[{"status":"public","_id":"1349","scopus_import":"1","ddc":["576"],"file_date_updated":"2020-07-14T12:44:45Z","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publist_id":"5900","oa":1,"date_updated":"2025-09-22T08:13:19Z","month":"07","publisher":"ACM","quality_controlled":"1","pubrep_id":"650","has_accepted_license":"1","citation":{"apa":"Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., &#38; Trubenova, B. (2016). When non-elitism outperforms elitism for crossing fitness valleys. In <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i> (pp. 1163–1170). Denver, CO, USA: ACM. <a href=\"https://doi.org/10.1145/2908812.2908909\">https://doi.org/10.1145/2908812.2908909</a>","mla":"Oliveto, Pietro, et al. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>, ACM, 2016, pp. 1163–70, doi:<a href=\"https://doi.org/10.1145/2908812.2908909\">10.1145/2908812.2908909</a>.","short":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, B. Trubenova, in:, Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–1170.","ista":"Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. 2016. When non-elitism outperforms elitism for crossing fitness valleys. Proceedings of the Genetic and Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation conference, 1163–1170.","chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” In <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>, 1163–70. ACM, 2016. <a href=\"https://doi.org/10.1145/2908812.2908909\">https://doi.org/10.1145/2908812.2908909</a>.","ama":"Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. When non-elitism outperforms elitism for crossing fitness valleys. In: <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>. ACM; 2016:1163-1170. doi:<a href=\"https://doi.org/10.1145/2908812.2908909\">10.1145/2908812.2908909</a>","ieee":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism outperforms elitism for crossing fitness valleys,” in <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>, Denver, CO, USA, 2016, pp. 1163–1170."},"page":"1163 - 1170","article_processing_charge":"No","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"type":"conference","title":"When non-elitism outperforms elitism for crossing fitness valleys","language":[{"iso":"eng"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","conference":{"start_date":"2016-07-20","name":"GECCO: Genetic and evolutionary computation conference","location":"Denver, CO, USA","end_date":"2016-07-24"},"license":"https://creativecommons.org/licenses/by/4.0/","date_created":"2018-12-11T11:51:31Z","doi":"10.1145/2908812.2908909","year":"2016","publication":"Proceedings of the Genetic and Evolutionary Computation Conference 2016 ","date_published":"2016-07-20T00:00:00Z","file":[{"date_updated":"2020-07-14T12:44:45Z","creator":"system","file_size":979026,"content_type":"application/pdf","date_created":"2018-12-12T10:16:27Z","checksum":"a1896e39e4113f2711e46b435d5f3e69","relation":"main_file","access_level":"open_access","file_name":"IST-2016-650-v1+1_p1163-oliveto.pdf","file_id":"5214"}],"external_id":{"isi":["000382659200147"]},"abstract":[{"text":"Crossing fitness valleys is one of the major obstacles to function optimization. In this paper we investigate how the structure of the fitness valley, namely its depth d and length ℓ, influence the runtime of different strategies for crossing these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis algorithm. While the (1+1) EA has to jump across the valley to a point of higher fitness because it does not accept decreasing moves, the non-elitist algorithms may cross the valley by accepting worsening moves. We show that while the runtime of the (1+1) EA algorithm depends critically on the length of the valley, the runtimes of the non-elitist algorithms depend crucially only on the depth of the valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of small length. Moreover, we show that both SSWM and Metropolis can also efficiently optimize a rugged function consisting of consecutive valleys.","lang":"eng"}],"oa_version":"Published Version","author":[{"last_name":"Oliveto","full_name":"Oliveto, Pietro","first_name":"Pietro"},{"orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","last_name":"Paixao","full_name":"Paixao, Tiago"},{"first_name":"Jorge","last_name":"Heredia","full_name":"Heredia, Jorge"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"last_name":"Trubenova","full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora","orcid":"0000-0002-6873-2967"}],"day":"20"},{"publist_id":"5889","oa":1,"date_updated":"2025-09-22T08:01:07Z","status":"public","corr_author":"1","_id":"1356","scopus_import":"1","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:46Z","ddc":["570"],"quality_controlled":"1","pubrep_id":"769","volume":202,"citation":{"apa":"Barton, N. H. (2016). Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.115.184796\">https://doi.org/10.1534/genetics.115.184796</a>","mla":"Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” <i>Genetics</i>, vol. 202, no. 1, Genetics Society of America, 2016, pp. 3–4, doi:<a href=\"https://doi.org/10.1534/genetics.115.184796\">10.1534/genetics.115.184796</a>.","short":"N.H. Barton, Genetics 202 (2016) 3–4.","ista":"Barton NH. 2016. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”. Genetics. 202(1), 3–4.","chicago":"Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.115.184796\">https://doi.org/10.1534/genetics.115.184796</a>.","ama":"Barton NH. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” <i>Genetics</i>. 2016;202(1):3-4. doi:<a href=\"https://doi.org/10.1534/genetics.115.184796\">10.1534/genetics.115.184796</a>","ieee":"N. H. Barton, “Sewall Wright on evolution in Mendelian populations and the ‘Shifting Balance,’” <i>Genetics</i>, vol. 202, no. 1. Genetics Society of America, pp. 3–4, 2016."},"has_accepted_license":"1","page":"3 - 4","article_processing_charge":"No","month":"01","intvolume":"       202","publisher":"Genetics Society of America","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:51:33Z","doi":"10.1534/genetics.115.184796","year":"2016","publication_status":"published","title":"Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"oa_version":"Submitted Version","issue":"1","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"day":"05","publication":"Genetics","external_id":{"isi":["000367718100002"]},"date_published":"2016-01-05T00:00:00Z","file":[{"date_updated":"2020-07-14T12:44:46Z","creator":"system","file_size":112674,"date_created":"2018-12-12T10:08:26Z","content_type":"application/pdf","checksum":"3562b89c821a4be84edf2b6ebd870cf5","access_level":"open_access","relation":"main_file","file_id":"4687","file_name":"IST-2017-769-v1+1_SewallWright1931.pdf"}]},{"month":"03","publisher":"Genetics Society of America","intvolume":"       202","has_accepted_license":"1","citation":{"apa":"Barton, N. H. (2016). Richard Hudson and Norman Kaplan on the coalescent process. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.116.187542\">https://doi.org/10.1534/genetics.116.187542</a>","mla":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” <i>Genetics</i>, vol. 202, no. 3, Genetics Society of America, 2016, pp. 865–66, doi:<a href=\"https://doi.org/10.1534/genetics.116.187542\">10.1534/genetics.116.187542</a>.","ista":"Barton NH. 2016. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 202(3), 865–866.","short":"N.H. Barton, Genetics 202 (2016) 865–866.","chicago":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.116.187542\">https://doi.org/10.1534/genetics.116.187542</a>.","ama":"Barton NH. Richard Hudson and Norman Kaplan on the coalescent process. <i>Genetics</i>. 2016;202(3):865-866. doi:<a href=\"https://doi.org/10.1534/genetics.116.187542\">10.1534/genetics.116.187542</a>","ieee":"N. H. Barton, “Richard Hudson and Norman Kaplan on the coalescent process,” <i>Genetics</i>, vol. 202, no. 3. Genetics Society of America, pp. 865–866, 2016."},"quality_controlled":"1","volume":202,"pubrep_id":"768","article_processing_charge":"No","page":"865 - 866","_id":"1357","corr_author":"1","status":"public","ddc":["576"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:46Z","scopus_import":"1","oa":1,"publist_id":"5888","date_updated":"2025-09-22T07:56:18Z","external_id":{"isi":["000371596400001"]},"date_published":"2016-03-01T00:00:00Z","file":[{"file_size":130779,"content_type":"application/pdf","date_created":"2018-12-12T10:15:09Z","date_updated":"2020-07-14T12:44:46Z","creator":"system","relation":"main_file","access_level":"open_access","file_name":"IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf","file_id":"5127","checksum":"b2174bab2de1d1142900062a150f35c9"}],"publication":"Genetics","issue":"3","oa_version":"Submitted Version","day":"01","author":[{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"publication_status":"published","isi":1,"language":[{"iso":"eng"}],"title":"Richard Hudson and Norman Kaplan on the coalescent process","type":"journal_article","date_created":"2018-12-11T11:51:33Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2016","doi":"10.1534/genetics.116.187542"},{"date_created":"2018-12-11T11:51:34Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2016","article_number":"12307","doi":"10.1038/ncomms12307","publication_status":"published","language":[{"iso":"eng"}],"isi":1,"type":"journal_article","title":"Intrinsic limits to gene regulation by global crosstalk","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","day":"04","author":[{"full_name":"Friedlander, Tamar","last_name":"Friedlander","first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Prizak","full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000380858400001"]},"file":[{"creator":"system","date_updated":"2020-07-14T12:44:46Z","content_type":"application/pdf","date_created":"2018-12-12T10:12:01Z","file_size":861805,"checksum":"fe3f3a1526d180b29fe691ab11435b78","file_name":"IST-2016-627-v1+1_ncomms12307.pdf","file_id":"4919","access_level":"open_access","relation":"main_file"},{"file_id":"4920","file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","access_level":"open_access","relation":"main_file","checksum":"164864a1a675f3ad80e9917c27aba07f","date_created":"2018-12-12T10:12:02Z","content_type":"application/pdf","file_size":1084703,"creator":"system","date_updated":"2020-07-14T12:44:46Z"}],"date_published":"2016-08-04T00:00:00Z","publication":"Nature Communications","abstract":[{"lang":"eng","text":"Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements."}],"oa":1,"related_material":{"record":[{"id":"6071","status":"public","relation":"dissertation_contains"}]},"publist_id":"5887","date_updated":"2026-04-08T13:54:24Z","corr_author":"1","_id":"1358","status":"public","file_date_updated":"2020-07-14T12:44:46Z","department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"ddc":["576"],"scopus_import":"1","citation":{"ista":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307.","short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).","apa":"Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., &#38; Tkačik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>","mla":"Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>, vol. 7, 12307, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>.","ieee":"T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","ama":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>","chicago":"Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>."},"has_accepted_license":"1","volume":7,"pubrep_id":"627","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"ec_funded":1,"article_processing_charge":"No","month":"08","publisher":"Nature Publishing Group","intvolume":"         7"},{"publication":"PNAS","date_published":"2016-04-19T00:00:00Z","external_id":{"isi":["000374393800056"],"pmid":["27044080"]},"abstract":[{"text":"The role of gene interactions in the evolutionary process has long\r\nbeen controversial. Although some argue that they are not of\r\nimportance, because most variation is additive, others claim that\r\ntheir effect in the long term can be substantial. Here, we focus on\r\nthe long-term effects of genetic interactions under directional\r\nselection assuming no mutation or dominance, and that epistasis is\r\nsymmetrical overall. We ask by how much the mean of a complex\r\ntrait can be increased by selection and analyze two extreme\r\nregimes, in which either drift or selection dominate the dynamics\r\nof allele frequencies. In both scenarios, epistatic interactions affect\r\nthe long-term response to selection by modulating the additive\r\ngenetic variance. When drift dominates, we extend Robertson\r\n’\r\ns\r\n[Robertson A (1960)\r\nProc R Soc Lond B Biol Sci\r\n153(951):234\r\n−\r\n249]\r\nargument to show that, for any form of epistasis, the total response\r\nof a haploid population is proportional to the initial total genotypic\r\nvariance. In contrast, the total response of a diploid population is\r\nincreased by epistasis, for a given initial genotypic variance. When\r\nselection dominates, we show that the total selection response can\r\nonly be increased by epistasis when s\r\nome initially deleterious alleles\r\nbecome favored as the genetic background changes. We find a sim-\r\nple approximation for this effect and show that, in this regime, it is\r\nthe structure of the genotype - phenotype map that matters and not\r\nthe variance components of the population.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/","open_access":"1"}],"issue":"16","author":[{"orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","last_name":"Paixao","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"day":"19","publication_status":"published","article_type":"original","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","title":"The effect of gene interactions on the long-term response to selection","language":[{"iso":"eng"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:34Z","doi":"10.1073/pnas.1518830113","year":"2016","month":"04","intvolume":"       113","publisher":"National Academy of Sciences","volume":113,"quality_controlled":"1","citation":{"chicago":"Paixao, Tiago, and Nicholas H Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” <i>PNAS</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1518830113\">https://doi.org/10.1073/pnas.1518830113</a>.","ama":"Paixao T, Barton NH. The effect of gene interactions on the long-term response to selection. <i>PNAS</i>. 2016;113(16):4422-4427. doi:<a href=\"https://doi.org/10.1073/pnas.1518830113\">10.1073/pnas.1518830113</a>","ieee":"T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term response to selection,” <i>PNAS</i>, vol. 113, no. 16. National Academy of Sciences, pp. 4422–4427, 2016.","apa":"Paixao, T., &#38; Barton, N. H. (2016). The effect of gene interactions on the long-term response to selection. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1518830113\">https://doi.org/10.1073/pnas.1518830113</a>","mla":"Paixao, Tiago, and Nicholas H. Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” <i>PNAS</i>, vol. 113, no. 16, National Academy of Sciences, 2016, pp. 4422–27, doi:<a href=\"https://doi.org/10.1073/pnas.1518830113\">10.1073/pnas.1518830113</a>.","ista":"Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 4422–4427.","short":"T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427."},"page":"4422 - 4427","article_processing_charge":"No","ec_funded":1,"status":"public","corr_author":"1","_id":"1359","scopus_import":"1","ddc":["570"],"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publist_id":"5886","oa":1,"date_updated":"2026-06-18T17:31:02Z"},{"abstract":[{"lang":"eng","text":"Background and aims Angiosperms display remarkable diversity in flower colour, implying that transitions between pigmentation phenotypes must have been common. Despite progress in understanding transitions between anthocyanin (blue, purple, pink or red) and unpigmented (white) flowers, little is known about the evolutionary patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented flowers. This study investigates the relative rates of evolutionary transitions between different combinations of yellow- and anthocyanin-pigmentation phenotypes in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on anthocyanin and yellow floral pigmentation for 369 species across the tribe. We then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative methods to estimate transition rates among pigmentation phenotypes across the phylogeny. Key Results In contrast to previous studies we found a bias towards transitions involving a gain in pigmentation, although transitions to phenotypes with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite the dominance of yellow and anthocyanin-pigmented taxa, transitions between these phenotypes are constrained to move through a white intermediate stage, whereas transitions to double-pigmentation are very rare. The most abundant transitions are between anthocyanin-pigmented and unpigmented flowers, and similarly the most abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented flowers. Conclusions Our findings show that pigment evolution is limited by the presence of other floral pigments. This interaction between anthocyanin and yellow pigments constrains the breadth of potential floral diversity observed in nature. In particular, they suggest that selection has repeatedly acted to promote the spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore, the correlation between transition rates and polymorphism suggests that the forces causing and maintaining variance in the short term reflect evolutionary processes on longer time scales."}],"date_published":"2016-06-01T00:00:00Z","external_id":{"isi":["000379733800004"]},"publication":"Annals of Botany","day":"01","author":[{"orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas","last_name":"Ellis","first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Field","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","orcid":"0000-0002-4014-8478"}],"issue":"7","oa_version":"None","isi":1,"language":[{"iso":"eng"}],"title":"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae","type":"journal_article","publication_status":"published","year":"2016","doi":"10.1093/aob/mcw043","acknowledgement":"We thank Melinda Pickup, Spencer Barrett, Nick Barton and four anonymous reviewers for helpful discussions on previous versions  of  this  manuscript.  We  also  thank  Jana  Porsche  for her efforts in tracking down the more obscure references.","date_created":"2018-12-11T11:51:42Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Oxford University Press","intvolume":"       117","month":"06","article_processing_charge":"No","page":"1133 - 1140","citation":{"mla":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” <i>Annals of Botany</i>, vol. 117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:<a href=\"https://doi.org/10.1093/aob/mcw043\">10.1093/aob/mcw043</a>.","apa":"Ellis, T., &#38; Field, D. (2016). Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. <i>Annals of Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/aob/mcw043\">https://doi.org/10.1093/aob/mcw043</a>","ista":"Ellis T, Field D. 2016. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. 117(7), 1133–1140.","short":"T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140.","ama":"Ellis T, Field D. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. <i>Annals of Botany</i>. 2016;117(7):1133-1140. doi:<a href=\"https://doi.org/10.1093/aob/mcw043\">10.1093/aob/mcw043</a>","chicago":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” <i>Annals of Botany</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/aob/mcw043\">https://doi.org/10.1093/aob/mcw043</a>.","ieee":"T. Ellis and D. Field, “Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae,” <i>Annals of Botany</i>, vol. 117, no. 7. Oxford University Press, pp. 1133–1140, 2016."