[{"type":"journal_article","publication":"Genetics","citation":{"short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883.","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.300748\">https://doi.org/10.1534/genetics.118.300748</a>.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., &#38; Pickup, M. (2018). Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.300748\">https://doi.org/10.1534/genetics.118.300748</a>","mla":"Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” <i>Genetics</i>, vol. 209, no. 3, Genetics Society of America, 2018, pp. 861–83, doi:<a href=\"https://doi.org/10.1534/genetics.118.300748\">10.1534/genetics.118.300748</a>.","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 209(3), 861–883.","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system,” <i>Genetics</i>, vol. 209, no. 3. Genetics Society of America, pp. 861–883, 2018.","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. <i>Genetics</i>. 2018;209(3):861-883. doi:<a href=\"https://doi.org/10.1534/genetics.118.300748\">10.1534/genetics.118.300748</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ec_funded":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self- and non-self recognition. Most work has focused on diversification within self-recognition systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI system. For this model the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and in general is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate to high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a non-self recognition SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a self recognition system common in flowering plants."}],"isi":1,"date_published":"2018-07-01T00:00:00Z","external_id":{"isi":["000437171700017"]},"title":"Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system","publication_status":"published","project":[{"name":"Mating system and the evolutionary dynamics of hybrid zones","_id":"25B36484-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"329960"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"date_updated":"2025-04-15T06:50:00Z","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"article_processing_charge":"No","issue":"3","day":"01","article_type":"original","publisher":"Genetics Society of America","page":"861-883","year":"2018","language":[{"iso":"eng"}],"_id":"316","oa_version":"Preprint","status":"public","month":"07","oa":1,"volume":209,"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/"}],"record":[{"status":"public","relation":"research_data","id":"9813"}]},"date_created":"2018-12-11T11:45:47Z","author":[{"orcid":"0000-0002-7214-0171","full_name":"Bodova, Katarina","last_name":"Bodova","first_name":"Katarina","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas","full_name":"Priklopil, Tadeas","last_name":"Priklopil"},{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","full_name":"Pickup, Melinda","last_name":"Pickup","orcid":"0000-0001-6118-0541"}],"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/node/80098.abstract"}],"intvolume":"       209","doi":"10.1534/genetics.118.300748","scopus_import":"1"},{"ddc":["576"],"_id":"33","file_date_updated":"2020-07-14T12:46:06Z","status":"public","oa_version":"Published Version","article_number":"e5325","oa":1,"month":"10","author":[{"first_name":"Johanna","last_name":"Bertl","full_name":"Bertl, Johanna"},{"full_name":"Ringbauer, Harald","last_name":"Ringbauer","orcid":"0000-0002-4884-9682","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","first_name":"Harald"},{"last_name":"Blum","full_name":"Blum, Michaël","first_name":"Michaël"}],"volume":2018,"date_created":"2018-12-11T11:44:16Z","doi":"10.7717/peerj.5325","scopus_import":"1","intvolume":"      2018","article_processing_charge":"No","publist_id":"8022","has_accepted_license":"1","department":[{"_id":"NiBa"}],"publisher":"PeerJ","issue":"10","day":"01","license":"https://creativecommons.org/licenses/by/4.0/","year":"2018","language":[{"iso":"eng"}],"abstract":[{"text":"Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species.","lang":"eng"}],"quality_controlled":"1","title":"Can secondary contact following range expansion be distinguished from barriers to gene flow?","publication_status":"published","date_updated":"2023-10-17T12:24:43Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000447204400001"],"pmid":["30294507"]},"date_published":"2018-10-01T00:00:00Z","isi":1,"type":"journal_article","acknowledgement":"Johanna Bertl was supported by the Vienna Graduate School of Population Genetics (Austrian Science Fund (FWF): W1225-B20) and worked on this project while employed at the Department of Statistics and Operations Research, University of Vienna, Austria. This article was developed in the framework of the Grenoble Alpes Data Institute, which is supported by the French National Research Agency under the “Investissments d’avenir” program (ANR-15-IDEX-02).","file":[{"checksum":"3334886c4b39678db4c4b74299ca14ba","relation":"main_file","content_type":"application/pdf","file_size":1328344,"file_id":"5692","access_level":"open_access","creator":"dernst","date_updated":"2020-07-14T12:46:06Z","file_name":"2018_PeerJ_Bertl.pdf","date_created":"2018-12-17T10:46:06Z"}],"publication":"PeerJ","citation":{"ista":"Bertl J, Ringbauer H, Blum M. 2018. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018(10), e5325.","mla":"Bertl, Johanna, et al. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” <i>PeerJ</i>, vol. 2018, no. 10, e5325, PeerJ, 2018, doi:<a href=\"https://doi.org/10.7717/peerj.5325\">10.7717/peerj.5325</a>.","ieee":"J. Bertl, H. Ringbauer, and M. Blum, “Can secondary contact following range expansion be distinguished from barriers to gene flow?,” <i>PeerJ</i>, vol. 2018, no. 10. PeerJ, 2018.","ama":"Bertl J, Ringbauer H, Blum M. Can secondary contact following range expansion be distinguished from barriers to gene flow? <i>PeerJ</i>. 2018;2018(10). doi:<a href=\"https://doi.org/10.7717/peerj.5325\">10.7717/peerj.5325</a>","short":"J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018).","apa":"Bertl, J., Ringbauer, H., &#38; Blum, M. (2018). Can secondary contact following range expansion be distinguished from barriers to gene flow? <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.5325\">https://doi.org/10.7717/peerj.5325</a>","chicago":"Bertl, Johanna, Harald Ringbauer, and Michaël Blum. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” <i>PeerJ</i>. PeerJ, 2018. <a href=\"https://doi.org/10.7717/peerj.5325\">https://doi.org/10.7717/peerj.5325</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1},{"year":"2018","language":[{"iso":"eng"}],"publist_id":"7784","article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"PeerJ","issue":"7","day":"30","author":[{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Camille","full_name":"Roux, Camille","last_name":"Roux"},{"first_name":"Pierre","full_name":"Gagnaire, Pierre","last_name":"Gagnaire"},{"first_name":"Jonathan","full_name":"Romiguier, Jonathan","last_name":"Romiguier"},{"first_name":"Nicolas","last_name":"Faivre","full_name":"Faivre, Nicolas"},{"full_name":"Welch, John","last_name":"Welch","first_name":"John"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}],"volume":2018,"date_created":"2018-12-11T11:44:50Z","doi":"10.7717/peerj.5198","scopus_import":"1","intvolume":"      2018","_id":"139","file_date_updated":"2020-07-14T12:44:48Z","ddc":["576"],"oa_version":"Published Version","status":"public","article_number":"30083438","oa":1,"month":"07","publication":"PeerJ","citation":{"short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018).","chicago":"Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier, Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” <i>PeerJ</i>. PeerJ, 2018. <a href=\"https://doi.org/10.7717/peerj.5198\">https://doi.org/10.7717/peerj.5198</a>.","apa":"Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J., &#38; Bierne, N. (2018). The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.5198\">https://doi.org/10.7717/peerj.5198</a>","mla":"Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” <i>PeerJ</i>, vol. 2018, no. 7, 30083438, PeerJ, 2018, doi:<a href=\"https://doi.org/10.7717/peerj.5198\">10.7717/peerj.5198</a>.","ista":"Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N. 2018. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018(7), 30083438.","ama":"Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. <i>PeerJ</i>. 2018;2018(7). doi:<a href=\"https://doi.org/10.7717/peerj.5198\">10.7717/peerj.5198</a>","ieee":"C. Fraisse <i>et al.</i>, “The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies,” <i>PeerJ</i>, vol. 2018, no. 7. PeerJ, 2018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","file":[{"file_size":1480792,"file_id":"5739","content_type":"application/pdf","relation":"main_file","checksum":"7d55ae22598a1c70759cd671600cff53","date_created":"2018-12-18T09:42:11Z","file_name":"2018_PeerJ_Fraisse.pdf","date_updated":"2020-07-14T12:44:48Z","access_level":"open_access","creator":"dernst"}],"abstract":[{"text":"Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed.","lang":"eng"}],"quality_controlled":"1","publication_status":"published","title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","date_updated":"2023-10-17T12:25:28Z","external_id":{"isi":["000440484800002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2018-07-30T00:00:00Z","isi":1},{"day":"30","publisher":"Genetics Society of America","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"type":"research_data_reference","article_processing_charge":"No","year":"2018","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., &#38; Pickup, M. (2018). Supplemental material for Bodova et al., 2018. Genetics Society of America. <a href=\"https://doi.org/10.25386/genetics.6148304.v1\">https://doi.org/10.25386/genetics.6148304.v1</a>","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society of America, 2018. <a href=\"https://doi.org/10.25386/genetics.6148304.v1\">https://doi.org/10.25386/genetics.6148304.v1</a>.","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material for Bodova et al., 2018, Genetics Society of America, <a href=\"https://doi.org/10.25386/genetics.6148304.v1\">10.25386/genetics.6148304.v1</a>.","mla":"Bodova, Katarina, et al. <i>Supplemental Material for Bodova et Al., 2018</i>. Genetics Society of America, 2018, doi:<a href=\"https://doi.org/10.25386/genetics.6148304.v1\">10.25386/genetics.6148304.v1</a>.","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental material for Bodova et al., 2018.” Genetics Society of America, 2018.","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material for Bodova et al., 2018. 2018. doi:<a href=\"https://doi.org/10.25386/genetics.6148304.v1\">10.25386/genetics.6148304.v1</a>"},"month":"04","oa":1,"status":"public","oa_version":"Published Version","_id":"9813","date_published":"2018-04-30T00:00:00Z","date_updated":"2025-04-15T07:17:08Z","title":"Supplemental material for Bodova et al., 2018","doi":"10.25386/genetics.6148304.v1","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"316"}]},"date_created":"2021-08-06T13:04:32Z","abstract":[{"text":"File S1 contains figures that clarify the following features: (i) effect of population size on the average number/frequency of SI classes, (ii) changes in the minimal completeness deficit in time for a single class, and (iii) diversification diagrams for all studied pathways, including the summary figure for k = 8. File S2 contains the code required for a stochastic simulation of the SLF system with an example. This file also includes the output in the form of figures and tables.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.25386/genetics.6148304.v1","open_access":"1"}],"author":[{"last_name":"Bod'ová","full_name":"Bod'ová, Katarína","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarína"},{"first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","full_name":"Priklopil, Tadeas","last_name":"Priklopil"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","last_name":"Pickup","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541"}]},{"file_date_updated":"2020-07-14T12:47:07Z","_id":"5583","status":"public","oa_version":"Published Version","oa":1,"month":"02","author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ellis","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254"}],"abstract":[{"text":"Data and scripts are provided in support of the manuscript \"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering\", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone.","lang":"eng"}],"date_created":"2018-12-12T12:31:39Z","related_material":{"record":[{"relation":"research_paper","id":"286","status":"public"}]},"doi":"10.15479/AT:ISTA:95","title":"Data and Python scripts supporting Python package FAPS","date_updated":"2025-04-15T07:11:03Z","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png"},"date_published":"2018-02-12T00:00:00Z","article_processing_charge":"No","datarep_id":"95","type":"research_data","has_accepted_license":"1","department":[{"_id":"NiBa"}],"file":[{"relation":"main_file","content_type":"text/csv","checksum":"fc6aab51439f2622ba6df8632e66fd4f","file_id":"5606","file_size":122048,"date_updated":"2020-07-14T12:47:07Z","access_level":"open_access","creator":"system","file_name":"IST-2018-95-v1+1_amajus_GPS_2012.csv","date_created":"2018-12-12T13:02:41Z"},{"date_created":"2018-12-12T13:02:42Z","file_name":"IST-2018-95-v1+2_offspring_SNPs_2012.csv","date_updated":"2020-07-14T12:47:07Z","creator":"system","access_level":"open_access","file_size":235980,"file_id":"5607","content_type":"text/csv","relation":"main_file","checksum":"92347586ae4f8a6eb7c04354797bf314"},{"access_level":"open_access","creator":"system","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:43Z","file_name":"IST-2018-95-v1+3_parents_SNPs_2012.csv","checksum":"3300813645a54e6c5c39f41917228354","content_type":"text/csv","relation":"main_file","file_id":"5608","file_size":311712},{"relation":"main_file","content_type":"application/zip","checksum":"e739fc473567fd8f39438b445fc46147","file_id":"5609","file_size":342090,"date_updated":"2020-07-14T12:47:07Z","creator":"system","access_level":"open_access","file_name":"IST-2018-95-v1+4_faps_scripts.zip","date_created":"2018-12-12T13:02:44Z"}],"publisher":"Institute of Science and Technology Austria","day":"12","license":"https://creativecommons.org/publicdomain/zero/1.0/","citation":{"apa":"Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:95\">https://doi.org/10.15479/AT:ISTA:95</a>","chicago":"Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:95\">https://doi.org/10.15479/AT:ISTA:95</a>.","short":"T. Ellis, (2018).","ama":"Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:95\">10.15479/AT:ISTA:95</a>","ieee":"T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018.","ista":"Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:95\">10.15479/AT:ISTA:95</a>.","mla":"Ellis, Thomas. <i>Data and Python Scripts Supporting Python Package FAPS</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:95\">10.15479/AT:ISTA:95</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","contributor":[{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"}],"year":"2018"},{"type":"journal_article","file":[{"file_name":"bartonetheridge.pdf","date_created":"2019-12-21T09:36:39Z","date_updated":"2020-07-14T12:47:09Z","access_level":"open_access","creator":"nbarton","file_id":"7199","file_size":2287682,"relation":"main_file","content_type":"application/pdf","checksum":"0b96f6db47e3e91b5e7d103b847c239d"}],"publication":"Theoretical Population Biology","citation":{"short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127.","chicago":"Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” <i>Theoretical Population Biology</i>. Academic Press, 2018. <a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">https://doi.org/10.1016/j.tpb.2017.11.007</a>.","apa":"Barton, N. H., &#38; Etheridge, A. (2018). Establishment in a new habitat by polygenic adaptation. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">https://doi.org/10.1016/j.tpb.2017.11.007</a>","ista":"Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 110–127.","mla":"Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” <i>Theoretical Population Biology</i>, vol. 122, no. 7, Academic Press, 2018, pp. 110–27, doi:<a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">10.1016/j.tpb.2017.11.007</a>.","ieee":"N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic adaptation,” <i>Theoretical Population Biology</i>, vol. 122, no. 7. Academic Press, pp. 110–127, 2018.","ama":"Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation. <i>Theoretical Population Biology</i>. 2018;122(7):110-127. doi:<a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">10.1016/j.tpb.2017.11.007</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ec_funded":1,"abstract":[{"text":"Maladapted individuals can only colonise a new habitat if they can evolve a\r\npositive growth rate fast enough to avoid extinction, a process known as evolutionary\r\nrescue. We treat log fitness at low density in the new habitat as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow the evolution\r\nof the growth rate; this assumes that the trait values of offspring of a\r\nsexual union are normally distributed around the mean of the parents’ trait\r\nvalues, with variance that depends only on the parents’ relatedness. The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe mean and genetic variance of the trait in the source population.\r\nThe chance of success becomes small if migrants come from a population\r\nwith mean growth rate in the new habitat more than a few standard deviations\r\nbelow zero; this chance depends roughly equally on the probability\r\nthat the initial founder is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring as a result of selection. The loss of genetic variation\r\nduring the founding event is substantial, but highly variable. With\r\ncontinued migration at rate M, establishment is inevitable; when migration\r\nis rare, the expected time to establishment decreases inversely with M.\r\nHowever, above a threshold migration rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation is held back by gene flow; above this\r\nthreshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder population\r\nwith mean and variance evolving deterministically. By assuming a constant\r\ngenetic variance, we also develop a diffusion approximation for the joint distribution\r\nof population size and trait mean, which extends to include stabilising\r\nselection and density regulation. Divergence of the population from its\r\nancestors causes partial reproductive isolation, which we measure through\r\nthe reproductive value of migrants into the newly established population.","lang":"eng"}],"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"date_published":"2018-07-01T00:00:00Z","external_id":{"isi":["000440392900014"]},"isi":1,"project":[{"grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation"}],"publication_status":"published","title":"Establishment in a new habitat by polygenic adaptation","date_updated":"2025-04-15T07:11:04Z","department":[{"_id":"NiBa"}],"publist_id":"7250","article_processing_charge":"No","has_accepted_license":"1","day":"01","issue":"7","publisher":"Academic Press","article_type":"original","page":"110-127","license":"https://creativecommons.org/licenses/by-nc/4.0/","year":"2018","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:09Z","_id":"564","ddc":["519","576"],"status":"public","oa_version":"Submitted Version","month":"07","oa":1,"volume":122,"related_material":{"record":[{"status":"public","id":"9842","relation":"research_data"}]},"date_created":"2018-12-11T11:47:12Z","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"},{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"}],"intvolume":"       122","doi":"10.1016/j.tpb.2017.11.007","scopus_import":"1"},{"page":"377 - 382","year":"2018","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"article_processing_charge":"No","publist_id":"7249","day":"01","issue":"1","publisher":"Genetics Society of America","article_type":"original","volume":208,"date_created":"2018-12-11T11:47:12Z","author":[{"last_name":"Charlesworth","full_name":"Charlesworth, Brian","first_name":"Brian"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/"}],"intvolume":"       208","doi":"10.1534/genetics.117.300426","scopus_import":"1","_id":"565","oa_version":"Published Version","status":"public","month":"01","oa":1,"publication":"Genetics","pmid":1,"citation":{"mla":"Charlesworth, Brian, and Nicholas H. Barton. “The Spread of an Inversion with Migration and Selection.” <i>Genetics</i>, vol. 208, no. 1, Genetics Society of America, 2018, pp. 377–82, doi:<a href=\"https://doi.org/10.1534/genetics.117.300426\">10.1534/genetics.117.300426</a>.","ista":"Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382.","ama":"Charlesworth B, Barton NH. The spread of an inversion with migration and selection. <i>Genetics</i>. 2018;208(1):377-382. doi:<a href=\"https://doi.org/10.1534/genetics.117.300426\">10.1534/genetics.117.300426</a>","ieee":"B. Charlesworth and N. H. Barton, “The spread of an inversion with migration and selection,” <i>Genetics</i>, vol. 208, no. 1. Genetics Society of America, pp. 377–382, 2018.","short":"B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382.","apa":"Charlesworth, B., &#38; Barton, N. H. (2018). The spread of an inversion with migration and selection. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.117.300426\">https://doi.org/10.1534/genetics.117.300426</a>","chicago":"Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion with Migration and Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.117.300426\">https://doi.org/10.1534/genetics.117.300426</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","abstract":[{"lang":"eng","text":"We re-examine the model of Kirkpatrick and Barton for the spread of an inversion into a local population. This model assumes that local selection maintains alleles at two or more loci, despite immigration of alternative alleles at these loci from another population. We show that an inversion is favored because it prevents the breakdown of linkage disequilibrium generated by migration; the selective advantage of an inversion is proportional to the amount of recombination between the loci involved, as in other cases where inversions are selected for. We derive expressions for the rate of spread of an inversion; when the loci covered by the inversion are tightly linked, these conditions deviate substantially from those proposed previously, and imply that an inversion can then have only a small advantage. "}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000419356300025"],"pmid":["29158424"]},"date_published":"2018-01-01T00:00:00Z","publication_status":"published","title":"The spread of an inversion with migration and selection","date_updated":"2025-06-03T11:31:54Z"},{"citation":{"short":"C. Fraisse, (2018).","chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/at:ista:/5757\">https://doi.org/10.15479/at:ista:/5757</a>.","apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:/5757\">https://doi.org/10.15479/at:ista:/5757</a>","ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>.","mla":"Fraisse, Christelle. <i>Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.”