[{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-01-01T00:00:00Z","publication":"Botany Letters","citation":{"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.","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.","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","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","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.","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."},"page":"80-92","abstract":[{"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.","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"None","_id":"5680","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone","intvolume":" 166","month":"01","publication_identifier":{"issn":["23818107"],"eissn":["23818115"]},"doi":"10.1080/23818107.2018.1545142","language":[{"iso":"eng"}],"external_id":{"isi":["000463802800009"]},"isi":1,"quality_controlled":"1","author":[{"last_name":"Andalo","first_name":"Christophe","full_name":"Andalo, Christophe"},{"full_name":"Burrus, Monique","first_name":"Monique","last_name":"Burrus"},{"last_name":"Paute","first_name":"Sandrine","full_name":"Paute, Sandrine"},{"full_name":"Lauzeral, Christine","first_name":"Christine","last_name":"Lauzeral"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field","full_name":"Field, David"}],"date_created":"2018-12-16T22:59:20Z","date_updated":"2023-08-24T14:34:12Z","volume":166,"year":"2019","publication_status":"published","publisher":"Taylor and Francis","department":[{"_id":"NiBa"}]},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"07","citation":{"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.","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).","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.","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","ieee":"R. M. Merrill et al., “Genetic dissection of assortative mating behavior,” PLoS Biology, vol. 17, no. 2. Public Library of Science, 2019.","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"},"publication":"PLoS Biology","date_published":"2019-02-07T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"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.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6022","intvolume":" 17","title":"Genetic dissection of assortative mating behavior","status":"public","ddc":["570"],"file":[{"content_type":"application/pdf","file_size":2005949,"creator":"dernst","file_name":"2019_PLOS_Merrill.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:17Z","date_created":"2019-02-18T14:57:24Z","checksum":"5f34001617ee729314ca520c049b1112","relation":"main_file","file_id":"6036"}],"oa_version":"Published Version","month":"02","external_id":{"isi":["000460317100001"]},"tmp":{"short":"CC0 (1.0)","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)"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1371/journal.pbio.2005902","language":[{"iso":"eng"}],"article_number":"e2005902","file_date_updated":"2020-07-14T12:47:17Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","year":"2019","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"publication_status":"published","related_material":{"record":[{"id":"9801","status":"public","relation":"research_data"}]},"author":[{"first_name":"Richard M.","last_name":"Merrill","full_name":"Merrill, Richard M."},{"full_name":"Rastas, Pasi","first_name":"Pasi","last_name":"Rastas"},{"full_name":"Martin, Simon H.","last_name":"Martin","first_name":"Simon H."},{"full_name":"Melo Hurtado, Maria C","id":"386D7308-F248-11E8-B48F-1D18A9856A87","first_name":"Maria C","last_name":"Melo Hurtado"},{"first_name":"Sarah","last_name":"Barker","full_name":"Barker, Sarah"},{"last_name":"Davey","first_name":"John","full_name":"Davey, John"},{"last_name":"Mcmillan","first_name":"W. Owen","full_name":"Mcmillan, W. Owen"},{"first_name":"Chris D.","last_name":"Jiggins","full_name":"Jiggins, Chris D."}],"volume":17,"date_updated":"2023-08-24T14:46:23Z","date_created":"2019-02-17T22:59:21Z"},{"date_created":"2021-08-06T11:34:56Z","date_updated":"2023-08-24T14:46:23Z","oa_version":"Published Version","author":[{"full_name":"Merrill, Richard M.","first_name":"Richard M.","last_name":"Merrill"},{"full_name":"Rastas, Pasi","first_name":"Pasi","last_name":"Rastas"},{"first_name":"Simon H.","last_name":"Martin","full_name":"Martin, Simon H."},{"full_name":"Melo Hurtado, Maria C","id":"386D7308-F248-11E8-B48F-1D18A9856A87","first_name":"Maria C","last_name":"Melo Hurtado"},{"last_name":"Barker","first_name":"Sarah","full_name":"Barker, Sarah"},{"full_name":"Davey, John","first_name":"John","last_name":"Davey"},{"last_name":"Mcmillan","first_name":"W. Owen","full_name":"Mcmillan, W. Owen"},{"first_name":"Chris D.","last_name":"Jiggins","full_name":"Jiggins, Chris D."}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6022"}]},"status":"public","title":"Raw behavioral data","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9801","year":"2019","type":"research_data_reference","doi":"10.1371/journal.pbio.2005902.s006","date_published":"2019-02-07T00:00:00Z","citation":{"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.","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).","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.","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","ieee":"R. M. Merrill et al., “Raw behavioral data.” Public Library of Science, 2019.","ama":"Merrill RM, Rastas P, Martin SH, et al. Raw behavioral data. 2019. doi:10.1371/journal.pbio.2005902.s006"},"month":"02","day":"07","article_processing_charge":"No"},{"abstract":[{"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.","lang":"eng"}],"issue":"6","type":"journal_article","file":[{"relation":"main_file","file_id":"6097","checksum":"f915885756057ec0ca5912a41f46a887","date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-11T16:12:54Z","access_level":"open_access","file_name":"2019_MolecularEcology_Faria.pdf","file_size":1510715,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","_id":"6095","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","ddc":["570"],"status":"public","intvolume":" 28","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-03-01T00:00:00Z","publication":"Molecular Ecology","citation":{"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.","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.","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","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","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.","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."},"page":"1375-1393","file_date_updated":"2020-07-14T12:47:19Z","license":"https://creativecommons.org/licenses/by/4.0/","author":[{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"last_name":"Chaube","first_name":"Pragya","full_name":"Chaube, Pragya"},{"full_name":"Morales, Hernán E.","last_name":"Morales","first_name":"Hernán E."},{"full_name":"Larsson, Tomas","first_name":"Tomas","last_name":"Larsson"},{"first_name":"Alan R.","last_name":"Lemmon","full_name":"Lemmon, Alan R."},{"full_name":"Lemmon, Emily M.","first_name":"Emily M.","last_name":"Lemmon"},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"last_name":"Panova","first_name":"Marina","full_name":"Panova, Marina"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"related_material":{"record":[{"id":"9837","relation":"research_data","status":"public"}]},"date_created":"2019-03-10T22:59:21Z","date_updated":"2023-08-24T14:50:27Z","volume":28,"year":"2019","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"month":"03","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"doi":"10.1111/mec.14972","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000465219200013"]},"oa":1,"isi":1,"quality_controlled":"1"},{"status":"public","ddc":["570"],"title":"Why structure matters","intvolume":" 8","_id":"6230","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_created":"2019-04-11T11:43:38Z","date_updated":"2020-07-14T12:47:24Z","checksum":"130d7544b57df4a6787e1263c2d7ea43","relation":"main_file","file_id":"6293","content_type":"application/pdf","file_size":298466,"creator":"dernst","file_name":"2019_eLife_Barton.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Great care is needed when interpreting claims about the genetic basis of human variation based on data from genome-wide association studies.","lang":"eng"}],"publication":"eLife","citation":{"ama":"Barton NH, Hermisson J, Nordborg M. Why structure matters. eLife. 2019;8. doi:10.7554/eLife.45380","ista":"Barton NH, Hermisson J, Nordborg M. 2019. Why structure matters. eLife. 8, e45380.","apa":"Barton, N. H., Hermisson, J., & Nordborg, M. (2019). Why structure matters. ELife. eLife Sciences Publications. 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.","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).","chicago":"Barton, Nicholas H, Joachim Hermisson, and Magnus Nordborg. “Why Structure Matters.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.45380."},"date_published":"2019-03-21T00:00:00Z","scopus_import":"1","day":"21","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"NiBa"}],"year":"2019","date_updated":"2023-08-25T08:59:38Z","date_created":"2019-04-07T21:59:15Z","volume":8,"author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"first_name":"Joachim","last_name":"Hermisson","full_name":"Hermisson, Joachim"},{"full_name":"Nordborg, Magnus","last_name":"Nordborg","first_name":"Magnus"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/body-height-bmi-disease-risk-co/"}]},"article_number":"e45380","file_date_updated":"2020-07-14T12:47:24Z","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000461988300001"]},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.45380","month":"03","publication_identifier":{"eissn":["2050084X"]}},{"language":[{"iso":"eng"}],"doi":"10.1111/mec.15048","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000474808300001"]},"publication_identifier":{"eissn":["1365294X"]},"month":"04","volume":28,"date_updated":"2023-08-25T10:37:30Z","date_created":"2019-05-19T21:59:15Z","author":[{"full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle"}],"department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","year":"2019","file_date_updated":"2020-07-14T12:47:31Z","date_published":"2019-04-01T00:00:00Z","page":"1579-1581","citation":{"short":"D. Field, C. Fraisse, Molecular Ecology 28 (2019) 1579–1581.","mla":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology, vol. 28, no. 7, Wiley, 2019, pp. 1579–81, doi:10.1111/mec.15048.","chicago":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.15048.","ama":"Field D, Fraisse C. Breaking down barriers in morning glories. Molecular ecology. 2019;28(7):1579-1581. doi:10.1111/mec.15048","ieee":"D. Field and C. Fraisse, “Breaking down barriers in morning glories,” Molecular ecology, vol. 28, no. 7. Wiley, pp. 1579–1581, 2019.","apa":"Field, D., & Fraisse, C. (2019). Breaking down barriers in morning glories. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15048","ista":"Field D, Fraisse C. 2019. Breaking down barriers in morning glories. Molecular ecology. 28(7), 1579–1581."},"publication":"Molecular ecology","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","file":[{"relation":"main_file","file_id":"6472","checksum":"521e3aff3e9263ddf2ffbfe0b6157715","date_created":"2019-05-20T11:49:06Z","date_updated":"2020-07-14T12:47:31Z","access_level":"open_access","file_name":"2019_MolecularEcology_Field.pdf","content_type":"application/pdf","file_size":367711,"creator":"dernst"}],"oa_version":"Published Version","intvolume":" 28","ddc":["580","576"],"title":"Breaking down barriers in morning glories","status":"public","_id":"6466","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"7","abstract":[{"text":"One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One \r\nproblem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the \r\nstudy is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates.","lang":"eng"}],"type":"journal_article"},{"type":"journal_article","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 (small nucleolar RNA). 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."}],"issue":"4","title":"The distribution of epistasis on simple fitness landscapes","status":"public","intvolume":" 15","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6467","oa_version":"Published Version","scopus_import":"1","day":"03","article_processing_charge":"No","article_type":"original","publication":"Biology Letters","citation":{"chicago":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters. Royal Society of London, 2019. https://doi.org/10.1098/rsbl.2018.0881.","mla":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters, vol. 15, no. 4, 0881, Royal Society of London, 2019, doi:10.1098/rsbl.2018.0881.","short":"C. Fraisse, J.J. Welch, Biology Letters 15 (2019).","ista":"Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness landscapes. Biology Letters. 15(4), 0881.","ieee":"C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness landscapes,” Biology Letters, vol. 15, no. 4. Royal Society of London, 2019.","apa":"Fraisse, C., & Welch, J. J. (2019). The distribution of epistasis on simple fitness landscapes. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2018.0881","ama":"Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes. Biology Letters. 2019;15(4). doi:10.1098/rsbl.2018.0881"},"date_published":"2019-04-03T00:00:00Z","article_number":"0881","ec_funded":1,"publication_status":"published","publisher":"Royal Society of London","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"year":"2019","pmid":1,"date_created":"2019-05-19T21:59:15Z","date_updated":"2023-08-25T10:34:41Z","volume":15,"author":[{"full_name":"Fraisse, Christelle","first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"},{"last_name":"Welch","first_name":"John J.","full_name":"Welch, John J."}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9798"},{"id":"9799","status":"public","relation":"research_data"}],"link":[{"relation":"supplementary_material","url":"https://dx.doi.org/10.6084/m9.figshare.c.4461008"}]},"month":"04","publication_identifier":{"eissn":["1744957X"],"issn":["17449561"]},"quality_controlled":"1","isi":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"oa":1,"external_id":{"pmid":["31014191"],"isi":["000465405300010"]},"main_file_link":[{"url":"https://doi.org/10.1098/rsbl.2018.0881","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1098/rsbl.2018.0881"},{"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"file_date_updated":"2020-07-14T12:47:34Z","volume":73,"date_created":"2019-07-14T21:59:20Z","date_updated":"2023-08-29T06:31:14Z","author":[{"full_name":"Trubenova, Barbora","last_name":"Trubenova","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Krejca, Martin ","last_name":"Krejca","first_name":"Martin "},{"first_name":"Per Kristian","last_name":"Lehre","full_name":"Lehre, Per Kristian"},{"full_name":"Kötzing, Timo","first_name":"Timo","last_name":"Kötzing"}],"department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","year":"2019","acknowledgement":"The authors would like to thank to Tiago Paixao and Nick Barton for useful comments and advice.","month":"07","language":[{"iso":"eng"}],"doi":"10.1111/evo.13784","project":[{"name":"Rate of Adaptation in Changing Environment","call_identifier":"H2020","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","grant_number":"704172"},{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000474031600001"]},"issue":"7","abstract":[{"text":"The environment changes constantly at various time scales and, in order to survive, species need to keep adapting. Whether these species succeed in avoiding extinction is a major evolutionary question. Using a multilocus evolutionary model of a mutation‐limited population adapting under strong selection, we investigate the effects of the frequency of environmental fluctuations on adaptation. Our results rely on an “adaptive‐walk” approximation and use mathematical methods from evolutionary computation theory to investigate the interplay between fluctuation frequency, the similarity of environments, and the number of loci contributing to adaptation. First, we assume a linear additive fitness function, but later generalize our results to include several types of epistasis. We show that frequent environmental changes prevent populations from reaching a fitness peak, but they may also prevent the large fitness loss that occurs after a single environmental change. Thus, the population can survive, although not thrive, in a wide range of conditions. Furthermore, we show that in a frequently changing environment, the similarity of threats that a population faces affects the level of adaptation that it is able to achieve. We check and supplement our analytical results with simulations.