--- _id: '1518' abstract: - lang: eng text: The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proved difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has a simple, recursive form, the size of such likelihood calculations explodes quickly with the number of individuals and applications of this framework have so far been mainly limited to small samples (pairs and triplets) for which the GF can be written by hand. Here we investigate several strategies for exploiting the inherent symmetries of the coalescent. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes that allows likelihood calculations from nontrivial samples. Using this strategy, we automated blockwise likelihood calculations for a general set of demographic scenarios in Mathematica. These histories may involve population size changes, continuous migration, discrete divergence, and admixture between multiple populations. To give a concrete example, we calculate the likelihood for a model of isolation with migration (IM), assuming two diploid samples without phase and outgroup information. We demonstrate the new inference scheme with an analysis of two individual butterfly genomes from the sister species Heliconius melpomene rosina and H. cydno. acknowledgement: "We thank Lynsey Bunnefeld for discussions throughout the project and Joshua Schraiber and one anonymous reviewer\r\nfor constructive comments on an earlier version of this manuscript. This work was supported by funding from the\r\nUnited Kingdom Natural Environment Research Council (to K.L.) (NE/I020288/1) and a grant from the European\r\nResearch Council (250152) (to N.H.B.)." article_processing_charge: No article_type: original author: - first_name: Konrad full_name: Lohse, Konrad last_name: Lohse - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Simon full_name: Martin, Simon last_name: Martin - 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: Lohse K, Chmelik M, Martin S, Barton NH. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 2016;202(2):775-786. doi:10.1534/genetics.115.183814 apa: Lohse, K., Chmelik, M., Martin, S., & Barton, N. H. (2016). Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.183814 chicago: Lohse, Konrad, Martin Chmelik, Simon Martin, and Nicholas H Barton. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.183814. ieee: K. Lohse, M. Chmelik, S. Martin, and N. H. Barton, “Efficient strategies for calculating blockwise likelihoods under the coalescent,” Genetics, vol. 202, no. 2. Genetics Society of America, pp. 775–786, 2016. ista: Lohse K, Chmelik M, Martin S, Barton NH. 2016. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 202(2), 775–786. mla: Lohse, Konrad, et al. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” Genetics, vol. 202, no. 2, Genetics Society of America, 2016, pp. 775–86, doi:10.1534/genetics.115.183814. short: K. Lohse, M. Chmelik, S. Martin, N.H. Barton, Genetics 202 (2016) 775–786. date_created: 2018-12-11T11:52:29Z date_published: 2016-02-01T00:00:00Z date_updated: 2022-05-24T09:16:22Z day: '01' ddc: - '570' department: - _id: KrCh - _id: NiBa doi: 10.1534/genetics.115.183814 ec_funded: 1 external_id: pmid: - '26715666' file: - access_level: open_access checksum: 41c9b5d72e7fe4624dd22dfe622337d5 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:51Z date_updated: 2020-07-14T12:45:00Z file_id: '5241' file_name: IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf file_size: 957466 relation: main_file file_date_updated: 2020-07-14T12:45:00Z has_accepted_license: '1' intvolume: ' 202' issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Preprint page: 775 - 786 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: Genetics publication_status: published publisher: Genetics Society of America publist_id: '5658' pubrep_id: '561' quality_controlled: '1' scopus_import: '1' status: public title: Efficient strategies for calculating blockwise likelihoods under the coalescent type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2016' ... --- _id: '1631' abstract: - lang: eng text: 'Ancestral processes are fundamental to modern population genetics and spatial structure has been the subject of intense interest for many years. Despite this interest, almost nothing is known about the distribution of the locations of pedigree or genetic ancestors. Using both spatially continuous and stepping-stone models, we show that the distribution of pedigree ancestors approaches a travelling wave, for which we develop two alternative approximations. The speed and width of the wave are sensitive to the local details of the model. After a short time, genetic ancestors spread far more slowly than pedigree ancestors, ultimately diffusing out with radius ## rather than spreading at constant speed. In contrast to the wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the local details of the models.' author: - first_name: Jerome full_name: Kelleher, Jerome last_name: Kelleher - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge - first_name: Amandine full_name: Véber, Amandine last_name: Véber - 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: Kelleher J, Etheridge A, Véber A, Barton NH. Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. 2016;108:1-12. doi:10.1016/j.tpb.2015.10.008 apa: Kelleher, J., Etheridge, A., Véber, A., & Barton, N. H. (2016). Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2015.10.008 chicago: Kelleher, Jerome, Alison Etheridge, Amandine Véber, and Nicholas H Barton. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” Theoretical Population Biology. Academic Press, 2016. https://doi.org/10.1016/j.tpb.2015.10.008. ieee: J. Kelleher, A. Etheridge, A. Véber, and N. H. Barton, “Spread of pedigree versus genetic ancestry in spatially distributed populations,” Theoretical Population Biology, vol. 108. Academic Press, pp. 1–12, 2016. ista: Kelleher J, Etheridge A, Véber A, Barton NH. 2016. Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. 108, 1–12. mla: Kelleher, Jerome, et al. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” Theoretical Population Biology, vol. 108, Academic Press, 2016, pp. 1–12, doi:10.1016/j.tpb.2015.10.008. short: J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population Biology 108 (2016) 1–12. date_created: 2018-12-11T11:53:08Z date_published: 2016-04-01T00:00:00Z date_updated: 2021-01-12T06:52:07Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1016/j.tpb.2015.10.008 ec_funded: 1 file: - access_level: open_access checksum: 6a65ba187994d4ad86c1c509e0ff482a content_type: application/pdf creator: system date_created: 2018-12-12T10:11:12Z date_updated: 2020-07-14T12:45:07Z file_id: '4865' file_name: IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf file_size: 1684043 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 108' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '04' oa: 1 oa_version: Published Version page: 1 - 12 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Theoretical Population Biology publication_status: published publisher: Academic Press publist_id: '5524' pubrep_id: '465' quality_controlled: '1' scopus_import: 1 status: public title: Spread of pedigree versus genetic ancestry in spatially distributed populations 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2016' ... --- _id: '1158' abstract: - lang: eng text: Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate "grey zone" of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation. acknowledgement: "European Research Council (ERC) https://erc.europa.eu/ (grant number ERC grant 232971). PopPhyl project. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/ (grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch) Center for high-performance computing of the SIB Swiss Institute of Bioinformatics and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité." article_number: e2000234 author: - first_name: Camille full_name: Roux, Camille last_name: Roux - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Jonathan full_name: Romiguier, Jonathan last_name: Romiguier - first_name: Youann full_name: Anciaux, Youann last_name: Anciaux - first_name: Nicolas full_name: Galtier, Nicolas last_name: Galtier - first_name: Nicolas full_name: Bierne, Nicolas last_name: Bierne citation: ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 2016;14(12). doi:10.1371/journal.pbio.2000234 apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234 chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” PLoS Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234. ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Shedding light on the grey zone of speciation along a continuum of genomic divergence,” PLoS Biology, vol. 14, no. 12. Public Library of Science, 2016. ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 14(12), e2000234. mla: Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” PLoS Biology, vol. 14, no. 12, e2000234, Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234. short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016). date_created: 2018-12-11T11:50:28Z date_published: 2016-12-27T00:00:00Z date_updated: 2023-02-23T14:11:16Z day: '27' ddc: - '576' department: - _id: BeVi - _id: NiBa doi: 10.1371/journal.pbio.2000234 file: - access_level: open_access checksum: 2bab63b068a9840efd532b9ae583f9bb content_type: application/pdf creator: system date_created: 2018-12-12T10:15:42Z date_updated: 2020-07-14T12:44:36Z file_id: '5164' file_name: IST-2017-742-v1+1_journal.pbio.2000234.pdf file_size: 2494348 relation: main_file file_date_updated: 2020-07-14T12:44:36Z has_accepted_license: '1' intvolume: ' 14' issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '6200' pubrep_id: '742' quality_controlled: '1' related_material: record: - id: '9862' relation: research_data status: public - id: '9863' relation: research_data status: public scopus_import: 1 status: public title: Shedding light on the grey zone of speciation along a continuum of genomic divergence 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2016' ... --- _id: '9862' article_processing_charge: No author: - first_name: Camille full_name: Roux, Camille last_name: Roux - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Jonathan full_name: Romiguier, Jonathan last_name: Romiguier - first_name: Youann full_name: Anciaux, Youann last_name: Anciaux - first_name: Nicolas full_name: Galtier, Nicolas last_name: Galtier - first_name: Nicolas full_name: Bierne, Nicolas last_name: Bierne citation: ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation study to test the robustness of ABC in face of recent times of divergence. 