</i> Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>.","ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:<a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","contributor":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse"},{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","first_name":"Gemma","last_name":"Puixeu Sala"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"year":"2018","keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"file":[{"checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","relation":"main_file","content_type":"application/zip","file_size":369837892,"file_id":"5758","creator":"cfraisse","access_level":"open_access","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS1.zip","date_created":"2018-12-19T14:19:52Z"},{"date_created":"2018-12-19T14:19:49Z","file_name":"FileS2.zip","date_updated":"2020-07-14T12:47:11Z","access_level":"open_access","creator":"cfraisse","file_size":84856909,"file_id":"5759","content_type":"application/zip","relation":"main_file","checksum":"3592e467b4d8206650860b612d6e12f3"},{"content_type":"text/plain","relation":"main_file","checksum":"c37ac5d5437c457338afc128c1240655","file_size":881133,"file_id":"5760","date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","access_level":"open_access","date_created":"2018-12-19T14:19:49Z","file_name":"FileS3.txt"},{"file_name":"FileS4.txt","date_created":"2018-12-19T14:19:49Z","access_level":"open_access","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","file_size":883742,"file_id":"5761","checksum":"943dfd14da61817441e33e3e3cb8cdb9","relation":"main_file","content_type":"text/plain"},{"access_level":"open_access","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:49Z","file_name":"FileS5.txt","checksum":"1c669b6c4690ec1bbca3e2da9f566d17","content_type":"text/plain","relation":"main_file","file_size":2495437,"file_id":"5762"},{"content_type":"text/plain","relation":"main_file","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","file_id":"5763","file_size":15913457,"date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","access_level":"open_access","date_created":"2018-12-19T14:19:50Z","file_name":"FileS6.txt"},{"file_id":"5764","file_size":2584120,"relation":"main_file","content_type":"text/plain","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","file_name":"FileS7.txt","date_created":"2018-12-19T14:19:50Z","date_updated":"2020-07-14T12:47:11Z","access_level":"open_access","creator":"cfraisse"},{"checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","content_type":"text/plain","relation":"main_file","file_id":"5765","file_size":2446059,"access_level":"open_access","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","file_name":"FileS8.txt"},{"date_created":"2018-12-19T14:19:50Z","file_name":"FileS9.txt","access_level":"open_access","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","file_id":"5766","file_size":100737,"checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","content_type":"text/plain","relation":"main_file"}],"publisher":"Institute of Science and Technology Austria","day":"19","article_processing_charge":"No","type":"research_data","has_accepted_license":"1","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"doi":"10.15479/at:ista:/5757","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","date_updated":"2025-04-15T08:18:38Z","date_published":"2018-12-19T00:00:00Z","author":[{"full_name":"Fraisse, Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"}],"abstract":[{"text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants.","lang":"eng"}],"date_created":"2018-12-19T14:22:35Z","related_material":{"record":[{"relation":"research_paper","id":"6089","status":"public"}]},"oa":1,"month":"12","_id":"5757","ec_funded":1,"file_date_updated":"2020-07-14T12:47:11Z","ddc":["576"],"status":"public","oa_version":"Published Version"},{"quality_controlled":"1","abstract":[{"lang":"eng","text":"We study the Fokker-Planck equation derived in the large system limit of the Markovian process describing the dynamics of quantitative traits. The Fokker-Planck equation is posed on a bounded domain and its transport and diffusion coefficients vanish on the domain's boundary. We first argue that, despite this degeneracy, the standard no-flux boundary condition is valid. We derive the weak formulation of the problem and prove the existence and uniqueness of its solutions by constructing the corresponding contraction semigroup on a suitable function space. Then, we prove that for the parameter regime with high enough mutation rate the problem exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next, we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt) method for approximation of observables (moments) of the Fokker-Planck solution, which can be interpreted as a nonlinear Galerkin approximation. The limited applicability of the DynMaxEnt method inspires us to introduce its modified version that is valid for the whole range of admissible parameters. Finally, we present several numerical experiments to demonstrate the performance of both the original and modified DynMaxEnt methods. We observe that in the parameter regimes where both methods are valid, the modified one exhibits slightly better approximation properties compared to the original one."}],"title":"Well posedness and maximum entropy approximation for the dynamics of quantitative traits","publication_status":"published","date_updated":"2024-10-09T20:58:45Z","date_published":"2018-08-01T00:00:00Z","isi":1,"external_id":{"arxiv":["1704.08757"],"isi":["000437962900012"]},"arxiv":1,"corr_author":"1","publication":"Physica D: Nonlinear Phenomena","citation":{"short":"K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.","apa":"Bodova, K., Haskovec, J., &#38; Markowich, P. (2018). Well posedness and maximum entropy approximation for the dynamics of quantitative traits. <i>Physica D: Nonlinear Phenomena</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.physd.2017.10.015\">https://doi.org/10.1016/j.physd.2017.10.015</a>","chicago":"Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” <i>Physica D: Nonlinear Phenomena</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.physd.2017.10.015\">https://doi.org/10.1016/j.physd.2017.10.015</a>.","ista":"Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 376–377, 108–120.","mla":"Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” <i>Physica D: Nonlinear Phenomena</i>, vol. 376–377, Elsevier, 2018, pp. 108–20, doi:<a href=\"https://doi.org/10.1016/j.physd.2017.10.015\">10.1016/j.physd.2017.10.015</a>.","ama":"Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. <i>Physica D: Nonlinear Phenomena</i>. 2018;376-377:108-120. doi:<a href=\"https://doi.org/10.1016/j.physd.2017.10.015\">10.1016/j.physd.2017.10.015</a>","ieee":"K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy approximation for the dynamics of quantitative traits,” <i>Physica D: Nonlinear Phenomena</i>, vol. 376–377. Elsevier, pp. 108–120, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"JH and PM are funded by KAUST baseline funds and grant no. 1000000193 .