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6643","date_created":"2019-07-16T06:08:31Z","date_updated":"2020-07-14T12:47:34Z","checksum":"9831ca65def2d62498c7b08338b6d237","file_name":"2019_Evolution_TrubenovaBarbora.pdf","access_level":"open_access","content_type":"application/pdf","file_size":815416,"creator":"apreinsp"}],"intvolume":" 73","ddc":["576"],"title":"Surfing on the seascape: Adaptation in a changing environment","status":"public","_id":"6637","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2019-07-01T00:00:00Z","page":"1356-1374","article_type":"original","citation":{"mla":"Trubenova, Barbora, et al. “Surfing on the Seascape: Adaptation in a Changing Environment.” Evolution, vol. 73, no. 7, Wiley, 2019, pp. 1356–74, doi:10.1111/evo.13784.","short":"B. Trubenova, M. Krejca, P.K. Lehre, T. Kötzing, Evolution 73 (2019) 1356–1374.","chicago":"Trubenova, Barbora, Martin Krejca, Per Kristian Lehre, and Timo Kötzing. “Surfing on the Seascape: Adaptation in a Changing Environment.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13784.","ama":"Trubenova B, Krejca M, Lehre PK, Kötzing T. Surfing on the seascape: Adaptation in a changing environment. Evolution. 2019;73(7):1356-1374. doi:10.1111/evo.13784","ista":"Trubenova B, Krejca M, Lehre PK, Kötzing T. 2019. Surfing on the seascape: Adaptation in a changing environment. Evolution. 73(7), 1356–1374.","ieee":"B. Trubenova, M. Krejca, P. K. Lehre, and T. Kötzing, “Surfing on the seascape: Adaptation in a changing environment,” Evolution, vol. 73, no. 7. Wiley, pp. 1356–1374, 2019.","apa":"Trubenova, B., Krejca, M., Lehre, P. K., & Kötzing, T. (2019). Surfing on the seascape: Adaptation in a changing environment. Evolution. Wiley. https://doi.org/10.1111/evo.13784"},"publication":"Evolution"},{"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2019-09-01T00:00:00Z","publication":"Evolution","citation":{"short":"H. Sachdeva, Evolution 73 (2019) 1729–1745.","mla":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution, vol. 73, no. 9, Wiley, 2019, pp. 1729–45, doi:10.1111/evo.13812.","chicago":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13812.","ama":"Sachdeva H. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 2019;73(9):1729-1745. doi:10.1111/evo.13812","ieee":"H. Sachdeva, “Effect of partial selfing and polygenic selection on establishment in a new habitat,” Evolution, vol. 73, no. 9. Wiley, pp. 1729–1745, 2019.","apa":"Sachdeva, H. (2019). Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. Wiley. https://doi.org/10.1111/evo.13812","ista":"Sachdeva H. 2019. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 73(9), 1729–1745."},"page":"1729-1745","abstract":[{"text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation‐selection balance in a large, partially selfing source population under selection involving multiple non‐identical loci. I then use individual‐based simulations to study the eco‐evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long‐term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed.","lang":"eng"}],"issue":"9","type":"journal_article","file":[{"date_created":"2019-09-17T10:56:27Z","date_updated":"2020-07-14T12:47:37Z","checksum":"772ce7035965153959b946a1033de1ca","relation":"main_file","file_id":"6881","content_type":"application/pdf","file_size":937573,"creator":"kschuh","file_name":"2019_Evolution_Sachdeva.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"6680","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["576"],"title":"Effect of partial selfing and polygenic selection on establishment in a new habitat","status":"public","intvolume":" 73","month":"09","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"doi":"10.1111/evo.13812","language":[{"iso":"eng"}],"external_id":{"isi":["000481300600001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"file_date_updated":"2020-07-14T12:47:37Z","author":[{"full_name":"Sachdeva, Himani","first_name":"Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"9802","relation":"research_data","status":"public"}]},"date_updated":"2023-08-29T06:43:58Z","date_created":"2019-07-25T09:08:28Z","volume":73,"year":"2019","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}]},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.0q2h6tk"}],"oa":1,"citation":{"mla":"Castro, João Pl, et al. Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice. Dryad, 2019, doi:10.5061/dryad.0q2h6tk.","short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, (2019).","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” Dryad, 2019. https://doi.org/10.5061/dryad.0q2h6tk.","ama":"Castro JP, Yancoskie MN, Marchini M, et al. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. 2019. doi:10.5061/dryad.0q2h6tk","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice, Dryad, 10.5061/dryad.0q2h6tk.","ieee":"J. P. Castro et al., “Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice.” Dryad, 2019.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. Dryad. https://doi.org/10.5061/dryad.0q2h6tk"},"doi":"10.5061/dryad.0q2h6tk","date_published":"2019-06-06T00:00:00Z","month":"06","day":"06","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9804","year":"2019","title":"Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","status":"public","publisher":"Dryad","department":[{"_id":"NiBa"}],"author":[{"last_name":"Castro","first_name":"João Pl","full_name":"Castro, João Pl"},{"full_name":"Yancoskie, Michelle N.","last_name":"Yancoskie","first_name":"Michelle N."},{"last_name":"Marchini","first_name":"Marta","full_name":"Marchini, Marta"},{"first_name":"Stefanie","last_name":"Belohlavy","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9849-498X","full_name":"Belohlavy, Stefanie"},{"full_name":"Hiramatsu, Layla","first_name":"Layla","last_name":"Hiramatsu"},{"first_name":"Marek","last_name":"Kučka","full_name":"Kučka, Marek"},{"full_name":"Beluch, William H.","last_name":"Beluch","first_name":"William H."},{"full_name":"Naumann, Ronald","first_name":"Ronald","last_name":"Naumann"},{"last_name":"Skuplik","first_name":"Isabella","full_name":"Skuplik, Isabella"},{"full_name":"Cobb, John","first_name":"John","last_name":"Cobb"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rolian, Campbell","last_name":"Rolian","first_name":"Campbell"},{"full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank","last_name":"Chan"}],"related_material":{"record":[{"id":"6713","status":"public","relation":"used_in_publication"}]},"date_updated":"2023-08-29T06:41:51Z","date_created":"2021-08-06T11:52:54Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"lang":"eng","text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response."}]},{"article_processing_charge":"No","day":"16","month":"07","date_published":"2019-07-16T00:00:00Z","doi":"10.5061/dryad.8tp0900","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.8tp0900"}],"citation":{"ama":"Sachdeva H. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. 2019. doi:10.5061/dryad.8tp0900","ista":"Sachdeva H. 2019. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat, Dryad, 10.5061/dryad.8tp0900.","ieee":"H. Sachdeva, “Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat.” Dryad, 2019.","apa":"Sachdeva, H. (2019). Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. Dryad. https://doi.org/10.5061/dryad.8tp0900","mla":"Sachdeva, Himani. Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat. Dryad, 2019, doi:10.5061/dryad.8tp0900.","short":"H. Sachdeva, (2019).","chicago":"Sachdeva, Himani. “Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Dryad, 2019. https://doi.org/10.5061/dryad.8tp0900."},"oa":1,"abstract":[{"text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation-selection balance in a large, partially selfing source population under selection involving multiple non-identical loci. I then use individual-based simulations to study the eco-evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long-term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed.","lang":"eng"}],"type":"research_data_reference","oa_version":"Published Version","date_created":"2021-08-06T11:45:11Z","date_updated":"2023-08-29T06:43:57Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6680"}]},"author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani","full_name":"Sachdeva, Himani"}],"publisher":"Dryad","department":[{"_id":"NiBa"}],"status":"public","title":"Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat","_id":"9802","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"author":[{"full_name":"Trubenova, Barbora","first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967"},{"full_name":"Hager, Reinmar","first_name":"Reinmar","last_name":"Hager"}],"volume":9,"date_updated":"2023-08-29T07:03:10Z","date_created":"2019-08-11T21:59:24Z","year":"2019","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:40Z","doi":"10.1002/ece3.5484","language":[{"iso":"eng"}],"external_id":{"isi":["000479973400001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"704172","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Rate of Adaptation in Changing Environment"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["20457758"]},"month":"09","file":[{"checksum":"adcb70af4901977d95b8747eeee01bd7","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-12T07:30:30Z","relation":"main_file","file_id":"6799","file_size":2839636,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_EcologyEvolution_Trubenova.pdf"}],"oa_version":"Published Version","_id":"6795","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 9","ddc":["576"],"status":"public","title":"Green beards in the light of indirect genetic effects","issue":"17","abstract":[{"lang":"eng","text":"The green‐beard effect is one proposed mechanism predicted to underpin the evolu‐tion of altruistic behavior. It relies on the recognition and the selective help of altruists to each other in order to promote and sustain altruistic behavior. However, this mechanism has often been dismissed as unlikely or uncommon, as it is assumed that both the signaling trait and altruistic trait need to be encoded by the same gene or through tightly linked genes. Here, we use models of indirect genetic effects (IGEs) to find the minimum correlation between the signaling and altruistic trait required for the evolution of the latter. We show that this correlation threshold depends on the strength of the interaction (influence of the green beard on the expression of the altruistic trait), as well as the costs and benefits of the altruistic behavior. We further show that this correlation does not necessarily have to be high and support our analytical results by simulations."}],"type":"journal_article","date_published":"2019-09-01T00:00:00Z","citation":{"short":"B. Trubenova, R. Hager, Ecology and Evolution 9 (2019) 9597–9608.","mla":"Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” Ecology and Evolution, vol. 9, no. 17, Wiley, 2019, pp. 9597–608, doi:10.1002/ece3.5484.","chicago":"Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” Ecology and Evolution. Wiley, 2019. https://doi.org/10.1002/ece3.5484.","ama":"Trubenova B, Hager R. Green beards in the light of indirect genetic effects. Ecology and Evolution. 2019;9(17):9597-9608. doi:10.1002/ece3.5484","ieee":"B. Trubenova and R. Hager, “Green beards in the light of indirect genetic effects,” Ecology and Evolution, vol. 9, no. 17. Wiley, pp. 9597–9608, 2019.","apa":"Trubenova, B., & Hager, R. (2019). Green beards in the light of indirect genetic effects. Ecology and Evolution. Wiley. https://doi.org/10.1002/ece3.5484","ista":"Trubenova B, Hager R. 2019. Green beards in the light of indirect genetic effects. Ecology and Evolution. 9(17), 9597–9608."},"publication":"Ecology and Evolution","page":"9597-9608","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1"},{"file_date_updated":"2020-07-14T12:47:42Z","ec_funded":1,"author":[{"last_name":"Puixeu Sala","first_name":"Gemma","orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","full_name":"Puixeu Sala, Gemma"},{"full_name":"Pickup, Melinda","last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David"},{"full_name":"Barrett, Spencer C.H.","last_name":"Barrett","first_name":"Spencer C.H."}],"related_material":{"record":[{"id":"9803","status":"public","relation":"research_data"},{"status":"public","relation":"dissertation_contains","id":"14058"}]},"date_created":"2019-08-25T22:00:51Z","date_updated":"2023-08-29T07:17:07Z","volume":224,"year":"2019","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publisher":"Wiley","month":"11","publication_identifier":{"eissn":["1469-8137"]},"doi":"10.1111/nph.16050","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000481376500001"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"abstract":[{"lang":"eng","text":"* Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less information is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life‐cycle dynamics.\r\n* Here, we investigated patterns of genetically based sexual dimorphism in vegetative and reproductive traits of a wind‐pollinated dioecious plant, Rumex hastatulus, across three life‐cycle stages using open‐pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species.\r\n* The direction and degree of sexual dimorphism was highly variable among populations and life‐cycle stages. Sex‐specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races.\r\n* Sex‐specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life‐cycle."}],"issue":"3","type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":2314016,"creator":"apreinsp","file_name":"2019_NewPhytologist_Puixeu.pdf","access_level":"open_access","date_created":"2019-08-27T12:44:54Z","date_updated":"2020-07-14T12:47:42Z","checksum":"6370e7567d96b7b562e77d8b89653f80","relation":"main_file","file_id":"6833"}],"_id":"6831","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics","ddc":["570"],"status":"public","intvolume":" 224","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","publication":"New Phytologist","citation":{"short":"G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, New Phytologist 224 (2019) 1108–1120.","mla":"Puixeu Sala, Gemma, et al. “Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” New Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1108–20, doi:10.1111/nph.16050.","chicago":"Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16050.","ama":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. 2019;224(3):1108-1120. doi:10.1111/nph.16050","ieee":"G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1108–1120, 2019.","apa":"Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. Wiley. https://doi.org/10.1111/nph.16050","ista":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. 224(3), 1108–1120."},"article_type":"original","page":"1108-1120"},{"author":[{"first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma"},{"full_name":"Pickup, Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup"},{"full_name":"Field, David","last_name":"Field","first_name":"David"},{"full_name":"Barrett, Spencer C.H.","first_name":"Spencer C.H.","last_name":"Barrett"}],"related_material":{"record":[{"id":"14058","status":"public","relation":"used_in_publication"},{"id":"6831","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-06T11:48:42Z","date_updated":"2023-08-29T07:17:07Z","oa_version":"Published Version","year":"2019","_id":"9803","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics","status":"public","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publisher":"Dryad","abstract":[{"lang":"eng","text":"Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life-cycle dynamics. Here, we investigate patterns of genetically-based sexual dimorphism in vegetative and reproductive traits of a wind-pollinated dioecious plant, Rumex hastatulus, across three life-cycle stages using open-pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species. The direction and degree of sexual dimorphism was highly variable among populations and life-cycle stages. Sex-specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races. Sex-specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life cycle."}],"type":"research_data_reference","doi":"10.5061/dryad.n1701c9","date_published":"2019-07-22T00:00:00Z","citation":{"chicago":"Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” Dryad, 2019. https://doi.org/10.5061/dryad.n1701c9.","short":"G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, (2019).","mla":"Puixeu Sala, Gemma, et al. Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics. Dryad, 2019, doi:10.5061/dryad.n1701c9.","apa":"Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. Dryad. https://doi.org/10.5061/dryad.n1701c9","ieee":"G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics.” Dryad, 2019.","ista":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics, Dryad, 10.5061/dryad.n1701c9.","ama":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. 2019. doi:10.5061/dryad.n1701c9"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.n1701c9"}],"oa":1,"day":"22","month":"07","article_processing_charge":"No"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"05","citation":{"chicago":"Sella, Guy, and Nicholas H Barton. “Thinking about the Evolution of Complex Traits in the Era of Genome-Wide Association Studies.” Annual Review of Genomics and Human Genetics. Annual Reviews, 2019. https://doi.org/10.1146/annurev-genom-083115-022316.","mla":"Sella, Guy, and Nicholas H. Barton. “Thinking about the Evolution of Complex Traits in the Era of Genome-Wide Association Studies.” Annual Review of Genomics and Human Genetics, vol. 20, Annual Reviews, 2019, pp. 461–93, doi:10.1146/annurev-genom-083115-022316.","short":"G. Sella, N.H. Barton, Annual Review of Genomics and Human Genetics 20 (2019) 461–493.","ista":"Sella G, Barton NH. 2019. Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. 20, 461–493.","ieee":"G. Sella and N. H. Barton, “Thinking about the evolution of complex traits in the era of genome-wide association studies,” Annual Review of Genomics and Human Genetics, vol. 20. Annual Reviews, pp. 461–493, 2019.","apa":"Sella, G., & Barton, N. H. (2019). Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genom-083115-022316","ama":"Sella G, Barton NH. Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. 2019;20:461-493. doi:10.1146/annurev-genom-083115-022316"},"publication":"Annual Review of Genomics and Human Genetics","page":"461-493","date_published":"2019-07-05T00:00:00Z","type":"journal_article","abstract":[{"text":"Many traits of interest are highly heritable and genetically complex, meaning that much of the variation they exhibit arises from differences at numerous loci in the genome. Complex traits and their evolution have been studied for more than a century, but only in the last decade have genome-wide association studies (GWASs) in humans begun to reveal their genetic basis. Here, we bring these threads of research together to ask how findings from GWASs can further our understanding of the processes that give rise to heritable variation in complex traits and of the genetic basis of complex trait evolution in response to changing selection pressures (i.e., of polygenic adaptation). Conversely, we ask how evolutionary thinking helps us to interpret findings from GWASs and informs related efforts of practical importance.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6855","intvolume":" 20","status":"public","ddc":["576"],"title":"Thinking about the evolution of complex traits in the era of genome-wide association studies","file":[{"checksum":"23d3978cf4739a89ce2c3e779f9305ca","date_updated":"2020-07-14T12:47:42Z","date_created":"2019-09-09T07:22:12Z","relation":"main_file","file_id":"6862","content_type":"application/pdf","file_size":411491,"creator":"dernst","access_level":"open_access","file_name":"2019_AnnualReview_Sella.pdf"}],"oa_version":"Published Version","publication_identifier":{"issn":["1527-8204"],"eissn":["1545-293X"]},"month":"07","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["31283361"],"isi":["000485148400020"]},"quality_controlled":"1","isi":1,"doi":"10.1146/annurev-genom-083115-022316","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:42Z","pmid":1,"year":"2019","department":[{"_id":"NiBa"}],"publisher":"Annual Reviews","publication_status":"published","author":[{"first_name":"Guy","last_name":"Sella","full_name":"Sella, Guy"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"volume":20,"date_created":"2019-09-07T14:28:29Z","date_updated":"2023-08-29T07:49:38Z"},{"type":"journal_article","issue":"2","title":"Is speciation driven by cycles of mixing and isolation?","ddc":["570"],"status":"public","intvolume":" 6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6858","file":[{"date_created":"2020-10-02T09:16:44Z","date_updated":"2020-10-02T09:16:44Z","success":1,"checksum":"571d60fa21a568607d1fd04e119da88c","file_id":"8595","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":106463,"file_name":"2019_NSR_Barton.pdf","access_level":"open_access"}],"oa_version":"Published Version","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","article_type":"review","page":"291-292","publication":"National Science Review","citation":{"ama":"Barton NH. Is speciation driven by cycles of mixing and isolation? National Science Review. 2019;6(2):291-292. doi:10.1093/nsr/nwy113","ista":"Barton NH. 2019. Is speciation driven by cycles of mixing and isolation? National Science Review. 6(2), 291–292.","ieee":"N. H. Barton, “Is speciation driven by cycles of mixing and isolation?,” National Science Review, vol. 6, no. 2. Oxford University Press, pp. 291–292, 2019.","apa":"Barton, N. H. (2019). Is speciation driven by cycles of mixing and isolation? National Science Review. Oxford University Press. https://doi.org/10.1093/nsr/nwy113","mla":"Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” National Science Review, vol. 6, no. 2, Oxford University Press, 2019, pp. 291–92, doi:10.1093/nsr/nwy113.","short":"N.H. Barton, National Science Review 6 (2019) 291–292.","chicago":"Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” National Science Review. Oxford University Press, 2019. https://doi.org/10.1093/nsr/nwy113."},"date_published":"2019-03-01T00:00:00Z","file_date_updated":"2020-10-02T09:16:44Z","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"year":"2019","date_created":"2019-09-07T14:43:02Z","date_updated":"2023-08-29T07:51:09Z","volume":6,"author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"month":"03","publication_identifier":{"eissn":["2053-714X"],"issn":["2095-5138"]},"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000467957400025"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/nsr/nwy113"},{"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","article_type":"original","publication":"BioEssays","citation":{"short":"B. Giese, J.L. Friess, M.F. Schetelig, N.H. Barton, P. Messer, F. Debarre, H. Meimberg, N. Windbichler, C. Boete, BioEssays 41 (2019).","mla":"Giese, B., et al. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays, vol. 41, no. 11, 1900151, Wiley, 2019, doi:10.1002/bies.201900151.","chicago":"Giese, B, J L Friess, M F Schetelig, Nicholas H Barton, Philip Messer, Florence Debarre, H Meimberg, N Windbichler, and C Boete. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays. Wiley, 2019. https://doi.org/10.1002/bies.201900151.","ama":"Giese B, Friess JL, Schetelig MF, et al. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 2019;41(11). doi:10.1002/bies.201900151","apa":"Giese, B., Friess, J. L., Schetelig, M. F., Barton, N. H., Messer, P., Debarre, F., … Boete, C. (2019). Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. Wiley. https://doi.org/10.1002/bies.201900151","ieee":"B. Giese et al., “Gene Drives: Dynamics and regulatory matters – A report from the workshop ‘Evaluation of spatial and temporal control of Gene Drives’, 4 – 5 April 2019, Vienna,” BioEssays, vol. 41, no. 11. Wiley, 2019.","ista":"Giese B, Friess JL, Schetelig MF, Barton NH, Messer P, Debarre F, Meimberg H, Windbichler N, Boete C. 2019. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 41(11), 1900151."},"abstract":[{"lang":"eng","text":"Gene Drives are regarded as future tools with a high potential for population control. Due to their inherent ability to overcome the rules of Mendelian inheritance, gene drives (GD) may spread genes rapidly through populations of sexually reproducing organisms. A release of organisms carrying a GD would constitute a paradigm shift in the handling of genetically modified organisms because gene drive organisms (GDO) are designed to drive their transgenes into wild populations and thereby increase the number of GDOs. The rapid development in this field and its focus on wild populations demand a prospective risk assessment with a focus on exposure related aspects. Presently, it is unclear how adequate risk management could be guaranteed to limit the spread of GDs in time and space, in order to avoid potential adverse effects in socio‐ecological systems.\r\n\r\nThe recent workshop on the “Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight into the potential population dynamic behavior of GDs and appropriate measures of control. Scientists from France, Germany, England, and the USA discussed both topics in this meeting on April 4–5, 2019. This article summarizes results of the workshop."}],"issue":"11","type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":193248,"access_level":"open_access","file_name":"2019_BioEssays_Giese.pdf","checksum":"8cc7551bff70b2658f8d5630f228ee12","date_updated":"2020-07-14T12:47:42Z","date_created":"2019-10-11T06:59:26Z","file_id":"6939","relation":"main_file"}],"ddc":["570"],"title":"Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna","status":"public","intvolume":" 41","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6857","month":"11","publication_identifier":{"eissn":["1521-1878"]},"language":[{"iso":"eng"}],"doi":"10.1002/bies.201900151","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000489502000001"]},"file_date_updated":"2020-07-14T12:47:42Z","article_number":"1900151","date_created":"2019-09-07T14:40:03Z","date_updated":"2023-08-30T06:56:26Z","volume":41,"author":[{"last_name":"Giese","first_name":"B","full_name":"Giese, B"},{"first_name":"J L","last_name":"Friess","full_name":"Friess, J L"},{"first_name":"M F ","last_name":"Schetelig","full_name":"Schetelig, M F "},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Philip","last_name":"Messer","full_name":"Messer, Philip"},{"full_name":"Debarre, Florence","first_name":"Florence","last_name":"Debarre"},{"full_name":"Meimberg, H","last_name":"Meimberg","first_name":"H"},{"last_name":"Windbichler","first_name":"N","full_name":"Windbichler, N"},{"full_name":"Boete, C","last_name":"Boete","first_name":"C"}],"publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"year":"2019"},{"oa":1,"tmp":{"short":"CC0 (1.0)","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)"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.tb2rbnzwk"}],"citation":{"ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019. doi:10.5061/DRYAD.TB2RBNZWK","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?, Dryad, 10.5061/DRYAD.TB2RBNZWK.","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?” Dryad, 2019.","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. (2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK","mla":"Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019).","chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK."},"date_published":"2019-12-02T00:00:00Z","doi":"10.5061/DRYAD.TB2RBNZWK","month":"12","day":"02","article_processing_charge":"No","_id":"13067","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","ddc":["570"],"title":"Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?","status":"public","department":[{"_id":"NiBa"}],"publisher":"Dryad","author":[{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"last_name":"Zagrodzka","first_name":"Zuzanna","full_name":"Zagrodzka, Zuzanna"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"last_name":"Butlin","first_name":"Roger","full_name":"Butlin, Roger"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7205"}]},"date_updated":"2023-09-06T14:48:57Z","date_created":"2023-05-23T16:36:27Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"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 postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Postzygotic 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 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterised 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 postzygotic barriers contributing to ecotype divergence and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.","lang":"eng"}]},{"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"isi":["000505069600008"],"pmid":["31840052"]},"quality_controlled":"1","isi":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020"}],"doi":"10.1126/sciadv.aav9963","language":[{"iso":"eng"}],"month":"12","publication_identifier":{"issn":["2375-2548"]},"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"AAAS","author":[{"full_name":"Morales, Hernán E.","first_name":"Hernán E.","last_name":"Morales"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"first_name":"Tomas","last_name":"Larsson","full_name":"Larsson, Tomas"},{"full_name":"Panova, Marina","first_name":"Marina","last_name":"Panova"},{"first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"date_updated":"2023-09-06T15:35:56Z","date_created":"2020-01-29T15:58:27Z","volume":5,"article_number":"eaav9963","file_date_updated":"2020-07-14T12:47:57Z","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","publication":"Science Advances","citation":{"chicago":"Morales, Hernán E., Rui Faria, Kerstin Johannesson, Tomas Larsson, Marina Panova, Anja M Westram, and Roger K. Butlin. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances. AAAS, 2019. https://doi.org/10.1126/sciadv.aav9963.","short":"H.E. Morales, R. Faria, K. Johannesson, T. Larsson, M. Panova, A.M. Westram, R.K. Butlin, Science Advances 5 (2019).","mla":"Morales, Hernán E., et al. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances, vol. 5, no. 12, eaav9963, AAAS, 2019, doi:10.1126/sciadv.aav9963.","apa":"Morales, H. E., Faria, R., Johannesson, K., Larsson, T., Panova, M., Westram, A. M., & Butlin, R. K. (2019). Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. AAAS. https://doi.org/10.1126/sciadv.aav9963","ieee":"H. E. Morales et al., “Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast,” Science Advances, vol. 5, no. 12. AAAS, 2019.","ista":"Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin RK. 2019. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 5(12), eaav9963.","ama":"Morales HE, Faria R, Johannesson K, et al. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 2019;5(12). doi:10.1126/sciadv.aav9963"},"article_type":"original","date_published":"2019-12-04T00:00:00Z","scopus_import":"1","day":"04","article_processing_charge":"No","has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7393","status":"public","ddc":["570"],"title":"Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast","intvolume":" 5","file":[{"checksum":"af99a5dcdc66c6d6102051faf3be48d8","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-02-03T13:33:25Z","file_id":"7442","relation":"main_file","creator":"dernst","file_size":1869449,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_ScienceAdvances_Morales.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow.","lang":"eng"}],"issue":"12"},{"oa_version":"None","ddc":["576"],"status":"public","title":"Mathematical models in population genetics","_id":"8281","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"We review the history of population genetics, starting with its origins a century ago from the synthesis between Mendel and Darwin's ideas, through to the recent development of sophisticated schemes of inference from sequence data, based on the coalescent. We explain the close relation between the coalescent and a diffusion process, which we illustrate by their application to understand spatial structure. We summarise the powerful methods available for analysis of multiple loci, when linkage equilibrium can be assumed, and then discuss approaches to the more challenging case, where associations between alleles require that we follow genotype, rather than allele, frequencies. Though we can hardly cover the whole of population genetics, we give an overview of the current state of the subject, and future challenges to it."}],"type":"book_chapter","date_published":"2019-07-29T00:00:00Z","page":"115-144","citation":{"short":"N.H. Barton, A. Etheridge, in:, D. Balding, I. Moltke, J. Marioni (Eds.), Handbook of Statistical Genomics, 4th ed., Wiley, 2019, pp. 115–144.","mla":"Barton, Nicholas H., and Alison Etheridge. “Mathematical Models in Population Genetics.” Handbook of Statistical Genomics, edited by David Balding et al., 4th ed., Wiley, 2019, pp. 115–44, doi:10.1002/9781119487845.ch4.","chicago":"Barton, Nicholas H, and Alison Etheridge. “Mathematical Models in Population Genetics.” In Handbook of Statistical Genomics, edited by David Balding, Ida Moltke, and John Marioni, 4th ed., 115–44. Wiley, 2019. https://doi.org/10.1002/9781119487845.ch4.","ama":"Barton NH, Etheridge A. Mathematical models in population genetics. In: Balding D, Moltke I, Marioni J, eds. Handbook of Statistical Genomics. 