[{"article_processing_charge":"No","date_published":"2017-07-18T00:00:00Z","date_created":"2021-08-09T14:02:34Z","title":"Modelling and simulation details","year":"2017","doi":"10.1371/journal.pcbi.1005609.s001","month":"07","author":[{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta","last_name":"Lukacisinova","first_name":"Marta","orcid":"0000-0002-2519-8004"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","orcid":"0000-0002-2519-824X"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","first_name":"Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953"}],"date_updated":"2025-09-10T11:11:52Z","publisher":"Public Library of Science","oa_version":"Published Version","abstract":[{"lang":"eng","text":"This text provides additional information about the model, a derivation of the analytic results in Eq (4), and details about simulations of an additional parameter set."}],"citation":{"ama":"Lukacisinova M, Novak S, Paixao T. Modelling and simulation details. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s001\">10.1371/journal.pcbi.1005609.s001</a>","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Modelling and simulation details.” Public Library of Science, 2017.","mla":"Lukacisinova, Marta, et al. <i>Modelling and Simulation Details</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s001\">10.1371/journal.pcbi.1005609.s001</a>.","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Modelling and simulation details, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s001\">10.1371/journal.pcbi.1005609.s001</a>.","apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Modelling and simulation details. 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Lukacisinova, S. Novak, and T. Paixao, “Extensions of the model.” Public Library of Science, 2017.","ama":"Lukacisinova M, Novak S, Paixao T. Extensions of the model. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s002\">10.1371/journal.pcbi.1005609.s002</a>","apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Extensions of the model. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s002\">https://doi.org/10.1371/journal.pcbi.1005609.s002</a>","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Extensions of the Model.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s002\">https://doi.org/10.1371/journal.pcbi.1005609.s002</a>.","mla":"Lukacisinova, Marta, et al. <i>Extensions of the Model</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s002\">10.1371/journal.pcbi.1005609.s002</a>.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Extensions of the model, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s002\">10.1371/journal.pcbi.1005609.s002</a>.","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017)."},"doi":"10.1371/journal.pcbi.1005609.s002","month":"07","author":[{"orcid":"0000-0002-2519-8004","last_name":"Lukacisinova","first_name":"Marta","full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","orcid":"0000-0002-2519-824X"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","first_name":"Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953"}],"date_updated":"2025-09-10T11:11:52Z","date_created":"2021-08-09T14:05:24Z","title":"Extensions of the model","article_processing_charge":"No","date_published":"2017-07-18T00:00:00Z","year":"2017"},{"status":"public","type":"research_data_reference","day":"18","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"696"}]},"publisher":"Public Library of Science","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Based on the intuitive derivation of the dynamics of SIM allele frequency pM in the main text, we present a heuristic prediction for the long-term SIM allele frequencies with χ > 1 stresses and compare it to numerical simulations."}],"citation":{"ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Heuristic prediction for multiple stresses.” Public Library of Science, 2017.","ama":"Lukacisinova M, Novak S, Paixao T. Heuristic prediction for multiple stresses. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s003\">10.1371/journal.pcbi.1005609.s003</a>","apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Heuristic prediction for multiple stresses. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s003\">https://doi.org/10.1371/journal.pcbi.1005609.s003</a>","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Heuristic Prediction for Multiple Stresses.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s003\">https://doi.org/10.1371/journal.pcbi.1005609.s003</a>.","mla":"Lukacisinova, Marta, et al. <i>Heuristic Prediction for Multiple Stresses</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s003\">10.1371/journal.pcbi.1005609.s003</a>.","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Heuristic prediction for multiple stresses, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s003\">10.1371/journal.pcbi.1005609.s003</a>."},"department":[{"_id":"ToBo"},{"_id":"CaGu"},{"_id":"NiBa"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9851","month":"07","doi":"10.1371/journal.pcbi.1005609.s003","author":[{"full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004","first_name":"Marta","last_name":"Lukacisinova"},{"first_name":"Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","last_name":"Paixao","first_name":"Tiago"}],"date_updated":"2025-09-10T11:11:52Z","date_published":"2017-07-18T00:00:00Z","article_processing_charge":"No","date_created":"2021-08-09T14:08:14Z","title":"Heuristic prediction for multiple stresses","year":"2017"},{"publisher":"Public Library of Science","oa_version":"Published Version","abstract":[{"text":"We show how different combination strategies affect the fraction of individuals that are multi-resistant.","lang":"eng"}],"citation":{"ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Resistance frequencies for different combination strategies.” Public Library of Science, 2017.","ama":"Lukacisinova M, Novak S, Paixao T. Resistance frequencies for different combination strategies. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s004\">10.1371/journal.pcbi.1005609.s004</a>","apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Resistance frequencies for different combination strategies. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s004\">https://doi.org/10.1371/journal.pcbi.1005609.s004</a>","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Resistance Frequencies for Different Combination Strategies.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s004\">https://doi.org/10.1371/journal.pcbi.1005609.s004</a>.","mla":"Lukacisinova, Marta, et al. <i>Resistance Frequencies for Different Combination Strategies</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s004\">10.1371/journal.pcbi.1005609.s004</a>.","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Resistance frequencies for different combination strategies, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s004\">10.1371/journal.pcbi.1005609.s004</a>."},"department":[{"_id":"ToBo"},{"_id":"CaGu"},{"_id":"NiBa"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9852","status":"public","type":"research_data_reference","day":"18","related_material":{"record":[{"relation":"used_in_publication","id":"696","status":"public"}]},"date_published":"2017-07-18T00:00:00Z","article_processing_charge":"No","date_created":"2021-08-09T14:11:40Z","title":"Resistance frequencies for different combination strategies","year":"2017","doi":"10.1371/journal.pcbi.1005609.s004","month":"07","date_updated":"2025-09-10T11:11:52Z","author":[{"orcid":"0000-0002-2519-8004","first_name":"Marta","last_name":"Lukacisinova","full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2519-824X","first_name":"Sebastian","last_name":"Novak","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"}]},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9856","department":[{"_id":"NiBa"}],"citation":{"chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Additional Likelihood Analyses and Results.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pbio.2001894.s014\">https://doi.org/10.1371/journal.pbio.2001894.s014</a>.","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Supporting Information concerning additional likelihood analyses and results. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2001894.s014\">https://doi.org/10.1371/journal.pbio.2001894.s014</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).","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 additional likelihood analyses and results, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2001894.s014\">10.1371/journal.pbio.2001894.s014</a>.","mla":"Schmidt, Tom, et al. <i>Supporting Information Concerning Additional Likelihood Analyses and Results</i>. 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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>","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).","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. 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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>"},"oa_version":"Published Version","_id":"9858","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"NiBa"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"990","ec_funded":1,"department":[{"_id":"NiBa"}],"issue":"6","pmid":1,"page":"1478 - 1493 ","has_accepted_license":"1","day":"01","corr_author":"1","publication":"Evolution; International Journal of Organic Evolution","year":"2017","date_created":"2018-12-11T11:49:34Z","file_date_updated":"2020-07-14T12:48:18Z","pubrep_id":"977","ddc":["576"],"language":[{"iso":"eng"}],"author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani","first_name":"Himani","last_name":"Sachdeva"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","oa":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"doi":"10.1111/evo.13252","file":[{"date_updated":"2020-07-14T12:48:18Z","relation":"main_file","content_type":"application/pdf","file_size":625260,"file_id":"6329","date_created":"2019-04-17T07:37:04Z","access_level":"open_access","file_name":"2017_Evolution_Sachdeva_supplement.pdf","creator":"dernst","checksum":"6d4c38cb1347fd43620d1736c6df5c79"},{"creator":"dernst","checksum":"f1d90dd8831b44baf49b4dd176f263af","file_name":"2017_Evolution_Sachdeva_article.pdf","access_level":"open_access","date_created":"2019-04-17T07:37:04Z","file_id":"6330","file_size":520110,"date_updated":"2020-07-14T12:48:18Z","content_type":"application/pdf","relation":"main_file"}],"intvolume":"        71","scopus_import":"1","citation":{"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>.","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.","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>","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>","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."},"abstract":[{"lang":"eng","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."}],"oa_version":"Submitted Version","publisher":"Wiley-Blackwell","type":"journal_article","publication_identifier":{"issn":["0014-3820"]},"status":"public","volume":71,"publist_id":"6409","title":"Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow","article_processing_charge":"No","date_published":"2017-06-01T00:00:00Z","isi":1,"external_id":{"pmid":["28419447"],"isi":["000403014800005"]},"quality_controlled":"1","date_updated":"2025-07-10T12:02:04Z","month":"06"},{"date_published":"2017-05-30T00:00:00Z","article_processing_charge":"No","isi":1,"title":"Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti","publist_id":"6464","volume":15,"month":"05","quality_controlled":"1","date_updated":"2026-07-06T13:53:54Z","external_id":{"isi":["000402520000012"]},"publisher":"Public Library of Science","abstract":[{"text":"Dengue-suppressing Wolbachia strains are promising tools for arbovirus control, particularly as they have the potential to self-spread following local introductions. To test this, we followed the frequency of the transinfected Wolbachia strain wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated locations within the city in early 2013. Spatial spread was analysed graphically using interpolation and by