--- _id: '12265' acknowledgement: We are very grateful to the authors of the commentaries for the interesting discussion and to Luke Holman for handling this set of manuscripts. Part of this work was funded by the Austrian Science Fund FWF (grant P 32166). article_processing_charge: Yes (via OA deal) article_type: letter_note author: - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Parvathy full_name: Surendranadh, Parvathy id: 455235B8-F248-11E8-B48F-1D18A9856A87 last_name: Surendranadh - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Westram AM, Stankowski S, Surendranadh P, Barton NH. Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. 2022;35(9):1200-1205. doi:10.1111/jeb.14082' apa: 'Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022). Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14082' chicago: 'Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H Barton. “Reproductive Isolation, Speciation, and the Value of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of Evolutionary Biology. Wiley, 2022. https://doi.org/10.1111/jeb.14082.' ieee: 'A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?,’” Journal of Evolutionary Biology, vol. 35, no. 9. Wiley, pp. 1200–1205, 2022.' ista: 'Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. 35(9), 1200–1205.' mla: 'Westram, Anja M., et al. “Reproductive Isolation, Speciation, and the Value of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of Evolutionary Biology, vol. 35, no. 9, Wiley, 2022, pp. 1200–05, doi:10.1111/jeb.14082.' short: A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary Biology 35 (2022) 1200–1205. date_created: 2023-01-16T09:59:37Z date_published: 2022-09-01T00:00:00Z date_updated: 2023-08-04T09:53:41Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/jeb.14082 external_id: isi: - '000849851100009' file: - access_level: open_access checksum: 27268009e5eec030bc10667a4ac5ed4c content_type: application/pdf creator: dernst date_created: 2023-01-30T10:14:09Z date_updated: 2023-01-30T10:14:09Z file_id: '12449' file_name: 2022_JourEvoBiology_Westram_Response.pdf file_size: 349603 relation: main_file success: 1 file_date_updated: 2023-01-30T10:14:09Z has_accepted_license: '1' intvolume: ' 35' isi: 1 issue: '9' keyword: - Ecology - Evolution - Behavior and Systematics language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 1200-1205 project: - _id: 05959E1C-7A3F-11EA-A408-12923DDC885E grant_number: P32166 name: The maintenance of alternative adaptive peaks in snapdragons publication: Journal of Evolutionary Biology publication_identifier: eissn: - 1420-9101 issn: - 1010-061X publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '12264' relation: other status: public scopus_import: '1' status: public title: 'Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 35 year: '2022' ... --- _id: '10787' abstract: - lang: eng text: "A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a ‘fixed-state’ approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m−1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments.\r\nThis article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’." acknowledgement: This research was partly funded by the Austrian Science Fund (FWF) [FWF P-32896B]. article_processing_charge: No article_type: original author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Oluwafunmilola O full_name: Olusanya, Oluwafunmilola O id: 41AD96DC-F248-11E8-B48F-1D18A9856A87 last_name: Olusanya orcid: 0000-0003-1971-8314 citation: ama: 'Barton NH, Olusanya OO. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 2022;377(1848). doi:10.1098/rstb.2021.0009' apa: 'Barton, N. H., & Olusanya, O. O. (2022). The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2021.0009' chicago: 'Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a Metapopulation to a Changing Environment.” Philosophical Transactions of the Royal Society B: Biological Sciences. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0009.' ieee: 'N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing environment,” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1848. The Royal Society, 2022.' ista: 'Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1848).' mla: 'Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation to a Changing Environment.” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1848, The Royal Society, 2022, doi:10.1098/rstb.2021.0009.' short: 'N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).' date_created: 2022-02-21T16:08:10Z date_published: 2022-04-11T00:00:00Z date_updated: 2024-01-26T12:00:53Z day: '11' ddc: - '570' department: - _id: GradSch - _id: NiBa doi: 10.1098/rstb.2021.0009 external_id: isi: - '000758140300001' pmid: - '35184588' file: - access_level: open_access checksum: 3b0243738f01bf3c07e0d7e8dc64f71d content_type: application/pdf creator: dernst date_created: 2022-08-02T06:14:32Z date_updated: 2022-08-02T06:14:32Z file_id: '11719' file_name: 2022_PhilosophicalTransactionsRSB_Barton.pdf file_size: 1349672 relation: main_file success: 1 file_date_updated: 2022-08-02T06:14:32Z has_accepted_license: '1' intvolume: ' 377' isi: 1 issue: '1848' keyword: - General Agricultural and Biological Sciences - General Biochemistry - Genetics and Molecular Biology language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8 grant_number: P32896 name: Causes and consequences of population fragmentation publication: 'Philosophical Transactions of the Royal Society B: Biological Sciences' publication_identifier: eissn: - 1471-2970 issn: - 0962-8436 publication_status: published publisher: The Royal Society quality_controlled: '1' related_material: record: - id: '14711' relation: dissertation_contains status: public scopus_import: '1' status: public title: The response of a metapopulation to a changing environment tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 377 year: '2022' ... --- _id: '10658' abstract: - lang: eng text: We analyse how migration from a large mainland influences genetic load and population numbers on an island, in a scenario where fitness-affecting variants are unconditionally deleterious, and where numbers decline with increasing load. Our analysis shows that migration can have qualitatively different effects, depending on the total mutation target and fitness effects of deleterious variants. In particular, we find that populations exhibit a genetic Allee effect across a wide range of parameter combinations, when variants are partially recessive, cycling between low-load (large-population) and high-load (sink) states. Increased migration reduces load in the sink state (by increasing heterozygosity) but further inflates load in the large-population state (by hindering purging). We identify various critical parameter thresholds at which one or other stable state collapses, and discuss how these thresholds are influenced by the genetic versus demographic effects of migration. Our analysis is based on a ‘semi-deterministic’ analysis, which accounts for genetic drift but neglects demographic stochasticity. We also compare against simulations which account for both demographic stochasticity and drift. Our results clarify the importance of gene flow as a key determinant of extinction risk in peripheral populations, even in the absence of ecological gradients. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (part I)’. acknowledgement: This research was partly funded by the Austrian Science Fund (FWF) (grant no. P-32896B). article_number: '20210010' article_processing_charge: No article_type: original author: - first_name: Himani full_name: Sachdeva, Himani last_name: Sachdeva - first_name: Oluwafunmilola O full_name: Olusanya, Oluwafunmilola O id: 41AD96DC-F248-11E8-B48F-1D18A9856A87 last_name: Olusanya orcid: 0000-0003-1971-8314 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Sachdeva H, Olusanya OO, Barton NH. Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. 2022;377(1846). doi:10.1098/rstb.2021.0010' apa: 'Sachdeva, H., Olusanya, O. O., & Barton, N. H. (2022). Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. The Royal Society. https://doi.org/10.1098/rstb.2021.0010' chicago: 'Sachdeva, Himani, Oluwafunmilola O Olusanya, and Nicholas H Barton. “Genetic Load and Extinction in Peripheral Populations: The Roles of Migration, Drift and Demographic Stochasticity.” Philosophical Transactions of the Royal Society B. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0010.' ieee: 'H. Sachdeva, O. O. Olusanya, and N. H. Barton, “Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity,” Philosophical Transactions of the Royal Society B, vol. 377, no. 1846. The Royal Society, 2022.' ista: 'Sachdeva H, Olusanya OO, Barton NH. 2022. Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. 377(1846), 20210010.' mla: 'Sachdeva, Himani, et al. “Genetic Load and Extinction in Peripheral Populations: The Roles of Migration, Drift and Demographic Stochasticity.” Philosophical Transactions of the Royal Society B, vol. 377, no. 1846, 20210010, The Royal Society, 2022, doi:10.1098/rstb.2021.0010.' short: H. Sachdeva, O.O. Olusanya, N.H. Barton, Philosophical Transactions of the Royal Society B 377 (2022). date_created: 2022-01-24T10:34:53Z date_published: 2022-01-24T00:00:00Z date_updated: 2024-01-26T12:00:53Z day: '24' ddc: - '576' department: - _id: GradSch - _id: NiBa doi: 10.1098/rstb.2021.0010 external_id: isi: - '000745854300008' pmid: - '35067097' file: - access_level: open_access checksum: 04ca9e2f0e344d680b947f2457df8d0a content_type: application/pdf creator: oolusany date_created: 2022-01-24T10:34:45Z date_updated: 2022-01-24T10:34:45Z file_id: '10659' file_name: rstb.2021.0010.pdf file_size: 1845792 relation: main_file file_date_updated: 2022-01-24T10:34:45Z has_accepted_license: '1' intvolume: ' 377' isi: 1 issue: '1846' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 project: - _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8 grant_number: P32896 name: Causes and consequences of population fragmentation publication: Philosophical Transactions of the Royal Society B publication_identifier: eissn: - 1471-2970 issn: - 0962-8436 publication_status: published publisher: The Royal Society quality_controlled: '1' related_material: link: - relation: earlier_version url: https://doi.org/10.1101/2021.08.05.455207 record: - id: '14711' relation: dissertation_contains status: public status: public title: 'Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 377 year: '2022' ... --- _id: '11411' abstract: - lang: eng text: Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium, which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use 2 types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1,000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity. acknowledged_ssus: - _id: ScienComp acknowledgement: "Part of this work was funded by Marie Curie COFUND Doctoral Fellowship and Austrian Science Fund FWF (grant P32166).\r\nWe thank the many volunteers and friends who have contributed to data collection in the field site over the years, in particular those who have managed field seasons: Barbora Trubenova, Maria Clara Melo, Tom Ellis, Eva Cereghetti, Lenka Matejovicova, Beatriz Pablo Carmona. Frederic Ferrer and Eva Salmerón Mateu have been immensely helpful with logistics at our informal field station, El Serrat de Planoles. We thank Sean Stankowski for technical help in\r\nproducing figure 1. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp)." article_number: iyac083 article_processing_charge: No article_type: original author: - first_name: Parvathy full_name: Surendranadh, Parvathy id: 455235B8-F248-11E8-B48F-1D18A9856A87 last_name: Surendranadh - first_name: Louise S full_name: Arathoon, Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon orcid: 0000-0003-1771-714X - first_name: Carina full_name: Baskett, Carina id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87 last_name: Baskett orcid: 0000-0002-7354-8574 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 2022;221(3). doi:10.1093/genetics/iyac083 apa: Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. Oxford University Press. https://doi.org/10.1093/genetics/iyac083 chicago: Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Genetics. Oxford University Press, 2022. https://doi.org/10.1093/genetics/iyac083. ieee: P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus,” Genetics, vol. 221, no. 3. Oxford University Press, 2022. ista: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 221(3), iyac083. mla: Surendranadh, Parvathy, et al. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Genetics, vol. 221, no. 3, iyac083, Oxford University Press, 2022, doi:10.1093/genetics/iyac083. short: P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, Genetics 221 (2022). date_created: 2022-05-26T13:44:50Z date_published: 2022-07-01T00:00:00Z date_updated: 2024-02-21T12:38:33Z day: '01' ddc: - '576' department: - _id: GradSch - _id: NiBa doi: 10.1093/genetics/iyac083 external_id: isi: - '000803735800001' pmid: - '35639938' file: - access_level: open_access checksum: cc2d56deb608bd53c5cc02f03a875107 content_type: application/pdf creator: larathoo date_created: 2022-05-26T12:48:15Z date_updated: 2022-05-26T12:48:15Z file_id: '11412' file_name: Manuscript.pdf file_size: 885374 relation: main_file success: 1 - access_level: open_access checksum: 693742595b6c7ed809423be01460d083 content_type: application/pdf creator: larathoo date_created: 2022-05-26T12:48:21Z date_updated: 2022-05-26T12:48:21Z file_id: '11413' file_name: SupplementalMaterial.pdf file_size: 1401704 relation: main_file success: 1 file_date_updated: 2022-05-26T12:48:21Z has_accepted_license: '1' intvolume: ' 221' isi: 1 issue: '3' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version pmid: 1 project: - _id: 05959E1C-7A3F-11EA-A408-12923DDC885E grant_number: P32166 name: The maintenance of alternative adaptive peaks in snapdragons publication: Genetics publication_identifier: eissn: - 1943-2631 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: record: - id: '14651' relation: dissertation_contains status: public - id: '11321' relation: research_data status: public - id: '9192' relation: research_data status: public scopus_import: '1' status: public title: Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 221 year: '2022' ... --- _id: '11321' abstract: - lang: eng text: 'Here are the research data underlying the publication "Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus" Further information are summed up in the README document. ' article_processing_charge: No author: - first_name: Parvathy full_name: Surendranadh, Parvathy id: 455235B8-F248-11E8-B48F-1D18A9856A87 last_name: Surendranadh - first_name: Louise S full_name: Arathoon, Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon orcid: 0000-0003-1771-714X - first_name: Carina full_name: Baskett, Carina id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87 last_name: Baskett orcid: 0000-0002-7354-8574 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2022. doi:10.15479/at:ista:11321 apa: Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11321 chicago: Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11321. ieee: P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2022. ista: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, 10.15479/at:ista:11321. mla: Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11321. short: P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2022). contributor: - contributor_type: project_member first_name: Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon - contributor_type: project_member first_name: Carina id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87 last_name: Baskett orcid: 0000-0002-7354-8574 - contributor_type: project_member first_name: David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - contributor_type: project_member first_name: Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - contributor_type: project_member first_name: Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 date_created: 2022-04-22T09:42:24Z date_published: 2022-04-28T00:00:00Z date_updated: 2024-02-21T12:41:09Z day: '28' ddc: - '570' department: - _id: GradSch - _id: NiBa doi: 10.15479/at:ista:11321 file: - access_level: open_access checksum: 96c1b86cdf25481f2a52972fcc45ca7f content_type: application/x-zip-compressed creator: larathoo date_created: 2022-04-22T09:39:03Z date_updated: 2022-04-22T09:39:03Z file_id: '11326' file_name: Data_Code.zip file_size: 13260571 relation: main_file success: 1 file_date_updated: 2022-04-22T09:39:03Z has_accepted_license: '1' month: '04' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '11411' relation: used_in_publication status: public - id: '9192' relation: earlier_version status: public - id: '8254' relation: earlier_version status: public status: public title: Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '12081' abstract: - lang: eng text: 'Selection accumulates information in the genome—it guides stochastically evolving populations toward states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright–Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation, and recombination. Finally, the cost of maintaining information depends on how it is encoded: Specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap.' acknowledgement: We thank Ksenia Khudiakova, Wiktor Młynarski, Sean Stankowski, and two anonymous reviewers for discussions and comments on the manuscript. G.T. and M.H. acknowledge funding from the Human Frontier Science Program Grant RGP0032/2018. N.B. acknowledges funding from ERC Grant 250152 “Information and Evolution.” article_number: e2123152119 article_processing_charge: No article_type: original author: - first_name: Michal full_name: Hledik, Michal id: 4171253A-F248-11E8-B48F-1D18A9856A87 last_name: Hledik - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: '1' citation: ama: Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 2022;119(36). doi:10.1073/pnas.2123152119 apa: Hledik, M., Barton, N. H., & Tkačik, G. (2022). Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2123152119 chicago: Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2123152119. ieee: M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information in evolution,” Proceedings of the National Academy of Sciences, vol. 119, no. 36. Proceedings of the National Academy of Sciences, 2022. ista: Hledik M, Barton NH, Tkačik G. 2022. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 119(36), e2123152119. mla: Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences, vol. 119, no. 36, e2123152119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2123152119. short: M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences 119 (2022). date_created: 2022-09-11T22:01:55Z date_published: 2022-08-29T00:00:00Z date_updated: 2024-03-06T14:22:51Z day: '29' ddc: - '570' department: - _id: NiBa - _id: GaTk doi: 10.1073/pnas.2123152119 ec_funded: 1 external_id: isi: - '000889278400014' pmid: - '36037343' file: - access_level: open_access checksum: 6dec51f6567da9039982a571508a8e4d content_type: application/pdf creator: dernst date_created: 2022-09-12T08:08:12Z date_updated: 2022-09-12T08:08:12Z file_id: '12091' file_name: 2022_PNAS_Hledik.pdf file_size: 2165752 relation: main_file success: 1 file_date_updated: 2022-09-12T08:08:12Z has_accepted_license: '1' intvolume: ' 119' isi: 1 issue: '36' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 2665AAFE-B435-11E9-9278-68D0E5697425 grant_number: RGP0034/2018 name: Can evolution minimize spurious signaling crosstalk to reach optimal performance? publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' related_material: record: - id: '15020' relation: dissertation_contains status: public scopus_import: '1' status: public title: Accumulation and maintenance of information in evolution tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 119 year: '2022' ... --- _id: '11388' abstract: - lang: eng text: "In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Stefanie full_name: Belohlavy, Stefanie id: 43FE426A-F248-11E8-B48F-1D18A9856A87 last_name: Belohlavy orcid: 0000-0002-9849-498X citation: ama: Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:10.15479/at:ista:11388 apa: Belohlavy, S. (2022). The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11388 chicago: Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11388. ieee: S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022. ista: Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria. mla: Belohlavy, Stefanie. The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11388. short: S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022. date_created: 2022-05-16T16:49:18Z date_published: 2022-05-18T00:00:00Z date_updated: 2023-08-29T06:41:51Z day: '18' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/at:ista:11388 file: - access_level: open_access checksum: 4d75e6a619df7e8a9d6e840aee182380 content_type: application/pdf creator: sbelohla date_created: 2022-05-19T13:03:13Z date_updated: 2023-05-20T22:30:03Z embargo: 2023-05-19 file_id: '11398' file_name: thesis_sb_final_pdfa.pdf file_size: 8247240 relation: main_file - access_level: closed checksum: 7a5d8b6dd0ca00784f860075b0a7d8f0 content_type: application/x-zip-compressed creator: sbelohla date_created: 2022-05-19T13:07:47Z date_updated: 2023-05-20T22:30:03Z embargo_to: open_access file_id: '11399' file_name: thesis_sb_final.zip file_size: 7094 relation: source_file file_date_updated: 2023-05-20T22:30:03Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '98' publication_identifier: isbn: - 978-3-99078-018-3 publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6713' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: The genetic basis of complex traits studied via analysis of evolve and resequence experiments tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '10535' abstract: - lang: eng text: Realistic models of biological processes typically involve interacting components on multiple scales, driven by changing environment and inherent stochasticity. Such models are often analytically and numerically intractable. We revisit a dynamic maximum entropy method that combines a static maximum entropy with a quasi-stationary approximation. This allows us to reduce stochastic non-equilibrium dynamics expressed by the Fokker-Planck equation to a simpler low-dimensional deterministic dynamics, without the need to track microscopic details. Although the method has been previously applied to a few (rather complicated) applications in population genetics, our main goal here is to explain and to better understand how the method works. We demonstrate the usefulness of the method for two widely studied stochastic problems, highlighting its accuracy in capturing important macroscopic quantities even in rapidly changing non-stationary conditions. For the Ornstein-Uhlenbeck process, the method recovers the exact dynamics whilst for a stochastic island model with migration from other habitats, the approximation retains high macroscopic accuracy under a wide range of scenarios in a dynamic environment. acknowledged_ssus: - _id: ScienComp acknowledgement: "Computational resources for the study were provided by the Institute of Science and Technology, Austria.\r\nKB received funding from the Scientific Grant Agency of the Slovak Republic under the Grants Nos. 1/0755/19 and 1/0521/20." article_number: e1009661 article_processing_charge: No article_type: original author: - first_name: Katarína full_name: Bod'ová, Katarína id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87 last_name: Bod'ová orcid: 0000-0002-7214-0171 - first_name: Eniko full_name: Szep, Eniko id: 485BB5A4-F248-11E8-B48F-1D18A9856A87 last_name: Szep - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Bodova K, Szep E, Barton NH. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 2021;17(12). doi:10.1371/journal.pcbi.1009661 apa: Bodova, K., Szep, E., & Barton, N. H. (2021). Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009661 chicago: Bodova, Katarina, Eniko Szep, and Nicholas H Barton. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009661. ieee: K. Bodova, E. Szep, and N. H. Barton, “Dynamic maximum entropy provides accurate approximation of structured population dynamics,” PLoS Computational Biology, vol. 17, no. 12. Public Library of Science, 2021. ista: Bodova K, Szep E, Barton NH. 2021. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 17(12), e1009661. mla: Bodova, Katarina, et al. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational Biology, vol. 17, no. 12, e1009661, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009661. short: K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021). date_created: 2021-12-12T23:01:27Z date_published: 2021-12-01T00:00:00Z date_updated: 2022-08-01T10:48:04Z day: '01' ddc: - '570' department: - _id: NiBa - _id: GaTk doi: 10.1371/journal.pcbi.1009661 external_id: arxiv: - '2102.03669' pmid: - '34851948' file: - access_level: open_access checksum: dcd185d4f7e0acee25edf1d6537f447e content_type: application/pdf creator: dernst date_created: 2022-05-16T08:53:11Z date_updated: 2022-05-16T08:53:11Z file_id: '11383' file_name: 2021_PLOsComBio_Bodova.pdf file_size: 2299486 relation: main_file success: 1 file_date_updated: 2022-05-16T08:53:11Z has_accepted_license: '1' intvolume: ' 17' issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Computational Biology publication_identifier: eissn: - 1553-7358 issn: - 1553-734X publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Dynamic maximum entropy provides accurate approximation of structured population dynamics tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2021' ... --- _id: '8708' abstract: - lang: eng text: The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study ‘replicated’ instances of secondary contact between closely related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry‐informative panel of such SNPs. We then compared their frequencies in newly sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi‐stable variants (Dobzhansky‐Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact. acknowledgement: Data used in this work were partly produced through the genotyping and sequencing facilities of ISEM and LabEx CeMEB, an ANR ‘Investissements d'avenir’ program (ANR‐10‐LABX‐04‐01) This project benefited from the Montpellier Bioinformatics Biodiversity platform supported by the LabEx CeMEB. We thank Norah Saarman, Grant Pogson, Célia Gosset and Pierre‐Alexandre Gagnaire for providing samples. This work was funded by a Languedoc‐Roussillon ‘Chercheur(se)s d'Avenir’ grant (Connect7 project). P. Strelkov was supported by the Russian Science Foundation project 19‐74‐20024. This is article 2020‐240 of Institut des Sciences de l'Evolution de Montpellier. article_processing_charge: No article_type: original author: - first_name: Alexis full_name: Simon, Alexis last_name: Simon - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Tahani full_name: El Ayari, Tahani last_name: El Ayari - first_name: Cathy full_name: Liautard‐Haag, Cathy last_name: Liautard‐Haag - first_name: Petr full_name: Strelkov, Petr last_name: Strelkov - first_name: John J full_name: Welch, John J last_name: Welch - first_name: Nicolas full_name: Bierne, Nicolas last_name: Bierne citation: ama: Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology. 2021;34(1):208-223. doi:10.1111/jeb.13709 apa: Simon, A., Fraisse, C., El Ayari, T., Liautard‐Haag, C., Strelkov, P., Welch, J. J., & Bierne, N. (2021). How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13709 chicago: Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard‐Haag, Petr Strelkov, John J Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Journal of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13709. ieee: A. Simon et al., “How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels,” Journal of Evolutionary Biology, vol. 34, no. 1. Wiley, pp. 208–223, 2021. ista: Simon A, Fraisse C, El Ayari T, Liautard‐Haag C, Strelkov P, Welch JJ, Bierne N. 2021. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology. 34(1), 208–223. mla: Simon, Alexis, et al. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Journal of Evolutionary Biology, vol. 34, no. 1, Wiley, 2021, pp. 208–23, doi:10.1111/jeb.13709. short: A. Simon, C. Fraisse, T. El Ayari, C. Liautard‐Haag, P. Strelkov, J.J. Welch, N. Bierne, Journal of Evolutionary Biology 34 (2021) 208–223. date_created: 2020-10-25T23:01:20Z date_published: 2021-01-01T00:00:00Z date_updated: 2023-08-04T11:04:11Z day: '01' department: - _id: BeVi - _id: NiBa doi: 10.1111/jeb.13709 external_id: isi: - '000579599700001' pmid: - '33045123' intvolume: ' 34' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/818559 month: '01' oa: 1 oa_version: Preprint page: 208-223 pmid: 1 publication: Journal of Evolutionary Biology publication_identifier: eissn: - '14209101' issn: - 1010061X publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '13073' relation: research_data status: public scopus_import: '1' status: public title: How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 34 year: '2021' ... --- _id: '8743' abstract: - lang: eng text: 'Montane cloud forests are areas of high endemism, and are one of the more vulnerable terrestrial ecosystems to climate change. Thus, understanding how they both contribute to the generation of biodiversity, and will respond to ongoing climate change, are important and related challenges. The widely accepted model for montane cloud forest dynamics involves upslope forcing of their range limits with global climate warming. However, limited climate data provides some support for an alternative model, where range limits are forced downslope with climate warming. Testing between these two models is challenging, due to the inherent limitations of climate and pollen records. We overcome this with an alternative source of historical information, testing between competing model predictions using genomic data and demographic analyses for a species of beetle tightly associated to an oceanic island cloud forest. Results unequivocally support the alternative model: populations that were isolated at higher elevation peaks during the Last Glacial Maximum are now in contact and hybridizing at lower elevations. Our results suggest that genomic data are a rich source of information to further understand how montane cloud forest biodiversity originates, and how it is likely to be impacted by ongoing climate change.' acknowledgement: 'This work was financed by the Spanish Agencia Estatal de Investigación (CGL2017‐85718‐P), awarded to BCE, and co‐financed by FEDER. It was also supported by the Spanish Ministerio de Ciencia, Innovación y Universidades (EQC2018‐004418‐P), awarded to BCE. AS‐C was funded by the Spanish Ministerio de Ciencia, Innovación y Universidades through an FPU PhD fellowship (FPU014/02948). The authors thank Instituto Tecnológico y de Energías Renovables (ITER), S.A for providing access to the Teide High‐Performance Computing facility (Teide‐HPC). Fieldwork was supported by collecting permit AFF 107/17 (sigma number 2017‐00572) kindly provided by the Cabildo of Tenerife. The authors wish to thank the following for field work and sample sorting and identification: A. J. Pérez‐Delgado, H. López, and C. Andújar. We also thank V. García‐Olivares for assistance with laboratory and bioinformatic work.' article_processing_charge: No article_type: original author: - first_name: Antonia full_name: Salces-Castellano, Antonia last_name: Salces-Castellano - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Paula full_name: Arribas, Paula last_name: Arribas - first_name: Jairo full_name: Patino, Jairo last_name: Patino - first_name: 'Dirk N. ' full_name: 'Karger, Dirk N. ' last_name: Karger - first_name: Roger full_name: Butlin, Roger last_name: Butlin - first_name: Brent C. full_name: Emerson, Brent C. last_name: Emerson citation: ama: Salces-Castellano A, Stankowski S, Arribas P, et al. Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. 2021;75(2):231-244. doi:10.1111/evo.14111 apa: Salces-Castellano, A., Stankowski, S., Arribas, P., Patino, J., Karger, D. N., Butlin, R., & Emerson, B. C. (2021). Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. Wiley. https://doi.org/10.1111/evo.14111 chicago: Salces-Castellano, Antonia, Sean Stankowski, Paula Arribas, Jairo Patino, Dirk N. Karger, Roger Butlin, and Brent C. Emerson. “Long-Term Cloud Forest Response to Climate Warming Revealed by Insect Speciation History.” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14111. ieee: A. Salces-Castellano et al., “Long-term cloud forest response to climate warming revealed by insect speciation history,” Evolution, vol. 75, no. 2. Wiley, pp. 231–244, 2021. ista: Salces-Castellano A, Stankowski S, Arribas P, Patino J, Karger DN, Butlin R, Emerson BC. 2021. Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. 75(2), 231–244. mla: Salces-Castellano, Antonia, et al. “Long-Term Cloud Forest Response to Climate Warming Revealed by Insect Speciation History.” Evolution, vol. 75, no. 2, Wiley, 2021, pp. 231–44, doi:10.1111/evo.14111. short: A. Salces-Castellano, S. Stankowski, P. Arribas, J. Patino, D.N. Karger, R. Butlin, B.C. Emerson, Evolution 75 (2021) 231–244. date_created: 2020-11-08T23:01:26Z date_published: 2021-02-01T00:00:00Z date_updated: 2023-08-04T11:09:49Z day: '01' department: - _id: NiBa doi: 10.1111/evo.14111 external_id: isi: - '000583190600001' pmid: - '33078844' intvolume: ' 75' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://hdl.handle.net/10261/223937 month: '02' oa: 1 oa_version: Submitted Version page: 231-244 pmid: 1 publication: Evolution publication_identifier: eissn: - 1558-5646 issn: - 0014-3820 publication_status: published publisher: Wiley quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1111/evo.14225 scopus_import: '1' status: public title: Long-term cloud forest response to climate warming revealed by insect speciation history type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 75 year: '2021' ... --- _id: '8928' abstract: - lang: eng text: Domestication is a human‐induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species‐specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species‐specific and supported by the few historical records available. acknowledgement: This work was supported by the EU Marie Curie Career Integration grant (FP7‐PEOPLE‐2011‐CIG grant agreement PCIG10‐GA‐2011‐304164) attributed to CS. SA was supported by a PhD fellowship from the French Région PACA and the Plant Breeding division of INRA, in partnership with Gautier Semences. CF was supported by an Austrian Science Foundation FWF grant (Project M 2463‐B29). Authors thank Mathilde Causse and Beatriz Vicoso for their team leading. Thanks to the Italian Eggplant Genome Consortium, which includes the DISAFA, Plant Genetics and Breeding (University of Torino), the Biotechnology Department (University of Verona), the CREA‐ORL in Montanaso Lombardo (LO) and the ENEA in Rome for providing access to the eggplant genome reference. Thanks to CRB‐lég ( https://www6.paca.inra.fr/gafl_eng/Vegetables-GRC ) for managing and providing the genetic resources, to Marie‐Christine Daunay and Alain Palloix (INRA UR1052) for assistance in choosing the biological material used, to Muriel Latreille and Sylvain Santoni from the UMR AGAP (INRA Montpellier, France) for their help with RNAseq library preparation, to Jean‐Paul Bouchet and Jacques Lagnel (INRA UR1052) for their Bioinformatics assistance. article_processing_charge: No article_type: original author: - first_name: Stéphanie full_name: Arnoux, Stéphanie last_name: Arnoux - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Christopher full_name: Sauvage, Christopher last_name: Sauvage citation: ama: Arnoux S, Fraisse C, Sauvage C. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 2021;34(2):270-283. doi:10.1111/jeb.13723 apa: Arnoux, S., Fraisse, C., & Sauvage, C. (2021). Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13723 chicago: Arnoux, Stéphanie, Christelle Fraisse, and Christopher Sauvage. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Journal of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13723. ieee: S. Arnoux, C. Fraisse, and C. Sauvage, “Genomic inference of complex domestication histories in three Solanaceae species,” Journal of Evolutionary Biology, vol. 34, no. 2. Wiley, pp. 270–283, 2021. ista: Arnoux S, Fraisse C, Sauvage C. 2021. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 34(2), 270–283. mla: Arnoux, Stéphanie, et al. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Journal of Evolutionary Biology, vol. 34, no. 2, Wiley, 2021, pp. 270–83, doi:10.1111/jeb.13723. short: S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021) 270–283. date_created: 2020-12-06T23:01:16Z date_published: 2021-02-01T00:00:00Z date_updated: 2023-08-04T11:19:26Z day: '01' department: - _id: NiBa doi: 10.1111/jeb.13723 external_id: isi: - '000587769700001' pmid: - '33107098' intvolume: ' 34' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/jeb.13723 month: '02' oa: 1 oa_version: Published Version page: 270-283 pmid: 1 project: - _id: 2662AADE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02463 name: Sex chromosomes and species barriers publication: Journal of Evolutionary Biology publication_identifier: eissn: - '14209101' issn: - 1010061X publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '13065' relation: research_data status: public scopus_import: '1' status: public title: Genomic inference of complex domestication histories in three Solanaceae species type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 34 year: '2021' ... --- _id: '9100' abstract: - lang: eng text: 'Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we ''dive under the surface'' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model‐based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity.' acknowledgement: "We would like to thank all the participants in the speciation symposium of the Marine Evolution Conference in Sweden for the interesting discussions and to all the contributors to this special\r\nissue. We thank Nicolas Bierne and Wolf Blanckenhorn (reviewer and editor, respectively) for valuable suggestions during the revision of the manuscript, and Roger K. Butlin and Anja M. Westram for very helpful comments on a previous draft. We would also like to thank Wolf Blanckenhorn and Nicola Cook, the Editor in Chief and the Managing Editor of the Journal of Evolutionary Biology, respectively, for the encouragement and support in putting together this special issue, and to all reviewers involved. RF was financed by the European Union's Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie Grant Agreement Number 706376 and is currently financed by the FEDER Funds through the Operational Competitiveness Factors Program COMPETE and by National Funds through the Foundation for Science and Technology (FCT) within the scope of the project ‘Hybrabbid' (PTDC/BIA-EVL/30628/2017-POCI-01-0145-FEDER-030628). KJ was funded by the Swedish\r\nResearch Council, VR. SS was supported by NERC and ERC funding awarded to Roger K. Butlin." article_processing_charge: No article_type: original author: - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski citation: ama: 'Faria R, Johannesson K, Stankowski S. Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. 2021;34(1):4-15. doi:10.1111/jeb.13756' apa: 'Faria, R., Johannesson, K., & Stankowski, S. (2021). Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13756' chicago: 'Faria, Rui, Kerstin Johannesson, and Sean Stankowski. “Speciation in Marine Environments: Diving under the Surface.” Journal of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13756.' ieee: 'R. Faria, K. Johannesson, and S. Stankowski, “Speciation in marine environments: Diving under the surface,” Journal of Evolutionary Biology, vol. 34, no. 1. Wiley, pp. 4–15, 2021.' ista: 'Faria R, Johannesson K, Stankowski S. 2021. Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. 34(1), 4–15.' mla: 'Faria, Rui, et al. “Speciation in Marine Environments: Diving under the Surface.” Journal of Evolutionary Biology, vol. 34, no. 1, Wiley, 2021, pp. 4–15, doi:10.1111/jeb.13756.' short: R. Faria, K. Johannesson, S. Stankowski, Journal of Evolutionary Biology 34 (2021) 4–15. date_created: 2021-02-07T23:01:13Z date_published: 2021-01-18T00:00:00Z date_updated: 2023-08-07T13:42:08Z day: '18' ddc: - '570' department: - _id: NiBa doi: 10.1111/jeb.13756 external_id: isi: - '000608367500001' file: - access_level: open_access checksum: 5755856a5368d4b4cdd6fad5ab27f4d1 content_type: application/pdf creator: dernst date_created: 2021-02-09T09:04:02Z date_updated: 2021-02-09T09:04:02Z file_id: '9108' file_name: 2021_JourEvolBiology_Faria.pdf file_size: 561340 relation: main_file success: 1 file_date_updated: 2021-02-09T09:04:02Z has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 4-15 publication: Journal of Evolutionary Biology publication_identifier: eissn: - '14209101' issn: - 1010061X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Speciation in marine environments: Diving under the surface' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 34 year: '2021' ... --- _id: '9168' abstract: - lang: eng text: Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems. acknowledged_ssus: - _id: ScienComp acknowledgement: "The computations were performed with the IST Austria High-Performance Computing (HPC) Cluster and the Institut Français de Bioinformatique (IFB) Core Cluster. We are grateful to Nick Barton and Beatriz Vicoso for critical comments on the model and the manuscript. We also thank Brian Charlesworth, Stuart Baird, and an anonymous reviewer for insightful comments.\r\nC.F. was supported by an Austrian Science Foundation FWF grant (Project M 2463-B29)." article_number: iyaa025 article_processing_charge: No article_type: original author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Himani full_name: Sachdeva, Himani id: 42377A0A-F248-11E8-B48F-1D18A9856A87 last_name: Sachdeva citation: ama: 'Fraisse C, Sachdeva H. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. 2021;217(2). doi:10.1093/genetics/iyaa025' apa: 'Fraisse, C., & Sachdeva, H. (2021). The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. Genetics Society of America. https://doi.org/10.1093/genetics/iyaa025' chicago: 'Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” Genetics. Genetics Society of America, 2021. https://doi.org/10.1093/genetics/iyaa025.' ieee: 'C. Fraisse and H. Sachdeva, “The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes,” Genetics, vol. 217, no. 2. Genetics Society of America, 2021.' ista: 'Fraisse C, Sachdeva H. 2021. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. 217(2), iyaa025.' mla: 'Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” Genetics, vol. 217, no. 2, iyaa025, Genetics Society of America, 2021, doi:10.1093/genetics/iyaa025.' short: C. Fraisse, H. Sachdeva, Genetics 217 (2021). date_created: 2021-02-18T14:41:30Z date_published: 2021-02-01T00:00:00Z date_updated: 2023-08-07T13:47:01Z day: '01' department: - _id: NiBa doi: 10.1093/genetics/iyaa025 external_id: isi: - '000637218100005' intvolume: ' 217' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/genetics/iyaa025 month: '02' oa: 1 oa_version: Published Version project: - _id: 2662AADE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02463 name: Sex chromosomes and species barriers publication: Genetics publication_identifier: issn: - 1943-2631 publication_status: published publisher: Genetics Society of America quality_controlled: '1' status: public title: 'The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 217 year: '2021' ... --- _id: '9119' abstract: - lang: eng text: 'We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single‐population or two‐population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.' article_processing_charge: No article_type: original author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Iva full_name: Popovic, Iva last_name: Popovic - first_name: Clément full_name: Mazoyer, Clément last_name: Mazoyer - first_name: Bruno full_name: Spataro, Bruno last_name: Spataro - first_name: Stéphane full_name: Delmotte, Stéphane last_name: Delmotte - first_name: Jonathan full_name: Romiguier, Jonathan last_name: Romiguier - first_name: Étienne full_name: Loire, Étienne last_name: Loire - first_name: Alexis full_name: Simon, Alexis last_name: Simon - first_name: Nicolas full_name: Galtier, Nicolas last_name: Galtier - first_name: Laurent full_name: Duret, Laurent last_name: Duret - first_name: Nicolas full_name: Bierne, Nicolas last_name: Bierne - first_name: Xavier full_name: Vekemans, Xavier last_name: Vekemans - first_name: Camille full_name: Roux, Camille last_name: Roux citation: ama: 'Fraisse C, Popovic I, Mazoyer C, et al. DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. 2021;21:2629-2644. doi:10.1111/1755-0998.13323' apa: 'Fraisse, C., Popovic, I., Mazoyer, C., Spataro, B., Delmotte, S., Romiguier, J., … Roux, C. (2021). DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13323' chicago: 'Fraisse, Christelle, Iva Popovic, Clément Mazoyer, Bruno Spataro, Stéphane Delmotte, Jonathan Romiguier, Étienne Loire, et al. “DILS: Demographic Inferences with Linked Selection by Using ABC.” Molecular Ecology Resources. Wiley, 2021. https://doi.org/10.1111/1755-0998.13323.' ieee: 'C. Fraisse et al., “DILS: Demographic inferences with linked selection by using ABC,” Molecular Ecology Resources, vol. 21. Wiley, pp. 2629–2644, 2021.' ista: 'Fraisse C, Popovic I, Mazoyer C, Spataro B, Delmotte S, Romiguier J, Loire É, Simon A, Galtier N, Duret L, Bierne N, Vekemans X, Roux C. 2021. DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. 21, 2629–2644.' mla: 'Fraisse, Christelle, et al. “DILS: Demographic Inferences with Linked Selection by Using ABC.” Molecular Ecology Resources, vol. 21, Wiley, 2021, pp. 2629–44, doi:10.1111/1755-0998.13323.' short: C. Fraisse, I. Popovic, C. Mazoyer, B. Spataro, S. Delmotte, J. Romiguier, É. Loire, A. Simon, N. Galtier, L. Duret, N. Bierne, X. Vekemans, C. Roux, Molecular Ecology Resources 21 (2021) 2629–2644. date_created: 2021-02-14T23:01:14Z date_published: 2021-01-15T00:00:00Z date_updated: 2023-08-07T13:45:18Z day: '15' department: - _id: NiBa doi: 10.1111/1755-0998.13323 external_id: isi: - '000614183100001' intvolume: ' 21' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2020.06.15.151597v2 month: '01' oa: 1 oa_version: Preprint page: 2629-2644 publication: Molecular Ecology Resources publication_identifier: eissn: - '17550998' issn: - 1755098X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'DILS: Demographic inferences with linked selection by using ABC' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 21 year: '2021' ... --- _id: '9375' abstract: - lang: eng text: Genetic variation segregates as linked sets of variants, or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. And yet, genomic data often lack haplotype information, due to constraints in sequencing technologies. Here we present “haplotagging”, a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species the geographic clines for the major wing pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the centre of the hybrid zone. We propose that shared warning signalling (Müllerian mimicry) may couple the cline shifts seen in both species, and facilitate the parallel co-emergence of a novel hybrid morph in both co-mimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations. acknowledgement: 'We thank Felicity Jones for input into experimental design, helpful discussion and improving the manuscript. We thank the Rolian, Jiggins, Chan and Jones Labs members for support, insightful scientific discussion and improving the manuscript. We thank the Rolian lab members, the Animal Resource Centre staff at the University of Calgary, and Caroline Schmid and Ann-Katrin Geysel at the Friedrich Miescher Laboratory for animal husbandry. We thank Christa Lanz, Rebecca Schwab and Ilja Bezrukov for assistance with high-throughput sequencing and associated data processing; Andre Noll and the MPI Tübingen IT team for computational support. We thank Ben Haller and Richard Durbin for helpful discussions. We thank David M. Kingsley for thoughtful input that has greatly improved our manuscript. J.I.M. is supported by a Research Fellowship from St. John’s College, Cambridge. A.D. was supported by a European Research Council Consolidator Grant (No. 617279 “EvolRecombAdapt”, P/I Felicity Jones). C.R. is supported by Discovery Grant #4181932 from the Natural Sciences and Engineering Research Council of Canada and by the Faculty of Veterinary Medicine at the University of Calgary. C.D.J. is supported by a BBSRC grant BB/R007500 and a European Research Council Advanced Grant (No. 339873 “SpeciationGenetics”). M.K. and Y.F.C. are supported by the Max Planck Society and a European Research Council Starting Grant (No. 639096 “HybridMiX”).' article_number: e2015005118 article_processing_charge: No article_type: original author: - first_name: Joana I. full_name: Meier, Joana I. last_name: Meier - first_name: Patricio A. full_name: Salazar, Patricio A. last_name: Salazar - first_name: Marek full_name: Kučka, Marek last_name: Kučka - first_name: Robert William full_name: Davies, Robert William last_name: Davies - first_name: Andreea full_name: Dréau, Andreea last_name: Dréau - first_name: Ismael full_name: Aldás, Ismael last_name: Aldás - first_name: Olivia Box full_name: Power, Olivia Box last_name: Power - first_name: Nicola J. full_name: Nadeau, Nicola J. last_name: Nadeau - first_name: Jon R. full_name: Bridle, Jon R. last_name: Bridle - first_name: Campbell full_name: Rolian, Campbell last_name: Rolian - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: W. Owen full_name: McMillan, W. Owen last_name: McMillan - first_name: Chris D. full_name: Jiggins, Chris D. last_name: Jiggins - first_name: Yingguang Frank full_name: Chan, Yingguang Frank last_name: Chan citation: ama: Meier JI, Salazar PA, Kučka M, et al. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. 2021;118(25). doi:10.1073/pnas.2015005118 apa: Meier, J. I., Salazar, P. A., Kučka, M., Davies, R. W., Dréau, A., Aldás, I., … Chan, Y. F. (2021). Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2015005118 chicago: Meier, Joana I., Patricio A. Salazar, Marek Kučka, Robert William Davies, Andreea Dréau, Ismael Aldás, Olivia Box Power, et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” PNAS. Proceedings of the National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2015005118. ieee: J. I. Meier et al., “Haplotype tagging reveals parallel formation of hybrid races in two butterfly species,” PNAS, vol. 118, no. 25. Proceedings of the National Academy of Sciences, 2021. ista: Meier JI, Salazar PA, Kučka M, Davies RW, Dréau A, Aldás I, Power OB, Nadeau NJ, Bridle JR, Rolian C, Barton NH, McMillan WO, Jiggins CD, Chan YF. 2021. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. 118(25), e2015005118. mla: Meier, Joana I., et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” PNAS, vol. 118, no. 25, e2015005118, Proceedings of the National Academy of Sciences, 2021, doi:10.1073/pnas.2015005118. short: J.I. Meier, P.A. Salazar, M. Kučka, R.W. Davies, A. Dréau, I. Aldás, O.B. Power, N.J. Nadeau, J.R. Bridle, C. Rolian, N.H. Barton, W.O. McMillan, C.D. Jiggins, Y.F. Chan, PNAS 118 (2021). date_created: 2021-05-07T17:10:21Z date_published: 2021-06-21T00:00:00Z date_updated: 2023-08-08T13:33:09Z day: '21' ddc: - '570' department: - _id: NiBa doi: 10.1073/pnas.2015005118 external_id: isi: - '000671755600001' pmid: - '34155138' file: - access_level: open_access checksum: cb30c6166b2132ee60d616b31a1a7c29 content_type: application/pdf creator: dernst date_created: 2022-03-08T08:18:16Z date_updated: 2022-03-08T08:18:16Z file_id: '10835' file_name: 2021_PNAS_Meier.pdf file_size: 20592929 relation: main_file success: 1 file_date_updated: 2022-03-08T08:18:16Z has_accepted_license: '1' intvolume: ' 118' isi: 1 issue: '25' language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: PNAS publication_identifier: eissn: - 0027-8424 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Haplotype tagging reveals parallel formation of hybrid races in two butterfly species tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 118 year: '2021' ... --- _id: '9394' abstract: - lang: eng text: 'Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow.' acknowledgement: 'We are very grateful to Irena Senčić for technical assistance and to Michelle Kortyna and Sean Holland at the Center for Anchored Phylogenomics for assistance with data collection. RKB was funded by the Natural Environment Research Council and by the European Research Council. KJ was funded by the Swedish Research Councils VR and Formas (Linnaeus Grant: 217‐2008‐1719). JL was funded by a studentship from the Leverhulme Centre for Advanced Biological Modelling. AMW was funded by the European Union''s Horizon 2020 research and innovation program under Marie Skłodowska‐Curie Grant agreement no. 797747. RF was funded by the European Union''s Horizon 2020 research and innovation programme under the Marie Sklodowska‐Curie Grant agreement No. 706376 and by FEDER Funds through the Operational Competitiveness Factors Program—COMPETE and by National Funds through FCT—Foundation for Science and Technology within the scope of the project “Hybrabbid” (PTDC/BIA‐EVL/30628/2017‐ POCI‐01‐0145‐FEDER‐030628). We are grateful to other members of the Littorina research group for helpful discussions. We thank Claire Mérot and an anonymous referee for insightful comments on an earlier version. ' article_processing_charge: No article_type: original author: - first_name: Eva L. full_name: Koch, Eva L. last_name: Koch - first_name: Hernán E. full_name: Morales, Hernán E. last_name: Morales - first_name: Jenny full_name: Larsson, Jenny last_name: Larsson - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Alan R. full_name: Lemmon, Alan R. last_name: Lemmon - first_name: E. Moriarty full_name: Lemmon, E. Moriarty last_name: Lemmon - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: Koch EL, Morales HE, Larsson J, et al. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. 2021;5(3):196-213. doi:10.1002/evl3.227 apa: Koch, E. L., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. Wiley. https://doi.org/10.1002/evl3.227 chicago: Koch, Eva L., Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Evolution Letters. Wiley, 2021. https://doi.org/10.1002/evl3.227. ieee: E. L. Koch et al., “Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis,” Evolution Letters, vol. 5, no. 3. Wiley, pp. 196–213, 2021. ista: Koch EL, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. 5(3), 196–213. mla: Koch, Eva L., et al. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Evolution Letters, vol. 5, no. 3, Wiley, 2021, pp. 196–213, doi:10.1002/evl3.227. short: E.L. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, Evolution Letters 5 (2021) 196–213. date_created: 2021-05-16T22:01:47Z date_published: 2021-05-07T00:00:00Z date_updated: 2023-08-08T13:34:08Z day: '07' ddc: - '570' department: - _id: NiBa doi: 10.1002/evl3.227 ec_funded: 1 external_id: isi: - '000647846200001' file: - access_level: open_access checksum: 023b1608e311f0fda30593ba3d0a4e0b content_type: application/pdf creator: cchlebak date_created: 2021-10-15T08:26:02Z date_updated: 2021-10-15T08:26:02Z file_id: '10142' file_name: 2021_EvolutionLetters_Koch.pdf file_size: 3021108 relation: main_file success: 1 file_date_updated: 2021-10-15T08:26:02Z has_accepted_license: '1' intvolume: ' 5' isi: 1 issue: '3' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 196-213 project: - _id: 265B41B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '797747' name: Theoretical and empirical approaches to understanding Parallel Adaptation publication: Evolution Letters publication_identifier: eissn: - 2056-3744 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '12987' relation: research_data status: public scopus_import: '1' status: public title: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 5 year: '2021' ... --- _id: '9392' abstract: - lang: eng text: 'Humans conceptualize the diversity of life by classifying individuals into types we call ‘species’1. The species we recognize influence political and financial decisions and guide our understanding of how units of diversity evolve and interact. Although the idea of species may seem intuitive, a debate about the best way to define them has raged even before Darwin2. So much energy has been devoted to the so-called ‘species problem’ that no amount of discourse will ever likely solve it2,3. Dozens of species concepts are currently recognized3, but we lack a concrete understanding of how much researchers actually disagree and the factors that cause them to think differently1,2. To address this, we used a survey to quantify the species problem for the first time. The results indicate that the disagreement is extensive: two randomly chosen respondents will most likely disagree on the nature of species. The probability of disagreement is not predicted by researcher experience or broad study system, but tended to be lower among researchers with similar focus, training and who study the same organism. Should we see this diversity of perspectives as a problem? We argue that we should not.' acknowledgement: We thank Christopher Cooney, Martin Garlovsky, Anja M. Westram, Carina Baskett, Stefanie Belohlavy, Michal Hledik, Arka Pal, Nicholas H. Barton, Roger K. Butlin and members of the University of Sheffield Speciation Journal Club for feedback on draft survey questions and/or comments on a draft manuscript. Three anonymous reviewers gave thoughtful feedback that improved the manuscript. We thank Ahmad Nadeem, who was paid to build the Shiny app. We are especially grateful to everyone who took part in the survey. Ethical approval for the survey was obtained through the University of Sheffield Ethics Review Procedure (Application 029768). S.S. was supported by a NERC grant awarded to Roger K. Butlin. article_processing_charge: No article_type: original author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Mark full_name: Ravinet, Mark last_name: Ravinet citation: ama: Stankowski S, Ravinet M. Quantifying the use of species concepts. Current Biology. 2021;31(9):R428-R429. doi:10.1016/j.cub.2021.03.060 apa: Stankowski, S., & Ravinet, M. (2021). Quantifying the use of species concepts. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2021.03.060 chicago: Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” Current Biology. Cell Press, 2021. https://doi.org/10.1016/j.cub.2021.03.060. ieee: S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” Current Biology, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021. ista: Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), R428–R429. mla: Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” Current Biology, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:10.1016/j.cub.2021.03.060. short: S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429. date_created: 2021-05-16T22:01:46Z date_published: 2021-05-10T00:00:00Z date_updated: 2023-08-08T13:34:38Z day: '10' department: - _id: NiBa doi: 10.1016/j.cub.2021.03.060 external_id: isi: - '000654741200004' pmid: - '33974865' intvolume: ' 31' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cub.2021.03.060 month: '05' oa: 1 oa_version: Published Version page: R428-R429 pmid: 1 publication: Current Biology publication_identifier: eissn: - '18790445' issn: - '09609822' publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: Quantifying the use of species concepts type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 31 year: '2021' ... --- _id: '12987' abstract: - lang: eng text: Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome. article_processing_charge: No author: - first_name: Eva full_name: Koch, Eva last_name: Koch - first_name: Hernán E. full_name: Morales, Hernán E. last_name: Morales - first_name: Jenny full_name: Larsson, Jenny last_name: Larsson - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Alan R. full_name: Lemmon, Alan R. last_name: Lemmon - first_name: E. Moriarty full_name: Lemmon, E. Moriarty last_name: Lemmon - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: 'Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. 2021. doi:10.5061/DRYAD.ZGMSBCCB4' apa: 'Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4' chicago: 'Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4.' ieee: 'E. Koch et al., “Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.' ista: 'Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4.' mla: 'Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4.' short: E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, (2021). date_created: 2023-05-16T12:34:09Z date_published: 2021-04-10T00:00:00Z date_updated: 2023-08-08T13:34:07Z day: '10' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.ZGMSBCCB4 has_accepted_license: '1' license: https://creativecommons.org/publicdomain/zero/1.0/ main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.zgmsbccb4 month: '04' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '9394' relation: used_in_publication status: public status: public title: 'Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis' tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '9410' abstract: - lang: eng text: Antibiotic concentrations vary dramatically in the body and the environment. Hence, understanding the dynamics of resistance evolution along antibiotic concentration gradients is critical for predicting and slowing the emergence and spread of resistance. While it has been shown that increasing the concentration of an antibiotic slows resistance evolution, how adaptation to one antibiotic concentration correlates with fitness at other points along the gradient has not received much attention. Here, we selected populations of Escherichia coli at several points along a concentration gradient for three different antibiotics, asking how rapidly resistance evolved and whether populations became specialized to the antibiotic concentration they were selected on. Populations selected at higher concentrations evolved resistance more slowly but exhibited equal or higher fitness across the whole gradient. Populations selected at lower concentrations evolved resistance rapidly, but overall fitness in the presence of antibiotics was lower. However, these populations readily adapted to higher concentrations upon subsequent selection. Our results indicate that resistance management strategies must account not only for the rates of resistance evolution but also for the fitness of evolved strains. acknowledgement: We would like to thank Martin Ackermann, Camilo Barbosa, Nick Barton, Jonathan Bollback, Sebastian Bonhoeffer, Nick Colegrave, Calin Guet, Alex Hall, Sally Otto, Tiago Paixao, Srdjan Sarikas, Hinrich Schulenburg, Marjon de Vos and Michael Whitlock for insightful support. article_number: '20200913' article_processing_charge: No author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Hildegard full_name: Uecker, Hildegard id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87 last_name: Uecker orcid: 0000-0001-9435-2813 - first_name: Paul full_name: Neve, Paul last_name: Neve citation: ama: Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic concentration gradients. Biology letters. 2021;17(5). doi:10.1098/rsbl.2020.0913 apa: Lagator, M., Uecker, H., & Neve, P. (2021). Adaptation at different points along antibiotic concentration gradients. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2020.0913 chicago: Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters. Royal Society of London, 2021. https://doi.org/10.1098/rsbl.2020.0913. ieee: M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along antibiotic concentration gradients,” Biology letters, vol. 17, no. 5. Royal Society of London, 2021. ista: Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913. mla: Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters, vol. 17, no. 5, 20200913, Royal Society of London, 2021, doi:10.1098/rsbl.2020.0913. short: M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021). date_created: 2021-05-23T22:01:43Z date_published: 2021-05-12T00:00:00Z date_updated: 2023-08-08T13:44:35Z day: '12' ddc: - '570' department: - _id: NiBa doi: 10.1098/rsbl.2020.0913 ec_funded: 1 external_id: isi: - '000651501400001' pmid: - ' 33975485' file: - access_level: open_access checksum: 9c13c1f5af7609c97c741f11d293188a content_type: application/pdf creator: kschuh date_created: 2021-05-25T14:09:03Z date_updated: 2021-05-25T14:09:03Z file_id: '9425' file_name: 2021_BiologyLetters_Lagator.pdf file_size: 726759 relation: main_file success: 1 file_date_updated: 2021-05-25T14:09:03Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Biology letters publication_identifier: eissn: - 1744957X publication_status: published publisher: Royal Society of London quality_controlled: '1' scopus_import: '1' status: public title: Adaptation at different points along antibiotic concentration gradients tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 17 year: '2021' ... --- _id: '9470' abstract: - lang: eng text: A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance. acknowledgement: We thank the editor, two helpful reviewers, Roger Butlin, Kerstin Johannesson, Valentina Peona, Rike Stelkens, Julie Blommaert, Nick Barton, and João Alpedrinha for helpful comments that improved the manuscript. The authors acknowledge funding from the Swedish Research Council Formas (2017-01597 to AS), the Swedish Research Council Vetenskapsrådet (2016-05139 to AS, 2019-04452 to TS) and from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 757451 to TS). ELB was funded by a Carl Tryggers grant awarded to Tanja Slotte. Anja M. Westram was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 797747. Inês Fragata was funded by a Junior Researcher contract from FCT (CEECIND/02616/2018). article_processing_charge: No author: - first_name: Emma L. full_name: Berdan, Emma L. last_name: Berdan - first_name: Alexandre full_name: Blanckaert, Alexandre last_name: Blanckaert - first_name: Tanja full_name: Slotte, Tanja last_name: Slotte - first_name: Alexander full_name: Suh, Alexander last_name: Suh - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Inês full_name: Fragata, Inês last_name: Fragata citation: ama: 'Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 2021;30(12):2710-2723. doi:10.1111/mec.15936' apa: 'Berdan, E. L., Blanckaert, A., Slotte, T., Suh, A., Westram, A. M., & Fragata, I. (2021). Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15936' chicago: 'Berdan, Emma L., Alexandre Blanckaert, Tanja Slotte, Alexander Suh, Anja M Westram, and Inês Fragata. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology. Wiley, 2021. https://doi.org/10.1111/mec.15936.' ieee: 'E. L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A. M. Westram, and I. Fragata, “Unboxing mutations: Connecting mutation types with evolutionary consequences,” Molecular Ecology, vol. 30, no. 12. Wiley, pp. 2710–2723, 2021.' ista: 'Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. 2021. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 30(12), 2710–2723.' mla: 'Berdan, Emma L., et al. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology, vol. 30, no. 12, Wiley, 2021, pp. 2710–23, doi:10.1111/mec.15936.' short: E.L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A.M. Westram, I. Fragata, Molecular Ecology 30 (2021) 2710–2723. date_created: 2021-06-06T22:01:31Z date_published: 2021-06-01T00:00:00Z date_updated: 2023-08-08T13:59:18Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/mec.15936 ec_funded: 1 external_id: isi: - '000652056400001' file: - access_level: open_access checksum: e6f4731365bde2614b333040a08265d8 content_type: application/pdf creator: kschuh date_created: 2021-06-11T15:34:53Z date_updated: 2021-06-11T15:34:53Z file_id: '9545' file_name: 2021_MolecularEcology_Berdan.pdf file_size: 1031978 relation: main_file success: 1 file_date_updated: 2021-06-11T15:34:53Z has_accepted_license: '1' intvolume: ' 30' isi: 1 issue: '12' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '06' oa: 1 oa_version: Published Version page: 2710-2723 project: - _id: 265B41B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '797747' name: Theoretical and empirical approaches to understanding Parallel Adaptation publication: Molecular Ecology publication_identifier: eissn: - 1365294X issn: - '09621083' publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Unboxing mutations: Connecting mutation types with evolutionary consequences' tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 30 year: '2021' ... --- _id: '9816' abstract: - lang: eng text: "Aims: Mass antigen testing programs have been challenged because of an alleged insufficient specificity, leading to a large number of false positives. The objective of this study is to derive a lower bound of the specificity of the SD Biosensor Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020 we calculate a lower confidence bound for the specificity. As positive test results were not systematically verified by PCR tests, we base the lower bound on a worst case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332 persons from 79 counties were tested. The lowest positivity rate was observed in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This implies a test specificity of at least 99.6% (97.5% one-sided lower confidence bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests a higher specificity compared to earlier studies in spite of the underlying worst case assumption and the application in a mass testing setting. The actual specificity is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible at the time of testing. To our knowledge, this estimate constitutes the first bound obtained from large scale practical use of an antigen test." acknowledgement: We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová for very helpful comments. We also thank Matej Mišík for discussion and information regarding the Slovak testing data and Ag-Test used. article_number: e0255267 article_processing_charge: Yes article_type: original author: - first_name: Michal full_name: Hledik, Michal id: 4171253A-F248-11E8-B48F-1D18A9856A87 last_name: Hledik - first_name: Jitka full_name: Polechova, Jitka id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 - first_name: Mathias full_name: Beiglböck, Mathias last_name: Beiglböck - first_name: Anna Nele full_name: Herdina, Anna Nele last_name: Herdina - first_name: Robert full_name: Strassl, Robert last_name: Strassl - first_name: Martin full_name: Posch, Martin last_name: Posch citation: ama: Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0255267 apa: Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., & Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0255267 chicago: Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina, Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0255267. ieee: M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch, “Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021. ista: Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 16(7), e0255267. mla: Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE, vol. 16, no. 7, e0255267, Public Library of Science, 2021, doi:10.1371/journal.pone.0255267. short: M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch, PLoS ONE 16 (2021). date_created: 2021-08-08T22:01:26Z date_published: 2021-07-29T00:00:00Z date_updated: 2023-08-10T14:26:32Z day: '29' ddc: - '610' department: - _id: NiBa doi: 10.1371/journal.pone.0255267 external_id: isi: - '000685248200095' pmid: - '34324553' file: - access_level: open_access checksum: ae4df60eb62f4491278588548d0c1f93 content_type: application/pdf creator: asandaue date_created: 2021-08-09T11:52:14Z date_updated: 2021-08-09T11:52:14Z file_id: '9835' file_name: 2021_PLoSONE_Hledík.pdf file_size: 773921 relation: main_file success: 1 file_date_updated: 2021-08-09T11:52:14Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS ONE publication_identifier: eissn: - 1932-6203 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 16 year: '2021' ... --- _id: '9252' abstract: - lang: eng text: 'This paper analyses the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat‐dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.' acknowledgement: We thank the reviewers for their helpful comments, and also our colleagues, for illuminating discussions over the long gestation of this paper. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Eniko full_name: Szep, Eniko id: 485BB5A4-F248-11E8-B48F-1D18A9856A87 last_name: Szep - first_name: Himani full_name: Sachdeva, Himani id: 42377A0A-F248-11E8-B48F-1D18A9856A87 last_name: Sachdeva - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Szep E, Sachdeva H, Barton NH. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. 2021;75(5):1030-1045. doi:10.1111/evo.14210' apa: 'Szep, E., Sachdeva, H., & Barton, N. H. (2021). Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. Wiley. https://doi.org/10.1111/evo.14210' chicago: 'Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Polygenic Local Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14210.' ieee: 'E. Szep, H. Sachdeva, and N. H. Barton, “Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model,” Evolution, vol. 75, no. 5. Wiley, pp. 1030–1045, 2021.' ista: 'Szep E, Sachdeva H, Barton NH. 2021. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. 