4th ed. Wiley; 2019:115-144. doi:10.1002/9781119487845.ch4","ieee":"N. H. Barton and A. Etheridge, “Mathematical models in population genetics,” in Handbook of statistical genomics, 4th ed., D. Balding, I. Moltke, and J. Marioni, Eds. 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In: Handbook of statistical genomics. , 115–144."},"publication":"Handbook of statistical genomics","article_processing_charge":"No","day":"29","date_created":"2020-08-21T04:25:39Z","date_updated":"2023-09-08T11:24:15Z","edition":"4","author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"}],"department":[{"_id":"NiBa"}],"publisher":"Wiley","editor":[{"full_name":"Balding, David","first_name":"David","last_name":"Balding"},{"full_name":"Moltke, Ida","first_name":"Ida","last_name":"Moltke"},{"full_name":"Marioni, John","first_name":"John","last_name":"Marioni"}],"publication_status":"published","year":"2019","language":[{"iso":"eng"}],"doi":"10.1002/9781119487845.ch4","isi":1,"quality_controlled":"1","external_id":{"isi":["000261343000003"]},"publication_identifier":{"isbn":["9781119429142"]},"month":"07"},{"month":"01","day":"09","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.2kb6fh4"}],"citation":{"ama":"Barton NH. Data from: The consequences of an introgression event. 2019. doi:10.5061/dryad.2kb6fh4","ista":"Barton NH. 2019. Data from: The consequences of an introgression event, Dryad, 10.5061/dryad.2kb6fh4.","apa":"Barton, N. H. (2019). Data from: The consequences of an introgression event. Dryad. https://doi.org/10.5061/dryad.2kb6fh4","ieee":"N. H. Barton, “Data from: The consequences of an introgression event.” Dryad, 2019.","mla":"Barton, Nicholas H. Data from: The Consequences of an Introgression Event. Dryad, 2019, doi:10.5061/dryad.2kb6fh4.","short":"N.H. Barton, (2019).","chicago":"Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.” Dryad, 2019. https://doi.org/10.5061/dryad.2kb6fh4."},"oa":1,"date_published":"2019-01-09T00:00:00Z","doi":"10.5061/dryad.2kb6fh4","type":"research_data_reference","abstract":[{"text":"The spread of adaptive alleles is fundamental to evolution, and in theory, this process is well‐understood. However, only rarely can we follow this process—whether it originates from the spread of a new mutation, or by introgression from another population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP). The species are usually reproductively isolated from each other, but in 2002 and 2006, bursts of hybridization were observed, when F1 hybrids became abundant. Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event, these declined over the following years. In contrast, after 2006, an insecticide resistance allele that had established in A. gambiae spread into A. coluzzi, and rose to high frequency there, over 6 years (~75 generations). Whole genome sequences of 74 individuals showed that A. gambiae SNP from across the genome had become common in the A. coluzzi population, but that most of these were clustered in 34 genes around the resistance locus. A new set of SNP from 25 of these genes were assayed over time; over the 4 years since near‐fixation of the resistance allele; some remained common, whereas others declined. What do these patterns tell us about this introgression event?","lang":"eng"}],"title":"Data from: The consequences of an introgression event","status":"public","publisher":"Dryad","department":[{"_id":"NiBa"}],"year":"2019","_id":"9805","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-08-06T12:03:50Z","date_updated":"2023-09-19T10:06:07Z","oa_version":"Published Version","author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"40"}]}},{"oa":1,"project":[{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"}],"doi":"10.15479/at:ista:th6071","supervisor":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["2663-337X"]},"year":"2019","publication_status":"published","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","first_name":"Roshan"}],"related_material":{"record":[{"id":"1358","status":"public","relation":"part_of_dissertation"},{"id":"955","relation":"part_of_dissertation","status":"public"}]},"date_created":"2019-03-06T16:16:10Z","date_updated":"2023-09-22T10:00:48Z","file_date_updated":"2020-07-14T12:47:18Z","citation":{"short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.","mla":"Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071.","chicago":"Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071.","ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071","apa":"Prizak, R. (2019). Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019.","ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria."},"page":"189","date_published":"2019-03-11T00:00:00Z","day":"11","article_processing_charge":"No","has_accepted_license":"1","_id":"6071","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Coevolution of transcription factors and their binding sites in sequence space","status":"public","ddc":["576"],"oa_version":"Published Version","file":[{"checksum":"e60a72de35d270b31f1a23d50f224ec0","date_created":"2019-03-06T16:05:07Z","date_updated":"2020-07-14T12:47:18Z","file_id":"6072","relation":"main_file","creator":"rprizak","content_type":"application/pdf","file_size":20995465,"access_level":"open_access","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf"},{"relation":"source_file","file_id":"6073","title":"Latex files","checksum":"67c2630333d05ebafef5f018863a8465","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-06T16:09:39Z","access_level":"closed","file_name":"thesis_v2_merge.zip","content_type":"application/zip","file_size":85705272,"creator":"rprizak"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Transcription factors, by binding to specific sequences on the DNA, control the precise spatio-temporal expression of genes inside a cell. However, this specificity is limited, leading to frequent incorrect binding of transcription factors that might have deleterious consequences on the cell. By constructing a biophysical model of TF-DNA binding in the context of gene regulation, I will first explore how regulatory constraints can strongly shape the distribution of a population in sequence space. Then, by directly linking this to a picture of multiple types of transcription factors performing their functions simultaneously inside the cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions between transcription factors and binding sites that lead to erroneous regulatory states -- and understand the constraints this places on the design of regulatory systems. I will then develop a generic theoretical framework to investigate the coevolution of multiple transcription factors and multiple binding sites, in the context of a gene regulatory network that performs a certain function. As a particular tractable version of this problem, I will consider the evolution of two transcription factors when they transmit upstream signals to downstream target genes. Specifically, I will describe the evolutionary steady states and the evolutionary pathways involved, along with their timescales, of a system that initially undergoes a transcription factor duplication event. To connect this important theoretical model to the prominent biological event of transcription factor duplication giving rise to paralogous families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription factors, a major family in humans, and focus on the patterns of evolution that paralogs have undergone in their various protein domains in the recent past. "}]},{"file":[{"access_level":"open_access","file_name":"2019_NewPhytologist_Pickup.pdf","content_type":"application/pdf","file_size":1511958,"creator":"dernst","relation":"main_file","file_id":"7011","checksum":"21e4c95599bbcaf7c483b89954658672","date_created":"2019-11-13T08:15:05Z","date_updated":"2020-07-14T12:47:42Z"}],"oa_version":"Published Version","intvolume":" 224","ddc":["570"],"title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","status":"public","_id":"6856","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","abstract":[{"lang":"eng","text":"Plant mating systems play a key role in structuring genetic variation both within and between species. In hybrid zones, the outcomes and dynamics of hybridization are usually interpreted as the balance between gene flow and selection against hybrids. Yet, mating systems can introduce selective forces that alter these expectations; with diverse outcomes for the level and direction of gene flow depending on variation in outcrossing and whether the mating systems of the species pair are the same or divergent. We present a survey of hybridization in 133 species pairs from 41 plant families and examine how patterns of hybridization vary with mating system. We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and the frequency of reproductive isolating barriers vary in relation to mating system/s of the species pair. We combine these results with a simulation model and examples from the literature to address two general themes: (i) the two‐way interaction between introgression and the evolution of reproductive systems, and (ii) how mating system can facilitate or restrict interspecific gene flow. We conclude that examining mating system with hybridization provides unique opportunities to understand divergence and the processes underlying reproductive isolation."}],"type":"journal_article","date_published":"2019-11-01T00:00:00Z","page":"1035-1047","article_type":"original","citation":{"short":"M. Pickup, N.H. Barton, Y. Brandvain, C. Fraisse, S. Yakimowski, T. Dixit, C. Lexer, E. Cereghetti, D. Field, New Phytologist 224 (2019) 1035–1047.","mla":"Pickup, Melinda, et al. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1035–47, doi:10.1111/nph.16180.","chicago":"Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse, Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16180.","ama":"Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 2019;224(3):1035-1047. doi:10.1111/nph.16180","apa":"Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit, T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. Wiley. https://doi.org/10.1111/nph.16180","ieee":"M. Pickup et al., “Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1035–1047, 2019.","ista":"Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047."},"publication":"New Phytologist","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","volume":224,"date_updated":"2023-10-18T08:47:08Z","date_created":"2019-09-07T14:35:40Z","author":[{"first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Brandvain, Yaniv","first_name":"Yaniv","last_name":"Brandvain"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle"},{"full_name":"Yakimowski, Sarah","last_name":"Yakimowski","first_name":"Sarah"},{"full_name":"Dixit, Tanmay","last_name":"Dixit","first_name":"Tanmay"},{"full_name":"Lexer, Christian","first_name":"Christian","last_name":"Lexer"},{"full_name":"Cereghetti, Eva","last_name":"Cereghetti","first_name":"Eva","id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63"},{"full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field"}],"publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2019","ec_funded":1,"file_date_updated":"2020-07-14T12:47:42Z","language":[{"iso":"eng"}],"doi":"10.1111/nph.16180","project":[{"grant_number":"329960","_id":"25B36484-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Mating system and the evolutionary dynamics of hybrid zones"},{"grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425","name":"Sex chromosomes and species barriers","call_identifier":"FWF"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["31505037"]},"publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"month":"11"},{"project":[{"grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000462585100006"],"pmid":["30590559"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/molbev/msy246","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"month":"03","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Oxford University Press","publication_status":"published","pmid":1,"year":"2019","volume":36,"date_created":"2019-03-10T22:59:19Z","date_updated":"2024-02-21T13:59:17Z","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5757"}]},"author":[{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle"},{"orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","first_name":"Gemma","full_name":"Puixeu Sala, Gemma"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"page":"500-515","citation":{"mla":"Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution, vol. 36, no. 3, Oxford University Press, 2019, pp. 500–15, doi:10.1093/molbev/msy246.","short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515.","chicago":"Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/molbev/msy246.","ama":"Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 2019;36(3):500-515. doi:10.1093/molbev/msy246","ista":"Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 36(3), 500–515.","apa":"Fraisse, C., Puixeu Sala, G., & Vicoso, B. (2019). Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy246","ieee":"C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy of selection in drosophila melanogaster,” Molecular biology and evolution, vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019."},"publication":"Molecular biology and evolution","date_published":"2019-03-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 36","status":"public","title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","_id":"6089","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general."}]},{"article_number":"022423","date_created":"2019-03-10T22:59:20Z","date_updated":"2024-02-28T13:12:06Z","volume":99,"author":[{"full_name":"Carballo-Pacheco, Martín","first_name":"Martín","last_name":"Carballo-Pacheco"},{"full_name":"Desponds, Jonathan","last_name":"Desponds","first_name":"Jonathan"},{"first_name":"Tatyana","last_name":"Gavrilchenko","full_name":"Gavrilchenko, Tatyana"},{"full_name":"Mayer, Andreas","last_name":"Mayer","first_name":"Andreas"},{"full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","first_name":"Roshan"},{"first_name":"Gautam","last_name":"Reddy","full_name":"Reddy, Gautam"},{"full_name":"Nemenman, Ilya","first_name":"Ilya","last_name":"Nemenman"},{"last_name":"Mora","first_name":"Thierry","full_name":"Mora, Thierry"}],"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"American Physical Society","year":"2019","month":"02","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.99.022423","quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000459916500007"]},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract","open_access":"1"}],"abstract":[{"text":"Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems, leading to crosstalk between ligand-receptor pairs. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of noncognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway. Here we quantify the optimal precision of sensing the concentrations of multiple ligands by a collection of promiscuous receptors. We demonstrate that crosstalk can improve precision in concentration sensing and discrimination tasks. To achieve superior precision, the additional information about ligand concentrations contained in short binding events of the noncognate ligand should be exploited. We present a proofreading scheme to realize an approximate estimation of multiple ligand concentrations that reaches a precision close to the derived optimal bounds. Our results help rationalize the observed ubiquity of receptor crosstalk in molecular sensing.","lang":"eng"}],"issue":"2","type":"journal_article","oa_version":"Preprint","title":"Receptor crosstalk improves concentration sensing of multiple ligands","status":"public","intvolume":" 99","_id":"6090","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"26","article_processing_charge":"No","scopus_import":"1","date_published":"2019-02-26T00:00:00Z","publication":"Physical Review E","citation":{"ama":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 2019;99(2). doi:10.1103/PhysRevE.99.022423","ista":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G, Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 99(2), 022423.","ieee":"M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American Physical Society, 2019.","apa":"Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R., Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423","mla":"Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423, American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423.","short":"M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).","chicago":"Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423."