[{"_id":"9857","author":[{"first_name":"Tom","last_name":"Schmidt","full_name":"Schmidt, Tom"},{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rasic, Gordana","first_name":"Gordana","last_name":"Rasic"},{"full_name":"Turley, Andrew","first_name":"Andrew","last_name":"Turley"},{"full_name":"Montgomery, Brian","first_name":"Brian","last_name":"Montgomery"},{"full_name":"Iturbe Ormaetxe, Inaki","last_name":"Iturbe Ormaetxe","first_name":"Inaki"},{"last_name":"Cook","first_name":"Peter","full_name":"Cook, Peter"},{"last_name":"Ryan","first_name":"Peter","full_name":"Ryan, Peter"},{"first_name":"Scott","last_name":"Ritchie","full_name":"Ritchie, Scott"},{"first_name":"Ary","last_name":"Hoffmann","full_name":"Hoffmann, Ary"},{"first_name":"Scott","last_name":"O’Neill","full_name":"O’Neill, Scott"},{"full_name":"Turelli, Michael","last_name":"Turelli","first_name":"Michael"}],"oa_version":"Published Version","article_processing_charge":"No","department":[{"_id":"NiBa"}],"date_created":"2021-08-10T07:41:52Z","month":"05","title":"Supporting information concerning observed wMel frequencies and analyses of habitat variables","publisher":"Public Library of Science ","date_updated":"2023-09-22T10:02:51Z","year":"2017","citation":{"ieee":"T. Schmidt <i>et al.</i>, “Supporting information concerning observed wMel frequencies and analyses of habitat variables.” Public Library of Science , 2017.","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables.” Public Library of Science , 2017. <a href=\"https://doi.org/10.1371/journal.pbio.2001894.s015\">https://doi.org/10.1371/journal.pbio.2001894.s015</a>.","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Supporting information concerning observed wMel frequencies and analyses of habitat variables. Public Library of Science . <a href=\"https://doi.org/10.1371/journal.pbio.2001894.s015\">https://doi.org/10.1371/journal.pbio.2001894.s015</a>","ama":"Schmidt T, Barton NH, Rasic G, et al. Supporting information concerning observed wMel frequencies and analyses of habitat variables. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001894.s015\">10.1371/journal.pbio.2001894.s015</a>","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting information concerning observed wMel frequencies and analyses of habitat variables, Public Library of Science , <a href=\"https://doi.org/10.1371/journal.pbio.2001894.s015\">10.1371/journal.pbio.2001894.s015</a>.","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).","mla":"Schmidt, Tom, et al. <i>Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables</i>. Public Library of Science , 2017, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001894.s015\">10.1371/journal.pbio.2001894.s015</a>."},"date_published":"2017-05-30T00:00:00Z","type":"research_data_reference","doi":"10.1371/journal.pbio.2001894.s015","day":"30","related_material":{"record":[{"status":"public","id":"951","relation":"used_in_publication"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public"},{"related_material":{"record":[{"relation":"used_in_publication","id":"951","status":"public"}]},"status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2017","citation":{"ieee":"T. Schmidt <i>et al.</i>, “Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics.” Public Library of Science, 2017.","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pbio.2001894.s016\">https://doi.org/10.1371/journal.pbio.2001894.s016</a>.","ama":"Schmidt T, Barton NH, Rasic G, et al. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001894.s016\">10.1371/journal.pbio.2001894.s016</a>","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2001894.s016\">https://doi.org/10.1371/journal.pbio.2001894.s016</a>","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2001894.s016\">10.1371/journal.pbio.2001894.s016</a>.","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).","mla":"Schmidt, Tom, et al. <i>Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001894.s016\">10.1371/journal.pbio.2001894.s016</a>."},"date_updated":"2023-09-22T10:02:51Z","type":"research_data_reference","date_published":"2017-05-30T00:00:00Z","day":"30","doi":"10.1371/journal.pbio.2001894.s016","publisher":"Public Library of Science","_id":"9858","author":[{"full_name":"Schmidt, Tom","last_name":"Schmidt","first_name":"Tom"},{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rasic, Gordana","last_name":"Rasic","first_name":"Gordana"},{"first_name":"Andrew","last_name":"Turley","full_name":"Turley, Andrew"},{"full_name":"Montgomery, Brian","last_name":"Montgomery","first_name":"Brian"},{"first_name":"Inaki","last_name":"Iturbe Ormaetxe","full_name":"Iturbe Ormaetxe, Inaki"},{"full_name":"Cook, Peter","last_name":"Cook","first_name":"Peter"},{"last_name":"Ryan","first_name":"Peter","full_name":"Ryan, Peter"},{"full_name":"Ritchie, Scott","last_name":"Ritchie","first_name":"Scott"},{"first_name":"Ary","last_name":"Hoffmann","full_name":"Hoffmann, Ary"},{"first_name":"Scott","last_name":"O’Neill","full_name":"O’Neill, Scott"},{"first_name":"Michael","last_name":"Turelli","full_name":"Turelli, Michael"}],"date_created":"2021-08-10T07:47:07Z","department":[{"_id":"NiBa"}],"article_processing_charge":"No","oa_version":"Published Version","title":"Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics","month":"05"},{"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Evolution; International Journal of Organic Evolution","month":"06","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"oa_version":"Submitted Version","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"creator":"dernst","file_id":"6329","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2017_Evolution_Sachdeva_supplement.pdf","date_updated":"2020-07-14T12:48:18Z","checksum":"6d4c38cb1347fd43620d1736c6df5c79","file_size":625260,"date_created":"2019-04-17T07:37:04Z"},{"creator":"dernst","file_id":"6330","relation":"main_file","access_level":"open_access","file_name":"2017_Evolution_Sachdeva_article.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:48:18Z","checksum":"f1d90dd8831b44baf49b4dd176f263af","file_size":520110,"date_created":"2019-04-17T07:37:04Z"}],"type":"journal_article","date_published":"2017-06-01T00:00:00Z","publist_id":"6409","oa":1,"publication_identifier":{"issn":["00143820"]},"file_date_updated":"2020-07-14T12:48:18Z","quality_controlled":"1","ec_funded":1,"page":"1478 - 1493 ","publisher":"Wiley-Blackwell","issue":"6","author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani","full_name":"Sachdeva, Himani"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"}],"scopus_import":"1","pmid":1,"_id":"990","intvolume":"        71","pubrep_id":"977","title":"Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow","department":[{"_id":"NiBa"}],"article_processing_charge":"No","date_created":"2018-12-11T11:49:34Z","publication_status":"published","ddc":["576"],"volume":71,"external_id":{"pmid":["28419447"],"isi":["000403014800005"]},"isi":1,"citation":{"ieee":"H. Sachdeva and N. H. Barton, “Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow,” <i>Evolution; International Journal of Organic Evolution</i>, vol. 71, no. 6. Wiley-Blackwell, pp. 1478–1493, 2017.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Divergence and Evolution of Assortative Mating in a Polygenic Trait Model of Speciation with Gene Flow.” <i>Evolution; International Journal of Organic Evolution</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/evo.13252\">https://doi.org/10.1111/evo.13252</a>.","ama":"Sachdeva H, Barton NH. Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. <i>Evolution; International Journal of Organic Evolution</i>. 2017;71(6):1478-1493. doi:<a href=\"https://doi.org/10.1111/evo.13252\">10.1111/evo.13252</a>","apa":"Sachdeva, H., &#38; Barton, N. H. (2017). Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. <i>Evolution; International Journal of Organic Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/evo.13252\">https://doi.org/10.1111/evo.13252</a>","ista":"Sachdeva H, Barton NH. 2017. Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. 71(6), 1478–1493.","short":"H. Sachdeva, N.H. Barton, Evolution; International Journal of Organic Evolution 71 (2017) 1478–1493.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Divergence and Evolution of Assortative Mating in a Polygenic Trait Model of Speciation with Gene Flow.” <i>Evolution; International Journal of Organic Evolution</i>, vol. 71, no. 6, Wiley-Blackwell, 2017, pp. 1478–93, doi:<a href=\"https://doi.org/10.1111/evo.13252\">10.1111/evo.13252</a>."},"year":"2017","date_updated":"2025-05-28T11:42:51Z","abstract":[{"text":"Assortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few-locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two-deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration-selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual-based simulations.","lang":"eng"}],"day":"01","doi":"10.1111/evo.13252"},{"page":"124","file_date_updated":"2021-02-22T13:42:47Z","publisher":"Institute of Science and Technology Austria","_id":"1125","author":[{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","last_name":"Novak","first_name":"Sebastian"}],"publication_status":"published","date_created":"2018-12-11T11:50:17Z","article_processing_charge":"No","department":[{"_id":"NiBa"}],"alternative_title":["ISTA Thesis"],"title":"Evolutionary proccesses in variable emvironments","ddc":["576"],"date_updated":"2025-05-28T11:57:05Z","year":"2016","citation":{"ista":"Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria.","mla":"Novak, Sebastian. <i>Evolutionary Proccesses in Variable Emvironments</i>. Institute of Science and Technology Austria, 2016.","short":"S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of Science and Technology Austria, 2016.","ieee":"S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of Science and Technology Austria, 2016.","chicago":"Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute of Science and Technology Austria, 2016.","apa":"Novak, S. (2016). <i>Evolutionary proccesses in variable emvironments</i>. Institute of Science and Technology Austria.","ama":"Novak S. Evolutionary proccesses in variable emvironments. 2016."},"degree_awarded":"PhD","day":"01","abstract":[{"text":"Natural environments are never constant but subject to spatial and temporal change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial to understand the\r\nimpact of environmental variation on evolutionary processes. In this thesis, I present\r\nthree topics that share the common theme of environmental variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst, I show how a temporally fluctuating environment gives rise to second-order\r\nselection on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations are adapted to their environment, mutation rates are minimized. I argue\r\nthat a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly subjected to diverse environmental challenges, and I outline implications of\r\nthe presented results to antibiotic treatment strategies.\r\nSecond, I discuss my work on the evolution of dispersal. Besides reproducing\r\nknown results about the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes in dispersal type frequencies as a source for selection for increased\r\npropensities to disperse. This concept contains effects of relatedness that are known\r\nto promote dispersal, and I explain how it identifies other forces selecting for dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances of phenotypic traits under multivariate stabilizing\r\nselection. For the case of constant environments, I generalize known formulae of\r\nequilibrium variances to multiple traits and discuss how the genetic variance of a focal\r\ntrait is influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary work aiming at including environmental fluctuations in the form of moving\r\ntrait optima into the model.","lang":"eng"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","oa_version":"Published Version","month":"07","file":[{"access_level":"closed","relation":"main_file","file_id":"6811","creator":"dernst","date_created":"2019-08-13T09:01:00Z","file_size":3564901,"checksum":"81dcc838dfcf7aa0b1a27ecf4fe2da4e","date_updated":"2019-08-13T09:01:00Z","file_name":"Novak_thesis.pdf","content_type":"application/pdf"},{"content_type":"application/pdf","file_name":"2016_Novak_Thesis.pdf","date_updated":"2021-02-22T13:42:47Z","checksum":"30808d2f7ca920e09f63a95cdc49bffd","file_size":2814384,"date_created":"2021-02-22T13:42:47Z","creator":"dernst","file_id":"9186","access_level":"open_access","relation":"main_file","success":1}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","related_material":{"record":[{"id":"2023","relation":"part_of_dissertation","status":"public"}]},"date_published":"2016-07-01T00:00:00Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6235","oa":1},{"publication_identifier":{"issn":["2663-337X"]},"publist_id":"6229","oa":1,"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"}],"type":"dissertation","date_published":"2016-07-01T00:00:00Z","file":[{"date_updated":"2019-08-13T08:53:52Z","file_name":"Tugrul_thesis_w_signature_page.pdf","content_type":"application/pdf","date_created":"2019-08-13T08:53:52Z","checksum":"66cb61a59943e4fb7447c6a86be5ef51","file_size":3695257,"file_id":"6810","creator":"dernst","relation":"main_file","access_level":"closed"},{"date_updated":"2021-02-22T11:45:20Z","file_name":"2016_Tugrul_Thesis.pdf","content_type":"application/pdf","date_created":"2021-02-22T11:45:20Z","checksum":"293e388d70563760f6b24c3e66283dda","file_size":3880811,"file_id":"9182","creator":"dernst","success":1,"relation":"main_file","access_level":"open_access"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","related_material":{"record":[{"status":"public","id":"5554","relation":"research_data"},{"status":"public","relation":"part_of_dissertation","id":"1666"}]},"oa_version":"Published Version","month":"07","has_accepted_license":"1","language":[{"iso":"eng"}],"day":"01","degree_awarded":"PhD","abstract":[{"text":"Evolution of gene regulation is important for phenotypic evolution and diversity. Sequence-specific binding of regulatory proteins is one of the key regulatory mechanisms determining gene expression. Although there has been intense interest in evolution of regulatory binding sites in the last decades, a theoretical understanding is far from being complete. In this thesis, I aim at a better understanding of the evolution of transcriptional regulatory binding sequences by using biophysical and population genetic models.\r\nIn the first part of the thesis, I discuss how to formulate the evolutionary dynamics of binding se- quences in a single isolated binding site and in promoter/enhancer regions. I develop a theoretical framework bridging between a thermodynamical model for transcription and a mutation-selection-drift model for monomorphic populations. I mainly address the typical evolutionary rates, and how they de- pend on biophysical parameters (e.g. binding length and specificity) and population genetic parameters (e.g. population size and selection strength).