},"volume":117,"quality_controlled":"1","department":[{"_id":"NiBa"}],"scopus_import":"1","corr_author":"1","_id":"1382","status":"public","date_updated":"2025-09-22T07:32:44Z","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5550"}]},"publist_id":"5828"},{"publisher":"Institute of Science and Technology Austria","supervisor":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton"}],"month":"02","OA_place":"publisher","article_processing_charge":"No","page":"130","citation":{"ista":"Ellis T. 2016. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute of Science and Technology Austria.","short":"T. Ellis, The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone, Institute of Science and Technology Austria, 2016.","apa":"Ellis, T. (2016). <i>The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">https://doi.org/10.15479/AT:ISTA:TH_526 </a>","mla":"Ellis, Thomas. <i>The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">10.15479/AT:ISTA:TH_526 </a>.","ieee":"T. Ellis, “The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone,” Institute of Science and Technology Austria, 2016.","chicago":"Ellis, Thomas. “The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">https://doi.org/10.15479/AT:ISTA:TH_526 </a>.","ama":"Ellis T. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">10.15479/AT:ISTA:TH_526 </a>"},"has_accepted_license":"1","pubrep_id":"526","file_date_updated":"2025-07-03T06:24:39Z","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"ddc":["576"],"degree_awarded":"PhD","corr_author":"1","_id":"1398","status":"public","date_updated":"2026-04-09T10:52:07Z","oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"5553"},{"id":"5551","relation":"dissertation_contains","status":"public"},{"id":"5552","status":"public","relation":"dissertation_contains"}]},"publist_id":"5809","abstract":[{"text":"Hybrid zones represent evolutionary laboratories, where recombination brings together alleles in combinations which have not previously been tested by selection. This provides an excellent opportunity to test the effect of molecular variation on fitness, and how this variation is able to spread through populations in a natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for two loci controlling the distribution of yellow and magenta floral pigments. Where the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine to give striking transgressive variation for flower colour. The sharp transition in phenotype over ~1km implies strong selection maintaining the hybrid zone. An indirect assay of pollinator visitation in the field found that pollinators forage in a positive-frequency dependent manner on Antirrhinum, matching previous data on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds demonstrated assortative mating for pigmentation alleles, and that pollinator behaviour alone is sufficient to explain this pattern. Selection by pollinators should be sufficiently strong to maintain the hybrid zone, although other mechanisms may be at work. At a broader scale I examined evolutionary transitions between yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection has acted strate that pollinators are a major determinant of reproductive success and mating patterns in wild Antirrhinum.","lang":"eng"}],"date_published":"2016-02-18T00:00:00Z","file":[{"date_created":"2025-07-03T06:24:17Z","content_type":"application/pdf","file_size":7590862,"creator":"dernst","date_updated":"2025-07-03T06:24:17Z","file_name":"2016_Thesis_Ellis_noSignatures.pdf","file_id":"19957","relation":"main_file","access_level":"open_access","checksum":"f0f7c260e19ec1416824b165afe2d5fd"},{"date_created":"2018-12-12T10:14:51Z","content_type":"application/pdf","file_size":11928241,"creator":"system","date_updated":"2025-07-03T06:24:39Z","file_name":"IST-2016-526-v1+1_Ellis_signed_thesis.pdf","file_id":"5106","access_level":"closed","relation":"main_file","checksum":"a89b17ff27cf92c9a15f6b3d46bd7e53"}],"day":"18","author":[{"last_name":"Ellis","full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","orcid":"0000-0002-8511-0254"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"title":"The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone","type":"dissertation","publication_status":"published","year":"2016","publication_identifier":{"issn":["2663-337X"]},"acknowledgement":"I am indebted to many people for their support during my PhD, but I particularly wish to thank Nick Barton for his guidance and intuition, and for encouraging me to take the time to look beyond the immediate topic of my PhD to understand the broader context. I am also especially grateful to David Field his bottomless patience, invaluable advice on experimental design, analysis and scientific writing, and for tireless work on the population surveys and genomic work without most of my thesis could not have happened. \r\n\r\nIt has been a pleasure to work with the combined strengths of the groups at The John Innes Centre, University of Toulouse and IST