}},{"ddc":["576"],"status":"public","title":"An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","intvolume":" 8","_id":"6713","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"relation":"main_file","file_id":"6721","date_created":"2019-07-29T07:41:18Z","date_updated":"2020-07-14T12:47:38Z","checksum":"fa0936fe58f0d9e3f8e75038570e5a17","file_name":"2019_eLife_Castro.pdf","access_level":"open_access","file_size":6748249,"content_type":"application/pdf","creator":"apreinsp"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.","lang":"eng"}],"publication":"eLife","citation":{"short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, ELife 8 (2019).","mla":"Castro, João Pl, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife, vol. 8, e42014, eLife Sciences Publications, 2019, doi:10.7554/eLife.42014.","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42014.","ama":"Castro JP, Yancoskie MN, Marchini M, et al. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 2019;8. doi:10.7554/eLife.42014","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.42014","ieee":"J. P. Castro et al., “An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice,” eLife, vol. 8. eLife Sciences Publications, 2019.","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 8, e42014."},"date_published":"2019-06-06T00:00:00Z","scopus_import":"1","day":"06","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"NiBa"}],"year":"2019","pmid":1,"date_updated":"2024-03-28T23:30:23Z","date_created":"2019-07-28T21:59:17Z","volume":8,"author":[{"full_name":"Castro, João Pl","last_name":"Castro","first_name":"João Pl"},{"last_name":"Yancoskie","first_name":"Michelle N.","full_name":"Yancoskie, Michelle N."},{"first_name":"Marta","last_name":"Marchini","full_name":"Marchini, Marta"},{"full_name":"Belohlavy, Stefanie","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9849-498X","first_name":"Stefanie","last_name":"Belohlavy"},{"full_name":"Hiramatsu, Layla","last_name":"Hiramatsu","first_name":"Layla"},{"first_name":"Marek","last_name":"Kučka","full_name":"Kučka, Marek"},{"first_name":"William H.","last_name":"Beluch","full_name":"Beluch, William H."},{"full_name":"Naumann, Ronald","first_name":"Ronald","last_name":"Naumann"},{"first_name":"Isabella","last_name":"Skuplik","full_name":"Skuplik, Isabella"},{"full_name":"Cobb, John","first_name":"John","last_name":"Cobb"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"last_name":"Rolian","first_name":"Campbell","full_name":"Rolian, Campbell"},{"first_name":"Yingguang Frank","last_name":"Chan","full_name":"Chan, Yingguang Frank"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9804"},{"id":"11388","status":"public","relation":"dissertation_contains"}]},"article_number":"e42014","file_date_updated":"2020-07-14T12:47:38Z","isi":1,"quality_controlled":"1","external_id":{"pmid":["31169497"],"isi":["000473588700001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/eLife.42014","month":"06"},{"publication":"PLoS Biology","citation":{"ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.","apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372","ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372.","ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372","chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372.","short":"J. Polechova, PLoS Biology 16 (2018).","mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005372."},"date_published":"2018-06-15T00:00:00Z","scopus_import":1,"day":"15","has_accepted_license":"1","ddc":["576"],"title":"Is the sky the limit? On the expansion threshold of a species’ range","status":"public","intvolume":" 16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"315","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":6968201,"access_level":"open_access","file_name":"2017_PLOS_Polechova.pdf","checksum":"908c52751bba30c55ed36789e5e4c84d","date_updated":"2020-07-14T12:46:01Z","date_created":"2019-01-22T08:30:03Z","file_id":"5870","relation":"main_file"}],"type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"6","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.2005372","month":"06","publication_identifier":{"issn":["15449173"]},"publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"year":"2018","date_created":"2018-12-11T11:45:46Z","date_updated":"2023-02-23T14:10:16Z","volume":16,"author":[{"last_name":"Polechova","first_name":"Jitka","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","full_name":"Polechova, Jitka"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9839"}]},"article_number":"e2005372","file_date_updated":"2020-07-14T12:46:01Z","publist_id":"7550"},{"related_material":{"record":[{"id":"6095","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"first_name":"Pragya","last_name":"Chaube","full_name":"Chaube, Pragya"},{"full_name":"Morales, Hernán E.","first_name":"Hernán E.","last_name":"Morales"},{"last_name":"Larsson","first_name":"Tomas","full_name":"Larsson, Tomas"},{"full_name":"Lemmon, Alan R.","last_name":"Lemmon","first_name":"Alan R."},{"full_name":"Lemmon, Emily M.","last_name":"Lemmon","first_name":"Emily M."},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"full_name":"Panova, Marina","last_name":"Panova","first_name":"Marina"},{"full_name":"Ravinet, Mark","first_name":"Mark","last_name":"Ravinet"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"oa_version":"Published Version","date_created":"2021-08-09T12:46:39Z","date_updated":"2023-08-24T14:50:26Z","_id":"9837","year":"2018","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"NiBa"}],"publisher":"Dryad","title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","status":"public","abstract":[{"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.","lang":"eng"}],"type":"research_data_reference","date_published":"2018-10-09T00:00:00Z","doi":"10.5061/dryad.72cg113","citation":{"ieee":"R. Faria et al., “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113","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. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, 10.5061/dryad.72cg113.","ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113.","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, (2018).","mla":"Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.72cg113"}],"article_processing_charge":"No","day":"09","month":"10"},{"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"publisher":"eLife Sciences Publications","publication_status":"published","acknowledgement":"We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions.","year":"2018","volume":7,"date_created":"2018-12-11T11:46:23Z","date_updated":"2023-09-11T12:49:17Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9840"}]},"author":[{"full_name":"Payne, Pavel","id":"35F78294-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2711-9453","first_name":"Pavel","last_name":"Payne"},{"full_name":"Geyrhofer, Lukas","first_name":"Lukas","last_name":"Geyrhofer"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P"}],"article_number":"e32035","publist_id":"7400","ec_funded":1,"file_date_updated":"2020-07-14T12:46:25Z","project":[{"call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000431035800001"]},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.32035","month":"03","intvolume":" 7","status":"public","title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","ddc":["576"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"423","file":[{"creator":"dernst","file_size":3533881,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_eLife_Payne.pdf","checksum":"447cf6e680bdc3c01062a8737d876569","date_updated":"2020-07-14T12:46:25Z","date_created":"2018-12-17T10:36:07Z","file_id":"5689","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"citation":{"mla":"Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications, 2018, doi:10.7554/eLife.32035.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32035.","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035.","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” eLife, vol. 7. eLife Sciences Publications, 2018.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32035"},"publication":"eLife","date_published":"2018-03-09T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"09"},{"abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"type":"research_data_reference","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"423"}]},"author":[{"first_name":"Pavel","last_name":"Payne","id":"35F78294-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2711-9453","full_name":"Payne, Pavel"},{"last_name":"Geyrhofer","first_name":"Lukas","full_name":"Geyrhofer, Lukas"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P"}],"oa_version":"Published Version","date_created":"2021-08-09T13:10:02Z","date_updated":"2023-09-11T12:49:17Z","year":"2018","_id":"9840","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"status":"public","title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","article_processing_charge":"No","day":"12","month":"03","doi":"10.5061/dryad.42n44","date_published":"2018-03-12T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.42n44"}],"oa":1,"citation":{"chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. https://doi.org/10.5061/dryad.42n44.","mla":"Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44.","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. https://doi.org/10.5061/dryad.42n44","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44"}},{"date_updated":"2023-09-11T13:41:22Z","date_created":"2018-12-11T11:47:12Z","volume":122,"author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"}],"related_material":{"record":[{"id":"9842","relation":"research_data","status":"public"}]},"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Academic Press","year":"2018","file_date_updated":"2020-07-14T12:47:09Z","ec_funded":1,"publist_id":"7250","language":[{"iso":"eng"}],"doi":"10.1016/j.tpb.2017.11.007","isi":1,"quality_controlled":"1","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000440392900014"]},"oa":1,"month":"07","oa_version":"Submitted Version","file":[{"checksum":"0b96f6db47e3e91b5e7d103b847c239d","date_updated":"2020-07-14T12:47:09Z","date_created":"2019-12-21T09:36:39Z","file_id":"7199","relation":"main_file","creator":"nbarton","file_size":2287682,"content_type":"application/pdf","access_level":"open_access","file_name":"bartonetheridge.pdf"}],"status":"public","title":"Establishment in a new habitat by polygenic adaptation","ddc":["519","576"],"intvolume":" 122","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"564","abstract":[{"text":"Maladapted individuals can only colonise a new habitat if they can evolve a\r\npositive growth rate fast enough to avoid extinction, a process known as evolutionary\r\nrescue. We treat log fitness at low density in the new habitat as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow the evolution\r\nof the growth rate; this assumes that the trait values of offspring of a\r\nsexual union are normally distributed around the mean of the parents’ trait\r\nvalues, with variance that depends only on the parents’ relatedness. The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe mean and genetic variance of the trait in the source population.\r\nThe chance of success becomes small if migrants come from a population\r\nwith mean growth rate in the new habitat more than a few standard deviations\r\nbelow zero; this chance depends roughly equally on the probability\r\nthat the initial founder is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring as a result of selection. The loss of genetic variation\r\nduring the founding event is substantial, but highly variable. With\r\ncontinued migration at rate M, establishment is inevitable; when migration\r\nis rare, the expected time to establishment decreases inversely with M.\r\nHowever, above a threshold migration rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation is held back by gene flow; above this\r\nthreshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder population\r\nwith mean and variance evolving deterministically. By assuming a constant\r\ngenetic variance, we also develop a diffusion approximation for the joint distribution\r\nof population size and trait mean, which extends to include stabilising\r\nselection and density regulation. Divergence of the population from its\r\nancestors causes partial reproductive isolation, which we measure through\r\nthe reproductive value of migrants into the newly established population.","lang":"eng"}],"issue":"7","type":"journal_article","date_published":"2018-07-01T00:00:00Z","article_type":"original","page":"110-127","publication":"Theoretical Population Biology","citation":{"chicago":"Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology. Academic Press, 2018. https://doi.org/10.1016/j.tpb.2017.11.007.","short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127.","mla":"Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology, vol. 122, no. 7, Academic Press, 2018, pp. 110–27, doi:10.1016/j.tpb.2017.11.007.","apa":"Barton, N. H., & Etheridge, A. (2018). Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.11.007","ieee":"N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic adaptation,” Theoretical Population Biology, vol. 122, no. 7. Academic Press, pp. 110–127, 2018.","ista":"Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 110–127.","ama":"Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 2018;122(7):110-127. doi:10.1016/j.tpb.2017.11.007"},"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"publist_id":"7251","author":[{"orcid":"0000-0002-4884-9682","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","last_name":"Ringbauer","first_name":"Harald","full_name":"Ringbauer, Harald"},{"id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander","last_name":"Kolesnikov","full_name":"Kolesnikov, Alexander"},{"full_name":"Field, David","last_name":"Field","first_name":"David"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"200"}]},"date_updated":"2023-09-11T13:42:38Z","date_created":"2018-12-11T11:47:12Z","volume":208,"year":"2018","publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"},{"_id":"ChLa"}],"month":"03","doi":"10.1534/genetics.117.300638","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/205484v1","open_access":"1"}],"external_id":{"isi":["000426219600025"]},"quality_controlled":"1","isi":1,"abstract":[{"text":"In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes\r\nthan geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation to model the effects of a barrier on the geographical spread of ancestry backwards in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographical covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow.","lang":"eng"}],"issue":"3","type":"journal_article","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"563","status":"public","title":"Estimating barriers to gene flow from distorted isolation-by-distance patterns","intvolume":" 208","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-03-01T00:00:00Z","publication":"Genetics","citation":{"ieee":"H. Ringbauer, A. Kolesnikov, D. Field, and N. H. Barton, “Estimating barriers to gene flow from distorted isolation-by-distance patterns,” Genetics, vol. 208, no. 3. Genetics Society of America, pp. 1231–1245, 2018.","apa":"Ringbauer, H., Kolesnikov, A., Field, D., & Barton, N. H. (2018). Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300638","ista":"Ringbauer H, Kolesnikov A, Field D, Barton NH. 2018. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 208(3), 1231–1245.","ama":"Ringbauer H, Kolesnikov A, Field D, Barton NH. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 2018;208(3):1231-1245. doi:10.1534/genetics.117.300638","chicago":"Ringbauer, Harald, Alexander Kolesnikov, David Field, and Nicholas H Barton. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300638.","short":"H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245.","mla":"Ringbauer, Harald, et al. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics, vol. 208, no. 3, Genetics Society of America, 2018, pp. 1231–45, doi:10.1534/genetics.117.300638."