fitting a statistical model describing the position and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and 0.52 km2), we observed slow but steady spatial spread, at about 100–200 m per year, roughly consistent with theoretical predictions. In contrast, the smallest release (0.11 km2) produced erratic temporal and spatial dynamics, with little evidence of spread after 2 years. This is consistent with the prediction concerning fitness-decreasing Wolbachia transinfections that a minimum release area is needed to achieve stable local establishment and spread in continuous habitats. Our graphical and likelihood analyses produced broadly consistent estimates of wave speed and wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental heterogeneity will affect large-scale Wolbachia transformations of urban mosquito populations. The persistence and spread of Wolbachia in release areas meeting minimum area requirements indicates the promise of successful large-scale population transfo","lang":"eng"}],"scopus_import":"1","citation":{"ama":"Schmidt T, Barton NH, Rasic G, et al. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. <i>PLoS Biology</i>. 2017;15(5). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001894\">10.1371/journal.pbio.2001894</a>","ieee":"T. Schmidt <i>et al.</i>, “Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti,” <i>PLoS Biology</i>, vol. 15, no. 5. Public Library of Science, 2017.","mla":"Schmidt, Tom, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” <i>PLoS Biology</i>, vol. 15, no. 5, e2001894, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001894\">10.1371/journal.pbio.2001894</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. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 15(5), e2001894.","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, PLoS Biology 15 (2017).","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2001894\">https://doi.org/10.1371/journal.pbio.2001894</a>","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” <i>PLoS Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pbio.2001894\">https://doi.org/10.1371/journal.pbio.2001894</a>."},"article_number":"e2001894","oa_version":"Published Version","status":"public","type":"journal_article","publication_identifier":{"issn":["1544-9173"]},"related_material":{"record":[{"status":"public","relation":"research_data","id":"9856"},{"id":"9858","relation":"research_data","status":"public"},{"id":"9857","relation":"research_data","status":"public"}]},"date_created":"2018-12-11T11:49:22Z","year":"2017","intvolume":"        15","publication_status":"published","oa":1,"doi":"10.1371/journal.pbio.2001894","file":[{"creator":"system","checksum":"107d290bd1159ec77b734eb2824b01c8","file_name":"IST-2017-843-v1+1_journal.pbio.2001894.pdf","access_level":"open_access","date_created":"2018-12-12T10:08:30Z","file_id":"4691","file_size":5541206,"content_type":"application/pdf","date_updated":"2020-07-14T12:48:16Z","relation":"main_file"}],"language":[{"iso":"eng"}],"ddc":["576"],"author":[{"full_name":"Schmidt, Tom","first_name":"Tom","last_name":"Schmidt"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"full_name":"Rasic, Gordana","first_name":"Gordana","last_name":"Rasic"},{"last_name":"Turley","first_name":"Andrew","full_name":"Turley, Andrew"},{"full_name":"Montgomery, Brian","first_name":"Brian","last_name":"Montgomery"},{"last_name":"Iturbe Ormaetxe","first_name":"Inaki","full_name":"Iturbe Ormaetxe, Inaki"},{"first_name":"Peter","last_name":"Cook","full_name":"Cook, Peter"},{"full_name":"Ryan, Peter","last_name":"Ryan","first_name":"Peter"},{"full_name":"Ritchie, Scott","last_name":"Ritchie","first_name":"Scott"},{"full_name":"Hoffmann, Ary","first_name":"Ary","last_name":"Hoffmann"},{"first_name":"Scott","last_name":"O’Neill","full_name":"O’Neill, Scott"},{"last_name":"Turelli","first_name":"Michael","full_name":"Turelli, Michael"}],"file_date_updated":"2020-07-14T12:48:16Z","pubrep_id":"843","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","_id":"951","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"issue":"5","publication":"PLoS Biology","day":"30"},{"oa_version":"Published Version","citation":{"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>","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>.","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>.","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).","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>.","ieee":"T. Schmidt <i>et al.</i>, “Supporting information concerning observed wMel frequencies and analyses of habitat variables.” Public Library of Science, 2017.","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>"},"department":[{"_id":"NiBa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9857","publisher":"Public Library of Science","day":"30","related_material":{"record":[{"id":"951","relation":"used_in_publication","status":"public"}]},"status":"public","type":"research_data_reference","year":"2017","date_published":"2017-05-30T00:00:00Z","article_processing_charge":"No","date_created":"2021-08-10T07:41:52Z","title":"Supporting information concerning observed wMel frequencies and analyses of habitat variables","date_updated":"2026-07-06T13:53:55Z","author":[{"first_name":"Tom","last_name":"Schmidt","full_name":"Schmidt, Tom"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"},{"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"},{"last_name":"Iturbe Ormaetxe","first_name":"Inaki","full_name":"Iturbe Ormaetxe, Inaki"},{"last_name":"Cook","first_name":"Peter","full_name":"Cook, Peter"},{"first_name":"Peter","last_name":"Ryan","full_name":"Ryan, Peter"},{"full_name":"Ritchie, Scott","last_name":"Ritchie","first_name":"Scott"},{"full_name":"Hoffmann, Ary","first_name":"Ary","last_name":"Hoffmann"},{"first_name":"Scott","last_name":"O’Neill","full_name":"O’Neill, Scott"},{"full_name":"Turelli, Michael","last_name":"Turelli","first_name":"Michael"}],"doi":"10.1371/journal.pbio.2001894.s015","month":"05"},{"related_material":{"record":[{"id":"9849","relation":"research_data","status":"public"},{"id":"9850","relation":"research_data","status":"public"},{"status":"public","id":"9851","relation":"research_data"},{"id":"9852","relation":"research_data","status":"public"},{"relation":"dissertation_contains","id":"6263","status":"public"}]},"status":"public","type":"journal_article","publication_identifier":{"issn":["1553-734X"]},"article_number":"e1005609","citation":{"ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” <i>PLoS Computational Biology</i>, vol. 13, no. 7. Public Library of Science, 2017.","ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. 