\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions. \r\n\r\n","type":"journal_article","author":[{"last_name":"Bodova","full_name":"Bodova, Katarina","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina"},{"first_name":"Jan","full_name":"Haskovec, Jan","last_name":"Haskovec"},{"first_name":"Peter","full_name":"Markowich, Peter","last_name":"Markowich"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.08757"}],"volume":"376-377","date_created":"2018-12-11T11:47:28Z","doi":"10.1016/j.physd.2017.10.015","scopus_import":"1","_id":"607","oa_version":"Submitted Version","status":"public","oa":1,"month":"08","page":"108-120","year":"2018","language":[{"iso":"eng"}],"publist_id":"7198","article_processing_charge":"No","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Elsevier","day":"01"},{"ec_funded":1,"abstract":[{"text":"Escaping local optima is one of the major obstacles to function optimisation. Using the metaphor of a fitness landscape, local optima correspond to hills separated by fitness valleys that have to be overcome. We define a class of fitness valleys of tunable difficulty by considering their length, representing the Hamming path between the two optima and their depth, the drop in fitness. For this function class we present a runtime comparison between stochastic search algorithms using different search strategies. The (1+1) EA is a simple and well-studied evolutionary algorithm that has to jump across the valley to a point of higher fitness because it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population genetics, are both able to cross the fitness valley by accepting worsening moves. We show that the runtime of the (1+1) EA depends critically on the length of the valley while the runtimes of the non-elitist algorithms depend crucially on the depth of the valley. Moreover, we show that both SSWM and Metropolis can also efficiently optimise a rugged function consisting of consecutive valleys.","lang":"eng"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2018-05-01T00:00:00Z","external_id":{"isi":["000428239300010"]},"publication_status":"published","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091"}],"title":"How to escape local optima in black box optimisation when non elitism outperforms elitism","date_updated":"2025-04-15T08:22:22Z","type":"journal_article","file":[{"file_size":691245,"file_id":"4674","checksum":"7d92f5d7be81e387edeec4f06442791c","content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T10:08:14Z","file_name":"IST-2018-1014-v1+1_2018_Paixao_Escape.pdf","creator":"system","access_level":"open_access","date_updated":"2020-07-14T12:47:54Z"}],"pubrep_id":"1014","publication":"Algorithmica","citation":{"short":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 80 (2018) 1604–1633.","apa":"Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., &#38; Trubenova, B. (2018). How to escape local optima in black box optimisation when non elitism outperforms elitism. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-017-0369-2\">https://doi.org/10.1007/s00453-017-0369-2</a>","chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” <i>Algorithmica</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00453-017-0369-2\">https://doi.org/10.1007/s00453-017-0369-2</a>.","ista":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2018. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 80(5), 1604–1633.","mla":"Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” <i>Algorithmica</i>, vol. 80, no. 5, Springer, 2018, pp. 1604–33, doi:<a href=\"https://doi.org/10.1007/s00453-017-0369-2\">10.1007/s00453-017-0369-2</a>.","ama":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape local optima in black box optimisation when non elitism outperforms elitism. <i>Algorithmica</i>. 2018;80(5):1604-1633. doi:<a href=\"https://doi.org/10.1007/s00453-017-0369-2\">10.1007/s00453-017-0369-2</a>","ieee":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How to escape local optima in black box optimisation when non elitism outperforms elitism,” <i>Algorithmica</i>, vol. 80, no. 5. Springer, pp. 1604–1633, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"723","file_date_updated":"2020-07-14T12:47:54Z","ddc":["576"],"status":"public","oa_version":"Published Version","month":"05","oa":1,"volume":80,"date_created":"2018-12-11T11:48:09Z","author":[{"full_name":"Oliveto, Pietro","last_name":"Oliveto","first_name":"Pietro"},{"orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","last_name":"Paixao","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pérez Heredia, Jorge","last_name":"Pérez Heredia","first_name":"Jorge"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"full_name":"Trubenova, Barbora","last_name":"Trubenova","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora"}],"intvolume":"        80","doi":"10.1007/s00453-017-0369-2","scopus_import":"1","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"article_processing_charge":"No","publist_id":"6957","has_accepted_license":"1","day":"01","issue":"5","publisher":"Springer","page":"1604 - 1633","year":"2018","language":[{"iso":"eng"}]},{"abstract":[{"text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.72cg113"}],"author":[{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"first_name":"Pragya","full_name":"Chaube, Pragya","last_name":"Chaube"},{"last_name":"Morales","full_name":"Morales, Hernán E.","first_name":"Hernán E."},{"full_name":"Larsson, Tomas","last_name":"Larsson","first_name":"Tomas"},{"last_name":"Lemmon","full_name":"Lemmon, Alan R.","first_name":"Alan R."},{"first_name":"Emily M.","last_name":"Lemmon","full_name":"Lemmon, Emily M."},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"first_name":"Marina","full_name":"Panova, Marina","last_name":"Panova"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","last_name":"Westram","full_name":"Westram, Anja M"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"related_material":{"record":[{"status":"public","id":"6095","relation":"used_in_publication"}]},"date_created":"2021-08-09T12:46:39Z","date_updated":"2023-08-24T14:50:26Z","title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","doi":"10.5061/dryad.72cg113","date_published":"2018-10-09T00:00:00Z","status":"public","oa_version":"Published Version","_id":"9837","oa":1,"month":"10","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. <a href=\"https://doi.org/10.5061/dryad.72cg113\">https://doi.org/10.5061/dryad.72cg113</a>","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.72cg113\">https://doi.org/10.5061/dryad.72cg113</a>.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, (2018).","ieee":"R. Faria <i>et al.</i>, “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, <a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>.","mla":"Faria, Rui, et al. <i>Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>."},"year":"2018","type":"research_data_reference","article_processing_charge":"No","department":[{"_id":"NiBa"}],"publisher":"Dryad","day":"09"},{"oa":1,"month":"03","_id":"9840","oa_version":"Published Version","status":"public","doi":"10.5061/dryad.42n44","title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","date_updated":"2025-04-15T08:17:50Z","date_published":"2018-03-12T00:00:00Z","author":[{"id":"35F78294-F248-11E8-B48F-1D18A9856A87","first_name":"Pavel","full_name":"Payne, Pavel","last_name":"Payne","orcid":"0000-0002-2711-9453"},{"first_name":"Lukas","full_name":"Geyrhofer, Lukas","last_name":"Geyrhofer"},{"full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback"}],"abstract":[{"text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.42n44"}],"date_created":"2021-08-09T13:10:02Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"423"}]},"publisher":"Dryad","day":"12","article_processing_charge":"No","type":"research_data_reference","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"citation":{"chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.42n44\">https://doi.org/10.5061/dryad.42n44</a>.