},"page":"1231-1245"},{"oa_version":"Preprint","status":"public","title":"Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system","intvolume":" 209","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"316","abstract":[{"lang":"eng","text":"Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self- and non-self recognition. Most work has focused on diversification within self-recognition systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI system. For this model the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and in general is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate to high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a non-self recognition SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a self recognition system common in flowering plants."}],"issue":"3","type":"journal_article","date_published":"2018-07-01T00:00:00Z","article_type":"original","page":"861-883","publication":"Genetics","citation":{"apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300748","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system,” Genetics, vol. 209, no. 3. Genetics Society of America, pp. 861–883, 2018.","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 209(3), 861–883.","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 2018;209(3):861-883. doi:10.1534/genetics.118.300748","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300748.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883.","mla":"Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics, vol. 209, no. 3, Genetics Society of America, 2018, pp. 861–83, doi:10.1534/genetics.118.300748."},"day":"01","article_processing_charge":"No","scopus_import":"1","date_updated":"2023-09-11T13:57:43Z","date_created":"2018-12-11T11:45:47Z","volume":209,"author":[{"full_name":"Bodova, Katarina","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","first_name":"Katarina","last_name":"Bodova"},{"last_name":"Priklopil","first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","full_name":"Priklopil, Tadeas"},{"last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Pickup, Melinda","first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/"}],"record":[{"relation":"research_data","status":"public","id":"9813"}]},"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Genetics Society of America","year":"2018","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1534/genetics.118.300748","isi":1,"quality_controlled":"1","project":[{"_id":"25B36484-B435-11E9-9278-68D0E5697425","grant_number":"329960","name":"Mating system and the evolutionary dynamics of hybrid zones","call_identifier":"FP7"},{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"external_id":{"isi":["000437171700017"]},"main_file_link":[{"url":"https://www.biorxiv.org/node/80098.abstract","open_access":"1"}],"oa":1,"month":"07"},{"month":"04","day":"30","article_processing_charge":"No","date_published":"2018-04-30T00:00:00Z","doi":"10.25386/genetics.6148304.v1","main_file_link":[{"url":"https://doi.org/10.25386/genetics.6148304.v1","open_access":"1"}],"oa":1,"citation":{"short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).","mla":"Bodova, Katarina, et al. Supplemental Material for Bodova et Al., 2018. Genetics Society of America, 2018, doi:10.25386/genetics.6148304.v1.","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society of America, 2018. https://doi.org/10.25386/genetics.6148304.v1.","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material for Bodova et al., 2018. 2018. doi:10.25386/genetics.6148304.v1","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental material for Bodova et al., 2018.” Genetics Society of America, 2018.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Supplemental material for Bodova et al., 2018. Genetics Society of America. https://doi.org/10.25386/genetics.6148304.v1","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material for Bodova et al., 2018, Genetics Society of America, 10.25386/genetics.6148304.v1."},"abstract":[{"lang":"eng","text":"File S1 contains figures that clarify the following features: (i) effect of population size on the average number/frequency of SI classes, (ii) changes in the minimal completeness deficit in time for a single class, and (iii) diversification diagrams for all studied pathways, including the summary figure for k = 8. File S2 contains the code required for a stochastic simulation of the SLF system with an example. This file also includes the output in the form of figures and tables."}],"type":"research_data_reference","author":[{"full_name":"Bod'ová, Katarína","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bod'ová","first_name":"Katarína"},{"full_name":"Priklopil, Tadeas","first_name":"Tadeas","last_name":"Priklopil","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup","full_name":"Pickup, Melinda"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"316"}]},"date_created":"2021-08-06T13:04:32Z","date_updated":"2023-09-11T13:57:42Z","oa_version":"Published Version","year":"2018","_id":"9813","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Supplemental material for Bodova et al., 2018","status":"public","publisher":"Genetics Society of America","department":[{"_id":"NiBa"},{"_id":"GaTk"}]},{"type":"journal_article","abstract":[{"text":"Escaping local optima is one of the major obstacles to function optimisation. Using the metaphor of a fitness landscape, local optima correspond to hills separated by fitness valleys that have to be overcome. We define a class of fitness valleys of tunable difficulty by considering their length, representing the Hamming path between the two optima and their depth, the drop in fitness. For this function class we present a runtime comparison between stochastic search algorithms using different search strategies. The (1+1) EA is a simple and well-studied evolutionary algorithm that has to jump across the valley to a point of higher fitness because it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population genetics, are both able to cross the fitness valley by accepting worsening moves. We show that the runtime of the (1+1) EA depends critically on the length of the valley while the runtimes of the non-elitist algorithms depend crucially on the depth of the valley. Moreover, we show that both SSWM and Metropolis can also efficiently optimise a rugged function consisting of consecutive valleys.","lang":"eng"}],"issue":"5","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"723","status":"public","title":"How to escape local optima in black box optimisation when non elitism outperforms elitism","ddc":["576"],"intvolume":" 80","pubrep_id":"1014","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4674","checksum":"7d92f5d7be81e387edeec4f06442791c","date_created":"2018-12-12T10:08:14Z","date_updated":"2020-07-14T12:47:54Z","access_level":"open_access","file_name":"IST-2018-1014-v1+1_2018_Paixao_Escape.pdf","file_size":691245,"content_type":"application/pdf","creator":"system"}],"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"Algorithmica","citation":{"chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica. Springer, 2018. https://doi.org/10.1007/s00453-017-0369-2.","mla":"Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica, vol. 80, no. 5, Springer, 2018, pp. 1604–33, doi:10.1007/s00453-017-0369-2.","short":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 80 (2018) 1604–1633.","ista":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2018. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 80(5), 1604–1633.","apa":"Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2018). How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. Springer. https://doi.org/10.1007/s00453-017-0369-2","ieee":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How to escape local optima in black box optimisation when non elitism outperforms elitism,” Algorithmica, vol. 80, no. 5. Springer, pp. 1604–1633, 2018.","ama":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 2018;80(5):1604-1633. doi:10.1007/s00453-017-0369-2"},"page":"1604 - 1633","date_published":"2018-05-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:54Z","publist_id":"6957","ec_funded":1,"year":"2018","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"Springer","author":[{"full_name":"Oliveto, Pietro","last_name":"Oliveto","first_name":"Pietro"},{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago"},{"full_name":"Pérez Heredia, Jorge","first_name":"Jorge","last_name":"Pérez Heredia"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","first_name":"Barbora","full_name":"Trubenova, Barbora"}],"date_created":"2018-12-11T11:48:09Z","date_updated":"2023-09-11T14:11:35Z","volume":80,"month":"05","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000428239300010"]},"quality_controlled":"1","isi":1,"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091"}],"doi":"10.1007/s00453-017-0369-2","language":[{"iso":"eng"}]},{"publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2018","volume":209,"date_created":"2018-12-11T11:45:36Z","date_updated":"2023-09-13T08:22:32Z","author":[{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"publist_id":"7617","isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000440014100020"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/early/2017/11/30/227082"}],"language":[{"iso":"eng"}],"doi":"10.1534/genetics.118.301018","month":"08","intvolume":" 209","status":"public","title":"Introgression of a block of genome under infinitesimal selection","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"282","oa_version":"Submitted Version","type":"journal_article","issue":"4","abstract":[{"text":"Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci.","lang":"eng"}],"page":"1279 - 1303","citation":{"mla":"Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:10.1534/genetics.118.301018.","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301018.","ama":"Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. Genetics. 2018;209(4):1279-1303. doi:10.1534/genetics.118.301018","ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303.","apa":"Sachdeva, H., & Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301018","ieee":"H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” Genetics, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018."},"publication":"Genetics","date_published":"2018-08-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"author":[{"first_name":"Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"date_created":"2018-12-11T11:44:18Z","date_updated":"2023-09-18T08:10:29Z","volume":210,"year":"2018","publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"doi":"10.1534/genetics.118.301429","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000452315900021"]},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/379578v1","open_access":"1"}],"quality_controlled":"1","isi":1,"month":"12","publication_identifier":{"issn":["00166731"]},"oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"39","title":"Replicability of introgression under linked, polygenic selection","status":"public","intvolume":" 210","abstract":[{"text":"We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation.","lang":"eng"}],"issue":"4","type":"journal_article","date_published":"2018-12-04T00:00:00Z","publication":"Genetics","citation":{"chicago":"Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301429.","short":"H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429.","ieee":"H. Sachdeva and N. H. Barton, “Replicability of introgression under linked, polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America, pp. 1411–1427, 2018.","apa":"Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429","ista":"Sachdeva H, Barton NH. 2018. Replicability of introgression under linked, polygenic selection. Genetics. 210(4), 1411–1427.","ama":"Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429"},"article_type":"original","page":"1411-1427","day":"04","article_processing_charge":"No","scopus_import":"1"},{"publist_id":"8017","file_date_updated":"2020-07-14T12:46:16Z","volume":115,"date_created":"2018-12-11T11:44:18Z","date_updated":"2023-09-18T08:36:49Z","author":[{"full_name":"Tavares, Hugo","last_name":"Tavares","first_name":"Hugo"},{"first_name":"Annabel","last_name":"Whitley","full_name":"Whitley, Annabel"},{"full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"full_name":"Bradley, Desmond","first_name":"Desmond","last_name":"Bradley"},{"full_name":"Couchman, Matthew","last_name":"Couchman","first_name":"Matthew"},{"full_name":"Copsey, Lucy","first_name":"Lucy","last_name":"Copsey"},{"full_name":"Elleouet, Joane","first_name":"Joane","last_name":"Elleouet"},{"full_name":"Burrus, Monique","last_name":"Burrus","first_name":"Monique"},{"last_name":"Andalo","first_name":"Christophe","full_name":"Andalo, Christophe"},{"full_name":"Li, Miaomiao","last_name":"Li","first_name":"Miaomiao"},{"full_name":"Li, Qun","last_name":"Li","first_name":"Qun"},{"last_name":"Xue","first_name":"Yongbiao","full_name":"Xue, Yongbiao"},{"full_name":"Rebocho, Alexandra B","last_name":"Rebocho","first_name":"Alexandra B"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Coen, Enrico","last_name":"Coen","first_name":"Enrico"}],"publisher":"National Academy of Sciences","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2018","acknowledgement":" ERC Grant 201252 (to N.H.B.)","publication_identifier":{"issn":["00278424"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1801832115","quality_controlled":"1","isi":1,"external_id":{"isi":["000448040500065"],"pmid":["30297406"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"issue":"43","abstract":[{"text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5683","date_updated":"2020-07-14T12:46:16Z","date_created":"2018-12-17T08:44:03Z","checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1","file_name":"11006.full.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1911302,"creator":"dernst"}],"intvolume":" 115","status":"public","title":"Selection and gene flow shape genomic islands that control floral guides","ddc":["570"],"_id":"38","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","has_accepted_license":"1","day":"23","scopus_import":"1","date_published":"2018-10-23T00:00:00Z","page":"11006 - 11011","citation":{"ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115","ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011.","ieee":"H. Tavares et al., “Selection and gene flow shape genomic islands that control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018.","apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115","mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:10.1073/pnas.1801832115.","short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1801832115."},"publication":"PNAS"},{"status":"public","title":"The consequences of an introgression event","ddc":["576"],"intvolume":" 27","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"40","oa_version":"Published Version","file":[{"file_size":295452,"content_type":"application/pdf","creator":"apreinsp","access_level":"open_access","file_name":"2018_MolecularEcology_BartonNick.pdf","date_updated":"2020-07-14T12:46:22Z","date_created":"2019-07-19T06:54:46Z","relation":"main_file","file_id":"6652"}],"type":"journal_article","abstract":[{"text":"Hanemaaijer et al. (Molecular Ecology, 27, 2018) describe the genetic consequences of the introgression of an insecticide resistance allele into a mosquito population. Linked alleles initially increased, but many of these later declined. It is hard to determine whether this decline was due to counter‐selection, rather than simply to chance.","lang":"eng"}],"issue":"24","article_type":"letter_note","page":"4973-4975","publication":"Molecular Ecology","citation":{"short":"N.H. Barton, Molecular Ecology 27 (2018) 4973–4975.","mla":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology, vol. 27, no. 24, Wiley, 2018, pp. 4973–75, doi:10.1111/mec.14950.","chicago":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology. Wiley, 2018. https://doi.org/10.1111/mec.14950.","ama":"Barton NH. The consequences of an introgression event. Molecular Ecology. 2018;27(24):4973-4975. doi:10.1111/mec.14950","ieee":"N. H. Barton, “The consequences of an introgression event,” Molecular Ecology, vol. 27, no. 24. Wiley, pp. 4973–4975, 2018.","apa":"Barton, N. H. (2018). The consequences of an introgression event. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14950","ista":"Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 4973–4975."