2016. doi:10.1371/journal.pbio.2000234.s016 apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Simulation study to test the robustness of ABC in face of recent times of divergence. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s016 chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.s016. ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Simulation study to test the robustness of ABC in face of recent times of divergence.” Public Library of Science, 2016. ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation study to test the robustness of ABC in face of recent times of divergence, Public Library of Science, 10.1371/journal.pbio.2000234.s016. mla: Roux, Camille, et al. Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s016. short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016). date_created: 2021-08-10T08:20:17Z date_updated: 2023-02-21T16:21:20Z day: '27' department: - _id: BeVi - _id: NiBa doi: 10.1371/journal.pbio.2000234.s016 month: '12' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1158' relation: used_in_publication status: public status: public title: Simulation study to test the robustness of ABC in face of recent times of divergence type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2016' ... --- _id: '9863' article_processing_charge: No author: - first_name: Camille full_name: Roux, Camille last_name: Roux - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Jonathan full_name: Romiguier, Jonathan last_name: Romiguier - first_name: Youann full_name: Anciaux, Youann last_name: Anciaux - first_name: Nicolas full_name: Galtier, Nicolas last_name: Galtier - first_name: Nicolas full_name: Bierne, Nicolas last_name: Bierne citation: ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions of surveyed individuals, geographic locations and summary statistics. 2016. doi:10.1371/journal.pbio.2000234.s017 apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Accessions of surveyed individuals, geographic locations and summary statistics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s017 chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.s017. ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Accessions of surveyed individuals, geographic locations and summary statistics.” Public Library of Science, 2016. ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions of surveyed individuals, geographic locations and summary statistics, Public Library of Science, 10.1371/journal.pbio.2000234.s017. mla: Roux, Camille, et al. Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s017. short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016). date_created: 2021-08-10T08:22:52Z date_updated: 2023-02-21T16:21:20Z day: '27' department: - _id: BeVi - _id: NiBa doi: 10.1371/journal.pbio.2000234.s017 month: '12' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1158' relation: used_in_publication status: public status: public title: Accessions of surveyed individuals, geographic locations and summary statistics type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2016' ... --- _id: '1125' abstract: - lang: eng text: "Natural environments are never constant but subject to spatial and temporal change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial to understand the\r\nimpact of environmental variation on evolutionary processes. In this thesis, I present\r\nthree topics that share the common theme of environmental variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst, I show how a temporally fluctuating environment gives rise to second-order\r\nselection on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations are adapted to their environment, mutation rates are minimized. I argue\r\nthat a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly subjected to diverse environmental challenges, and I outline implications of\r\nthe presented results to antibiotic treatment strategies.\r\nSecond, I discuss my work on the evolution of dispersal. Besides reproducing\r\nknown results about the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes in dispersal type frequencies as a source for selection for increased\r\npropensities to disperse. This concept contains effects of relatedness that are known\r\nto promote dispersal, and I explain how it identifies other forces selecting for dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances of phenotypic traits under multivariate stabilizing\r\nselection. For the case of constant environments, I generalize known formulae of\r\nequilibrium variances to multiple traits and discuss how the genetic variance of a focal\r\ntrait is influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary work aiming at including environmental fluctuations in the form of moving\r\ntrait optima into the model." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak orcid: 0000-0002-2519-824X citation: ama: Novak S. Evolutionary proccesses in variable emvironments. 2016. apa: Novak, S. (2016). Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria. chicago: Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute of Science and Technology Austria, 2016. ieee: S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of Science and Technology Austria, 2016. ista: Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria. mla: Novak, Sebastian. Evolutionary Proccesses in Variable Emvironments. Institute of Science and Technology Austria, 2016. short: S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of Science and Technology Austria, 2016. date_created: 2018-12-11T11:50:17Z date_published: 2016-07-01T00:00:00Z date_updated: 2023-09-07T11:55:53Z day: '01' ddc: - '576' degree_awarded: PhD department: - _id: NiBa file: - access_level: closed checksum: 81dcc838dfcf7aa0b1a27ecf4fe2da4e content_type: application/pdf creator: dernst date_created: 2019-08-13T09:01:00Z date_updated: 2019-08-13T09:01:00Z file_id: '6811' file_name: Novak_thesis.pdf file_size: 3564901 relation: main_file - access_level: open_access checksum: 30808d2f7ca920e09f63a95cdc49bffd content_type: application/pdf creator: dernst date_created: 2021-02-22T13:42:47Z date_updated: 2021-02-22T13:42:47Z file_id: '9186' file_name: 2016_Novak_Thesis.pdf file_size: 2814384 relation: main_file success: 1 file_date_updated: 2021-02-22T13:42:47Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '124' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6235' related_material: record: - id: '2023' 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: Evolutionary proccesses in variable emvironments type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2016' ... --- _id: '1358' abstract: - lang: eng text: 'Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements.' article_number: '12307' author: - first_name: Tamar full_name: Friedlander, Tamar id: 36A5845C-F248-11E8-B48F-1D18A9856A87 last_name: Friedlander - first_name: Roshan full_name: Prizak, Roshan id: 4456104E-F248-11E8-B48F-1D18A9856A87 last_name: Prizak - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - 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: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 2016;7. doi:10.1038/ncomms12307 apa: Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., & Tkačik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms12307 chicago: Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms12307. ieee: T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” Nature Communications, vol. 7. Nature Publishing Group, 2016. ista: Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307. mla: Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications, vol. 7, 12307, Nature Publishing Group, 2016, doi:10.1038/ncomms12307. short: T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016). date_created: 2018-12-11T11:51:34Z date_published: 2016-08-04T00:00:00Z date_updated: 2023-09-07T12:53:49Z day: '04' ddc: - '576' department: - _id: GaTk - _id: NiBa - _id: CaGu doi: 10.1038/ncomms12307 ec_funded: 1 file: - access_level: open_access checksum: fe3f3a1526d180b29fe691ab11435b78 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:01Z date_updated: 2020-07-14T12:44:46Z file_id: '4919' file_name: IST-2016-627-v1+1_ncomms12307.pdf file_size: 861805 relation: main_file - access_level: open_access checksum: 164864a1a675f3ad80e9917c27aba07f content_type: application/pdf creator: system date_created: 2018-12-12T10:12:02Z date_updated: 2020-07-14T12:44:46Z file_id: '4920' file_name: IST-2016-627-v1+2_ncomms12307-s1.pdf file_size: 1084703 relation: main_file file_date_updated: 2020-07-14T12:44:46Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5887' pubrep_id: '627' quality_controlled: '1' related_material: record: - id: '6071' relation: dissertation_contains status: public scopus_import: 1 status: public title: Intrinsic limits to gene regulation by global crosstalk 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2016' ... --- _id: '9710' abstract: - lang: eng text: Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects. 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 citation: ama: 'Barton NH. Data from: How does epistasis influence the response to selection? 2016. doi:10.5061/dryad.s5s7r' apa: 'Barton, N. H. (2016). Data from: How does epistasis influence the response to selection? Dryad. https://doi.org/10.5061/dryad.s5s7r' chicago: 'Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response to Selection?” Dryad, 2016. https://doi.org/10.5061/dryad.s5s7r.' ieee: 'N. H. Barton, “Data from: How does epistasis influence the response to selection?” Dryad, 2016.' ista: 'Barton NH. 2016. Data from: How does epistasis influence the response to selection?, Dryad, 10.5061/dryad.s5s7r.' mla: 'Barton, Nicholas H. Data from: How Does Epistasis Influence the Response to Selection? Dryad, 2016, doi:10.5061/dryad.s5s7r.' short: N.H. Barton, (2016). date_created: 2021-07-23T11:45:47Z date_published: 2016-09-23T00:00:00Z date_updated: 2023-09-20T11:17:47Z day: '23' department: - _id: NiBa doi: 10.5061/dryad.s5s7r main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.s5s7r month: '09' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '1199' relation: used_in_publication status: public status: public title: 'Data from: How does epistasis influence the response to selection?' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2016' ... --- _id: '9864' abstract: - lang: eng text: Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima. article_processing_charge: No author: - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Harold full_name: de Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: de Vladar orcid: 0000-0002-5985-7653 - first_name: Tomasz full_name: Włodarski, Tomasz last_name: Włodarski - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:10.6084/m9.figshare.4315652.v1 apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J. P. (2016). Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. The Royal Society. https://doi.org/10.6084/m9.figshare.4315652.v1 chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. https://doi.org/10.6084/m9.figshare.4315652.v1. ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.” The Royal Society, 2016. ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family, The Royal Society, 10.6084/m9.figshare.4315652.v1. mla: Fernandes Redondo, Rodrigo A., et al. Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family. The Royal Society, 2016, doi:10.6084/m9.figshare.4315652.v1. short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016). date_created: 2021-08-10T08:29:47Z date_published: 2016-12-14T00:00:00Z date_updated: 2023-09-20T11:56:33Z day: '14' department: - _id: NiBa - _id: JoBo doi: 10.6084/m9.figshare.4315652.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.4315652.v1 month: '12' oa: 1 oa_version: Published Version publisher: The Royal Society related_material: record: - id: '1077' relation: used_in_publication status: public status: public title: Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2016' ... --- _id: '1382' abstract: - lang: eng text: Background and aims Angiosperms display remarkable diversity in flower colour, implying that transitions between pigmentation phenotypes must have been common. Despite progress in understanding transitions between anthocyanin (blue, purple, pink or red) and unpigmented (white) flowers, little is known about the evolutionary patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented flowers. This study investigates the relative rates of evolutionary transitions between different combinations of yellow- and anthocyanin-pigmentation phenotypes in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on anthocyanin and yellow floral pigmentation for 369 species across the tribe. We then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative methods to estimate transition rates among pigmentation phenotypes across the phylogeny. Key Results In contrast to previous studies we found a bias towards transitions involving a gain in pigmentation, although transitions to phenotypes with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite the dominance of yellow and anthocyanin-pigmented taxa, transitions between these phenotypes are constrained to move through a white intermediate stage, whereas transitions to double-pigmentation are very rare. The most abundant transitions are between anthocyanin-pigmented and unpigmented flowers, and similarly the most abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented flowers. Conclusions Our findings show that pigment evolution is limited by the presence of other floral pigments. This interaction between anthocyanin and yellow pigments constrains the breadth of potential floral diversity observed in nature. In particular, they suggest that selection has repeatedly acted to promote the spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore, the correlation between transition rates and polymorphism suggests that the forces causing and maintaining variance in the short term reflect evolutionary processes on longer time scales. acknowledgement: We thank Melinda Pickup, Spencer Barrett, Nick Barton and four anonymous reviewers for helpful discussions on previous versions of this manuscript. We also thank Jana Porsche for her efforts in tracking down the more obscure references. author: - first_name: Thomas full_name: Ellis, Thomas id: 3153D6D4-F248-11E8-B48F-1D18A9856A87 last_name: Ellis orcid: 0000-0002-8511-0254 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 citation: ama: Ellis T, Field D. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. 2016;117(7):1133-1140. doi:10.1093/aob/mcw043 apa: Ellis, T., & Field, D. (2016). Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. Oxford University Press. https://doi.org/10.1093/aob/mcw043 chicago: Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany. Oxford University Press, 2016. https://doi.org/10.1093/aob/mcw043. ieee: T. Ellis and D. Field, “Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae,” Annals of Botany, vol. 117, no. 7. Oxford University Press, pp. 1133–1140, 2016. ista: Ellis T, Field D. 2016. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. 117(7), 1133–1140. mla: Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany, vol. 117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:10.1093/aob/mcw043. short: T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140. date_created: 2018-12-11T11:51:42Z date_published: 2016-06-01T00:00:00Z date_updated: 2024-02-21T13:49:53Z day: '1' department: - _id: NiBa doi: 10.1093/aob/mcw043 intvolume: ' 117' issue: '7' language: - iso: eng month: '06' oa_version: None page: 1133 - 1140 publication: Annals of Botany publication_status: published publisher: Oxford University Press publist_id: '5828' quality_controlled: '1' related_material: record: - id: '5550' relation: popular_science status: public scopus_import: 1 status: public title: Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 117 year: '2016' ...