\r\nIn the second part of the thesis, I analyse empirical data for a better evolutionary and biophysical understanding of sequence-specific binding of bacterial RNA polymerase. First, I infer selection on regulatory and non-regulatory binding sites of RNA polymerase in the E. coli K12 genome. Second, I infer the chemical potential of RNA polymerase, an important but unknown physical parameter defining the threshold energy for strong binding. Furthermore, I try to understand the relation between the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial isolates by constructing a simple but biophysically motivated gene expression model. Lastly, I lay out a statistical framework to predict adaptive point mutations in de novo promoter evolution in a selection experiment.","lang":"eng"}],"year":"2016","citation":{"ista":"Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria.","short":"M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of Science and Technology Austria, 2016.","mla":"Tugrul, Murat. <i>Evolution of Transcriptional Regulatory Sequences</i>. Institute of Science and Technology Austria, 2016.","chicago":"Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute of Science and Technology Austria, 2016.","ieee":"M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute of Science and Technology Austria, 2016.","apa":"Tugrul, M. (2016). <i>Evolution of transcriptional regulatory sequences</i>. Institute of Science and Technology Austria.","ama":"Tugrul M. Evolution of transcriptional regulatory sequences. 2016."},"date_updated":"2025-05-28T11:57:04Z","acknowledgement":"This PhD thesis may not have been completed without the help and care I received from some peo- ple during my PhD life. I am especially grateful to Tiago Paixao, Gasper Tkacik, Nick Barton, not only for their scientific advices but also for their patience and support. I thank Calin Guet and Jonathan Bollback for allowing me to “play around” in their labs and get some experience on experimental evolution. I thank Magdalena Steinrueck and Fabienne Jesse for collaborating and sharing their experimental data with me. I thank Johannes Jaeger for reviewing my thesis. I thank all members of Barton group (aka bartonians) for their feedback, and all workers of IST Austria for making the best working conditions. Lastly, I thank two special women, Nejla Sag ̆lam and Setenay Dog ̆an, for their continuous support and encouragement. I truly had a great chance of having right people around me.","ddc":["576"],"department":[{"_id":"NiBa"}],"article_processing_charge":"No","date_created":"2018-12-11T11:50:19Z","publication_status":"published","title":"Evolution of transcriptional regulatory sequences","alternative_title":["ISTA Thesis"],"_id":"1131","author":[{"id":"37C323C6-F248-11E8-B48F-1D18A9856A87","full_name":"Tugrul, Murat","orcid":"0000-0002-8523-0758","last_name":"Tugrul","first_name":"Murat"}],"publisher":"Institute of Science and Technology Austria","page":"89","file_date_updated":"2021-02-22T11:45:20Z"},{"language":[{"iso":"eng"}],"oa_version":"Published Version","article_number":"e2000234","month":"12","has_accepted_license":"1","publication":"PLoS Biology","file":[{"creator":"system","file_id":"5164","relation":"main_file","access_level":"open_access","file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:36Z","file_size":2494348,"checksum":"2bab63b068a9840efd532b9ae583f9bb","date_created":"2018-12-12T10:15:42Z"}],"status":"public","related_material":{"record":[{"status":"public","relation":"research_data","id":"9862"},{"id":"9863","relation":"research_data","status":"public"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"publist_id":"6200","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2016-12-27T00:00:00Z","publisher":"Public Library of Science","quality_controlled":"1","file_date_updated":"2020-07-14T12:44:36Z","date_created":"2018-12-11T11:50:28Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publication_status":"published","intvolume":"        14","title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","pubrep_id":"742","scopus_import":1,"_id":"1158","issue":"12","author":[{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle","last_name":"Fraisse"},{"full_name":"Romiguier, Jonathan","first_name":"Jonathan","last_name":"Romiguier"},{"first_name":"Youann","last_name":"Anciaux","full_name":"Anciaux, Youann"},{"full_name":"Galtier, Nicolas","last_name":"Galtier","first_name":"Nicolas"},{"first_name":"Nicolas","last_name":"Bierne","full_name":"Bierne, Nicolas"}],"volume":14,"acknowledgement":"European Research Council (ERC) https://erc.europa.eu/ (grant number ERC grant 232971). PopPhyl project. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/ (grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch) Center for high-performance computing of the SIB Swiss Institute of Bioinformatics and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité.","ddc":["576"],"day":"27","doi":"10.1371/journal.pbio.2000234","abstract":[{"lang":"eng","text":"Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate &quot;grey zone&quot; of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation."}],"year":"2016","citation":{"apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Shedding light on the grey zone of speciation along a continuum of genomic divergence. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234\">https://doi.org/10.1371/journal.pbio.2000234</a>","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light on the grey zone of speciation along a continuum of genomic divergence. <i>PLoS Biology</i>. 2016;14(12). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234\">10.1371/journal.pbio.2000234</a>","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” <i>PLoS Biology</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234\">https://doi.org/10.1371/journal.pbio.2000234</a>.","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Shedding light on the grey zone of speciation along a continuum of genomic divergence,” <i>PLoS Biology</i>, vol. 14, no. 12. Public Library of Science, 2016.","mla":"Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” <i>PLoS Biology</i>, vol. 14, no. 12, e2000234, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234\">10.1371/journal.pbio.2000234</a>.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016).","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 14(12), e2000234."},"date_updated":"2023-02-23T14:11:16Z"},{"ddc":["576"],"volume":6,"acknowledgement":"H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund Thattai for critical discussions and suggestions.","year":"2016","citation":{"ista":"Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.","mla":"Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” <i>Scientific Reports</i>, vol. 6, 38840, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep38840\">10.1038/srep38840</a>.","short":"H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).","chicago":"Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep38840\">https://doi.org/10.1038/srep38840</a>.","ieee":"H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","apa":"Sachdeva, H., Barma, M., &#38; Rao, M. (2016). Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep38840\">https://doi.org/10.1038/srep38840</a>","ama":"Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep38840\">10.1038/srep38840</a>"},"date_updated":"2021-01-12T06:48:50Z","abstract":[{"text":"A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner-this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging.","lang":"eng"}],"day":"19","doi":"10.1038/srep38840","file_date_updated":"2020-07-14T12:44:37Z","quality_controlled":"1","publisher":"Nature Publishing Group","author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani"},{"last_name":"Barma","first_name":"Mustansir","full_name":"Barma, Mustansir"},{"full_name":"Rao, Madan","first_name":"Madan","last_name":"Rao"}],"scopus_import":1,"_id":"1172","intvolume":"         6","title":"Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae","pubrep_id":"737","department":[{"_id":"NiBa"}],"date_created":"2018-12-11T11:50:32Z","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"checksum":"cb378732da885ea4959ec5b845fb6e52","file_size":760967,"date_created":"2018-12-12T10:12:56Z","content_type":"application/pdf","file_name":"IST-2017-737-v1+1_srep38840.pdf","date_updated":"2020-07-14T12:44:37Z","access_level":"open_access","relation":"main_file","creator":"system","file_id":"4977"}],"type":"journal_article","date_published":"2016-12-19T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publist_id":"6183","language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Scientific Reports","article_number":"38840","month":"12","oa_version":"Published Version"},{"ddc":["576"],"volume":108,"abstract":[{"text":"Ancestral processes are fundamental to modern population genetics and spatial structure has been the subject of intense interest for many years. Despite this interest, almost nothing is known about the distribution of the locations of pedigree or genetic ancestors. Using both spatially continuous and stepping-stone models, we show that the distribution of pedigree ancestors approaches a travelling wave, for which we develop two alternative approximations. The speed and width of the wave are sensitive to the local details of the model. After a short time, genetic ancestors spread far more slowly than pedigree ancestors, ultimately diffusing out with radius ## rather than spreading at constant speed. In contrast to the wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the local details of the models.","lang":"eng"}],"day":"01","doi":"10.1016/j.tpb.2015.10.008","year":"2016","citation":{"ieee":"J. Kelleher, A. Etheridge, A. Véber, and N. H. Barton, “Spread of pedigree versus genetic ancestry in spatially distributed populations,” <i>Theoretical Population Biology</i>, vol. 108. Academic Press, pp. 1–12, 2016.","chicago":"Kelleher, Jerome, Alison Etheridge, Amandine Véber, and Nicholas H Barton. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” <i>Theoretical Population Biology</i>. Academic Press, 2016. <a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">https://doi.org/10.1016/j.tpb.2015.10.008</a>.","apa":"Kelleher, J., Etheridge, A., Véber, A., &#38; Barton, N. H. (2016). Spread of pedigree versus genetic ancestry in spatially distributed populations. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">https://doi.org/10.1016/j.tpb.2015.10.008</a>","ama":"Kelleher J, Etheridge A, Véber A, Barton NH. Spread of pedigree versus genetic ancestry in spatially distributed populations. <i>Theoretical Population Biology</i>. 2016;108:1-12. doi:<a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">10.1016/j.tpb.2015.10.008</a>","ista":"Kelleher J, Etheridge A, Véber A, Barton NH. 2016. Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. 108, 1–12.","mla":"Kelleher, Jerome, et al. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” <i>Theoretical Population Biology</i>, vol. 108, Academic Press, 2016, pp. 1–12, doi:<a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">10.1016/j.tpb.2015.10.008</a>.","short":"J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population Biology 108 (2016) 1–12."},"date_updated":"2021-01-12T06:52:07Z","publisher":"Academic Press","file_date_updated":"2020-07-14T12:45:07Z","ec_funded":1,"quality_controlled":"1","page":"1 - 12","intvolume":"       108","pubrep_id":"465","title":"Spread of pedigree versus genetic ancestry in spatially distributed populations","department":[{"_id":"NiBa"}],"date_created":"2018-12-11T11:53:08Z","publication_status":"published","author":[{"first_name":"Jerome","last_name":"Kelleher","full_name":"Kelleher, Jerome"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"},{"last_name":"Véber","first_name":"Amandine","full_name":"Véber, Amandine"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":1,"_id":"1631","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"creator":"system","file_id":"4865","relation":"main_file","access_level":"open_access","file_name":"IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:07Z","file_size":1684043,"checksum":"6a65ba187994d4ad86c1c509e0ff482a","date_created":"2018-12-12T10:11:12Z"}],"publist_id":"5524","oa":1,"type":"journal_article","date_published":"2016-04-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"month":"04","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"Theoretical Population Biology"},{"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"date_updated":"2024-02-21T13:49:54Z","citation":{"mla":"Ellis, Thomas, and David Field. <i>Flower Colour Data and Phylogeny (NEXUS) Files</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>.","short":"T. Ellis, D. Field, (2016).","ista":"Ellis T, Field D. 2016. Flower colour data and phylogeny (NEXUS) files, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>.","ama":"Ellis T, Field D. Flower colour data and phylogeny (NEXUS) files. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>","apa":"Ellis, T., &#38; Field, D. (2016). Flower colour data and phylogeny (NEXUS) files. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:34\">https://doi.org/10.15479/AT:ISTA:34</a>","ieee":"T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute of Science and Technology Austria, 2016.","chicago":"Ellis, Thomas, and David Field. “Flower Colour Data and Phylogeny (NEXUS) Files.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:34\">https://doi.org/10.15479/AT:ISTA:34</a>."},"year":"2016","date_published":"2016-02-19T00:00:00Z","type":"research_data","doi":"10.15479/AT:ISTA:34","day":"19","abstract":[{"text":"We collected flower colour information on species in the tribe Antirrhineae from taxonomic literature. We also retreived molecular data from GenBank for as many of these species as possible to estimate phylogenetic relationships among these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny.\r\n\r\nFor full details of the methods see:\r\nEllis TJ and Field DL \"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)","lang":"eng"}],"oa":1,"publist_id":"5828","file":[{"content_type":"application/zip","file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip","date_updated":"2020-07-14T12:47:00Z","checksum":"950f85b80427d357bfeff09608ba02e9","file_size":4468543,"date_created":"2018-12-12T13:02:27Z","creator":"system","file_id":"5594","relation":"main_file","access_level":"open_access"}],"status":"public","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"1382","relation":"research_paper","status":"public"}]},"_id":"5550","has_accepted_license":"1","license":"https://creativecommons.org/publicdomain/zero/1.0/","author":[{"last_name":"Ellis","first_name":"Thomas","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David","first_name":"David","last_name":"Field"}],"datarep_id":"34","oa_version":"Published Version","article_processing_charge":"No","date_created":"2018-12-12T12:31:29Z","department":[{"_id":"NiBa"}],"month":"02","title":"Flower colour data and phylogeny (NEXUS) files","file_date_updated":"2020-07-14T12:47:00Z","publisher":"Institute of Science and Technology Austria"},{"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"date_updated":"2024-02-21T13:51:27Z","citation":{"ista":"Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>.","mla":"Ellis, Thomas. <i>Data on Pollinator Observations and Offpsring Phenotypes</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>.","short":"T. Ellis, (2016).","ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016.","chicago":"Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:35\">https://doi.org/10.15479/AT:ISTA:35</a>.","apa":"Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:35\">https://doi.org/10.15479/AT:ISTA:35</a>","ama":"Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>"},"year":"2016","date_published":"2016-02-19T00:00:00Z","type":"research_data","doi":"10.15479/AT:ISTA:35","day":"19","abstract":[{"lang":"eng","text":"Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid."}],"oa":1,"file":[{"checksum":"aa3eb85d52b110cd192aa23147c4d4f3","file_size":32775,"date_created":"2018-12-12T13:05:12Z","content_type":"application/zip","file_name":"IST-2016-35-v1+1_array_data.zip","date_updated":"2020-07-14T12:47:01Z","relation":"main_file","access_level":"open_access","creator":"system","file_id":"5640"}],"related_material":{"record":[{"status":"public","id":"1398","relation":"research_paper"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","_id":"5551","has_accepted_license":"1","author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ellis","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"}],"datarep_id":"35","oa_version":"Published Version","article_processing_charge":"No","department":[{"_id":"NiBa"}],"date_created":"2018-12-12T12:31:29Z","month":"02","title":"Data on pollinator observations and offpsring phenotypes","contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"file_date_updated":"2020-07-14T12:47:01Z","publisher":"Institute of Science and Technology Austria"},{"file":[{"access_level":"open_access","relation":"main_file","creator":"system","file_id":"5625","file_size":44905,"checksum":"cbc61b523d4d475a04a737d50dc470ef","date_created":"2018-12-12T13:03:07Z","content_type":"application/zip","file_name":"IST-2016-36-v1+1_tag_assay_archive.zip","date_updated":"2020-07-14T12:47:01Z"}],"related_material":{"record":[{"id":"1398","relation":"research_paper","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_updated":"2024-02-21T13:51:40Z","year":"2016","citation":{"mla":"Ellis, Thomas. <i>Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.</i> Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>.","short":"T. Ellis, (2016).","ista":"Ellis T. 2016. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data., Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>.","apa":"Ellis, T. (2016). Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:36\">https://doi.org/10.15479/AT:ISTA:36</a>","ama":"Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>","ieee":"T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.” Institute of Science and Technology Austria, 2016.","chicago":"Ellis, Thomas. “Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:36\">https://doi.org/10.15479/AT:ISTA:36</a>."},"date_published":"2016-02-19T00:00:00Z","type":"research_data","doi":"10.15479/AT:ISTA:36","day":"19","abstract":[{"lang":"eng","text":"Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016).\r\n\r\nSnapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012.\r\n\r\nAlso included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation."}],"oa":1,"file_date_updated":"2020-07-14T12:47:01Z","contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"publisher":"Institute of Science and Technology Austria","_id":"5552","has_accepted_license":"1","author":[{"last_name":"Ellis","first_name":"Thomas","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"}],"datarep_id":"36","oa_version":"Published Version","department":[{"_id":"NiBa"}],"date_created":"2018-12-12T12:31:30Z","article_processing_charge":"No","title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.","month":"02"},{"doi":"10.15479/AT:ISTA:37","day":"19","abstract":[{"lang":"eng","text":"Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset.\r\n\r\nOther data were retreived from an online database of this population at www.antspec.org."}],"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"date_updated":"2024-02-21T13:51:14Z","year":"2016","citation":{"ista":"Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>.","short":"D. Field, T. Ellis, (2016).","mla":"Field, David, and Thomas Ellis. <i>Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>.","chicago":"Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:37\">https://doi.org/10.15479/AT:ISTA:37</a>.","ieee":"D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012.” Institute of Science and Technology Austria, 2016.","apa":"Field, D., &#38; Ellis, T. (2016). Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:37\">https://doi.org/10.15479/AT:ISTA:37</a>","ama":"Field D, Ellis T. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>"},"date_published":"2016-02-19T00:00:00Z","type":"research_data","file":[{"file_id":"5620","creator":"system","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:47:01Z","content_type":"application/zip","file_name":"IST-2016-37-v1+1_paternity_archive.zip","date_created":"2018-12-12T13:03:02Z","file_size":132808,"checksum":"4ae751b1fa4897fa216241f975a57313"}],"ddc":["576"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"1398","relation":"research_paper"}]},"oa_version":"Published Version","department":[{"_id":"NiBa"}],"date_created":"2018-12-12T12:31:30Z","article_processing_charge":"No","month":"02","title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","_id":"5553","has_accepted_license":"1","author":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David","orcid":"0000-0002-4014-8478","last_name":"Field","first_name":"David"},{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","first_name":"Thomas","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254"}],"datarep_id":"37","publisher":"Institute of Science and Technology Austria","contributor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","contributor_type":"project_manager","first_name":"Nicholas H"}],"file_date_updated":"2020-07-14T12:47:01Z","keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"]},{"keyword":["RNAP binding","de novo promoter evolution","lac promoter"],"file_date_updated":"2020-07-14T12:47:01Z","contributor":[{"first_name":"Magdalena","last_name":"Steinrück","contributor_type":"researcher","id":"2C023F40-F248-11E8-B48F-1D18A9856A87"},{"id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Jesse","first_name":"Fabienne"}],"publisher":"Institute of Science and Technology Austria","datarep_id":"43","author":[{"id":"37C323C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8523-0758","full_name":"Tugrul, Murat","first_name":"Murat","last_name":"Tugrul"}],"has_accepted_license":"1","_id":"5554","month":"05","title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","date_created":"2018-12-12T12:31:30Z","article_processing_charge":"No","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"oa_version":"Published Version","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1131"}]},"file":[{"file_size":1123495,"checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2","date_created":"2018-12-12T13:03:08Z","content_type":"application/zip","file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip","date_updated":"2020-07-14T12:47:01Z","relation":"main_file","access_level":"open_access","creator":"system","file_id":"5626"}],"type":"research_data","date_published":"2016-05-12T00:00:00Z","year":"2016","citation":{"chicago":"Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:43\">https://doi.org/10.15479/AT:ISTA:43</a>.","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016.","apa":"Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:43\">https://doi.org/10.15479/AT:ISTA:43</a>","ama":"Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>","ista":"Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>.","short":"M. Tugrul, (2016).","mla":"Tugrul, Murat. <i>Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"date_updated":"2024-02-21T13:50:34Z","oa":1,"abstract":[{"text":"The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution.","lang":"eng"}],"day":"12","doi":"10.15479/AT:ISTA:43"},{"issue":"2","author":[{"last_name":"Lohse","first_name":"Konrad","full_name":"Lohse, Konrad"},{"full_name":"Chmelik, Martin","first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Martin","first_name":"Simon","full_name":"Martin, Simon"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"scopus_import":"1","pmid":1,"_id":"1518","intvolume":"       202","pubrep_id":"561","title":"Efficient strategies for calculating blockwise likelihoods under the coalescent","article_processing_charge":"No","department":[{"_id":"KrCh"},{"_id":"NiBa"}],"date_created":"2018-12-11T11:52:29Z","publication_status":"published","file_date_updated":"2020-07-14T12:45:00Z","ec_funded":1,"quality_controlled":"1","page":"775 - 786","article_type":"original","publisher":"Genetics Society of America","external_id":{"pmid":["26715666"]},"citation":{"apa":"Lohse, K., Chmelik, M., Martin, S., &#38; Barton, N. H. (2016). Efficient strategies for calculating blockwise likelihoods under the coalescent. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.115.183814\">https://doi.org/10.1534/genetics.115.183814</a>","ama":"Lohse K, Chmelik M, Martin S, Barton NH. Efficient strategies for calculating blockwise likelihoods under the coalescent. <i>Genetics</i>. 2016;202(2):775-786. doi:<a href=\"https://doi.org/10.1534/genetics.115.183814\">10.1534/genetics.115.183814</a>","chicago":"Lohse, Konrad, Martin Chmelik, Simon Martin, and Nicholas H Barton. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.115.183814\">https://doi.org/10.1534/genetics.115.183814</a>.","ieee":"K. Lohse, M. Chmelik, S. Martin, and N. H. Barton, “Efficient strategies for calculating blockwise likelihoods under the coalescent,” <i>Genetics</i>, vol. 202, no. 2. Genetics Society of America, pp. 775–786, 2016.","mla":"Lohse, Konrad, et al. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” <i>Genetics</i>, vol. 202, no. 2, Genetics Society of America, 2016, pp. 775–86, doi:<a href=\"https://doi.org/10.1534/genetics.115.183814\">10.1534/genetics.115.183814</a>.","short":"K. Lohse, M. Chmelik, S. Martin, N.H. Barton, Genetics 202 (2016) 775–786.","ista":"Lohse K, Chmelik M, Martin S, Barton NH. 2016. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 202(2), 775–786."},"year":"2016","date_updated":"2025-05-28T11:42:48Z","abstract":[{"lang":"eng","text":"The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proved difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has a simple, recursive form, the size of such likelihood calculations explodes quickly with the number of individuals and applications of this framework have so far been mainly limited to small samples (pairs and triplets) for which the GF can be written by hand. Here we investigate several strategies for exploiting the inherent symmetries of the coalescent. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes that allows likelihood calculations from nontrivial samples. Using this strategy, we automated blockwise likelihood calculations for a general set of demographic scenarios in Mathematica. These histories may involve population size changes, continuous migration, discrete divergence, and admixture between multiple populations. To give a concrete example, we calculate the likelihood for a model of isolation with migration (IM), assuming two diploid samples without phase and outgroup information. We demonstrate the new inference scheme with an analysis of two individual butterfly genomes from the sister species Heliconius melpomene rosina and H. cydno."}],"day":"01","doi":"10.1534/genetics.115.183814","ddc":["570"],"acknowledgement":"We thank Lynsey Bunnefeld for discussions throughout the project and Joshua Schraiber and one anonymous reviewer\r\nfor constructive comments on an earlier version of this manuscript. This work was supported by funding from the\r\nUnited Kingdom Natural Environment Research Council (to K.L.) (NE/I020288/1) and a grant from the European\r\nResearch Council (250152) (to N.H.B.).","volume":202,"has_accepted_license":"1","publication":"Genetics","month":"02","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"oa_version":"Preprint","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2016-02-01T00:00:00Z","publist_id":"5658","oa":1,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:45:00Z","content_type":"application/pdf","file_name":"IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf","date_created":"2018-12-12T10:16:51Z","file_size":957466,"checksum":"41c9b5d72e7fe4624dd22dfe622337d5","file_id":"5241","creator":"system","relation":"main_file","access_level":"open_access"}]},{"ddc":["576"],"date_updated":"2021-01-12T06:50:03Z","year":"2016","citation":{"short":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, B. Trubenova, in:, Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–1170.","mla":"Oliveto, Pietro, et al. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>, ACM, 2016, pp. 1163–70, doi:<a href=\"https://doi.org/10.1145/2908812.2908909\">10.1145/2908812.2908909</a>.","ista":"Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. 2016. When non-elitism outperforms elitism for crossing fitness valleys. Proceedings of the Genetic and Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation conference, 1163–1170.","ama":"Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. When non-elitism outperforms elitism for crossing fitness valleys. In: <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>. ACM; 2016:1163-1170. doi:<a href=\"https://doi.org/10.1145/2908812.2908909\">10.1145/2908812.2908909</a>","apa":"Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., &#38; Trubenova, B. (2016). When non-elitism outperforms elitism for crossing fitness valleys. In <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i> (pp. 1163–1170). Denver, CO, USA: ACM. <a href=\"https://doi.org/10.1145/2908812.2908909\">https://doi.org/10.1145/2908812.2908909</a>","ieee":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism outperforms elitism for crossing fitness valleys,” in <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>, Denver, CO, USA, 2016, pp. 1163–1170.","chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” In <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>, 1163–70. ACM, 2016. <a href=\"https://doi.org/10.1145/2908812.2908909\">https://doi.org/10.1145/2908812.2908909</a>."},"doi":"10.1145/2908812.2908909","day":"20","abstract":[{"text":"Crossing fitness valleys is one of the major obstacles to function optimization. In this paper we investigate how the structure of the fitness valley, namely its depth d and length ℓ, influence the runtime of different strategies for crossing these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis algorithm. While the (1+1) EA has to jump across the valley to a point of higher fitness because it does not accept decreasing moves, the non-elitist algorithms may cross the valley by accepting worsening moves. We show that while the runtime of the (1+1) EA algorithm depends critically on the length of the valley, the runtimes of the non-elitist algorithms depend crucially only on the depth of the valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of small length. Moreover, we show that both SSWM and Metropolis can also efficiently optimize a rugged function consisting of consecutive valleys.","lang":"eng"}],"page":"1163 - 1170","ec_funded":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:44:45Z","publisher":"ACM","_id":"1349","scopus_import":1,"author":[{"first_name":"Pietro","last_name":"Oliveto","full_name":"Oliveto, Pietro"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"},{"last_name":"Heredia","first_name":"Jorge","full_name":"Heredia, Jorge"},{"full_name":"Sudholt, Dirk","first_name":"Dirk","last_name":"Sudholt"},{"last_name":"Trubenova","first_name":"Barbora","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","date_created":"2018-12-11T11:51:31Z","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"pubrep_id":"650","title":"When non-elitism outperforms elitism for crossing fitness valleys","file":[{"date_created":"2018-12-12T10:16:27Z","file_size":979026,"checksum":"a1896e39e4113f2711e46b435d5f3e69","date_updated":"2020-07-14T12:44:45Z","content_type":"application/pdf","file_name":"IST-2016-650-v1+1_p1163-oliveto.pdf","access_level":"open_access","relation":"main_file","file_id":"5214","creator":"system"}],"status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2016-07-20T00:00:00Z","type":"conference","publist_id":"5900","oa":1,"language":[{"iso":"eng"}],"conference":{"location":"Denver, CO, USA","end_date":"2016-07-24","start_date":"2016-07-20","name":"GECCO: Genetic and evolutionary computation conference"},"publication":"Proceedings of the Genetic and Evolutionary Computation Conference 2016 ","has_accepted_license":"1","oa_version":"Published Version","project":[{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"month":"07"},{"publist_id":"5889","oa":1,"date_published":"2016-01-05T00:00:00Z","type":"journal_article","file":[{"file_name":"IST-2017-769-v1+1_SewallWright1931.