Austria. Thanks to Enrico Coen and his group for hosting me in Norwich in 2011 and especially for setting up the tag experiment. \r\n\r\nI thank David Field, Desmond Bradley and Maria Clara Melo-Hurtado for organising field collections, as well as Monique Burrus and Christophe Andalo and a large number of volunteers for their e ff orts helping with the field work. Furthermore I thank Coline Jaworski for providing seeds and for her input into the design of the experimental arrays, and Matthew Couchman for maintaining the database of. \r\n\r\nIn addition to those mentioned above, I am grateful to Melinda Pickup, Spencer Barrett, and four anonymous reviewers for their insightful comments on sections of this manuscript. I also thank Jana Porsche for her e ff orts in tracking down the more obscure references for chapter 5, and Jon Bollback for his advice about the analysis. \r\n\r\nI am indebted to Jon Ågren for his patience whilst I finished this thesis, and to Sylvia Cremer and Magnus Nordborg for taking the time to read and evaluate the thesis given a shorter deadline than was fair. \r\n\r\nA very positive aspect of my PhD has been the supportive atmosphere of IST. In particular, I have come to appreciate the enormous support from our group assistants Nicole Hotzy, Julia Asimakis, Christine Ostermann and Jerneja Beslagic. I also thank Christian Chaloupka and Stefan Hipfinger for their enthusiasm and readiness to help where possible in setting up our greenhouse and experiments. ","doi":"10.15479/AT:ISTA:TH_526 ","alternative_title":["ISTA Thesis"],"date_created":"2018-12-11T11:51:47Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"publist_id":"5798","oa":1,"date_updated":"2025-09-18T14:30:06Z","status":"public","_id":"1409","scopus_import":"1","ddc":["576"],"file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"NiBa"}],"pubrep_id":"772","volume":25,"quality_controlled":"1","has_accepted_license":"1","citation":{"ieee":"R. Abbott, N. H. Barton, and J. Good, “Genomics of hybridization and its evolutionary consequences,” <i>Molecular Ecology</i>, vol. 25, no. 11. Wiley-Blackwell, pp. 2325–2332, 2016.","chicago":"Abbott, Richard, Nicholas H Barton, and Jeffrey Good. “Genomics of Hybridization and Its Evolutionary Consequences.” <i>Molecular Ecology</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1111/mec.13685\">https://doi.org/10.1111/mec.13685</a>.","ama":"Abbott R, Barton NH, Good J. Genomics of hybridization and its evolutionary consequences. <i>Molecular Ecology</i>. 2016;25(11):2325-2332. doi:<a href=\"https://doi.org/10.1111/mec.13685\">10.1111/mec.13685</a>","ista":"Abbott R, Barton NH, Good J. 2016. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 25(11), 2325–2332.","short":"R. Abbott, N.H. Barton, J. Good, Molecular Ecology 25 (2016) 2325–2332.","mla":"Abbott, Richard, et al. “Genomics of Hybridization and Its Evolutionary Consequences.” <i>Molecular Ecology</i>, vol. 25, no. 11, Wiley-Blackwell, 2016, pp. 2325–32, doi:<a href=\"https://doi.org/10.1111/mec.13685\">10.1111/mec.13685</a>.","apa":"Abbott, R., Barton, N. H., &#38; Good, J. (2016). Genomics of hybridization and its evolutionary consequences. <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/mec.13685\">https://doi.org/10.1111/mec.13685</a>"},"page":"2325 - 2332","article_processing_charge":"No","month":"06","intvolume":"        25","publisher":"Wiley-Blackwell","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:51:51Z","doi":"10.1111/mec.13685","year":"2016","publication_status":"published","title":"Genomics of hybridization and its evolutionary consequences","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"oa_version":"Submitted Version","issue":"11","author":[{"first_name":"Richard","last_name":"Abbott","full_name":"Abbott, Richard"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton"},{"first_name":"Jeffrey","full_name":"Good, Jeffrey","last_name":"Good"}],"day":"08","publication":"Molecular Ecology","file":[{"access_level":"open_access","relation":"main_file","file_name":"IST-2017-772-v1+1_AbbotEtAl2016-3.pdf","file_id":"4797","checksum":"ede7d0b8a471754f71f17e2b20f3135b","file_size":226137,"date_created":"2018-12-12T10:10:12Z","content_type":"application/pdf","date_updated":"2020-07-14T12:44:53Z","creator":"system"}],"date_published":"2016-06-08T00:00:00Z","external_id":{"isi":["000378941100001"]}},{"author":[{"orcid":"0000-0002-7214-0171","full_name":"Bod'ová, Katarína","last_name":"Bod'ová","first_name":"Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"day":"06","oa_version":"Preprint","issue":"4","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.08344"}],"abstract":[{"lang":"eng","text":"Selection, mutation, and random drift affect the dynamics of allele frequencies and consequently of quantitative traits. While the macroscopic dynamics of quantitative traits can be measured, the underlying allele frequencies are typically unobserved. Can we understand how the macroscopic observables evolve