2017;13(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>","apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>.","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609.","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017)."},"abstract":[{"text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy.","lang":"eng"}],"scopus_import":"1","oa_version":"Published Version","publisher":"Public Library of Science","quality_controlled":"1","date_updated":"2026-08-07T22:31:08Z","external_id":{"isi":["000406619800014"]},"month":"07","publist_id":"7004","volume":13,"date_published":"2017-07-18T00:00:00Z","article_processing_charge":"No","isi":1,"title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","day":"18","publication":"PLoS Computational Biology","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"696","ec_funded":1,"issue":"7","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","ddc":["576"],"language":[{"iso":"eng"}],"author":[{"last_name":"Lukacisinova","first_name":"Marta","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","orcid":"0000-0002-2519-824X"},{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","last_name":"Paixao","first_name":"Tiago"}],"file_date_updated":"2020-07-14T12:47:46Z","pubrep_id":"894","intvolume":"        13","publication_status":"published","oa":1,"file":[{"date_created":"2018-12-12T10:15:01Z","file_id":"5117","creator":"system","checksum":"9143c290fa6458ed2563bff4b295554a","access_level":"open_access","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","file_size":3775716,"date_updated":"2020-07-14T12:47:46Z","relation":"main_file","content_type":"application/pdf"}],"doi":"10.1371/journal.pcbi.1005609","project":[{"call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"year":"2017","article_type":"original","date_created":"2018-12-11T11:47:58Z"},{"publisher":"Public Library of Science","oa_version":"Published Version","citation":{"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.","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>","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>","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>.","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>.","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.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016)."},"abstract":[{"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.","lang":"eng"}],"scopus_import":"1","article_number":"e2000234","type":"journal_article","status":"public","related_material":{"record":[{"status":"public","relation":"research_data","id":"9862"},{"status":"public","id":"9863","relation":"research_data"}]},"title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","isi":1,"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.","date_published":"2016-12-27T00:00:00Z","article_processing_charge":"No","volume":14,"publist_id":"6200","month":"12","external_id":{"isi":["000392120100008"]},"date_updated":"2025-09-22T09:55:10Z","quality_controlled":"1","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"issue":"12","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1158","publication":"PLoS Biology","day":"27","date_created":"2018-12-11T11:50:28Z","year":"2016","doi":"10.1371/journal.pbio.2000234","file":[{"checksum":"2bab63b068a9840efd532b9ae583f9bb","creator":"system","access_level":"open_access","file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","date_created":"2018-12-12T10:15:42Z","file_id":"5164","file_size":2494348,"date_updated":"2020-07-14T12:44:36Z","content_type":"application/pdf","relation":"main_file"}],"oa":1,"publication_status":"published","intvolume":"        14","pubrep_id":"742","file_date_updated":"2020-07-14T12:44:36Z","author":[{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"},{"last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"first_name":"Jonathan","last_name":"Romiguier","full_name":"Romiguier, Jonathan"},{"full_name":"Anciaux, Youann","last_name":"Anciaux","first_name":"Youann"},{"last_name":"Galtier","first_name":"Nicolas","full_name":"Galtier, Nicolas"},{"full_name":"Bierne, Nicolas","first_name":"Nicolas","last_name":"Bierne"}],"language":[{"iso":"eng"}],"ddc":["576"]},{"publisher":"Nature Publishing Group","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"}],"citation":{"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.","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>","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>.","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>","short":"H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).","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>."