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:46Z","file_size":112674,"checksum":"3562b89c821a4be84edf2b6ebd870cf5","date_created":"2018-12-12T10:08:26Z","creator":"system","file_id":"4687","relation":"main_file","access_level":"open_access"}],"status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","month":"01","publication":"Genetics","has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.1534/genetics.115.184796","day":"05","date_updated":"2021-01-12T06:50:07Z","citation":{"chicago":"Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.115.184796\">https://doi.org/10.1534/genetics.115.184796</a>.","ieee":"N. H. Barton, “Sewall Wright on evolution in Mendelian populations and the ‘Shifting Balance,’” <i>Genetics</i>, vol. 202, no. 1. Genetics Society of America, pp. 3–4, 2016.","apa":"Barton, N. H. (2016). Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.115.184796\">https://doi.org/10.1534/genetics.115.184796</a>","ama":"Barton NH. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” <i>Genetics</i>. 2016;202(1):3-4. doi:<a href=\"https://doi.org/10.1534/genetics.115.184796\">10.1534/genetics.115.184796</a>","ista":"Barton NH. 2016. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”. Genetics. 202(1), 3–4.","mla":"Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” <i>Genetics</i>, vol. 202, no. 1, Genetics Society of America, 2016, pp. 3–4, doi:<a href=\"https://doi.org/10.1534/genetics.115.184796\">10.1534/genetics.115.184796</a>.","short":"N.H. Barton, Genetics 202 (2016) 3–4."},"year":"2016","volume":202,"ddc":["570"],"publication_status":"published","department":[{"_id":"NiBa"}],"date_created":"2018-12-11T11:51:33Z","title":"Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”","pubrep_id":"769","intvolume":"       202","_id":"1356","scopus_import":1,"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"issue":"1","publisher":"Genetics Society of America","page":"3 - 4","quality_controlled":"1","file_date_updated":"2020-07-14T12:44:46Z"},{"has_accepted_license":"1","publication":"Genetics","oa_version":"Submitted Version","month":"03","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2016-03-01T00:00:00Z","publist_id":"5888","oa":1,"file":[{"file_id":"5127","creator":"system","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:44:46Z","file_name":"IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:15:09Z","checksum":"b2174bab2de1d1142900062a150f35c9","file_size":130779}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","scopus_import":1,"_id":"1357","issue":"3","author":[{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:51:33Z","department":[{"_id":"NiBa"}],"publication_status":"published","intvolume":"       202","title":"Richard Hudson and Norman Kaplan on the coalescent process","pubrep_id":"768","quality_controlled":"1","page":"865 - 866","file_date_updated":"2020-07-14T12:44:46Z","publisher":"Genetics Society of America","year":"2016","citation":{"apa":"Barton, N. H. (2016). Richard Hudson and Norman Kaplan on the coalescent process. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.116.187542\">https://doi.org/10.1534/genetics.116.187542</a>","ama":"Barton NH. Richard Hudson and Norman Kaplan on the coalescent process. <i>Genetics</i>. 2016;202(3):865-866. doi:<a href=\"https://doi.org/10.1534/genetics.116.187542\">10.1534/genetics.116.187542</a>","ieee":"N. H. Barton, “Richard Hudson and Norman Kaplan on the coalescent process,” <i>Genetics</i>, vol. 202, no. 3. Genetics Society of America, pp. 865–866, 2016.","chicago":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.116.187542\">https://doi.org/10.1534/genetics.116.187542</a>.","short":"N.H. Barton, Genetics 202 (2016) 865–866.","mla":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” <i>Genetics</i>, vol. 202, no. 3, Genetics Society of America, 2016, pp. 865–66, doi:<a href=\"https://doi.org/10.1534/genetics.116.187542\">10.1534/genetics.116.187542</a>.","ista":"Barton NH. 2016. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 202(3), 865–866."},"date_updated":"2021-01-12T06:50:07Z","day":"01","doi":"10.1534/genetics.116.187542","volume":202,"ddc":["576"]},{"publist_id":"5887","oa":1,"type":"journal_article","date_published":"2016-08-04T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","related_material":{"record":[{"status":"public","id":"6071","relation":"dissertation_contains"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","relation":"main_file","creator":"system","file_id":"4919","file_size":861805,"checksum":"fe3f3a1526d180b29fe691ab11435b78","date_created":"2018-12-12T10:12:01Z","content_type":"application/pdf","file_name":"IST-2016-627-v1+1_ncomms12307.pdf","date_updated":"2020-07-14T12:44:46Z"},{"file_id":"4920","creator":"system","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:44:46Z","content_type":"application/pdf","file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","date_created":"2018-12-12T10:12:02Z","file_size":1084703,"checksum":"164864a1a675f3ad80e9917c27aba07f"}],"article_number":"12307","month":"08","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"Nature Communications","language":[{"iso":"eng"}],"abstract":[{"text":"Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements.","lang":"eng"}],"day":"04","doi":"10.1038/ncomms12307","year":"2016","citation":{"apa":"Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., &#38; Tkačik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>","ama":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>","ieee":"T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","chicago":"Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>.","short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).","mla":"Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>, vol. 7, 12307, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>.","ista":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307."},"date_updated":"2023-09-07T12:53:49Z","ddc":["576"],"volume":7,"intvolume":"         7","pubrep_id":"627","title":"Intrinsic limits to gene regulation by global crosstalk","department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"date_created":"2018-12-11T11:51:34Z","publication_status":"published","author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar","last_name":"Friedlander","full_name":"Friedlander, Tamar"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan","first_name":"Roshan","last_name":"Prizak"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"scopus_import":1,"_id":"1358","publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:44:46Z","quality_controlled":"1","ec_funded":1},{"quality_controlled":"1","ec_funded":1,"page":"4422 - 4427","article_type":"original","publisher":"National Academy of Sciences","issue":"16","author":[{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":1,"_id":"1359","pmid":1,"intvolume":"       113","title":"The effect of gene interactions on the long-term response to selection","date_created":"2018-12-11T11:51:34Z","article_processing_charge":"No","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publication_status":"published","volume":113,"external_id":{"pmid":["27044080"]},"citation":{"ista":"Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 4422–4427.","short":"T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427.","mla":"Paixao, Tiago, and Nicholas H. Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” <i>PNAS</i>, vol. 113, no. 16, National Academy of Sciences, 2016, pp. 4422–27, doi:<a href=\"https://doi.org/10.1073/pnas.1518830113\">10.1073/pnas.1518830113</a>.","chicago":"Paixao, Tiago, and Nicholas H Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” <i>PNAS</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1518830113\">https://doi.org/10.1073/pnas.1518830113</a>.","ieee":"T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term response to selection,” <i>PNAS</i>, vol. 113, no. 16. National Academy of Sciences, pp. 4422–4427, 2016.","ama":"Paixao T, Barton NH. The effect of gene interactions on the long-term response to selection. <i>PNAS</i>. 2016;113(16):4422-4427. doi:<a href=\"https://doi.org/10.1073/pnas.1518830113\">10.1073/pnas.1518830113</a>","apa":"Paixao, T., &#38; Barton, N. H. (2016). The effect of gene interactions on the long-term response to selection. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1518830113\">https://doi.org/10.1073/pnas.1518830113</a>"},"year":"2016","date_updated":"2021-01-12T06:50:08Z","abstract":[{"text":"The role of gene interactions in the evolutionary process has long\r\nbeen controversial. Although some argue that they are not of\r\nimportance, because most variation is additive, others claim that\r\ntheir effect in the long term can be substantial. Here, we focus on\r\nthe long-term effects of genetic interactions under directional\r\nselection assuming no mutation or dominance, and that epistasis is\r\nsymmetrical overall. We ask by how much the mean of a complex\r\ntrait can be increased by selection and analyze two extreme\r\nregimes, in which either drift or selection dominate the dynamics\r\nof allele frequencies. In both scenarios, epistatic interactions affect\r\nthe long-term response to selection by modulating the additive\r\ngenetic variance. When drift dominates, we extend Robertson\r\n’\r\ns\r\n[Robertson A (1960)\r\nProc R Soc Lond B Biol Sci\r\n153(951):234\r\n−\r\n249]\r\nargument to show that, for any form of epistasis, the total response\r\nof a haploid population is proportional to the initial total genotypic\r\nvariance. In contrast, the total response of a diploid population is\r\nincreased by epistasis, for a given initial genotypic variance. When\r\nselection dominates, we show that the total selection response can\r\nonly be increased by epistasis when s\r\nome initially deleterious alleles\r\nbecome favored as the genetic background changes. We find a sim-\r\nple approximation for this effect and show that, in this regime, it is\r\nthe structure of the genotype - phenotype map that matters and not\r\nthe variance components of the population.","lang":"eng"}],"day":"19","doi":"10.1073/pnas.1518830113","language":[{"iso":"eng"}],"publication":"PNAS","month":"04","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/"}],"type":"journal_article","date_published":"2016-04-19T00:00:00Z","publist_id":"5886","oa":1},{"intvolume":"       117","month":"06","title":"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae","date_created":"2018-12-11T11:51:42Z","department":[{"_id":"NiBa"}],"publication_status":"published","oa_version":"None","issue":"7","author":[{"first_name":"Thomas","last_name":"Ellis","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David"}],"scopus_import":1,"publication":"Annals of Botany","_id":"1382","publisher":"Oxford University Press","language":[{"iso":"eng"}],"quality_controlled":"1","page":"1133 - 1140","publist_id":"5828","abstract":[{"text":"Background and aims Angiosperms display remarkable diversity in flower colour, implying that transitions between pigmentation phenotypes must have been common. Despite progress in understanding transitions between anthocyanin (blue, purple, pink or red) and unpigmented (white) flowers, little is known about the evolutionary patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented flowers. This study investigates the relative rates of evolutionary transitions between different combinations of yellow- and anthocyanin-pigmentation phenotypes in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on anthocyanin and yellow floral pigmentation for 369 species across the tribe. We then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative methods to estimate transition rates among pigmentation phenotypes across the phylogeny. Key Results In contrast to previous studies we found a bias towards transitions involving a gain in pigmentation, although transitions to phenotypes with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite the dominance of yellow and anthocyanin-pigmented taxa, transitions between these phenotypes are constrained to move through a white intermediate stage, whereas transitions to double-pigmentation are very rare. The most abundant transitions are between anthocyanin-pigmented and unpigmented flowers, and similarly the most abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented flowers. Conclusions Our findings show that pigment evolution is limited by the presence of other floral pigments. This interaction between anthocyanin and yellow pigments constrains the breadth of potential floral diversity observed in nature. In particular, they suggest that selection has repeatedly acted to promote the spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore, the correlation between transition rates and polymorphism suggests that the forces causing and maintaining variance in the short term reflect evolutionary processes on longer time scales.","lang":"eng"}],"day":"1","doi":"10.1093/aob/mcw043","type":"journal_article","date_published":"2016-06-01T00:00:00Z","year":"2016","citation":{"ista":"Ellis T, Field D. 2016. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. 117(7), 1133–1140.","mla":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” <i>Annals of Botany</i>, vol. 117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:<a href=\"https://doi.org/10.1093/aob/mcw043\">10.1093/aob/mcw043</a>.","short":"T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140.","chicago":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” <i>Annals of Botany</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/aob/mcw043\">https://doi.org/10.1093/aob/mcw043</a>.","ieee":"T. Ellis and D. Field, “Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae,” <i>Annals of Botany</i>, vol. 117, no. 7. Oxford University Press, pp. 1133–1140, 2016.","ama":"Ellis T, Field D. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. <i>Annals of Botany</i>. 2016;117(7):1133-1140. doi:<a href=\"https://doi.org/10.1093/aob/mcw043\">10.1093/aob/mcw043</a>","apa":"Ellis, T., &#38; Field, D. (2016). Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. <i>Annals of Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/aob/mcw043\">https://doi.org/10.1093/aob/mcw043</a>"},"date_updated":"2024-02-21T13:49:53Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5550"}]},"volume":117,"acknowledgement":"We thank Melinda Pickup, Spencer Barrett, Nick Barton and four anonymous reviewers for helpful discussions on previous versions  of  this  manuscript.  We  also  thank  Jana  Porsche  for her efforts in tracking down the more obscure references."}]