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., &#38; Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. <a href=\"https://doi.org/10.5061/dryad.42n44\">https://doi.org/10.5061/dryad.42n44</a>","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, <a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>.","mla":"Payne, Pavel, et al. <i>Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2018"},{"author":[{"first_name":"Hugo","full_name":"Tavares, Hugo","last_name":"Tavares"},{"full_name":"Whitley, Annabel","last_name":"Whitley","first_name":"Annabel"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bradley, Desmond","last_name":"Bradley","first_name":"Desmond"},{"first_name":"Matthew","last_name":"Couchman","full_name":"Couchman, Matthew"},{"first_name":"Lucy","last_name":"Copsey","full_name":"Copsey, Lucy"},{"last_name":"Elleouet","full_name":"Elleouet, Joane","first_name":"Joane"},{"first_name":"Monique","last_name":"Burrus","full_name":"Burrus, Monique"},{"first_name":"Christophe","last_name":"Andalo","full_name":"Andalo, Christophe"},{"first_name":"Miaomiao","last_name":"Li","full_name":"Li, Miaomiao"},{"first_name":"Qun","last_name":"Li","full_name":"Li, Qun"},{"full_name":"Xue, Yongbiao","last_name":"Xue","first_name":"Yongbiao"},{"first_name":"Alexandra B","full_name":"Rebocho, Alexandra B","last_name":"Rebocho"},{"full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"last_name":"Coen","full_name":"Coen, Enrico","first_name":"Enrico"}],"date_created":"2018-12-11T11:44:18Z","volume":115,"scopus_import":"1","doi":"10.1073/pnas.1801832115","intvolume":"       115","oa_version":"Published Version","status":"public","_id":"38","ddc":["570"],"file_date_updated":"2020-07-14T12:46:16Z","oa":1,"month":"10","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","page":"11006 - 11011","language":[{"iso":"eng"}],"year":"2018","has_accepted_license":"1","article_processing_charge":"No","publist_id":"8017","department":[{"_id":"NiBa"}],"publisher":"National Academy of Sciences","day":"23","issue":"43","quality_controlled":"1","abstract":[{"lang":"eng","text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation."}],"date_updated":"2025-07-10T11:52:32Z","publication_status":"published","title":"Selection and gene flow shape genomic islands that control floral guides","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"date_published":"2018-10-23T00:00:00Z","external_id":{"pmid":["30297406"],"isi":["000448040500065"]},"isi":1,"publication_identifier":{"issn":["0027-8424"]},"publication":"PNAS","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011.","mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” <i>PNAS</i>, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:<a href=\"https://doi.org/10.1073/pnas.1801832115\">10.1073/pnas.1801832115</a>.","ieee":"H. Tavares <i>et al.</i>, “Selection and gene flow shape genomic islands that control floral guides,” <i>PNAS</i>, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018.","ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. <i>PNAS</i>. 2018;115(43):11006-11011. doi:<a href=\"https://doi.org/10.1073/pnas.1801832115\">10.1073/pnas.1801832115</a>","short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1801832115\">https://doi.org/10.1073/pnas.1801832115</a>","chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1801832115\">https://doi.org/10.1073/pnas.1801832115</a>."},"pmid":1,"type":"journal_article","acknowledgement":" ERC Grant 201252 (to N.H.B.)","file":[{"checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1","relation":"main_file","content_type":"application/pdf","file_id":"5683","file_size":1911302,"creator":"dernst","access_level":"open_access","date_updated":"2020-07-14T12:46:16Z","file_name":"11006.full.pdf","date_created":"2018-12-17T08:44:03Z"}]},{"type":"journal_article","publication":"Genetics","citation":{"ieee":"H. Sachdeva and N. H. Barton, “Replicability of introgression under linked, polygenic selection,” <i>Genetics</i>, vol. 210, no. 4. Genetics Society of America, pp. 1411–1427, 2018.","ama":"Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic selection. <i>Genetics</i>. 2018;210(4):1411-1427. doi:<a href=\"https://doi.org/10.1534/genetics.118.301429\">10.1534/genetics.118.301429</a>","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under Linked, Polygenic Selection.” <i>Genetics</i>, vol. 210, no. 4, Genetics Society of America, 2018, pp. 1411–27, doi:<a href=\"https://doi.org/10.1534/genetics.118.301429\">10.1534/genetics.118.301429</a>.","ista":"Sachdeva H, Barton NH. 2018. Replicability of introgression under linked, polygenic selection. Genetics. 210(4), 1411–1427.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression under Linked, Polygenic Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.301429\">https://doi.org/10.1534/genetics.118.301429</a>.","apa":"Sachdeva, H., &#38; Barton, N. H. (2018). Replicability of introgression under linked, polygenic selection. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.301429\">https://doi.org/10.1534/genetics.118.301429</a>","short":"H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0016-6731"]},"quality_controlled":"1","abstract":[{"text":"We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation.","lang":"eng"}],"publication_status":"published","title":"Replicability of introgression under linked, polygenic selection","date_updated":"2025-07-10T11:52:33Z","isi":1,"date_published":"2018-12-04T00:00:00Z","external_id":{"isi":["000452315900021"]},"article_processing_charge":"No","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","article_type":"original","day":"04","issue":"4","page":"1411-1427","year":"2018","language":[{"iso":"eng"}],"_id":"39","oa_version":"Preprint","status":"public","oa":1,"month":"12","author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","full_name":"Sachdeva, Himani","last_name":"Sachdeva"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/379578v1"}],"volume":210,"date_created":"2018-12-11T11:44:18Z","doi":"10.1534/genetics.118.301429","scopus_import":"1","intvolume":"       210"},{"date_published":"2018-12-31T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["30599087"],"isi":["000454600500001"]},"isi":1,"date_updated":"2025-07-10T11:52:34Z","publication_status":"published","title":"The consequences of an introgression event","abstract":[{"text":"Hanemaaijer et al. (Molecular Ecology, 27, 2018) describe the genetic consequences of the introgression of an insecticide resistance allele into a mosquito population. Linked alleles initially increased, but many of these later declined. It is hard to determine whether this decline was due to counter‐selection, rather than simply to chance.","lang":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["1365-294X"]},"corr_author":"1","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"N. H. Barton, “The consequences of an introgression event,” <i>Molecular Ecology</i>, vol. 27, no. 24. Wiley, pp. 4973–4975, 2018.","ama":"Barton NH. The consequences of an introgression event. <i>Molecular Ecology</i>. 2018;27(24):4973-4975. doi:<a href=\"https://doi.org/10.1111/mec.14950\">10.1111/mec.14950</a>","ista":"Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 4973–4975.","mla":"Barton, Nicholas H. “The Consequences of an Introgression Event.” <i>Molecular Ecology</i>, vol. 27, no. 24, Wiley, 2018, pp. 4973–75, doi:<a href=\"https://doi.org/10.1111/mec.14950\">10.1111/mec.14950</a>.","chicago":"Barton, Nicholas H. “The Consequences of an Introgression Event.” <i>Molecular Ecology</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/mec.14950\">https://doi.org/10.1111/mec.14950</a>.","apa":"Barton, N. H. (2018). The consequences of an introgression event. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.14950\">https://doi.org/10.1111/mec.14950</a>","short":"N.H. Barton, Molecular Ecology 27 (2018) 4973–4975."