},"scopus_import":"1","article_number":"38840","oa_version":"Published Version","status":"public","type":"journal_article","article_processing_charge":"No","date_published":"2016-12-19T00:00:00Z","acknowledgement":"H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund Thattai for critical discussions and suggestions.","isi":1,"title":"Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae","publist_id":"6183","volume":6,"month":"12","date_updated":"2025-09-22T09:49:53Z","quality_controlled":"1","external_id":{"isi":["000389885900001"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","_id":"1172","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"NiBa"}],"publication":"Scientific Reports","day":"19","date_created":"2018-12-11T11:50:32Z","year":"2016","intvolume":"         6","oa":1,"publication_status":"published","file":[{"file_id":"4977","date_created":"2018-12-12T10:12:56Z","file_name":"IST-2017-737-v1+1_srep38840.pdf","access_level":"open_access","checksum":"cb378732da885ea4959ec5b845fb6e52","creator":"system","date_updated":"2020-07-14T12:44:37Z","relation":"main_file","content_type":"application/pdf","file_size":760967}],"doi":"10.1038/srep38840","ddc":["576"],"language":[{"iso":"eng"}],"author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani","first_name":"Himani","last_name":"Sachdeva"},{"full_name":"Barma, Mustansir","first_name":"Mustansir","last_name":"Barma"},{"first_name":"Madan","last_name":"Rao","full_name":"Rao, Madan"}],"file_date_updated":"2020-07-14T12:44:37Z","pubrep_id":"737"},{"type":"journal_article","status":"public","publisher":"Oxford University Press","abstract":[{"lang":"eng","text":"The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (Pool-Seq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpretation of selection signatures in most Evolve and Resequencing studies remains challenging. To facilitate the characterization of selection targets, we propose a new approach that reconstructs selected haplotypes from replicated time series, using Pool-Seq data. We identify selected haplotypes through the correlated frequencies of alleles carried by them. Computer simulations indicate that selected haplotype-blocks of several Mb can be reconstructed with high confidence and low error rates, even when allele frequencies change only by 20% across three replicates. Applying this method to real data from D. melanogaster populations adapting to a hot environment, we identify a selected haplotype-block of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations by experimental haplotyping, demonstrating the power and accuracy of our haplotype reconstruction from Pool-Seq data. We propose that the combination of allele frequency estimates with haplotype information will provide the key to understanding the dynamics of adaptive alleles. "}],"scopus_import":"1","citation":{"mla":"Franssen, Susan, et al. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” <i>Molecular Biology and Evolution</i>, vol. 34, no. 1, Oxford University Press, 2016, pp. 174–84, doi:<a href=\"https://doi.org/10.1093/molbev/msw210\">10.1093/molbev/msw210</a>.","short":"S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution 34 (2016) 174–184.","ista":"Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 34(1), 174–184.","apa":"Franssen, S., Barton, N. H., &#38; Schlötterer, C. (2016). Reconstruction of haplotype-blocks selected during experimental evolution. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msw210\">https://doi.org/10.1093/molbev/msw210</a>","chicago":"Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/molbev/msw210\">https://doi.org/10.1093/molbev/msw210</a>.","ama":"Franssen S, Barton NH, Schlötterer C. Reconstruction of haplotype-blocks selected during experimental evolution. <i>Molecular Biology and Evolution</i>. 2016;34(1):174-184. doi:<a href=\"https://doi.org/10.1093/molbev/msw210\">10.1093/molbev/msw210</a>","ieee":"S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks selected during experimental evolution.,” <i>Molecular Biology and Evolution</i>, vol. 34, no. 1. Oxford University Press, pp. 174–184, 2016."},"oa_version":"Submitted Version","month":"10","external_id":{"isi":["000396772000009"]},"quality_controlled":"1","date_updated":"2025-09-22T09:43:41Z","title":"Reconstruction of haplotype-blocks selected during experimental evolution.","date_published":"2016-10-03T00:00:00Z","article_processing_charge":"No","isi":1,"acknowledgement":"The authors thank all members of the Institute of Population\r\nGenetics for discussion and support on the project and par-\r\nticularly N. Barghi for helpful comments on earlier versions of\r\nthe  manuscript.  This  work  was  supported  by  the  European\r\nResearch Council (ERC) grants “ArchAdapt” and “250152”.","volume":34,"publist_id":"6155","publication":"Molecular Biology and Evolution","day":"03","page":"174 - 184","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1195","ec_funded":1,"issue":"1","department":[{"_id":"NiBa"}],"oa":1,"publication_status":"published","file":[{"file_id":"5223","date_created":"2018-12-12T10:16:35Z","file_name":"IST-2017-770-v1+1_FranssenEtAl_nofigs-1.pdf","access_level":"open_access","creator":"system","checksum":"1e78d3aaffcb40dc8b02b7b4666019e0","date_updated":"2020-07-14T12:44:38Z","content_type":"application/pdf","relation":"main_file","file_size":295274},{"checksum":"e13171843283774404c936c581b4543e","creator":"system","file_name":"IST-2017-770-v1+2_Fig1.pdf","access_level":"open_access","date_created":"2018-12-12T10:16:36Z","file_id":"5224","file_size":10902625,"content_type":"application/pdf","date_updated":"2020-07-14T12:44:38Z","relation":"main_file"},{"file_size":21437,"date_updated":"2020-07-14T12:44:38Z","content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T10:16:37Z","file_id":"5225","creator":"system","checksum":"63bc6e6e61f347594d8c00c37f874a0b","file_name":"IST-2017-770-v1+3_Fig2.pdf","access_level":"open_access"},{"file_id":"5226","date_created":"2018-12-12T10:16:38Z","file_name":"IST-2017-770-v1+4_Fig3.pdf","access_level":"open_access","creator":"system","checksum":"da87cc7c78808837f22a3dae1c8397f9","content_type":"application/pdf","date_updated":"2020-07-14T12:44:38Z","relation":"main_file","file_size":1172194},{"file_size":50045,"date_updated":"2020-07-14T12:44:38Z","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:16:38Z","file_id":"5227","creator":"system","checksum":"e47b2a0c32142f423b3100150c0294f8","file_name":"IST-2017-770-v1+5_Fig4.pdf","access_level":"open_access"},{"relation":"main_file","date_updated":"2020-07-14T12:44:38Z","content_type":"application/pdf","file_size":50705,"file_id":"5228","date_created":"2018-12-12T10:16:39Z","access_level":"open_access","file_name":"IST-2017-770-v1+6_Fig5.pdf","checksum":"a5a7d6b32e7e17d35d337d7ec2a9f6c9","creator":"system"}],"doi":"10.1093/molbev/msw210","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"intvolume":"        