75(5), 1030–1045.' mla: 'Szep, Eniko, et al. “Polygenic Local Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” Evolution, vol. 75, no. 5, Wiley, 2021, pp. 1030–45, doi:10.1111/evo.14210.' short: E. Szep, H. Sachdeva, N.H. Barton, Evolution 75 (2021) 1030–1045. date_created: 2021-03-20T08:22:10Z date_published: 2021-05-01T00:00:00Z date_updated: 2023-09-05T15:44:06Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/evo.14210 external_id: isi: - '000636966300001' file: - access_level: open_access checksum: b90fb5767d623602046fed03725e16ca content_type: application/pdf creator: kschuh date_created: 2021-08-11T13:39:19Z date_updated: 2021-08-11T13:39:19Z file_id: '9886' file_name: 2021_Evolution_Szep.pdf file_size: 734102 relation: main_file success: 1 file_date_updated: 2021-08-11T13:39:19Z has_accepted_license: '1' intvolume: ' 75' isi: 1 issue: '5' keyword: - Genetics - Ecology - Evolution - Behavior and Systematics - General Agricultural and Biological Sciences language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 1030-1045 publication: Evolution publication_identifier: eissn: - 1558-5646 issn: - 0014-3820 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '13062' relation: research_data status: public scopus_import: '1' status: public title: 'Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 75 year: '2021' ... --- _id: '9374' abstract: - lang: eng text: If there are no constraints on the process of speciation, then the number of species might be expected to match the number of available niches and this number might be indefinitely large. One possible constraint is the opportunity for allopatric divergence. In 1981, Felsenstein used a simple and elegant model to ask if there might also be genetic constraints. He showed that progress towards speciation could be described by the build‐up of linkage disequilibrium among divergently selected loci and between these loci and those contributing to other forms of reproductive isolation. Therefore, speciation is opposed by recombination, because it tends to break down linkage disequilibria. Felsenstein then introduced a crucial distinction between “two‐allele” models, which are subject to this effect, and “one‐allele” models, which are free from the recombination constraint. These fundamentally important insights have been the foundation for both empirical and theoretical studies of speciation ever since. acknowledgement: RKB was funded by the Natural Environment Research Council (NE/P012272/1 & NE/P001610/1), the European Research Council (693030 BARRIERS), and the Swedish Research Council (VR) (2018‐03695). MRS was funded by the National Science Foundation (Grant No. DEB1939290). article_processing_charge: No article_type: original author: - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin - first_name: Maria R. full_name: Servedio, Maria R. last_name: Servedio - first_name: Carole M. full_name: Smadja, Carole M. last_name: Smadja - first_name: Claudia full_name: Bank, Claudia last_name: Bank - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Samuel M. full_name: Flaxman, Samuel M. last_name: Flaxman - first_name: Tatiana full_name: Giraud, Tatiana last_name: Giraud - first_name: Robin full_name: Hopkins, Robin last_name: Hopkins - first_name: Erica L. full_name: Larson, Erica L. last_name: Larson - first_name: Martine E. full_name: Maan, Martine E. last_name: Maan - first_name: Joana full_name: Meier, Joana last_name: Meier - first_name: Richard full_name: Merrill, Richard last_name: Merrill - first_name: Mohamed A. F. full_name: Noor, Mohamed A. F. last_name: Noor - first_name: Daniel full_name: Ortiz‐Barrientos, Daniel last_name: Ortiz‐Barrientos - first_name: Anna full_name: Qvarnström, Anna last_name: Qvarnström citation: ama: Butlin RK, Servedio MR, Smadja CM, et al. Homage to Felsenstein 1981, or why are there so few/many species? Evolution. 2021;75(5):978-988. doi:10.1111/evo.14235 apa: Butlin, R. K., Servedio, M. R., Smadja, C. M., Bank, C., Barton, N. H., Flaxman, S. M., … Qvarnström, A. (2021). Homage to Felsenstein 1981, or why are there so few/many species? Evolution. Wiley. https://doi.org/10.1111/evo.14235 chicago: Butlin, Roger K., Maria R. Servedio, Carole M. Smadja, Claudia Bank, Nicholas H Barton, Samuel M. Flaxman, Tatiana Giraud, et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14235. ieee: R. K. Butlin et al., “Homage to Felsenstein 1981, or why are there so few/many species?,” Evolution, vol. 75, no. 5. Wiley, pp. 978–988, 2021. ista: Butlin RK, Servedio MR, Smadja CM, Bank C, Barton NH, Flaxman SM, Giraud T, Hopkins R, Larson EL, Maan ME, Meier J, Merrill R, Noor MAF, Ortiz‐Barrientos D, Qvarnström A. 2021. Homage to Felsenstein 1981, or why are there so few/many species? Evolution. 75(5), 978–988. mla: Butlin, Roger K., et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” Evolution, vol. 75, no. 5, Wiley, 2021, pp. 978–88, doi:10.1111/evo.14235. short: R.K. Butlin, M.R. Servedio, C.M. Smadja, C. Bank, N.H. Barton, S.M. Flaxman, T. Giraud, R. Hopkins, E.L. Larson, M.E. Maan, J. Meier, R. Merrill, M.A.F. Noor, D. Ortiz‐Barrientos, A. Qvarnström, Evolution 75 (2021) 978–988. date_created: 2021-05-06T04:34:47Z date_published: 2021-04-19T00:00:00Z date_updated: 2023-09-05T15:44:33Z day: '19' department: - _id: NiBa doi: 10.1111/evo.14235 external_id: isi: - '000647224000001' intvolume: ' 75' isi: 1 issue: '5' keyword: - Genetics - Ecology - Evolution - Behavior and Systematics - General Agricultural and Biological Sciences language: - iso: eng main_file_link: - open_access: '1' url: https://onlinelibrary.wiley.com/doi/10.1111/evo.14235 month: '04' oa: 1 oa_version: Published Version page: 978-988 publication: Evolution publication_identifier: eissn: - 1558-5646 issn: - 0014-3820 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Homage to Felsenstein 1981, or why are there so few/many species? tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 75 year: '2021' ... --- _id: '13062' abstract: - lang: eng text: 'This paper analyzes the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.' article_processing_charge: No author: - first_name: Eniko full_name: Szep, Eniko id: 485BB5A4-F248-11E8-B48F-1D18A9856A87 last_name: Szep - first_name: Himani full_name: Sachdeva, Himani id: 42377A0A-F248-11E8-B48F-1D18A9856A87 last_name: Sachdeva - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Szep E, Sachdeva H, Barton NH. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. 2021. doi:10.5061/DRYAD.8GTHT76P1' apa: 'Szep, E., Sachdeva, H., & Barton, N. H. (2021). Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. Dryad. https://doi.org/10.5061/DRYAD.8GTHT76P1' chicago: 'Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model.” Dryad, 2021. https://doi.org/10.5061/DRYAD.8GTHT76P1.' ieee: 'E. Szep, H. Sachdeva, and N. H. Barton, “Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model.” Dryad, 2021.' ista: 'Szep E, Sachdeva H, Barton NH. 2021. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model, Dryad, 10.5061/DRYAD.8GTHT76P1.' mla: 'Szep, Eniko, et al. Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model. Dryad, 2021, doi:10.5061/DRYAD.8GTHT76P1.' short: E. Szep, H. Sachdeva, N.H. Barton, (2021). date_created: 2023-05-23T16:17:02Z date_published: 2021-03-02T00:00:00Z date_updated: 2023-09-05T15:44:05Z day: '02' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.8GTHT76P1 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.8gtht76p1 month: '03' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '9252' relation: used_in_publication status: public status: public title: 'Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model' tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '9383' abstract: - lang: eng text: A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present‐day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us. acknowledgement: We thank M. Garlovsky, S. Martin, C. Cooney, C. Roux, J. Larson, and J. Mallet for critical feedback and for discussion. K. Lohse, M. de la Cámara, J. Cerca, M. A. Chase, C. Baskett, A. M. Westram, and N. H. Barton gave feedback on a draft of the manuscript. O. Seehausen, two anonymous reviewers, and the AE (Michael Kopp) provided comments that greatly improved the manuscript. V. Holzmann made many corrections to the proofs. G. Bisschop and K. Lohse kindly contributed the simulations and analyses presented in Box 3. We would also like to extend our thanks to everyone who took part in the speciation survey, which received ethical approval through the University of Sheffield Ethics Review Procedure (Application 029768). We are especially grateful to R. K. Butlin for stimulating discussion throughout the writing of the manuscript and for feedback on an earlier draft. article_processing_charge: No article_type: original author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Mark full_name: Ravinet, Mark last_name: Ravinet citation: ama: Stankowski S, Ravinet M. Defining the speciation continuum. Evolution. 2021;75(6):1256-1273. doi:10.1111/evo.14215 apa: Stankowski, S., & Ravinet, M. (2021). Defining the speciation continuum. Evolution. Oxford University Press. https://doi.org/10.1111/evo.14215 chicago: Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution. Oxford University Press, 2021. https://doi.org/10.1111/evo.14215. ieee: S. Stankowski and M. Ravinet, “Defining the speciation continuum,” Evolution, vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021. ista: Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution. 75(6), 1256–1273. mla: Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution, vol. 75, no. 6, Oxford University Press, 2021, pp. 1256–73, doi:10.1111/evo.14215. short: S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273. date_created: 2021-05-09T22:01:39Z date_published: 2021-03-22T00:00:00Z date_updated: 2023-10-18T08:16:01Z day: '22' ddc: - '570' department: - _id: NiBa doi: 10.1111/evo.14215 external_id: isi: - '000647226400001' file: - access_level: open_access checksum: 96f6ccf15d95a4e9f7c0b27eee570fa6 content_type: application/pdf creator: kschuh date_created: 2022-03-25T12:02:04Z date_updated: 2022-03-25T12:02:04Z file_id: '10921' file_name: 2021_Evolution_Stankowski.pdf file_size: 719991 relation: main_file success: 1 file_date_updated: 2022-03-25T12:02:04Z has_accepted_license: '1' intvolume: ' 75' isi: 1 issue: '6' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 1256-1273 publication: Evolution publication_identifier: eissn: - 1558-5646 issn: - 0014-3820 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Defining the speciation continuum tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 75 year: '2021' ... --- _id: '14984' abstract: - lang: eng text: Hybrid zones are narrow geographic regions where different populations, races or interbreeding species meet and mate, producing mixed ‘hybrid’ offspring. They are relatively common and can be found in a diverse range of organisms and environments. The study of hybrid zones has played an important role in our understanding of the origin of species, with hybrid zones having been described as ‘natural laboratories’. This is because they allow us to study,in situ, the conditions and evolutionary forces that enable divergent taxa to remain distinct despite some ongoing gene exchange between them. article_processing_charge: No author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Daria full_name: Shipilina, Daria id: 428A94B0-F248-11E8-B48F-1D18A9856A87 last_name: Shipilina orcid: 0000-0002-1145-9226 - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 citation: ama: 'Stankowski S, Shipilina D, Westram AM. Hybrid Zones. In: Encyclopedia of Life Sciences. Vol 2. eLS. Wiley; 2021. doi:10.1002/9780470015902.a0029355' apa: Stankowski, S., Shipilina, D., & Westram, A. M. (2021). Hybrid Zones. In Encyclopedia of Life Sciences (Vol. 2). Wiley. https://doi.org/10.1002/9780470015902.a0029355 chicago: Stankowski, Sean, Daria Shipilina, and Anja M Westram. “Hybrid Zones.” In Encyclopedia of Life Sciences, Vol. 2. ELS. Wiley, 2021. https://doi.org/10.1002/9780470015902.a0029355. ieee: S. Stankowski, D. Shipilina, and A. M. Westram, “Hybrid Zones,” in Encyclopedia of Life Sciences, vol. 2, Wiley, 2021. ista: 'Stankowski S, Shipilina D, Westram AM. 2021.Hybrid Zones. In: Encyclopedia of Life Sciences. vol. 2.' mla: Stankowski, Sean, et al. “Hybrid Zones.” Encyclopedia of Life Sciences, vol. 2, Wiley, 2021, doi:10.1002/9780470015902.a0029355. short: S. Stankowski, D. Shipilina, A.M. Westram, in:, Encyclopedia of Life Sciences, Wiley, 2021. date_created: 2024-02-14T12:05:50Z date_published: 2021-05-28T00:00:00Z date_updated: 2024-02-19T09:54:18Z day: '28' department: - _id: NiBa doi: 10.1002/9780470015902.a0029355 intvolume: ' 2' language: - iso: eng month: '05' oa_version: None publication: Encyclopedia of Life Sciences publication_identifier: eisbn: - '9780470015902' isbn: - '9780470016176' publication_status: published publisher: Wiley quality_controlled: '1' series_title: eLS status: public title: Hybrid Zones type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2021' ... --- _id: '9192' abstract: - lang: eng text: Here are the research data underlying the publication " Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus)." Further information are summed up in the README document. article_processing_charge: No author: - first_name: Parvathy full_name: Surendranadh, Parvathy id: 455235B8-F248-11E8-B48F-1D18A9856A87 last_name: Surendranadh - first_name: Louise S full_name: Arathoon, Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon orcid: 0000-0003-1771-714X - first_name: Carina full_name: Baskett, Carina id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87 last_name: Baskett orcid: 0000-0002-7354-8574 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2021. doi:10.15479/AT:ISTA:9192 apa: Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2021). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9192 chicago: Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9192. ieee: P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2021. ista: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2021. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9192. mla: Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9192. short: P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2021). contributor: - contributor_type: project_member first_name: Parvathy id: 455235B8-F248-11E8-B48F-1D18A9856A87 last_name: Surendranadh - contributor_type: project_member first_name: Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon - contributor_type: project_member first_name: Carina id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87 last_name: Baskett - contributor_type: project_member first_name: David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - contributor_type: project_member first_name: Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - contributor_type: project_leader first_name: Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 date_created: 2021-02-24T17:49:21Z date_published: 2021-02-26T00:00:00Z date_updated: 2024-02-21T12:41:09Z day: '26' ddc: - '576' department: - _id: GradSch - _id: NiBa doi: 10.15479/AT:ISTA:9192 file: - access_level: open_access checksum: f85537815809a8a4b7da9d01163f88c0 content_type: application/x-zip-compressed creator: larathoo date_created: 2021-02-24T17:45:13Z date_updated: 2021-02-24T17:45:13Z file_id: '9193' file_name: Data_Code.zip file_size: 5934452 relation: main_file success: 1 file_date_updated: 2021-02-24T17:45:13Z has_accepted_license: '1' month: '02' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '11411' relation: used_in_publication status: public - id: '11321' relation: later_version status: public - id: '8254' relation: earlier_version status: public status: public title: Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '7651' abstract: - lang: eng text: The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods. article_number: '20190721' article_processing_charge: No article_type: original author: - first_name: J. full_name: Larsson, J. last_name: Larsson - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: S. full_name: Bengmark, S. last_name: Bengmark - first_name: T. full_name: Lundh, T. last_name: Lundh - first_name: R. K. full_name: Butlin, R. K. last_name: Butlin citation: ama: Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. 2020;17(163). doi:10.1098/rsif.2019.0721 apa: Larsson, J., Westram, A. M., Bengmark, S., Lundh, T., & Butlin, R. K. (2020). A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2019.0721 chicago: Larsson, J., Anja M Westram, S. Bengmark, T. Lundh, and R. K. Butlin. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” Journal of The Royal Society Interface. The Royal Society, 2020. https://doi.org/10.1098/rsif.2019.0721. ieee: J. Larsson, A. M. Westram, S. Bengmark, T. Lundh, and R. K. Butlin, “A developmentally descriptive method for quantifying shape in gastropod shells,” Journal of The Royal Society Interface, vol. 17, no. 163. The Royal Society, 2020. ista: Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. 2020. A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. 17(163), 20190721. mla: Larsson, J., et al. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” Journal of The Royal Society Interface, vol. 17, no. 163, 20190721, The Royal Society, 2020, doi:10.1098/rsif.2019.0721. short: J. Larsson, A.M. Westram, S. Bengmark, T. Lundh, R.K. Butlin, Journal of The Royal Society Interface 17 (2020). date_created: 2020-04-08T15:19:17Z date_published: 2020-02-01T00:00:00Z date_updated: 2021-01-12T08:14:41Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1098/rsif.2019.0721 file: - access_level: open_access checksum: 4eb102304402f5c56432516b84df86d6 content_type: application/pdf creator: dernst date_created: 2020-04-14T12:31:16Z date_updated: 2020-07-14T12:48:01Z file_id: '7660' file_name: 2020_JournRoyalSociety_Larsson.pdf file_size: 1556190 relation: main_file file_date_updated: 2020-07-14T12:48:01Z has_accepted_license: '1' intvolume: ' 17' issue: '163' language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: Journal of The Royal Society Interface publication_identifier: eissn: - 1742-5662 issn: - 1742-5689 publication_status: published publisher: The Royal Society quality_controlled: '1' scopus_import: 1 status: public title: A developmentally descriptive method for quantifying shape in gastropod shells tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2020' ... --- _id: '9123' abstract: - lang: eng text: 'Inversions are chromosomal rearrangements where the order of genes is reversed. Inversions originate by mutation and can be under positive, negative or balancing selection. Selective effects result from potential disruptive effects on meiosis, gene disruption at inversion breakpoints and, importantly, the effects of inversions as modifiers of recombination rate: Recombination is strongly reduced in individuals heterozygous for an inversion, allowing for alleles at different loci to be inherited as a ‘block’. This may lead to a selective advantage whenever it is favourable to keep certain combinations of alleles associated, for example under local adaptation with gene flow. Inversions can cover a considerable part of a chromosome and contain numerous loci under different selection pressures, so that the resulting overall effects may be complex. Empirical data from various systems show that inversions may have a prominent role in local adaptation, speciation, parallel evolution, the maintenance of polymorphism and sex chromosome evolution.' article_processing_charge: No author: - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Roger full_name: Butlin, Roger last_name: Butlin - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson citation: ama: 'Westram AM, Faria R, Butlin R, Johannesson K. Inversions and Evolution. In: ELS. Wiley; 2020. doi:10.1002/9780470015902.a0029007' apa: Westram, A. M., Faria, R., Butlin, R., & Johannesson, K. (2020). Inversions and Evolution. In eLS. Wiley. https://doi.org/10.1002/9780470015902.a0029007 chicago: Westram, Anja M, Rui Faria, Roger Butlin, and Kerstin Johannesson. “Inversions and Evolution.” In ELS. Wiley, 2020. https://doi.org/10.1002/9780470015902.a0029007. ieee: A. M. Westram, R. Faria, R. Butlin, and K. Johannesson, “Inversions and Evolution,” in eLS, Wiley, 2020. ista: 'Westram AM, Faria R, Butlin R, Johannesson K. 2020.Inversions and Evolution. In: eLS. .' mla: Westram, Anja M., et al. “Inversions and Evolution.” ELS, Wiley, 2020, doi:10.1002/9780470015902.a0029007. short: A.M. Westram, R. Faria, R. Butlin, K. Johannesson, in:, ELS, Wiley, 2020. date_created: 2021-02-15T12:39:04Z date_published: 2020-05-16T00:00:00Z date_updated: 2021-02-15T13:18:16Z day: '16' department: - _id: NiBa doi: 10.1002/9780470015902.a0029007 language: - iso: eng month: '05' oa_version: None publication: eLS publication_identifier: isbn: - '9780470016176' - '9780470015902' publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Inversions and Evolution type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '13073' abstract: - lang: eng text: The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study "replicated" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact. article_processing_charge: No author: - first_name: Alexis full_name: Simon, Alexis last_name: Simon - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Tahani full_name: El Ayari, Tahani last_name: El Ayari - first_name: Cathy full_name: Liautard-Haag, Cathy last_name: Liautard-Haag - first_name: Petr full_name: Strelkov, Petr last_name: Strelkov - first_name: John full_name: Welch, John last_name: Welch - first_name: Nicolas full_name: Bierne, Nicolas last_name: Bierne citation: ama: Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. 2020. doi:10.5061/DRYAD.R4XGXD29N apa: Simon, A., Fraisse, C., El Ayari, T., Liautard-Haag, C., Strelkov, P., Welch, J., & Bierne, N. (2020). How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. Dryad. https://doi.org/10.5061/DRYAD.R4XGXD29N chicago: Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard-Haag, Petr Strelkov, John Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Dryad, 2020. https://doi.org/10.5061/DRYAD.R4XGXD29N. ieee: A. Simon et al., “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020. ista: Simon A, Fraisse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch J, Bierne N. 2020. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels, Dryad, 10.5061/DRYAD.R4XGXD29N. mla: Simon, Alexis, et al. How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels. Dryad, 2020, doi:10.5061/DRYAD.R4XGXD29N. short: A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020). date_created: 2023-05-23T16:48:27Z date_published: 2020-09-22T00:00:00Z date_updated: 2023-08-04T11:04:11Z day: '22' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.R4XGXD29N main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.r4xgxd29n month: '09' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '8708' relation: used_in_publication status: public status: public title: How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '13065' abstract: - lang: eng text: Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available. article_processing_charge: No author: - first_name: Stephanie full_name: Arnoux, Stephanie last_name: Arnoux - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Christopher full_name: Sauvage, Christopher last_name: Sauvage citation: ama: 'Arnoux S, Fraisse C, Sauvage C. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. 2020. doi:10.5061/DRYAD.Q2BVQ83HD' apa: 'Arnoux, S., Fraisse, C., & Sauvage, C. (2020). VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. Dryad. https://doi.org/10.5061/DRYAD.Q2BVQ83HD' chicago: 'Arnoux, Stephanie, Christelle Fraisse, and Christopher Sauvage. “VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Dryad, 2020. https://doi.org/10.5061/DRYAD.Q2BVQ83HD.' ieee: 'S. Arnoux, C. Fraisse, and C. Sauvage, “VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species.” Dryad, 2020.' ista: 'Arnoux S, Fraisse C, Sauvage C. 2020. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species, Dryad, 10.5061/DRYAD.Q2BVQ83HD.' mla: 'Arnoux, Stephanie, et al. VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species. Dryad, 2020, doi:10.5061/DRYAD.Q2BVQ83HD.' short: S. Arnoux, C. Fraisse, C. Sauvage, (2020). date_created: 2023-05-23T16:30:20Z date_published: 2020-10-19T00:00:00Z date_updated: 2023-08-04T11:19:26Z day: '19' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.Q2BVQ83HD main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.q2bvq83hd month: '10' oa: 1 oa_version: Published Version publisher: Dryad related_material: link: - relation: software url: https://github.com/starnoux/arnoux_et_al_2019 record: - id: '8928' relation: used_in_publication status: public status: public title: 'VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species' tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '7995' abstract: - lang: eng text: When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple‐effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis , occur in North Atlantic rocky‐shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size‐assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment. acknowledgement: We are very grateful to I. Sencic, L. Brettell, A.‐L. Liabot, J. Galindo, M. Ravinet, and A. Butlin for their help with field sampling and mating experiments. This work was funded by the Natural Environment Research Council, European Research Council and Swedish Research Council VR and we are also very grateful for the support of the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg. The simulations were performed on resources at Chalmers Centre for Computational Science and Engineering (C3SE) provided by the Swedish National Infrastructure for Computing (SNIC). AMW was funded by the European Union's Horizon 2020 research and innovation program under Marie Skłodowska‐Curie grant agreement no. 797747. article_processing_charge: No article_type: original author: - first_name: Samuel full_name: Perini, Samuel last_name: Perini - first_name: Marina full_name: Rafajlović, Marina last_name: Rafajlović - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. 2020;74(7):1482-1497. doi:10.1111/evo.14027 apa: Perini, S., Rafajlović, M., Westram, A. M., Johannesson, K., & Butlin, R. K. (2020). Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. Wiley. https://doi.org/10.1111/evo.14027 chicago: Perini, Samuel, Marina Rafajlović, Anja M Westram, Kerstin Johannesson, and Roger K. Butlin. “Assortative Mating, Sexual Selection, and Their Consequences for Gene Flow in Littorina.” Evolution. Wiley, 2020. https://doi.org/10.1111/evo.14027. ieee: S. Perini, M. Rafajlović, A. M. Westram, K. Johannesson, and R. K. Butlin, “Assortative mating, sexual selection, and their consequences for gene flow in Littorina,” Evolution, vol. 74, no. 7. Wiley, pp. 1482–1497, 2020. ista: Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. 2020. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. 74(7), 1482–1497. mla: Perini, Samuel, et al. “Assortative Mating, Sexual Selection, and Their Consequences for Gene Flow in Littorina.” Evolution, vol. 74, no. 7, Wiley, 2020, pp. 1482–97, doi:10.1111/evo.14027. short: S. Perini, M. Rafajlović, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution 74 (2020) 1482–1497. date_created: 2020-06-22T09:14:21Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-08-22T07:13:38Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/evo.14027 ec_funded: 1 external_id: isi: - '000539780800001' file: - access_level: open_access checksum: 56235bf1e2a9e25f96196bb13b6b754d content_type: application/pdf creator: dernst date_created: 2020-11-25T10:49:48Z date_updated: 2020-11-25T10:49:48Z file_id: '8808' file_name: 2020_Evolution_Perini.pdf file_size: 1080810 relation: main_file success: 1 file_date_updated: 2020-11-25T10:49:48Z has_accepted_license: '1' intvolume: ' 74' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1482-1497 project: - _id: 265B41B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '797747' name: Theoretical and empirical approaches to understanding Parallel Adaptation publication: Evolution publication_identifier: eissn: - '15585646' issn: - '00143820' publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '8809' relation: research_data status: public scopus_import: '1' status: public title: Assortative mating, sexual selection, and their consequences for gene flow in Littorina tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 74 year: '2020' ... --- _id: '8809' abstract: - lang: eng text: When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment. article_processing_charge: No author: - first_name: Samuel full_name: Perini, Samuel last_name: Perini - first_name: Marina full_name: Rafajlovic, Marina last_name: Rafajlovic - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger full_name: Butlin, Roger last_name: Butlin citation: ama: 'Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. 2020. doi:10.5061/dryad.qrfj6q5cn' apa: 'Perini, S., Rafajlovic, M., Westram, A. M., Johannesson, K., & Butlin, R. (2020). Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. Dryad. https://doi.org/10.5061/dryad.qrfj6q5cn' chicago: 'Perini, Samuel, Marina Rafajlovic, Anja M Westram, Kerstin Johannesson, and Roger Butlin. “Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina.” Dryad, 2020. https://doi.org/10.5061/dryad.qrfj6q5cn.' ieee: 'S. Perini, M. Rafajlovic, A. M. Westram, K. Johannesson, and R. Butlin, “Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina.” Dryad, 2020.' ista: 'Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. 2020. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina, Dryad, 10.5061/dryad.qrfj6q5cn.' mla: 'Perini, Samuel, et al. Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina. Dryad, 2020, doi:10.5061/dryad.qrfj6q5cn.' short: S. Perini, M. Rafajlovic, A.M. Westram, K. Johannesson, R. Butlin, (2020). date_created: 2020-11-25T11:07:25Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-08-22T07:13:37Z day: '01' department: - _id: NiBa doi: 10.5061/dryad.qrfj6q5cn has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.qrfj6q5cn month: '07' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '7995' relation: used_in_publication status: public status: public title: 'Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina' tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '8112' article_number: '20190530' article_processing_charge: No article_type: letter_note author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Barton NH. On the completion of speciation. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0530' apa: 'Barton, N. H. (2020). On the completion of speciation. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0530' chicago: 'Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0530.' ieee: 'N. H. Barton, “On the completion of speciation,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.' ista: 'Barton NH. 2020. On the completion of speciation. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190530.' mla: 'Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190530, The Royal Society, 2020, doi:10.1098/rstb.2019.0530.' short: 'N.H. Barton, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).' date_created: 2020-07-13T03:41:39Z date_published: 2020-07-12T00:00:00Z date_updated: 2023-08-22T07:53:52Z day: '12' department: - _id: NiBa doi: 10.1098/rstb.2019.0530 external_id: isi: - '000552662100002' pmid: - '32654647' intvolume: ' 375' isi: 1 issue: '1806' language: - iso: eng month: '07' oa_version: None pmid: 1 publication: 'Philosophical Transactions of the Royal Society. Series B: Biological Sciences' publication_identifier: eissn: - 1471-2970 issn: - 0962-8436 publication_status: published publisher: The Royal Society quality_controlled: '1' scopus_import: '1' status: public title: On the completion of speciation type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 375 year: '2020' ... --- _id: '8168' abstract: - lang: eng text: Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed. article_number: '20190528' article_processing_charge: No article_type: original author: - first_name: Jonna full_name: Kulmuni, Jonna last_name: Kulmuni - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin - first_name: Kay full_name: Lucek, Kay last_name: Lucek - first_name: Vincent full_name: Savolainen, Vincent last_name: Savolainen - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 citation: ama: 'Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society Series B: Biological sciences. 2020;375(1806). doi:10.1098/rstb.2019.0528' apa: 'Kulmuni, J., Butlin, R. K., Lucek, K., Savolainen, V., & Westram, A. M. (2020). Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0528' chicago: 'Kulmuni, Jonna, Roger K. Butlin, Kay Lucek, Vincent Savolainen, and Anja M Westram. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0528.' ieee: 'J. Kulmuni, R. K. Butlin, K. Lucek, V. Savolainen, and A. M. Westram, “Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers,” Philosophical Transactions of the Royal Society. Series B: Biological sciences, vol. 375, no. 1806. The Royal Society, 2020.' ista: 'Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. 2020. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological sciences. 375(1806), 20190528.' mla: 'Kulmuni, Jonna, et al. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190528, The Royal Society, 2020, doi:10.1098/rstb.2019.0528.' short: 'J. Kulmuni, R.K. Butlin, K. Lucek, V. Savolainen, A.M. Westram, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).' date_created: 2020-07-26T22:01:01Z date_published: 2020-07-12T00:00:00Z date_updated: 2023-08-22T08:21:31Z day: '12' department: - _id: NiBa doi: 10.1098/rstb.2019.0528 ec_funded: 1 external_id: isi: - '000552662100001' pmid: - '32654637' intvolume: ' 375' isi: 1 issue: '1806' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1098/rstb.2019.0528 month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 265B41B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '797747' name: Theoretical and empirical approaches to understanding Parallel Adaptation publication: 'Philosophical Transactions of the Royal Society. Series B: Biological sciences' publication_identifier: eissn: - 1471-2970 issn: - 0962-8436 publication_status: published publisher: The Royal Society quality_controlled: '1' scopus_import: '1' status: public title: 'Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 375 year: '2020' ... --- _id: '8167' abstract: - lang: eng text: The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions. acknowledgement: Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council. We thank Rui Faria, Nicola Nadeau, Martin Garlovsky and Hernan Morales for advice and/or useful discussion during the project. Richard Turney, Graciela Sotelo, Jenny Larson, Stéphane Loisel and Meghan Wharton participated in the collection and processing of samples. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield High-performance computer, ShARC. Jeffrey Feder and an anonymous reviewer provided comments that improved the manuscript. article_number: '20190545' article_processing_charge: No article_type: original author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Zuzanna B. full_name: Zagrodzka, Zuzanna B. last_name: Zagrodzka - first_name: Isobel full_name: Eyres, Isobel last_name: Eyres - first_name: Thomas full_name: Broquet, Thomas last_name: Broquet - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: 'Stankowski S, Westram AM, Zagrodzka ZB, et al. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0545' apa: 'Stankowski, S., Westram, A. M., Zagrodzka, Z. B., Eyres, I., Broquet, T., Johannesson, K., & Butlin, R. K. (2020). The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0545' chicago: 'Stankowski, Sean, Anja M Westram, Zuzanna B. Zagrodzka, Isobel Eyres, Thomas Broquet, Kerstin Johannesson, and Roger K. Butlin. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0545.' ieee: 'S. Stankowski et al., “The evolution of strong reproductive isolation between sympatric intertidal snails,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.' ista: 'Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K, Butlin RK. 2020. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190545.' mla: 'Stankowski, Sean, et al. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190545, The Royal Society, 2020, doi:10.1098/rstb.2019.0545.' short: 'S. Stankowski, A.M. Westram, Z.B. Zagrodzka, I. Eyres, T. Broquet, K. Johannesson, R.K. Butlin, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).' date_created: 2020-07-26T22:01:01Z date_published: 2020-07-12T00:00:00Z date_updated: 2023-08-22T08:22:13Z day: '12' department: - _id: NiBa doi: 10.1098/rstb.2019.0545 external_id: isi: - '000552662100014' pmid: - '32654639' intvolume: ' 375' isi: 1 issue: '1806' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1098/rstb.2019.0545 month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: 'Philosophical Transactions of the Royal Society. Series B: Biological Sciences' publication_identifier: eissn: - 1471-2970 publication_status: published publisher: The Royal Society quality_controlled: '1' scopus_import: '1' status: public title: The evolution of strong reproductive isolation between sympatric intertidal snails type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 375 year: '2020' ... --- _id: '8169' abstract: - lang: eng text: Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the ‘escape’ of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation. acknowledgement: This work was supported by a fellowship from the China Scholarship Council (CSC) to H.S., Swiss National Science Foundation (SNF) grant no. 31003A_149306 to C.L., doctoral programme grant W1225-B20 to a faculty team including C.L., and the University of Vienna. We thank members of J.L.’s lab for collecting samples, Michael Barfuss and Elfi Grasserbauer for help in the laboratory, the Next Generation Sequencing Platform of the University of Berne for sequencing, the Vienna Scientific Cluster (VSC) for access to computational resources, and Claus Vogel and members of the PopGen Vienna graduate school for helpful discussions. article_number: '20190544' article_processing_charge: No article_type: original author: - first_name: Huiying full_name: Shang, Huiying last_name: Shang - first_name: Jaqueline full_name: Hess, Jaqueline last_name: Hess - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Pär K. full_name: Ingvarsson, Pär K. last_name: Ingvarsson - first_name: Jianquan full_name: Liu, Jianquan last_name: Liu - first_name: Christian full_name: Lexer, Christian last_name: Lexer citation: ama: 'Shang H, Hess J, Pickup M, et al. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0544' apa: 'Shang, H., Hess, J., Pickup, M., Field, D., Ingvarsson, P. K., Liu, J., & Lexer, C. (2020). Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0544' chicago: 'Shang, Huiying, Jaqueline Hess, Melinda Pickup, David Field, Pär K. Ingvarsson, Jianquan Liu, and Christian Lexer. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0544.' ieee: 'H. Shang et al., “Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.' ista: 'Shang H, Hess J, Pickup M, Field D, Ingvarsson PK, Liu J, Lexer C. 2020. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190544.' mla: 'Shang, Huiying, et al. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190544, The Royal Society, 2020, doi:10.1098/rstb.2019.0544.' short: 'H. Shang, J. Hess, M. Pickup, D. Field, P.K. Ingvarsson, J. Liu, C. Lexer, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).' date_created: 2020-07-26T22:01:02Z date_published: 2020-07-12T00:00:00Z date_updated: 2023-08-22T08:23:24Z day: '12' department: - _id: NiBa doi: 10.1098/rstb.2019.0544 external_id: isi: - '000552662100013' pmid: - '32654641' intvolume: ' 375' isi: 1 issue: '1806' language: - iso: eng month: '07' oa_version: Published Version pmid: 1 publication: 'Philosophical Transactions of the Royal Society. Series B: Biological Sciences' publication_identifier: eissn: - '14712970' publication_status: published publisher: The Royal Society quality_controlled: '1' scopus_import: '1' status: public title: 'Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 375 year: '2020' ... --- _id: '9799' abstract: - lang: eng text: Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations. article_processing_charge: No author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: John J. full_name: Welch, John J. last_name: Welch citation: ama: Fraisse C, Welch JJ. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. 2020. doi:10.6084/m9.figshare.7957469.v1 apa: Fraisse, C., & Welch, J. J. (2020). Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. https://doi.org/10.6084/m9.figshare.7957469.v1 chicago: Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. https://doi.org/10.6084/m9.figshare.7957469.v1. ieee: C. Fraisse and J. J. Welch, “Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020. ista: Fraisse C, Welch JJ. 2020. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, 10.6084/m9.figshare.7957469.v1. mla: Fraisse, Christelle, and John J. Welch. Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes. Royal Society of London, 2020, doi:10.6084/m9.figshare.7957469.v1. short: C. Fraisse, J.J. Welch, (2020). date_created: 2021-08-06T11:26:57Z date_published: 2020-10-15T00:00:00Z date_updated: 2023-08-25T10:34:41Z day: '15' department: - _id: BeVi - _id: NiBa doi: 10.6084/m9.figshare.7957469.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.7957469.v1 month: '10' oa: 1 oa_version: Published Version publisher: Royal Society of London related_material: record: - id: '6467' relation: used_in_publication status: public status: public title: Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '9798' abstract: - lang: eng text: Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations. article_processing_charge: No author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: John J. full_name: Welch, John J. last_name: Welch citation: ama: Fraisse C, Welch JJ. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. 2020. doi:10.6084/m9.figshare.7957472.v1 apa: Fraisse, C., & Welch, J. J. (2020). Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. https://doi.org/10.6084/m9.figshare.7957472.v1 chicago: Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. https://doi.org/10.6084/m9.figshare.7957472.v1. ieee: C. Fraisse and J. J. Welch, “Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020. ista: Fraisse C, Welch JJ. 2020. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, 10.6084/m9.figshare.7957472.v1. mla: Fraisse, Christelle, and John J. Welch. Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes. Royal Society of London, 2020, doi:10.6084/m9.figshare.7957472.v1. short: C. Fraisse, J.J. Welch, (2020). date_created: 2021-08-06T11:18:15Z date_published: 2020-10-15T00:00:00Z date_updated: 2023-08-25T10:34:41Z day: '15' department: - _id: BeVi - _id: NiBa doi: 10.6084/m9.figshare.7957472.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.7957472.v1 month: '10' oa: 1 oa_version: Published Version publisher: Royal Society of London related_material: record: - id: '6467' relation: used_in_publication status: public status: public title: Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '7236' abstract: - lang: eng text: The biotic interactions hypothesis posits that biotic interactions are more important drivers of adaptation closer to the equator, evidenced by “stronger” contemporary interactions (e.g. greater interaction rates) and/or patterns of trait evolution consistent with a history of stronger interactions. Support for the hypothesis is mixed, but few studies span tropical and temperate regions while experimentally controlling for evolutionary history. Here, we integrate field observations and common garden experiments to quantify the relative importance of pollination and herbivory in a pair of tropical‐temperate congeneric perennial herbs. Phytolacca rivinoides and P. americana are pioneer species native to the Neotropics and the eastern USA, respectively. We compared plant‐pollinator and plant‐herbivore interactions between three tropical populations of P. rivinoides from Costa Rica and three temperate populations of P. americana from its northern range edge in Michigan and Ohio. For some metrics of interaction importance, we also included three subtropical populations of P. americana from its southern range edge in Florida. This approach confounds species and region but allows us, uniquely, to measure complementary proxies of interaction importance across a tropical‐temperate range in one system. To test the prediction that lower‐latitude plants are more reliant on insect pollinators, we quantified floral display and reward, insect visitation rates, and self‐pollination ability (autogamy). To test the prediction that lower‐latitude plants experience more herbivore pressure, we quantified herbivory rates, herbivore abundance, and leaf palatability. We found evidence supporting the biotic interactions hypothesis for most comparisons between P. rivinoides and north‐temperate P. americana (floral display, insect visitation, autogamy, herbivory, herbivore abundance, and young‐leaf palatability). Results for subtropical P. americana populations, however, were typically not intermediate between P. rivinoides and north‐temperate P. americana, as would be predicted by a linear latitudinal gradient in interaction importance. Subtropical young‐leaf palatability was intermediate, but subtropical mature leaves were the least palatable, and pollination‐related traits did not differ between temperate and subtropical regions. These nonlinear patterns of interaction importance suggest future work to relate interaction importance to climatic or biotic thresholds. In sum, we found that the biotic interactions hypothesis was more consistently supported at the larger spatial scale of our study. article_number: e01397 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Carina full_name: Baskett, Carina id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87 last_name: Baskett orcid: 0000-0002-7354-8574 - first_name: Lucy full_name: Schroeder, Lucy last_name: Schroeder - first_name: Marjorie G. full_name: Weber, Marjorie G. last_name: Weber - first_name: Douglas W. full_name: Schemske, Douglas W. last_name: Schemske citation: ama: Baskett C, Schroeder L, Weber MG, Schemske DW. Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. 2020;90(1). doi:10.1002/ecm.1397 apa: Baskett, C., Schroeder, L., Weber, M. G., & Schemske, D. W. (2020). Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. Wiley. https://doi.org/10.1002/ecm.1397 chicago: Baskett, Carina, Lucy Schroeder, Marjorie G. Weber, and Douglas W. Schemske. “Multiple Metrics of Latitudinal Patterns in Insect Pollination and Herbivory for a Tropical‐temperate Congener Pair.” Ecological Monographs. Wiley, 2020. https://doi.org/10.1002/ecm.1397. ieee: C. Baskett, L. Schroeder, M. G. Weber, and D. W. Schemske, “Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair,” Ecological Monographs, vol. 90, no. 1. Wiley, 2020. ista: Baskett C, Schroeder L, Weber MG, Schemske DW. 2020. Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. 90(1), e01397. mla: Baskett, Carina, et al. “Multiple Metrics of Latitudinal Patterns in Insect Pollination and Herbivory for a Tropical‐temperate Congener Pair.” Ecological Monographs, vol. 90, no. 1, e01397, Wiley, 2020, doi:10.1002/ecm.1397. short: C. Baskett, L. Schroeder, M.G. Weber, D.W. Schemske, Ecological Monographs 90 (2020). date_created: 2020-01-07T12:47:07Z date_published: 2020-02-01T00:00:00Z date_updated: 2023-09-05T15:43:19Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1002/ecm.1397 ec_funded: 1 external_id: isi: - '000508511600001' file: - access_level: open_access checksum: ab8130c6e68101f5a091d05324c36f08 content_type: application/pdf creator: dernst date_created: 2020-02-10T08:18:14Z date_updated: 2020-07-14T12:47:54Z file_id: '7469' file_name: 2020_EcologMono_Baskett.pdf file_size: 537941 relation: main_file file_date_updated: 2020-07-14T12:47:54Z has_accepted_license: '1' intvolume: ' 90' isi: 1 issue: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Ecological Monographs publication_identifier: eissn: - 1557-7015 issn: - 0012-9615 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 90 year: '2020' ... --- _id: '7205' abstract: - lang: eng text: Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the "Crab" and "Wave" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Post‐zygotic barriers might include genetic incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011 embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterized female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index, and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant post‐zygotic barriers contributing to ecotype divergence, and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females. article_processing_charge: No article_type: original author: - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Zuzanna full_name: Zagrodzka, Zuzanna last_name: Zagrodzka - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. 2020;33(3):342-351. doi:10.1111/jeb.13570 apa: Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. K. (2020). Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13570 chicago: Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger K. Butlin. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” Journal of Evolutionary Biology. Wiley, 2020. https://doi.org/10.1111/jeb.13570. ieee: K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. K. Butlin, “Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?,” Journal of Evolutionary Biology, vol. 33, no. 3. Wiley, pp. 342–351, 2020. ista: Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. 2020. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. 33(3), 342–351. mla: Johannesson, Kerstin, et al. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” Journal of Evolutionary Biology, vol. 33, no. 3, Wiley, 2020, pp. 342–51, doi:10.1111/jeb.13570. short: K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R.K. Butlin, Journal of Evolutionary Biology 33 (2020) 342–351. date_created: 2019-12-22T23:00:43Z date_published: 2020-03-01T00:00:00Z date_updated: 2023-09-06T14:48:57Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/jeb.13570 external_id: isi: - '000500954800001' pmid: - '31724256' file: - access_level: open_access checksum: 7534ff0839709c0c5265c12d29432f03 content_type: application/pdf creator: dernst date_created: 2020-09-22T09:42:18Z date_updated: 2020-09-22T09:42:18Z file_id: '8553' file_name: 2020_EvolBiology_Johannesson.pdf file_size: 885611 relation: main_file success: 1 file_date_updated: 2020-09-22T09:42:18Z has_accepted_license: '1' intvolume: ' 33' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 342-351 pmid: 1 publication: Journal of Evolutionary Biology publication_identifier: eissn: - '14209101' issn: - 1010061X publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '13067' relation: research_data status: public scopus_import: '1' status: public title: Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 33 year: '2020' ... --- _id: '8574' abstract: - lang: eng text: "This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes \r\nleave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes, such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful \r\ntool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real \r\nbehavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.\r\nWe give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both \r\ndrift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare \r\nthe results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook to further research. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Eniko full_name: Szep, Eniko id: 485BB5A4-F248-11E8-B48F-1D18A9856A87 last_name: Szep citation: ama: Szep E. Local adaptation in metapopulations. 2020. doi:10.15479/AT:ISTA:8574 apa: Szep, E. (2020). Local adaptation in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8574 chicago: Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8574. ieee: E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020. ista: Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria. mla: Szep, Eniko. Local Adaptation in Metapopulations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8574. short: E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020. date_created: 2020-09-28T07:33:38Z date_published: 2020-09-20T00:00:00Z date_updated: 2023-09-07T13:11:39Z day: '20' ddc: - '570' degree_awarded: PhD department: - _id: NiBa doi: 10.15479/AT:ISTA:8574 file: - access_level: open_access checksum: 20e71f015fbbd78fea708893ad634ed0 content_type: application/pdf creator: dernst date_created: 2020-09-28T07:25:35Z date_updated: 2020-09-28T07:25:35Z file_id: '8575' file_name: thesis_EnikoSzep_final.pdf file_size: 6354833 relation: main_file success: 1 - access_level: closed checksum: a8de2c14a1bb4e53c857787efbb289e1 content_type: application/x-zip-compressed creator: dernst date_created: 2020-09-28T07:25:37Z date_updated: 2020-09-28T07:25:37Z file_id: '8576' file_name: thesisFiles_EnikoSzep.zip file_size: 23020401 relation: source_file file_date_updated: 2020-09-28T07:25:37Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '158' publication_identifier: eissn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Local adaptation in metapopulations type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8254' abstract: - lang: eng text: "Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192." article_processing_charge: No author: - first_name: Louise S full_name: Arathoon, Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon orcid: 0000-0003-1771-714X citation: ama: Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:10.15479/AT:ISTA:8254 apa: Arathoon, L. S. (2020). Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8254 chicago: Arathoon, Louise S. “Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus).” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8254. ieee: L. S. Arathoon, “Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus).” Institute of Science and Technology Austria, 2020. ista: Arathoon LS. 2020. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus), Institute of Science and Technology Austria, 10.15479/AT:ISTA:8254. mla: Arathoon, Louise S. Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus). Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8254. short: L.S. Arathoon, (2020). contributor: - contributor_type: data_collector first_name: Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon - contributor_type: project_member first_name: Parvathy id: 455235B8-F248-11E8-B48F-1D18A9856A87 last_name: Surendranadh - contributor_type: project_member first_name: Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - contributor_type: project_member first_name: David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - contributor_type: project_member first_name: Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - contributor_type: project_member first_name: Carina id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87 last_name: Baskett date_created: 2020-08-12T12:49:23Z date_published: 2020-08-18T00:00:00Z date_updated: 2024-02-21T12:41:09Z day: '18' ddc: - '576' department: - _id: NiBa doi: 10.15479/AT:ISTA:8254 file: - access_level: open_access checksum: 4f1382ed4384751b6013398c11557bf6 content_type: application/x-zip-compressed creator: dernst date_created: 2020-08-18T08:03:23Z date_updated: 2020-08-18T08:03:23Z file_id: '8280' file_name: Data_Rcode_MathematicaNB.zip file_size: 5778420 relation: main_file success: 1 file_date_updated: 2020-08-18T08:03:23Z has_accepted_license: '1' month: '08' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '11321' relation: later_version status: public - id: '9192' relation: later_version status: public status: public title: Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus) tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '9839' abstract: - lang: eng text: 'More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.' article_processing_charge: No author: - first_name: Jitka full_name: Polechova, Jitka id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 citation: ama: 'Polechova J. Data from: Is the sky the limit? On the expansion threshold of a species’ range. 