without following these microscopic processes? This problem has been studied previously by analogy with statistical mechanics: the allele frequency distribution at each time point is approximated by the stationary form, which maximizes entropy. We explore the limitations of this method when mutation is small (4Nμ &lt; 1) so that populations are typically close to fixation, and we extend the theory in this regime to account for changes in mutation strength. We consider a single diallelic locus either under directional selection or with overdominance and then generalize to multiple unlinked biallelic loci with unequal effects. We find that the maximum-entropy approximation is remarkably accurate, even when mutation and selection change rapidly. "}],"publication":"Genetics","date_published":"2016-04-06T00:00:00Z","external_id":{"isi":["000373959100022"],"arxiv":["1510.08344"]},"doi":"10.1534/genetics.115.184127","year":"2016","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:51:55Z","type":"journal_article","title":"A general approximation for the dynamics of quantitative traits","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425"}],"isi":1,"language":[{"iso":"eng"}],"publication_status":"published","page":"1523 - 1548","ec_funded":1,"article_processing_charge":"No","quality_controlled":"1","volume":202,"citation":{"ieee":"K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” <i>Genetics</i>, vol. 202, no. 4. Genetics Society of America, pp. 1523–1548, 2016.","chicago":"Bodova, Katarina, Gašper Tkačik, and Nicholas H Barton. “A General Approximation for the Dynamics of Quantitative Traits.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.115.184127\">https://doi.org/10.1534/genetics.115.184127</a>.","ama":"Bodova K, Tkačik G, Barton NH. A general approximation for the dynamics of quantitative traits. <i>Genetics</i>. 2016;202(4):1523-1548. doi:<a href=\"https://doi.org/10.1534/genetics.115.184127\">10.1534/genetics.115.184127</a>","ista":"Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548.","short":"K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.","mla":"Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative Traits.” <i>Genetics</i>, vol. 202, no. 4, Genetics Society of America, 2016, pp. 1523–48, doi:<a href=\"https://doi.org/10.1534/genetics.115.184127\">10.1534/genetics.115.184127</a>.","apa":"Bodova, K., Tkačik, G., &#38; Barton, N. H. (2016). A general approximation for the dynamics of quantitative traits. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.115.184127\">https://doi.org/10.1534/genetics.115.184127</a>"},"intvolume":"       202","publisher":"Genetics Society of America","month":"04","date_updated":"2025-09-18T14:22:05Z","publist_id":"5787","oa":1,"scopus_import":"1","arxiv":1,"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"status":"public","_id":"1420","corr_author":"1"},{"corr_author":"1","_id":"1631","status":"public","file_date_updated":"2020-07-14T12:45:07Z","department":[{"_id":"NiBa"}],"ddc":["576"],"scopus_import":"1","oa":1,"publist_id":"5524","date_updated":"2025-09-18T10:51:58Z","month":"04","publisher":"Academic Press","intvolume":"       108","citation":{"apa":"Kelleher, J., Etheridge, A., Véber, A., &#38; Barton, N. H. (2016). Spread of pedigree versus genetic ancestry in spatially distributed populations. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">https://doi.org/10.1016/j.tpb.2015.10.008</a>","mla":"Kelleher, Jerome, et al. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” <i>Theoretical Population Biology</i>, vol. 108, Academic Press, 2016, pp. 1–12, doi:<a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">10.1016/j.tpb.2015.10.008</a>.","ista":"Kelleher J, Etheridge A, Véber A, Barton NH. 2016. Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. 108, 1–12.","short":"J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population Biology 108 (2016) 1–12.","chicago":"Kelleher, Jerome, Alison Etheridge, Amandine Véber, and Nicholas H Barton. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” <i>Theoretical Population Biology</i>. Academic Press, 2016. <a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">https://doi.org/10.1016/j.tpb.2015.10.008</a>.","ama":"Kelleher J, Etheridge A, Véber A, Barton NH. Spread of pedigree versus genetic ancestry in spatially distributed populations. <i>Theoretical Population Biology</i>. 2016;108:1-12. doi:<a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">10.1016/j.tpb.2015.10.008</a>","ieee":"J. Kelleher, A. Etheridge, A. Véber, and N. H. Barton, “Spread of pedigree versus genetic ancestry in spatially distributed populations,” <i>Theoretical Population Biology</i>, vol. 108. Academic Press, pp. 1–12, 2016."