},"date_published":"2018-12-31T00:00:00Z","scopus_import":"1","day":"31","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"year":"2018","pmid":1,"date_created":"2018-12-11T11:44:18Z","date_updated":"2023-09-19T10:06:08Z","volume":27,"author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"related_material":{"record":[{"id":"9805","status":"public","relation":"research_data"}]},"file_date_updated":"2020-07-14T12:46:22Z","publist_id":"8014","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["30599087"],"isi":["000454600500001"]},"language":[{"iso":"eng"}],"doi":"10.1111/mec.14950","month":"12","publication_identifier":{"issn":["1365294X"]}},{"issue":"1","abstract":[{"text":"We re-examine the model of Kirkpatrick and Barton for the spread of an inversion into a local population. This model assumes that local selection maintains alleles at two or more loci, despite immigration of alternative alleles at these loci from another population. We show that an inversion is favored because it prevents the breakdown of linkage disequilibrium generated by migration; the selective advantage of an inversion is proportional to the amount of recombination between the loci involved, as in other cases where inversions are selected for. We derive expressions for the rate of spread of an inversion; when the loci covered by the inversion are tightly linked, these conditions deviate substantially from those proposed previously, and imply that an inversion can then have only a small advantage. ","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 208","title":"The spread of an inversion with migration and selection","status":"public","_id":"565","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-01-01T00:00:00Z","page":"377 - 382","article_type":"original","citation":{"ama":"Charlesworth B, Barton NH. The spread of an inversion with migration and selection. Genetics. 2018;208(1):377-382. doi:10.1534/genetics.117.300426","apa":"Charlesworth, B., & Barton, N. H. (2018). The spread of an inversion with migration and selection. Genetics. Genetics . https://doi.org/10.1534/genetics.117.300426","ieee":"B. Charlesworth and N. H. Barton, “The spread of an inversion with migration and selection,” Genetics, vol. 208, no. 1. Genetics , pp. 377–382, 2018.","ista":"Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382.","short":"B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382.","mla":"Charlesworth, Brian, and Nicholas H. Barton. “The Spread of an Inversion with Migration and Selection.” Genetics, vol. 208, no. 1, Genetics , 2018, pp. 377–82, doi:10.1534/genetics.117.300426.","chicago":"Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion with Migration and Selection.” Genetics. Genetics , 2018. https://doi.org/10.1534/genetics.117.300426."},"publication":"Genetics","publist_id":"7249","volume":208,"date_updated":"2023-09-19T10:12:31Z","date_created":"2018-12-11T11:47:12Z","author":[{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"department":[{"_id":"NiBa"}],"publisher":"Genetics ","publication_status":"published","pmid":1,"year":"2018","month":"01","language":[{"iso":"eng"}],"doi":"10.1534/genetics.117.300426","quality_controlled":"1","isi":1,"external_id":{"pmid":["29158424"],"isi":["000419356300025"]},"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/","open_access":"1"}]},{"date_published":"2018-04-01T00:00:00Z","citation":{"ama":"Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. Genetics. 2018;208(4):1351-1355. doi:10.1534/genetics.118.300786","ieee":"J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests of selection,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1351–1355, 2018.","apa":"Novembre, J., & Barton, N. H. (2018). Tread lightly interpreting polygenic tests of selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300786","ista":"Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355.","short":"J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.","mla":"Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1351–55, doi:10.1534/genetics.118.300786.","chicago":"Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300786."},"publication":"Genetics","page":"1351 - 1355","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","pubrep_id":"1012","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4958","checksum":"3d838dc285df394376555b794b6a5ad1","date_updated":"2020-07-14T12:46:26Z","date_created":"2018-12-12T10:12:40Z","access_level":"open_access","file_name":"IST-2018-1012-v1+1_2018_Barton_Tread.pdf","content_type":"application/pdf","file_size":500129,"creator":"system"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"430","intvolume":" 208","status":"public","title":"Tread lightly interpreting polygenic tests of selection","ddc":["576"],"issue":"4","abstract":[{"lang":"eng","text":"In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly."}],"type":"journal_article","doi":"10.1534/genetics.118.300786","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000429094400005"]},"oa":1,"isi":1,"quality_controlled":"1","month":"04","author":[{"full_name":"Novembre, John","last_name":"Novembre","first_name":"John"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"volume":208,"date_created":"2018-12-11T11:46:26Z","date_updated":"2023-09-19T10:17:30Z","year":"2018","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","publication_status":"published","publist_id":"7393","file_date_updated":"2020-07-14T12:46:26Z"},{"publist_id":"7198","acknowledgement":"JH and PM are funded by KAUST baseline funds and grant no. 1000000193 .\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions. \r\n\r\n","year":"2018","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Elsevier","author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","first_name":"Katarina","last_name":"Bodova","full_name":"Bodova, Katarina"},{"first_name":"Jan","last_name":"Haskovec","full_name":"Haskovec, Jan"},{"first_name":"Peter","last_name":"Markowich","full_name":"Markowich, Peter"}],"date_created":"2018-12-11T11:47:28Z","date_updated":"2023-09-19T10:38:34Z","volume":"376-377","month":"08","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.08757"}],"external_id":{"arxiv":["1704.08757"],"isi":["000437962900012"]},"isi":1,"quality_controlled":"1","doi":"10.1016/j.physd.2017.10.015","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We study the Fokker-Planck equation derived in the large system limit of the Markovian process describing the dynamics of quantitative traits. The Fokker-Planck equation is posed on a bounded domain and its transport and diffusion coefficients vanish on the domain's boundary. We first argue that, despite this degeneracy, the standard no-flux boundary condition is valid. We derive the weak formulation of the problem and prove the existence and uniqueness of its solutions by constructing the corresponding contraction semigroup on a suitable function space. Then, we prove that for the parameter regime with high enough mutation rate the problem exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next, we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt) method for approximation of observables (moments) of the Fokker-Planck solution, which can be interpreted as a nonlinear Galerkin approximation. The limited applicability of the DynMaxEnt method inspires us to introduce its modified version that is valid for the whole range of admissible parameters. Finally, we present several numerical experiments to demonstrate the performance of both the original and modified DynMaxEnt methods. We observe that in the parameter regimes where both methods are valid, the modified one exhibits slightly better approximation properties compared to the original one."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"607","status":"public","title":"Well posedness and maximum entropy approximation for the dynamics of quantitative traits","oa_version":"Submitted Version","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Physica D: Nonlinear Phenomena","citation":{"ama":"Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015","apa":"Bodova, K., Haskovec, J., & Markowich, P. (2018). Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. Elsevier. https://doi.org/10.1016/j.physd.2017.10.015","ieee":"K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy approximation for the dynamics of quantitative traits,” Physica D: Nonlinear Phenomena, vol. 376–377. Elsevier, pp. 108–120, 2018.","ista":"Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 376–377, 108–120.","short":"K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.","mla":"Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena, vol. 376–377, Elsevier, 2018, pp. 108–20, doi:10.1016/j.physd.2017.10.015.","chicago":"Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015."},"page":"108-120","date_published":"2018-08-01T00:00:00Z"},{"abstract":[{"lang":"eng","text":"This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2018-963-v1+1_thesis.pdf","content_type":"application/pdf","file_size":5792935,"creator":"system","relation":"main_file","file_id":"5111","checksum":"8cc534d2b528ae017acf80874cce48c9","date_updated":"2020-07-14T12:45:23Z","date_created":"2018-12-12T10:14:55Z"},{"content_type":"application/zip","file_size":113365,"creator":"dernst","access_level":"closed","file_name":"2018_thesis_ringbauer_source.zip","checksum":"6af18d7e5a7e2728ceda2f41ee24f628","date_updated":"2020-07-14T12:45:23Z","date_created":"2019-04-05T09:30:12Z","relation":"source_file","file_id":"6224"}],"pubrep_id":"963","title":"Inferring recent demography from spatial genetic structure","status":"public","ddc":["576"],"_id":"200","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"21","has_accepted_license":"1","article_processing_charge":"No","date_published":"2018-02-21T00:00:00Z","page":"146","citation":{"ama":"Ringbauer H. Inferring recent demography from spatial genetic structure. 2018. doi:10.15479/AT:ISTA:th_963","ieee":"H. Ringbauer, “Inferring recent demography from spatial genetic structure,” Institute of Science and Technology Austria, 2018.","apa":"Ringbauer, H. (2018). Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_963","ista":"Ringbauer H. 2018. Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria.","short":"H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure, Institute of Science and Technology Austria, 2018.","mla":"Ringbauer, Harald. Inferring Recent Demography from Spatial Genetic Structure. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_963.","chicago":"Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_963."},"file_date_updated":"2020-07-14T12:45:23Z","publist_id":"7713","date_updated":"2023-09-20T12:00:56Z","date_created":"2018-12-11T11:45:10Z","author":[{"full_name":"Ringbauer, Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4884-9682","first_name":"Harald","last_name":"Ringbauer"}],"related_material":{"record":[{"id":"563","relation":"part_of_dissertation","status":"public"},{"id":"1074","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","year":"2018","month":"02","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","supervisor":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_963","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"}},{"day":"30","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-07-30T00:00:00Z","publication":"PeerJ","citation":{"short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018).","mla":"Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ, vol. 2018, no. 7, 30083438, PeerJ, 2018, doi:10.7717/peerj.5198.","chicago":"Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier, Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5198.","ama":"Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018;2018(7). doi:10.7717/peerj.5198","ieee":"C. Fraisse et al., “The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies,” PeerJ, vol. 2018, no. 7. PeerJ, 2018.","apa":"Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J., & Bierne, N. (2018). The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. PeerJ. https://doi.org/10.7717/peerj.5198","ista":"Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N. 2018. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018(7), 30083438."},"abstract":[{"text":"Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed.","lang":"eng"}],"issue":"7","type":"journal_article","file":[{"relation":"main_file","file_id":"5739","date_updated":"2020-07-14T12:44:48Z","date_created":"2018-12-18T09:42:11Z","checksum":"7d55ae22598a1c70759cd671600cff53","file_name":"2018_PeerJ_Fraisse.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1480792,"creator":"dernst"}],"oa_version":"Published Version","ddc":["576"],"title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","status":"public","intvolume":" 2018","_id":"139","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","language":[{"iso":"eng"}],"doi":"10.7717/peerj.5198","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000440484800002"]},"oa":1,"file_date_updated":"2020-07-14T12:44:48Z","publist_id":"7784","article_number":"30083438","date_updated":"2023-10-17T12:25:28Z","date_created":"2018-12-11T11:44:50Z","volume":2018,"author":[{"full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"},{"first_name":"Pierre","last_name":"Gagnaire","full_name":"Gagnaire, Pierre"},{"full_name":"Romiguier, Jonathan","first_name":"Jonathan","last_name":"Romiguier"},{"last_name":"Faivre","first_name":"Nicolas","full_name":"Faivre, Nicolas"},{"last_name":"Welch","first_name":"John","full_name":"Welch, John"},{"full_name":"Bierne, Nicolas","first_name":"Nicolas","last_name":"Bierne"}],"publication_status":"published","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"PeerJ","year":"2018"},{"article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2018-10-01T00:00:00Z","citation":{"ista":"Bertl J, Ringbauer H, Blum M. 2018. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018(10), e5325.","ieee":"J. Bertl, H. Ringbauer, and M. Blum, “Can secondary contact following range expansion be distinguished from barriers to gene flow?,” PeerJ, vol. 2018, no. 10. PeerJ, 2018.","apa":"Bertl, J., Ringbauer, H., & Blum, M. (2018). Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. PeerJ. https://doi.org/10.7717/peerj.5325","ama":"Bertl J, Ringbauer H, Blum M. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018;2018(10). doi:10.7717/peerj.5325","chicago":"Bertl, Johanna, Harald Ringbauer, and Michaël Blum. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5325.","mla":"Bertl, Johanna, et al. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ, vol. 2018, no. 10, e5325, PeerJ, 2018, doi:10.7717/peerj.5325.","short":"J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018)."},"publication":"PeerJ","issue":"10","abstract":[{"lang":"eng","text":"Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2018_PeerJ_Bertl.pdf","access_level":"open_access","file_size":1328344,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"5692","date_created":"2018-12-17T10:46:06Z","date_updated":"2020-07-14T12:46:06Z","checksum":"3334886c4b39678db4c4b74299ca14ba"}],"_id":"33","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 2018","ddc":["576"],"status":"public","title":"Can secondary contact following range expansion be distinguished from barriers to gene flow?","month":"10","doi":"10.7717/peerj.5325","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000447204400001"],"pmid":["30294507"]},"isi":1,"quality_controlled":"1","publist_id":"8022","file_date_updated":"2020-07-14T12:46:06Z","article_number":"e5325","author":[{"first_name":"Johanna","last_name":"Bertl","full_name":"Bertl, Johanna"},{"last_name":"Ringbauer","first_name":"Harald","orcid":"0000-0002-4884-9682","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","full_name":"Ringbauer, Harald"},{"full_name":"Blum, Michaël","last_name":"Blum","first_name":"Michaël"}],"volume":2018,"date_created":"2018-12-11T11:44:16Z","date_updated":"2023-10-17T12:24:43Z","pmid":1,"year":"2018","acknowledgement":"Johanna Bertl was supported by the Vienna Graduate School of Population Genetics (Austrian Science Fund (FWF): W1225-B20) and worked on this project while employed at the Department of Statistics and Operations Research, University of Vienna, Austria. This article was developed in the framework of the Grenoble Alpes Data Institute, which is supported by the French National Research Agency under the “Investissments d’avenir” program (ANR-15-IDEX-02).","department":[{"_id":"NiBa"}],"publisher":"PeerJ","publication_status":"published"},{"intvolume":" 18","status":"public","title":"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"286","oa_version":"None","type":"journal_article","issue":"5","abstract":[{"text":"Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time-consuming. Here, we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically derived error rates, the method performs as well as the widely used package Colony, but is faster by two orders of magnitude. Using simulations, we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open-pollinated arrays of the snapdragon Antirrhinum majus and find evidence for a high degree of multiple mating. Although we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in nonmodel systems. ","lang":"eng"}],"page":"988 - 999","citation":{"short":"T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999.","mla":"Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources, vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:10.1111/1755-0998.12782.","chicago":"Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources. Wiley, 2018. https://doi.org/10.1111/1755-0998.12782.","ama":"Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 2018;18(5):988-999. doi:10.1111/1755-0998.12782","apa":"Ellis, T., Field, D., & Barton, N. H. (2018). Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.12782","ieee":"T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering,” Molecular Ecology Resources, vol. 18, no. 5. Wiley, pp. 988–999, 2018.","ista":"Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 18(5), 988–999."},"publication":"Molecular Ecology Resources","date_published":"2018-09-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","acknowledgement":"ERC, Grant/Award Number: 250152","year":"2018","volume":18,"date_created":"2018-12-11T11:45:37Z","date_updated":"2024-02-21T13:45:00Z","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5583"}]},"author":[{"last_name":"Ellis","first_name":"Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","full_name":"Ellis, Thomas"},{"full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"ec_funded":1,"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000441753000007"]},"language":[{"iso":"eng"}],"doi":"10.1111/1755-0998.12782","month":"09"},{"type":"conference","abstract":[{"lang":"eng","text":"There has been renewed interest in modelling the behaviour of evolutionary algorithms by more traditional mathematical objects, such as ordinary differential equations or Markov chains. The advantage is that the analysis becomes greatly facilitated due to the existence of well established methods. However, this typically comes at the cost of disregarding information about the process. Here, we introduce the use of stochastic differential equations (SDEs) for the study of EAs. SDEs can produce simple analytical results for the dynamics of stochastic processes, unlike Markov chains which can produce rigorous but unwieldy expressions about the dynamics. On the other hand, unlike ordinary differential equations (ODEs), they do not discard information about the stochasticity of the process. We show that these are especially suitable for the analysis of fixed budget scenarios and present analogs of the additive and multiplicative drift theorems for SDEs. We exemplify the use of these methods for two model algorithms ((1+1) EA and RLS) on two canonical problems(OneMax and LeadingOnes)."}],"publist_id":"6255","_id":"1112","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","title":"An application of stochastic differential equations to evolutionary algorithms","publication_status":"published","status":"public","department":[{"_id":"NiBa"}],"publisher":"ACM","author":[{"last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"full_name":"Pérez Heredia, Jorge","last_name":"Pérez Heredia","first_name":"Jorge"}],"date_created":"2018-12-11T11:50:12Z","date_updated":"2021-01-12T06:48:22Z","oa_version":"None","scopus_import":1,"day":"12","month":"01","publication_identifier":{"isbn":["978-145034651-1"]},"publication":"Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms","citation":{"ista":"Paixao T, Pérez Heredia J. 2017. An application of stochastic differential equations to evolutionary algorithms. Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. FOGA: Foundations of Genetic Algorithms, 3–11.","apa":"Paixao, T., & Pérez Heredia, J. (2017). An application of stochastic differential equations to evolutionary algorithms. In Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms (pp. 3–11). Copenhagen, Denmark: ACM. https://doi.org/10.1145/3040718.3040729","ieee":"T. Paixao and J. Pérez Heredia, “An application of stochastic differential equations to evolutionary algorithms,” in Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, Copenhagen, Denmark, 2017, pp. 3–11.","ama":"Paixao T, Pérez Heredia J. An application of stochastic differential equations to evolutionary algorithms. In: Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. ACM; 2017:3-11. doi:10.1145/3040718.3040729","chicago":"Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms.” In Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, 3–11. ACM, 2017. https://doi.org/10.1145/3040718.3040729.","mla":"Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms.” Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11, doi:10.1145/3040718.3040729.","short":"T. Paixao, J. Pérez Heredia, in:, Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11."},"quality_controlled":"1","page":"3 - 11","conference":{"end_date":"2017-01-15","location":"Copenhagen, Denmark","start_date":"2017-01-12","name":"FOGA: Foundations of Genetic Algorithms"},"doi":"10.1145/3040718.3040729","date_published":"2017-01-12T00:00:00Z","language":[{"iso":"eng"}]},{"publist_id":"6160","ec_funded":1,"acknowledgement":"We thank Nick Barton, Katarína Bod’ová, and Sr\r\n-\r\ndan Sarikas for constructive feed-\r\nback and support. Furthermore, we would like to express our deep gratitude to the anonymous referees (one\r\nof whom, Jimmy Garnier, agreed to reveal his identity) and the editor Max Souza, for very helpful and\r\ndetailed comments and suggestions that significantly helped us to improve the manuscript. This project has\r\nreceived funding from the European Union’s Seventh Framework Programme for research, technological\r\ndevelopment and demonstration under Grant Agreement 618091 Speed of Adaptation in Population Genet-\r\nics and Evolutionary Computation (SAGE) and the European Research Council (ERC) Grant No. 250152\r\n(SN), from the Scientific Grant Agency of the Slovak Republic under the Grant 1/0459/13 and by the Slovak\r\nResearch and Development Agency under the Contract No. APVV-14-0378 (RK). RK would also like to\r\nthank IST Austria for its hospitality during the work on this project.","year":"2017","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Springer","author":[{"first_name":"Richard","last_name":"Kollár","full_name":"Kollár, Richard"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","first_name":"Sebastian","full_name":"Novak, Sebastian"}],"date_created":"2018-12-11T11:50:38Z","date_updated":"2021-01-12T06:48:58Z","volume":79,"month":"03","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1607.00944","open_access":"1"}],"quality_controlled":"1","project":[{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"},{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"doi":"10.1007/s11538-016-0244-3","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Variation in genotypes may be responsible for differences in dispersal rates, directional biases, and growth rates of individuals. These traits may favor certain genotypes and enhance their spatiotemporal spreading into areas occupied by the less advantageous genotypes. We study how these factors influence the speed of spreading in the case of two competing genotypes under the assumption that spatial variation of the total population is small compared to the spatial variation of the frequencies of the genotypes in the population. In that case, the dynamics of the frequency of one of the genotypes is approximately described by a generalized Fisher–Kolmogorov–Petrovskii–Piskunov (F–KPP) equation. This generalized F–KPP equation with (nonlinear) frequency-dependent diffusion and advection terms admits traveling wave solutions that characterize the invasion of the dominant genotype. Our existence results generalize the classical theory for traveling waves for the F–KPP with constant coefficients. Moreover, in the particular case of the quadratic (monostable) nonlinear growth–decay rate in the generalized F–KPP we study in detail the influence of the variance in diffusion and mean displacement rates of the two genotypes on the minimal wave propagation speed.","lang":"eng"}],"issue":"3","_id":"1191","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Existence of traveling waves for the generalized F–KPP equation","intvolume":" 79","oa_version":"Preprint","scopus_import":1,"day":"01","publication":"Bulletin of Mathematical Biology","citation":{"chicago":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology. Springer, 2017. https://doi.org/10.1007/s11538-016-0244-3.","short":"R. Kollár, S. Novak, Bulletin of Mathematical Biology 79 (2017) 525–559.","mla":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology, vol. 79, no. 3, Springer, 2017, pp. 525–59, doi:10.1007/s11538-016-0244-3.","apa":"Kollár, R., & Novak, S. (2017). Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. Springer. https://doi.org/10.1007/s11538-016-0244-3","ieee":"R. Kollár and S. Novak, “Existence of traveling waves for the generalized F–KPP equation,” Bulletin of Mathematical Biology, vol. 79, no. 3. Springer, pp. 525–559, 2017.","ista":"Kollár R, Novak S. 2017. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 79(3), 525–559.","ama":"Kollár R, Novak S. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 2017;79(3):525-559. doi:10.1007/s11538-016-0244-3"},"page":"525-559","date_published":"2017-03-01T00:00:00Z"},{"pubrep_id":"918","oa_version":"Published Version","file":[{"checksum":"273ab17f33305e4eaafd911ff88e7c5b","date_created":"2018-12-12T10:14:42Z","date_updated":"2020-07-14T12:47:10Z","file_id":"5096","relation":"main_file","creator":"system","file_size":8453470,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-918-v1+1_elife-28921-figures-v3.pdf"},{"creator":"system","file_size":1953221,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-918-v1+2_elife-28921-v3.pdf","checksum":"b433f90576c7be597cd43367946f8e7f","date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-12T10:14:43Z","file_id":"5097","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"570","intvolume":" 6","status":"public","title":"Regulatory network structure determines patterns of intermolecular epistasis","ddc":["576"],"abstract":[{"text":"Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site. In large part, this epistasis can be qualitatively attributed to the structure of the transcriptional regulatory system and could therefore be a common feature in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution. ","lang":"eng"}],"type":"journal_article","date_published":"2017-11-13T00:00:00Z","citation":{"short":"M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).","mla":"Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife, vol. 6, e28921, eLife Sciences Publications, 2017, doi:10.7554/eLife.28921.","chicago":"Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.28921.","ama":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 2017;6. doi:10.7554/eLife.28921","apa":"Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., & Guet, C. C. (2017). Regulatory network structure determines patterns of intermolecular epistasis. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.28921","ieee":"M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory network structure determines patterns of intermolecular epistasis,” eLife, vol. 6. eLife Sciences Publications, 2017.","ista":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. 2017. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 6, e28921."},"publication":"eLife","has_accepted_license":"1","day":"13","scopus_import":1,"author":[{"full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato"},{"id":"35F0286E-F248-11E8-B48F-1D18A9856A87","first_name":"Srdjan","last_name":"Sarikas","full_name":"Sarikas, Srdjan"},{"orcid":"0000-0003-1986-9753","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","last_name":"Acar","first_name":"Hande","full_name":"Acar, Hande"},{"first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"},{"full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"volume":6,"date_created":"2018-12-11T11:47:14Z","date_updated":"2021-01-12T08:03:15Z","year":"2017","department":[{"_id":"CaGu"},{"_id":"JoBo"},{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","publication_status":"published","ec_funded":1,"publist_id":"7244","file_date_updated":"2020-07-14T12:47:10Z","article_number":"e28921","doi":"10.7554/eLife.28921","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publication_identifier":{"issn":["2050084X"]},"month":"11"},{"publication_identifier":{"issn":["00368075"]},"day":"17","month":"11","scopus_import":1,"doi":"10.1126/science.aao3526","date_published":"2017-11-17T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ista":"Bradley D, Xu P, Mohorianu I, Whibley A, Field D, Tavares H, Couchman M, Copsey L, Carpenter R, Li M, Li Q, Xue Y, Dalmay T, Coen E. 2017. Evolution of flower color pattern through selection on regulatory small RNAs. Science. 358(6365), 925–928.","apa":"Bradley, D., Xu, P., Mohorianu, I., Whibley, A., Field, D., Tavares, H., … Coen, E. (2017). Evolution of flower color pattern through selection on regulatory small RNAs. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aao3526","ieee":"D. Bradley et al., “Evolution of flower color pattern through selection on regulatory small RNAs,” Science, vol. 358, no. 6365. American Association for the Advancement of Science, pp. 925–928, 2017.","ama":"Bradley D, Xu P, Mohorianu I, et al. Evolution of flower color pattern through selection on regulatory small RNAs. Science. 2017;358(6365):925-928. doi:10.1126/science.aao3526","chicago":"Bradley, Desmond, Ping Xu, Irina Mohorianu, Annabel Whibley, David Field, Hugo Tavares, Matthew Couchman, et al. “Evolution of Flower Color Pattern through Selection on Regulatory Small RNAs.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aao3526.","mla":"Bradley, Desmond, et al. “Evolution of Flower Color Pattern through Selection on Regulatory Small RNAs.” Science, vol. 358, no. 6365, American Association for the Advancement of Science, 2017, pp. 925–28, doi:10.1126/science.aao3526.","short":"D. Bradley, P. Xu, I. Mohorianu, A. Whibley, D. Field, H. Tavares, M. Couchman, L. Copsey, R. Carpenter, M. Li, Q. Li, Y. Xue, T. Dalmay, E. Coen, Science 358 (2017) 925–928."},"publication":"Science","page":"925 - 928","quality_controlled":"1","publist_id":"7193","issue":"6365","abstract":[{"text":"Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that population-wide differences in color patterns in snapdragon flowers are caused by an inverted duplication that generates sRNAs. The complexity and size of the transcripts indicate that the duplication represents an intermediate on the pathway to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating a yellow highlight at the site of pollinator entry. The inverted duplication exhibits steep clines in allele frequency in a natural hybrid zone, showing that the allele is under selection. Thus, regulatory interactions of evolutionarily recent sRNAs can be acted upon by selection and contribute to the evolution of phenotypic diversity.","lang":"eng"}],"type":"journal_article","author":[{"full_name":"Bradley, Desmond","first_name":"Desmond","last_name":"Bradley"},{"full_name":"Xu, Ping","first_name":"Ping","last_name":"Xu"},{"full_name":"Mohorianu, Irina","last_name":"Mohorianu","first_name":"Irina"},{"first_name":"Annabel","last_name":"Whibley","full_name":"Whibley, Annabel"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"},{"full_name":"Tavares, Hugo","last_name":"Tavares","first_name":"Hugo"},{"last_name":"Couchman","first_name":"Matthew","full_name":"Couchman, Matthew"},{"full_name":"Copsey, Lucy","first_name":"Lucy","last_name":"Copsey"},{"full_name":"Carpenter, Rosemary","first_name":"Rosemary","last_name":"Carpenter"},{"last_name":"Li","first_name":"Miaomiao","full_name":"Li, Miaomiao"},{"full_name":"Li, Qun","last_name":"Li","first_name":"Qun"},{"first_name":"Yongbiao","last_name":"Xue","full_name":"Xue, Yongbiao"},{"full_name":"Dalmay, Tamas","last_name":"Dalmay","first_name":"Tamas"},{"full_name":"Coen, Enrico","first_name":"Enrico","last_name":"Coen"}],"volume":358,"oa_version":"None","date_created":"2018-12-11T11:47:29Z","date_updated":"2021-01-12T08:06:10Z","year":"2017","_id":"611","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Association for the Advancement of Science","intvolume":" 358","department":[{"_id":"NiBa"}],"title":"Evolution of flower color pattern through selection on regulatory small RNAs","publication_status":"published","status":"public"}]