34","file_date_updated":"2020-07-14T12:44:38Z","pubrep_id":"770","ddc":["576"],"language":[{"iso":"eng"}],"author":[{"full_name":"Franssen, Susan","first_name":"Susan","last_name":"Franssen"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Schlötterer","first_name":"Christian","full_name":"Schlötterer, Christian"}],"date_created":"2018-12-11T11:50:39Z","year":"2016"},{"year":"2016","date_created":"2018-12-11T11:50:48Z","language":[{"iso":"eng"}],"author":[{"full_name":"Teitel, Zachary","first_name":"Zachary","last_name":"Teitel"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda","last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541"},{"first_name":"David","last_name":"Field","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David"},{"last_name":"Barrett","first_name":"Spencer","full_name":"Barrett, Spencer"}],"publication_status":"published","doi":"10.1111/plb.12336","intvolume":"        18","_id":"1224","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"1","department":[{"_id":"NiBa"}],"page":"98 - 103","day":"01","publication":"Plant Biology","volume":18,"publist_id":"6110","title":"The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant","article_processing_charge":"No","date_published":"2016-01-01T00:00:00Z","isi":1,"external_id":{"isi":["000369975700011"]},"date_updated":"2025-09-22T09:31:49Z","quality_controlled":"1","month":"01","citation":{"ama":"Teitel Z, Pickup M, Field D, Barrett S. The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant. <i>Plant Biology</i>. 2016;18(1):98-103. doi:<a href=\"https://doi.org/10.1111/plb.12336\">10.1111/plb.12336</a>","ieee":"Z. Teitel, M. Pickup, D. Field, and S. Barrett, “The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant,” <i>Plant Biology</i>, vol. 18, no. 1. Wiley-Blackwell, pp. 98–103, 2016.","mla":"Teitel, Zachary, et al. “The Dynamics of Resource Allocation and Costs of Reproduction in a Sexually Dimorphic, Wind-Pollinated Dioecious Plant.” <i>Plant Biology</i>, vol. 18, no. 1, Wiley-Blackwell, 2016, pp. 98–103, doi:<a href=\"https://doi.org/10.1111/plb.12336\">10.1111/plb.12336</a>.","ista":"Teitel Z, Pickup M, Field D, Barrett S. 2016. The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant. Plant Biology. 18(1), 98–103.","short":"Z. Teitel, M. Pickup, D. Field, S. Barrett, Plant Biology 18 (2016) 98–103.","apa":"Teitel, Z., Pickup, M., Field, D., &#38; Barrett, S. (2016). The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant. <i>Plant Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/plb.12336\">https://doi.org/10.1111/plb.12336</a>","chicago":"Teitel, Zachary, Melinda Pickup, David Field, and Spencer Barrett. “The Dynamics of Resource Allocation and Costs of Reproduction in a Sexually Dimorphic, Wind-Pollinated Dioecious Plant.” <i>Plant Biology</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1111/plb.12336\">https://doi.org/10.1111/plb.12336</a>."},"scopus_import":"1","abstract":[{"text":"Sexual dimorphism in resource allocation is expected to change during the life cycle of dioecious plants because of temporal differences between the sexes in reproductive investment. Given the potential for sex-specific differences in reproductive costs, resource availability may contribute to variation in reproductive allocation in females and males. Here, we used Rumex hastatulus, a dioecious, wind-pollinated annual plant, to investigate whether sexual dimorphism varies with life-history stage and nutrient availability, and determine whether allocation patterns differ depending on reproductive commitment. To examine if the costs of reproduction varied between the sexes, reproduction was either allowed or prevented through bud removal, and biomass allocation was measured at maturity. In a second experiment to assess variation in sexual dimorphism across the life cycle, and whether this varied with resource availability, plants were grown in high and low nutrients and allocation to roots, aboveground vegetative growth and reproduction were measured at three developmental stages. Males prevented from reproducing compensated with increased above- and belowground allocation to a much larger degree than females, suggesting that male reproductive costs reduce vegetative growth. The proportional allocation to roots, reproductive structures and aboveground vegetative growth varied between the sexes and among life-cycle stages, but not with nutrient treatment. Females allocated proportionally more resources to roots than males at peak flowering, but this pattern was reversed at reproductive maturity under low-nutrient conditions. Our study illustrates the importance of temporal dynamics in sex-specific resource allocation and provides support for high male reproductive costs in wind-pollinated plants.","lang":"eng"}],"oa_version":"None","publisher":"Wiley-Blackwell","type":"journal_article","status":"public"},{"type":"journal_article","status":"public","oa_version":"Preprint","citation":{"apa":"Uecker, H., &#38; Hermisson, J. (2016). The role of recombination in evolutionary rescue. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.115.180299\">https://doi.org/10.1534/genetics.115.180299</a>","chicago":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.115.180299\">https://doi.org/10.1534/genetics.115.180299</a>.","mla":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” <i>Genetics</i>, vol. 202, no. 2, Genetics Society of America, 2016, pp. 721–32, doi:<a href=\"https://doi.org/10.1534/genetics.115.180299\">10.1534/genetics.115.180299</a>.","ista":"Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue. Genetics. 202(2), 721–732.","short":"H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732.","ieee":"H. Uecker and J. Hermisson, “The role of recombination in evolutionary rescue,” <i>Genetics</i>, vol. 202, no. 2. Genetics Society of America, pp. 721–732, 2016.","ama":"Uecker H, Hermisson J. The role of recombination in evolutionary rescue. <i>Genetics</i>. 