2019. doi:10.5061/dryad.5vv37' apa: 'Polechova, J. (2019). Data from: Is the sky the limit? On the expansion threshold of a species’ range. Dryad. https://doi.org/10.5061/dryad.5vv37' chicago: 'Polechova, Jitka. “Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” Dryad, 2019. https://doi.org/10.5061/dryad.5vv37.' ieee: 'J. Polechova, “Data from: Is the sky the limit? On the expansion threshold of a species’ range.” Dryad, 2019.' ista: 'Polechova J. 2019. Data from: Is the sky the limit? On the expansion threshold of a species’ range, Dryad, 10.5061/dryad.5vv37.' mla: 'Polechova, Jitka. Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range. Dryad, 2019, doi:10.5061/dryad.5vv37.' short: J. Polechova, (2019). date_created: 2021-08-09T13:07:28Z date_published: 2019-06-22T00:00:00Z date_updated: 2023-02-23T11:14:30Z day: '22' department: - _id: NiBa doi: 10.5061/dryad.5vv37 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.5vv37 month: '06' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '315' relation: used_in_publication status: public status: public title: 'Data from: Is the sky the limit? On the expansion threshold of a species'' range' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '5911' abstract: - lang: eng text: Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polymorphisms are maintained by different processes, for example, divergent or balancing selection, or a mix of multiple processes. Moreover, the relative roles of selection, drift, mutation, and recombination will change over the lifetime of an inversion and within its area of distribution. We believe inversions are central to the evolution of many species, but we need many more data and new models to understand the complex mechanisms involved. article_processing_charge: No article_type: original author: - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 citation: ama: Faria R, Johannesson K, Butlin RK, Westram AM. Evolving inversions. Trends in Ecology and Evolution. 2019;34(3):239-248. doi:10.1016/j.tree.2018.12.005 apa: Faria, R., Johannesson, K., Butlin, R. K., & Westram, A. M. (2019). Evolving inversions. Trends in Ecology and Evolution. Elsevier. https://doi.org/10.1016/j.tree.2018.12.005 chicago: Faria, Rui, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Evolving Inversions.” Trends in Ecology and Evolution. Elsevier, 2019. https://doi.org/10.1016/j.tree.2018.12.005. ieee: R. Faria, K. Johannesson, R. K. Butlin, and A. M. Westram, “Evolving inversions,” Trends in Ecology and Evolution, vol. 34, no. 3. Elsevier, pp. 239–248, 2019. ista: Faria R, Johannesson K, Butlin RK, Westram AM. 2019. Evolving inversions. Trends in Ecology and Evolution. 34(3), 239–248. mla: Faria, Rui, et al. “Evolving Inversions.” Trends in Ecology and Evolution, vol. 34, no. 3, Elsevier, 2019, pp. 239–48, doi:10.1016/j.tree.2018.12.005. short: R. Faria, K. Johannesson, R.K. Butlin, A.M. Westram, Trends in Ecology and Evolution 34 (2019) 239–248. date_created: 2019-02-03T22:59:15Z date_published: 2019-03-01T00:00:00Z date_updated: 2023-08-24T14:29:48Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1016/j.tree.2018.12.005 ec_funded: 1 external_id: isi: - '000459899000013' file: - access_level: open_access checksum: ef24572d6ebcc1452c067e05410cc4a2 content_type: application/pdf creator: cziletti date_created: 2020-01-09T10:55:58Z date_updated: 2020-07-14T12:47:13Z file_id: '7245' file_name: 2019_Trends_Evolution_Faria.pdf file_size: 1946795 relation: main_file file_date_updated: 2020-07-14T12:47:13Z has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 239-248 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Trends in Ecology and Evolution publication_identifier: issn: - '01695347' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Evolving inversions tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 34 year: '2019' ... --- _id: '5680' abstract: - lang: eng text: Pollinators display a remarkable diversity of foraging strategies with flowering plants, from primarily mutualistic interactions to cheating through nectar robbery. Despite numerous studies on the effect of nectar robbing on components of plant fitness, its contribution to reproductive isolation is unclear. We experimentally tested the impact of different pollinator strategies in a natural hybrid zone between two subspecies of Antirrhinum majus with alternate flower colour guides. On either side of a steep cline in flower colour between Antirrhinum majus pseudomajus (magenta) and A. m. striatum (yellow), we quantified the behaviour of all floral visitors at different time points during the flowering season. Using long-run camera surveys, we quantify the impact of nectar robbing on the number of flowers visited per inflorescence and the flower probing time. We further experimentally tested the effect of nectar robbing on female reproductive success by manipulating the intensity of robbing. While robbing increased over time the number of legitimate visitors tended to decrease concomitantly. We found that the number of flowers pollinated on a focal inflorescence decreased with the number of prior robbing events. However, in the manipulative experiment, fruit set and fruit volume did not vary significantly between low robbing and control treatments. Our findings challenge the idea that robbers have a negative impact on plant fitness through female function. This study also adds to our understanding of the components of pollinator-mediated reproductive isolation and the maintenance of Antirrhinum hybrid zones. article_processing_charge: No author: - first_name: Christophe full_name: Andalo, Christophe last_name: Andalo - first_name: Monique full_name: Burrus, Monique last_name: Burrus - first_name: Sandrine full_name: Paute, Sandrine last_name: Paute - first_name: Christine full_name: Lauzeral, Christine last_name: Lauzeral - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 citation: ama: Andalo C, Burrus M, Paute S, Lauzeral C, Field D. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 2019;166(1):80-92. doi:10.1080/23818107.2018.1545142 apa: Andalo, C., Burrus, M., Paute, S., Lauzeral, C., & Field, D. (2019). Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. Taylor and Francis. https://doi.org/10.1080/23818107.2018.1545142 chicago: Andalo, Christophe, Monique Burrus, Sandrine Paute, Christine Lauzeral, and David Field. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany Letters. Taylor and Francis, 2019. https://doi.org/10.1080/23818107.2018.1545142. ieee: C. Andalo, M. Burrus, S. Paute, C. Lauzeral, and D. Field, “Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone,” Botany Letters, vol. 166, no. 1. Taylor and Francis, pp. 80–92, 2019. ista: Andalo C, Burrus M, Paute S, Lauzeral C, Field D. 2019. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 166(1), 80–92. mla: Andalo, Christophe, et al. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany Letters, vol. 166, no. 1, Taylor and Francis, 2019, pp. 80–92, doi:10.1080/23818107.2018.1545142. short: C. Andalo, M. Burrus, S. Paute, C. Lauzeral, D. Field, Botany Letters 166 (2019) 80–92. date_created: 2018-12-16T22:59:20Z date_published: 2019-01-01T00:00:00Z date_updated: 2023-08-24T14:34:12Z day: '01' department: - _id: NiBa doi: 10.1080/23818107.2018.1545142 external_id: isi: - '000463802800009' intvolume: ' 166' isi: 1 issue: '1' language: - iso: eng month: '01' oa_version: None page: 80-92 publication: Botany Letters publication_identifier: eissn: - '23818115' issn: - '23818107' publication_status: published publisher: Taylor and Francis quality_controlled: '1' scopus_import: '1' status: public title: Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 166 year: '2019' ... --- _id: '6022' abstract: - lang: eng text: The evolution of new species is made easier when traits under divergent ecological selection are also mating cues. Such ecological mating cues are now considered more common than previously thought, but we still know little about the genetic changes underlying their evolution or more generally about the genetic basis for assortative mating behaviors. Both tight physical linkage and the existence of large-effect preference loci will strengthen genetic associations between behavioral and ecological barriers, promoting the evolution of assortative mating. The warning patterns of Heliconius melpomene and H. cydno are under disruptive selection due to increased predation of nonmimetic hybrids and are used during mate recognition. We carried out a genome-wide quantitative trait locus (QTL) analysis of preference behaviors between these species and showed that divergent male preference has a simple genetic basis. We identify three QTLs that together explain a large proportion (approximately 60%) of the difference in preference behavior observed between the parental species. One of these QTLs is just 1.2 (0-4.8) centiMorgans (cM) from the major color pattern gene optix, and, individually, all three have a large effect on the preference phenotype. Genomic divergence between H. cydno and H. melpomene is high but broadly heterogenous, and admixture is reduced at the preference-optix color pattern locus but not the other preference QTLs. The simple genetic architecture we reveal will facilitate the evolution and maintenance of new species despite ongoing gene flow by coupling behavioral and ecological aspects of reproductive isolation. article_number: e2005902 article_processing_charge: No author: - first_name: Richard M. full_name: Merrill, Richard M. last_name: Merrill - first_name: Pasi full_name: Rastas, Pasi last_name: Rastas - first_name: Simon H. full_name: Martin, Simon H. last_name: Martin - first_name: Maria C full_name: Melo Hurtado, Maria C id: 386D7308-F248-11E8-B48F-1D18A9856A87 last_name: Melo Hurtado - first_name: Sarah full_name: Barker, Sarah last_name: Barker - first_name: John full_name: Davey, John last_name: Davey - first_name: W. Owen full_name: Mcmillan, W. Owen last_name: Mcmillan - first_name: Chris D. full_name: Jiggins, Chris D. last_name: Jiggins citation: ama: Merrill RM, Rastas P, Martin SH, et al. Genetic dissection of assortative mating behavior. PLoS Biology. 2019;17(2). doi:10.1371/journal.pbio.2005902 apa: Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Genetic dissection of assortative mating behavior. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005902 chicago: Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Genetic Dissection of Assortative Mating Behavior.” PLoS Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pbio.2005902. ieee: R. M. Merrill et al., “Genetic dissection of assortative mating behavior,” PLoS Biology, vol. 17, no. 2. Public Library of Science, 2019. ista: Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Genetic dissection of assortative mating behavior. PLoS Biology. 17(2), e2005902. mla: Merrill, Richard M., et al. “Genetic Dissection of Assortative Mating Behavior.” PLoS Biology, vol. 17, no. 2, e2005902, Public Library of Science, 2019, doi:10.1371/journal.pbio.2005902. short: R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, PLoS Biology 17 (2019). date_created: 2019-02-17T22:59:21Z date_published: 2019-02-07T00:00:00Z date_updated: 2023-08-24T14:46:23Z day: '07' ddc: - '570' department: - _id: NiBa doi: 10.1371/journal.pbio.2005902 external_id: isi: - '000460317100001' file: - access_level: open_access checksum: 5f34001617ee729314ca520c049b1112 content_type: application/pdf creator: dernst date_created: 2019-02-18T14:57:24Z date_updated: 2020-07-14T12:47:17Z file_id: '6036' file_name: 2019_PLOS_Merrill.pdf file_size: 2005949 relation: main_file file_date_updated: 2020-07-14T12:47:17Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: PLoS Biology publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '9801' relation: research_data status: public scopus_import: '1' status: public title: Genetic dissection of assortative mating behavior tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 17 year: '2019' ... --- _id: '9801' article_processing_charge: No author: - first_name: Richard M. full_name: Merrill, Richard M. last_name: Merrill - first_name: Pasi full_name: Rastas, Pasi last_name: Rastas - first_name: Simon H. full_name: Martin, Simon H. last_name: Martin - first_name: Maria C full_name: Melo Hurtado, Maria C id: 386D7308-F248-11E8-B48F-1D18A9856A87 last_name: Melo Hurtado - first_name: Sarah full_name: Barker, Sarah last_name: Barker - first_name: John full_name: Davey, John last_name: Davey - first_name: W. Owen full_name: Mcmillan, W. Owen last_name: Mcmillan - first_name: Chris D. full_name: Jiggins, Chris D. last_name: Jiggins citation: ama: Merrill RM, Rastas P, Martin SH, et al. Raw behavioral data. 2019. doi:10.1371/journal.pbio.2005902.s006 apa: Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Raw behavioral data. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005902.s006 chicago: Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Raw Behavioral Data.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pbio.2005902.s006. ieee: R. M. Merrill et al., “Raw behavioral data.” Public Library of Science, 2019. ista: Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Raw behavioral data, Public Library of Science, 10.1371/journal.pbio.2005902.s006. mla: Merrill, Richard M., et al. Raw Behavioral Data. Public Library of Science, 2019, doi:10.1371/journal.pbio.2005902.s006. short: R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, (2019). date_created: 2021-08-06T11:34:56Z date_published: 2019-02-07T00:00:00Z date_updated: 2023-08-24T14:46:23Z day: '07' department: - _id: NiBa doi: 10.1371/journal.pbio.2005902.s006 month: '02' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '6022' relation: used_in_publication status: public status: public title: Raw behavioral data type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '6095' abstract: - lang: eng text: Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients. article_processing_charge: No author: - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Pragya full_name: Chaube, Pragya last_name: Chaube - first_name: Hernán E. full_name: Morales, Hernán E. last_name: Morales - first_name: Tomas full_name: Larsson, Tomas last_name: Larsson - first_name: Alan R. full_name: Lemmon, Alan R. last_name: Lemmon - first_name: Emily M. full_name: Lemmon, Emily M. last_name: Lemmon - first_name: Marina full_name: Rafajlović, Marina last_name: Rafajlović - first_name: Marina full_name: Panova, Marina last_name: Panova - first_name: Mark full_name: Ravinet, Mark last_name: Ravinet - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: Faria R, Chaube P, Morales HE, et al. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 2019;28(6):1375-1393. doi:10.1111/mec.14972 apa: Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2019). Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14972 chicago: Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.14972. ieee: R. Faria et al., “Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes,” Molecular Ecology, vol. 28, no. 6. Wiley, pp. 1375–1393, 2019. ista: Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2019. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 28(6), 1375–1393. mla: Faria, Rui, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Molecular Ecology, vol. 28, no. 6, Wiley, 2019, pp. 1375–93, doi:10.1111/mec.14972. short: R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, Molecular Ecology 28 (2019) 1375–1393. date_created: 2019-03-10T22:59:21Z date_published: 2019-03-01T00:00:00Z date_updated: 2023-08-24T14:50:27Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/mec.14972 external_id: isi: - '000465219200013' file: - access_level: open_access checksum: f915885756057ec0ca5912a41f46a887 content_type: application/pdf creator: dernst date_created: 2019-03-11T16:12:54Z date_updated: 2020-07-14T12:47:19Z file_id: '6097' file_name: 2019_MolecularEcology_Faria.pdf file_size: 1510715 relation: main_file file_date_updated: 2020-07-14T12:47:19Z has_accepted_license: '1' intvolume: ' 28' isi: 1 issue: '6' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 1375-1393 publication: Molecular Ecology publication_identifier: eissn: - 1365-294X issn: - 0962-1083 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '9837' relation: research_data status: public scopus_import: '1' status: public title: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 28 year: '2019' ... --- _id: '6230' abstract: - lang: eng text: Great care is needed when interpreting claims about the genetic basis of human variation based on data from genome-wide association studies. article_number: e45380 article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Joachim full_name: Hermisson, Joachim last_name: Hermisson - first_name: Magnus full_name: Nordborg, Magnus last_name: Nordborg citation: ama: Barton NH, Hermisson J, Nordborg M. Why structure matters. eLife. 2019;8. doi:10.7554/eLife.45380 apa: Barton, N. H., Hermisson, J., & Nordborg, M. (2019). Why structure matters. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.45380 chicago: Barton, Nicholas H, Joachim Hermisson, and Magnus Nordborg. “Why Structure Matters.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.45380. ieee: N. H. Barton, J. Hermisson, and M. Nordborg, “Why structure matters,” eLife, vol. 8. eLife Sciences Publications, 2019. ista: Barton NH, Hermisson J, Nordborg M. 2019. Why structure matters. eLife. 8, e45380. mla: Barton, Nicholas H., et al. “Why Structure Matters.” ELife, vol. 8, e45380, eLife Sciences Publications, 2019, doi:10.7554/eLife.45380. short: N.H. Barton, J. Hermisson, M. Nordborg, ELife 8 (2019). date_created: 2019-04-07T21:59:15Z date_published: 2019-03-21T00:00:00Z date_updated: 2023-08-25T08:59:38Z day: '21' ddc: - '570' department: - _id: NiBa doi: 10.7554/eLife.45380 external_id: isi: - '000461988300001' file: - access_level: open_access checksum: 130d7544b57df4a6787e1263c2d7ea43 content_type: application/pdf creator: dernst date_created: 2019-04-11T11:43:38Z date_updated: 2020-07-14T12:47:24Z file_id: '6293' file_name: 2019_eLife_Barton.pdf file_size: 298466 relation: main_file file_date_updated: 2020-07-14T12:47:24Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: eLife publication_identifier: eissn: - 2050084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/body-height-bmi-disease-risk-co/ scopus_import: '1' status: public title: Why structure matters tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 8 year: '2019' ...