},"publication":"Molecular Ecology","file":[{"access_level":"open_access","creator":"apreinsp","date_updated":"2020-07-14T12:46:22Z","file_name":"2018_MolecularEcology_BartonNick.pdf","date_created":"2019-07-19T06:54:46Z","relation":"main_file","content_type":"application/pdf","file_id":"6652","file_size":295452}],"type":"journal_article","intvolume":"        27","scopus_import":"1","doi":"10.1111/mec.14950","date_created":"2018-12-11T11:44:18Z","related_material":{"record":[{"relation":"research_data","id":"9805","status":"public"}]},"volume":27,"author":[{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"month":"12","oa":1,"status":"public","oa_version":"Published Version","_id":"40","ddc":["576"],"file_date_updated":"2020-07-14T12:46:22Z","language":[{"iso":"eng"}],"year":"2018","page":"4973-4975","issue":"24","day":"31","article_type":"letter_note","publisher":"Wiley","department":[{"_id":"NiBa"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publist_id":"8014"},{"type":"journal_article","acknowledgement":"We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions.","file":[{"content_type":"application/pdf","relation":"main_file","checksum":"447cf6e680bdc3c01062a8737d876569","file_id":"5689","file_size":3533881,"date_updated":"2020-07-14T12:46:25Z","creator":"dernst","access_level":"open_access","date_created":"2018-12-17T10:36:07Z","file_name":"2018_eLife_Payne.pdf"}],"publication":"eLife","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).","apa":"Payne, P., Geyrhofer, L., Barton, N. H., &#38; Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.32035\">https://doi.org/10.7554/eLife.32035</a>","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.32035\">https://doi.org/10.7554/eLife.32035</a>.","mla":"Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” <i>ELife</i>, vol. 7, e32035, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.32035\">10.7554/eLife.32035</a>.","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035.","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.32035\">10.7554/eLife.32035</a>"},"ec_funded":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2018-03-09T00:00:00Z","external_id":{"isi":["000431035800001"]},"date_updated":"2025-03-31T16:00:24Z","title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","publication_status":"published","project":[{"grant_number":"648440","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"has_accepted_license":"1","article_processing_charge":"No","publist_id":"7400","day":"09","publisher":"eLife Sciences Publications","language":[{"iso":"eng"}],"year":"2018","article_number":"e32035","oa_version":"Published Version","status":"public","ddc":["576"],"_id":"423","file_date_updated":"2020-07-14T12:46:25Z","month":"03","oa":1,"date_created":"2018-12-11T11:46:23Z","related_material":{"record":[{"id":"9840","relation":"research_data","status":"public"}]},"volume":7,"author":[{"full_name":"Payne, Pavel","last_name":"Payne","orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87","first_name":"Pavel"},{"first_name":"Lukas","last_name":"Geyrhofer","full_name":"Geyrhofer, Lukas"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"},{"orcid":"0000-0002-4624-4612","last_name":"Bollback","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"         7","scopus_import":"1","doi":"10.7554/eLife.32035"},{"language":[{"iso":"eng"}],"year":"2018","page":"1351 - 1355","day":"01","issue":"4","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"has_accepted_license":"1","article_processing_charge":"No","publist_id":"7393","intvolume":"       208","scopus_import":"1","doi":"10.1534/genetics.118.300786","date_created":"2018-12-11T11:46:26Z","volume":208,"author":[{"first_name":"John","last_name":"Novembre","full_name":"Novembre, John"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"month":"04","oa":1,"oa_version":"Published Version","status":"public","_id":"430","ddc":["576"],"file_date_updated":"2020-07-14T12:46:26Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.","chicago":"Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.300786\">https://doi.org/10.1534/genetics.118.300786</a>.","apa":"Novembre, J., &#38; Barton, N. H. (2018). Tread lightly interpreting polygenic tests of selection. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.300786\">https://doi.org/10.1534/genetics.118.300786</a>","mla":"Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” <i>Genetics</i>, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1351–55, doi:<a href=\"https://doi.org/10.1534/genetics.118.300786\">10.1534/genetics.118.300786</a>.","ista":"Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355.","ieee":"J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests of selection,” <i>Genetics</i>, vol. 208, no. 4. Genetics Society of America, pp. 1351–1355, 2018.","ama":"Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. <i>Genetics</i>. 2018;208(4):1351-1355. doi:<a href=\"https://doi.org/10.1534/genetics.118.300786\">10.1534/genetics.118.300786</a>"},"publication":"Genetics","pubrep_id":"1012","file":[{"date_created":"2018-12-12T10:12:40Z","file_name":"IST-2018-1012-v1+1_2018_Barton_Tread.pdf","date_updated":"2020-07-14T12:46:26Z","access_level":"open_access","creator":"system","file_size":500129,"file_id":"4958","content_type":"application/pdf","relation":"main_file","checksum":"3d838dc285df394376555b794b6a5ad1"}],"type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"external_id":{"isi":["000429094400005"]},"date_published":"2018-04-01T00:00:00Z","date_updated":"2023-09-19T10:17:30Z","title":"Tread lightly interpreting polygenic tests of selection","publication_status":"published","quality_controlled":"1","abstract":[{"text":"In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly.","lang":"eng"}]},{"supervisor":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"type":"dissertation","OA_place":"publisher","alternative_title":["ISTA Thesis"],"file":[{"creator":"system","access_level":"open_access","date_updated":"2020-07-14T12:45:23Z","file_name":"IST-2018-963-v1+1_thesis.pdf","date_created":"2018-12-12T10:14:55Z","checksum":"8cc534d2b528ae017acf80874cce48c9","relation":"main_file","content_type":"application/pdf","file_id":"5111","file_size":5792935},{"relation":"source_file","content_type":"application/zip","checksum":"6af18d7e5a7e2728ceda2f41ee24f628","file_id":"6224","file_size":113365,"date_updated":"2020-07-14T12:45:23Z","creator":"dernst","access_level":"closed","file_name":"2018_thesis_ringbauer_source.zip","date_created":"2019-04-05T09:30:12Z"}],"pubrep_id":"963","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ieee":"H. Ringbauer, “Inferring recent demography from spatial genetic structure,” Institute of Science and Technology Austria, 2018.","ama":"Ringbauer H. Inferring recent demography from spatial genetic structure. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">10.15479/AT:ISTA:th_963</a>","ista":"Ringbauer H. 2018. Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria.","mla":"Ringbauer, Harald. <i>Inferring Recent Demography from Spatial Genetic Structure</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">10.15479/AT:ISTA:th_963</a>.","apa":"Ringbauer, H. (2018). <i>Inferring recent demography from spatial genetic structure</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">https://doi.org/10.15479/AT:ISTA:th_963</a>","chicago":"Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">https://doi.org/10.15479/AT:ISTA:th_963</a>.","short":"H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure, Institute of Science and Technology Austria, 2018."},"publication_identifier":{"issn":["2663-337X"]},"corr_author":"1","degree_awarded":"PhD","abstract":[{"text":"This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm.","lang":"eng"}],"date_published":"2018-02-21T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"date_updated":"2026-04-08T14:06:37Z","publication_status":"published","title":"Inferring recent demography from spatial genetic structure","department":[{"_id":"NiBa"}],"has_accepted_license":"1","publist_id":"7713","article_processing_charge":"No","day":"21","publisher":"Institute of Science and Technology Austria","page":"146","language":[{"iso":"eng"}],"year":"2018","status":"public","oa_version":"Published Version","_id":"200","file_date_updated":"2020-07-14T12:45:23Z","ddc":["576"],"month":"02","oa":1,"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"563"},{"id":"1074","relation":"part_of_dissertation","status":"public"}]},"date_created":"2018-12-11T11:45:10Z","author":[{"id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","first_name":"Harald","last_name":"Ringbauer","full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682"}],"doi":"10.15479/AT:ISTA:th_963"},{"publication":"Genetics","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Ringbauer H, Kolesnikov A, Field D, Barton NH. Estimating barriers to gene flow from distorted isolation-by-distance patterns. <i>Genetics</i>. 