2016;202(2):721-732. doi:<a href=\"https://doi.org/10.1534/genetics.115.180299\">10.1534/genetics.115.180299</a>"},"scopus_import":"1","abstract":[{"lang":"eng","text":"How likely is it that a population escapes extinction through adaptive evolution? The answer to this question is of great relevance in conservation biology, where we aim at species’ rescue and the maintenance of biodiversity, and in agriculture and medicine, where we seek to hamper the emergence of pesticide or drug resistance. By reshuffling the genome, recombination has two antagonistic effects on the probability of evolutionary rescue: It generates and it breaks up favorable gene combinations. Which of the two effects prevails depends on the fitness effects of mutations and on the impact of stochasticity on the allele frequencies. In this article, we analyze a mathematical model for rescue after a sudden environmental change when adaptation is contingent on mutations at two loci. The analysis reveals a complex nonlinear dependence of population survival on recombination. We moreover find that, counterintuitively, a fast eradication of the wild type can promote rescue in the presence of recombination. The model also shows that two-step rescue is not unlikely to happen and can even be more likely than single-step rescue (where adaptation relies on a single mutation), depending on the circumstances."}],"publisher":"Genetics Society of America","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/022020"}],"das_tickbox":"1","external_id":{"biorxivid":["10.1101/022020"],"isi":["000371304600028"]},"date_updated":"2026-06-22T14:07:01Z","quality_controlled":"1","month":"02","biorxivid":1,"volume":202,"publist_id":"6091","title":"The role of recombination in evolutionary rescue","acknowledgement":"This work was made possible by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for the United Nations Educational, Scientific, and Cultural Organization and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria) and European Research Council grant 250152 (to Nick Barton).","isi":1,"article_processing_charge":"No","date_published":"2016-02-01T00:00:00Z","day":"01","publication":"Genetics","ec_funded":1,"department":[{"_id":"NiBa"}],"issue":"2","_id":"1241","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"721 - 732","author":[{"id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","full_name":"Uecker, Hildegard","first_name":"Hildegard","last_name":"Uecker","orcid":"0000-0001-9435-2813"},{"last_name":"Hermisson","first_name":"Joachim","full_name":"Hermisson, Joachim"}],"language":[{"iso":"eng"}],"doi":"10.1534/genetics.115.180299","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"_id":"25B67606-B435-11E9-9278-68D0E5697425","name":"Evolutionary rescue"}],"oa":1,"publication_status":"published","intvolume":"       202","year":"2016","date_created":"2018-12-11T11:50:54Z"},{"page":"1163 - 1170","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1349","conference":{"location":"Denver, CO, USA","end_date":"2016-07-24","name":"GECCO: Genetic and evolutionary computation conference","start_date":"2016-07-20"},"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"ec_funded":1,"publication":"Proceedings of the Genetic and Evolutionary Computation Conference 2016 ","day":"20","date_created":"2018-12-11T11:51:31Z","year":"2016","oa":1,"publication_status":"published","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"file":[{"creator":"system","checksum":"a1896e39e4113f2711e46b435d5f3e69","access_level":"open_access","file_name":"IST-2016-650-v1+1_p1163-oliveto.pdf","date_created":"2018-12-12T10:16:27Z","file_id":"5214","file_size":979026,"date_updated":"2020-07-14T12:44:45Z","content_type":"application/pdf","relation":"main_file"}],"doi":"10.1145/2908812.2908909","file_date_updated":"2020-07-14T12:44:45Z","pubrep_id":"650","ddc":["576"],"language":[{"iso":"eng"}],"author":[{"full_name":"Oliveto, Pietro","last_name":"Oliveto","first_name":"Pietro"},{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao"},{"last_name":"Heredia","first_name":"Jorge","full_name":"Heredia, Jorge"},{"full_name":"Sudholt, Dirk","last_name":"Sudholt","first_name":"Dirk"},{"orcid":"0000-0002-6873-2967","last_name":"Trubenova","first_name":"Barbora","full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87"}],"publisher":"ACM","citation":{"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>.","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>","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.","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.","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>.","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.","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>"},"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"}],"scopus_import":"1","oa_version":"Published Version","type":"conference","status":"public","title":"When non-elitism outperforms elitism for crossing fitness valleys","article_processing_charge":"No","date_published":"2016-07-20T00:00:00Z","isi":1,"publist_id":"5900","month":"07","external_id":{"isi":["000382659200147"]},"quality_controlled":"1","date_updated":"2025-09-22T08:13:19Z"},{"isi":1,"article_processing_charge":"No","date_published":"2016-01-05T00:00:00Z","title":"Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”","publist_id":"5889","volume":202,"month":"01","quality_controlled":"1","date_updated":"2025-09-22T08:01:07Z","external_id":{"isi":["000367718100002"]},"publisher":"Genetics Society of America","oa_version":"Submitted Version","citation":{"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>","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.","ista":"Barton NH. 2016. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”. Genetics. 202(1), 3–4.","short":"N.H. Barton, Genetics 202 (2016) 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>.","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>.","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>"},"scopus_import":"1","status":"public","type":"journal_article","date_created":"2018-12-11T11:51:33Z","year":"2016","intvolume":"       202","doi":"10.1534/genetics.115.184796","file":[{"creator":"system","checksum":"3562b89c821a4be84edf2b6ebd870cf5","file_name":"IST-2017-769-v1+1_SewallWright1931.pdf","access_level":"open_access","date_created":"2018-12-12T10:08:26Z","file_id":"4687","file_size":112674,"relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:44:46Z"}],"publication_status":"published","oa":1,"author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"ddc":["570"],"language":[{"iso":"eng"}],"pubrep_id":"769","file_date_updated":"2020-07-14T12:44:46Z","has_accepted_license":"1","page":"3 - 4","department":[{"_id":"NiBa"}],"issue":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1356","publication":"Genetics","corr_author":"1","day":"05"},{"publisher":"Genetics Society of America","oa_version":"Submitted Version","scopus_import":"1","citation":{"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>.","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>","ista":"Barton NH. 2016. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 202(3), 865–866.","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>.","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.","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>"},"status":"public","type":"journal_article","isi":1,"date_published":"2016-03-01T00:00:00Z","article_processing_charge":"No","title":"Richard Hudson and Norman Kaplan on the coalescent process","publist_id":"5888","volume":202,"month":"03","date_updated":"2025-09-22T07:56:18Z","quality_controlled":"1","external_id":{"isi":["000371596400001"]},"has_accepted_license":"1","page":"865 - 866","issue":"3","department":[{"_id":"NiBa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1357","publication":"Genetics","corr_author":"1","day":"01","date_created":"2018-12-11T11:51:33Z","year":"2016","intvolume":"       202","doi":"10.1534/genetics.116.187542","file":[{"date_created":"2018-12-12T10:15:09Z","file_id":"5127","creator":"system","checksum":"b2174bab2de1d1142900062a150f35c9","access_level":"open_access","file_name":"IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf","file_size":130779,"date_updated":"2020-07-14T12:44:46Z","content_type":"application/pdf","relation":"main_file"}],"publication_status":"published","oa":1,"author":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"ddc":["576"],"language":[{"iso":"eng"}],"pubrep_id":"768","file_date_updated":"2020-07-14T12:44:46Z"},{"date_updated":"2026-04-08T13:54:24Z","quality_controlled":"1","external_id":{"isi":["000380858400001"]},"month":"08","publist_id":"5887","volume":7,"date_published":"2016-08-04T00:00:00Z","article_processing_charge":"No","isi":1,"title":"Intrinsic limits to gene regulation by global crosstalk","related_material":{"record":[{"status":"public","id":"6071","relation":"dissertation_contains"}]},"status":"public","type":"journal_article","scopus_import":"1","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"}],"article_number":"12307","citation":{"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.","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>","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>","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>.","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.","short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016)."},"oa_version":"Published Version","publisher":"Nature Publishing Group","ddc":["576"],"language":[{"iso":"eng"}],"author":[{"full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","last_name":"Friedlander","first_name":"Tamar"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan"},{"first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik"}],"file_date_updated":"2020-07-14T12:44:46Z","pubrep_id":"627","intvolume":"         7","oa":1,"publication_status":"published","doi":"10.1038/ncomms12307","file":[{"relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:44:46Z","file_size":861805,"file_id":"4919","date_created":"2018-12-12T10:12:01Z","file_name":"IST-2016-627-v1+1_ncomms12307.pdf","access_level":"open_access","checksum":"fe3f3a1526d180b29fe691ab11435b78","creator":"system"},{"file_id":"4920","date_created":"2018-12-12T10:12:02Z","access_level":"open_access","file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","creator":"system","checksum":"164864a1a675f3ad80e9917c27aba07f","date_updated":"2020-07-14T12:44:46Z","relation":"main_file","content_type":"application/pdf","file_size":1084703}],"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"}],"year":"2016","date_created":"2018-12-11T11:51:34Z","day":"04","publication":"Nature Communications","corr_author":"1","_id":"1358","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1"},{"year":"2016","article_type":"original","date_created":"2018-12-11T11:51:34Z","author":[{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"language":[{"iso":"eng"}],"intvolume":"       113","doi":"10.1073/pnas.1518830113","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","oa":1,"pmid":1,"issue":"16","ec_funded":1,"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"_id":"1359","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"4422 - 4427","day":"19","publication":"PNAS","corr_author":"1","publist_id":"5886","volume":113,"isi":1,"article_processing_charge":"No","date_published":"2016-04-19T00:00:00Z","title":"The effect of gene interactions on the long-term response to selection","date_updated":"2026-06-18T17:31:02Z","quality_controlled":"1","external_id":{"isi":["000374393800056"],"pmid":["27044080"]},"month":"04","oa_version":"Published Version","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"}],"citation":{"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>","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>.","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>.","short":"T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427.","ista":"Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 4422–4427."},"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/"}],"publisher":"National Academy of Sciences","status":"public","type":"journal_article"}]