2018;208(3):1231-1245. doi:<a href=\"https://doi.org/10.1534/genetics.117.300638\">10.1534/genetics.117.300638</a>","ieee":"H. Ringbauer, A. Kolesnikov, D. Field, and N. H. Barton, “Estimating barriers to gene flow from distorted isolation-by-distance patterns,” <i>Genetics</i>, vol. 208, no. 3. Genetics Society of America, pp. 1231–1245, 2018.","mla":"Ringbauer, Harald, et al. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” <i>Genetics</i>, vol. 208, no. 3, Genetics Society of America, 2018, pp. 1231–45, doi:<a href=\"https://doi.org/10.1534/genetics.117.300638\">10.1534/genetics.117.300638</a>.","ista":"Ringbauer H, Kolesnikov A, Field D, Barton NH. 2018. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 208(3), 1231–1245.","apa":"Ringbauer, H., Kolesnikov, A., Field, D., &#38; Barton, N. H. (2018). Estimating barriers to gene flow from distorted isolation-by-distance patterns. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.117.300638\">https://doi.org/10.1534/genetics.117.300638</a>","chicago":"Ringbauer, Harald, Alexander Kolesnikov, David Field, and Nicholas H Barton. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.117.300638\">https://doi.org/10.1534/genetics.117.300638</a>.","short":"H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245."},"type":"journal_article","quality_controlled":"1","abstract":[{"text":"In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes\r\nthan geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation to model the effects of a barrier on the geographical spread of ancestry backwards in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographical covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow.","lang":"eng"}],"isi":1,"external_id":{"isi":["000426219600025"]},"date_published":"2018-03-01T00:00:00Z","date_updated":"2026-04-08T14:06:35Z","title":"Estimating barriers to gene flow from distorted isolation-by-distance patterns","publication_status":"published","corr_author":"1","page":"1231-1245","language":[{"iso":"eng"}],"year":"2018","department":[{"_id":"NiBa"},{"_id":"ChLa"}],"publist_id":"7251","article_processing_charge":"No","issue":"3","day":"01","publisher":"Genetics Society of America","related_material":{"record":[{"status":"public","id":"200","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:47:12Z","volume":208,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/205484v1","open_access":"1"}],"author":[{"id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","first_name":"Harald","last_name":"Ringbauer","full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682"},{"last_name":"Kolesnikov","full_name":"Kolesnikov, Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander"},{"first_name":"David","last_name":"Field","full_name":"Field, David"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"intvolume":"       208","scopus_import":"1","doi":"10.1534/genetics.117.300638","status":"public","oa_version":"Preprint","_id":"563","month":"03","oa":1},{"month":"01","oa":1,"status":"public","oa_version":"Submitted Version","ddc":["576"],"_id":"1169","file_date_updated":"2020-07-14T12:44:37Z","intvolume":"       205","scopus_import":"1","doi":"10.1534/genetics.116.193946","date_created":"2018-12-11T11:50:31Z","volume":205,"author":[{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Novak","full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X"},{"first_name":"Richard","last_name":"Kollár","full_name":"Kollár, Richard"}],"issue":"1","day":"01","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"has_accepted_license":"1","publist_id":"6188","article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2017","page":"367 - 374","publication_identifier":{"issn":["0016-6731"]},"ec_funded":1,"date_published":"2017-01-01T00:00:00Z","isi":1,"external_id":{"isi":["000393677300025"]},"date_updated":"2025-07-10T11:50:13Z","title":"Spatial gene frequency waves under genotype dependent dispersal","project":[{"grant_number":"618091","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"},{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"publication_status":"published","abstract":[{"text":"Dispersal is a crucial factor in natural evolution, since it determines the habitat experienced by any population and defines the spatial scale of interactions between individuals. There is compelling evidence for systematic differences in dispersal characteristics within the same population, i.e., genotype-dependent dispersal. The consequences of genotype-dependent dispersal on other evolutionary phenomena, however, are poorly understood. In this article we investigate the effect of genotype-dependent dispersal on spatial gene frequency patterns, using a generalization of the classical diffusion model of selection and dispersal. Dispersal is characterized by the variance of dispersal (diffusion coefficient) and the mean displacement (directional advection term). We demonstrate that genotype-dependent dispersal may change the qualitative behavior of Fisher waves, which change from being “pulled” to being “pushed” wave fronts as the discrepancy in dispersal between genotypes increases. The speed of any wave is partitioned into components due to selection, genotype-dependent variance of dispersal, and genotype-dependent mean displacement. We apply our findings to wave fronts maintained by selection against heterozygotes. Furthermore, we identify a benefit of increased variance of dispersal, quantify its effect on the speed of the wave, and discuss the implications for the evolution of dispersal strategies.","lang":"eng"}],"quality_controlled":"1","file":[{"file_name":"IST-2016-727-v1+1_SFC_Genetics_final.pdf","date_created":"2018-12-12T10:10:43Z","date_updated":"2020-07-14T12:44:37Z","creator":"system","access_level":"open_access","file_id":"4833","file_size":361500,"relation":"main_file","content_type":"application/pdf","checksum":"7c8ab79cda1f92760bbbbe0f53175bfc"}],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"S. Novak, R. Kollár, Genetics 205 (2017) 367–374.","apa":"Novak, S., &#38; Kollár, R. (2017). Spatial gene frequency waves under genotype dependent dispersal. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.116.193946\">https://doi.org/10.1534/genetics.116.193946</a>","chicago":"Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype Dependent Dispersal.” <i>Genetics</i>. Genetics Society of America, 2017. <a href=\"https://doi.org/10.1534/genetics.116.193946\">https://doi.org/10.1534/genetics.116.193946</a>.","ista":"Novak S, Kollár R. 2017. Spatial gene frequency waves under genotype dependent dispersal. Genetics. 205(1), 367–374.","mla":"Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype Dependent Dispersal.” <i>Genetics</i>, vol. 205, no. 1, Genetics Society of America, 2017, pp. 367–74, doi:<a href=\"https://doi.org/10.1534/genetics.116.193946\">10.1534/genetics.116.193946</a>.","ama":"Novak S, Kollár R. Spatial gene frequency waves under genotype dependent dispersal. <i>Genetics</i>. 2017;205(1):367-374. doi:<a href=\"https://doi.org/10.1534/genetics.116.193946\">10.1534/genetics.116.193946</a>","ieee":"S. Novak and R. Kollár, “Spatial gene frequency waves under genotype dependent dispersal,” <i>Genetics</i>, vol. 205, no. 1. Genetics Society of America, pp. 367–374, 2017."},"publication":"Genetics","pubrep_id":"727"}]