},"has_accepted_license":"1","pubrep_id":"465","volume":108,"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"ec_funded":1,"article_processing_charge":"No","page":"1 - 12","publication_status":"published","isi":1,"language":[{"iso":"eng"}],"title":"Spread of pedigree versus genetic ancestry in spatially distributed populations","type":"journal_article","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"date_created":"2018-12-11T11:53:08Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2016","doi":"10.1016/j.tpb.2015.10.008","external_id":{"isi":["000372560000001"]},"file":[{"relation":"main_file","access_level":"open_access","file_id":"4865","file_name":"IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf","checksum":"6a65ba187994d4ad86c1c509e0ff482a","file_size":1684043,"content_type":"application/pdf","date_created":"2018-12-12T10:11:12Z","date_updated":"2020-07-14T12:45:07Z","creator":"system"}],"date_published":"2016-04-01T00:00:00Z","publication":"Theoretical Population Biology","abstract":[{"lang":"eng","text":"Ancestral processes are fundamental to modern population genetics and spatial structure has been the subject of intense interest for many years. Despite this interest, almost nothing is known about the distribution of the locations of pedigree or genetic ancestors. Using both spatially continuous and stepping-stone models, we show that the distribution of pedigree ancestors approaches a travelling wave, for which we develop two alternative approximations. The speed and width of the wave are sensitive to the local details of the model. After a short time, genetic ancestors spread far more slowly than pedigree ancestors, ultimately diffusing out with radius ## rather than spreading at constant speed. In contrast to the wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the local details of the models."}],"oa_version":"Published Version","day":"01","author":[{"first_name":"Jerome","full_name":"Kelleher, Jerome","last_name":"Kelleher"},{"first_name":"Alison","full_name":"Etheridge, Alison","last_name":"Etheridge"},{"first_name":"Amandine","full_name":"Véber, Amandine","last_name":"Véber"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}]},{"year":"2016","acknowledgement":"This work was made possible by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for the United Nations Educational, Scientific, and Cultural Organization and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria) and European Research Council grant 250152 (to Nick Barton).","doi":"10.1534/genetics.115.180299","date_created":"2018-12-11T11:50:54Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"language":[{"iso":"eng"}],"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"_id":"25B67606-B435-11E9-9278-68D0E5697425","name":"Evolutionary rescue"}],"type":"journal_article","title":"The role of recombination in evolutionary rescue","publication_status":"published","day":"01","author":[{"orcid":"0000-0001-9435-2813","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","first_name":"Hildegard","last_name":"Uecker","full_name":"Uecker, Hildegard"},{"full_name":"Hermisson, Joachim","last_name":"Hermisson","first_name":"Joachim"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/022020"}],"issue":"2","oa_version":"Preprint","abstract":[{"lang":"eng","text":"How likely is it that a population escapes extinction through adaptive evolution? The answer to this question is of great relevance in conservation biology, where we aim at species’ rescue and the maintenance of biodiversity, and in agriculture and medicine, where we seek to hamper the emergence of pesticide or drug resistance. By reshuffling the genome, recombination has two antagonistic effects on the probability of evolutionary rescue: It generates and it breaks up favorable gene combinations. Which of the two effects prevails depends on the fitness effects of mutations and on the impact of stochasticity on the allele frequencies. In this article, we analyze a mathematical model for rescue after a sudden environmental change when adaptation is contingent on mutations at two loci. The analysis reveals a complex nonlinear dependence of population survival on recombination. We moreover find that, counterintuitively, a fast eradication of the wild type can promote rescue in the presence of recombination. The model also shows that two-step rescue is not unlikely to happen and can even be more likely than single-step rescue (where adaptation relies on a single mutation), depending on the circumstances."}],"das_tickbox":"1","date_published":"2016-02-01T00:00:00Z","external_id":{"biorxivid":["10.1101/022020"],"isi":["000371304600028"]},"publication":"Genetics","date_updated":"2026-06-22T14:07:01Z","oa":1,"publist_id":"6091","department":[{"_id":"NiBa"}],"scopus_import":"1","_id":"1241","status":"public","ec_funded":1,"article_processing_charge":"No","page":"721 - 732","citation":{"ama":"Uecker H, Hermisson J. The role of recombination in evolutionary rescue. <i>Genetics</i>. 2016;202(2):721-732. doi:<a href=\"https://doi.org/10.1534/genetics.115.180299\">10.1534/genetics.115.180299</a>","chicago":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.115.180299\">https://doi.org/10.1534/genetics.115.180299</a>.","ieee":"H. Uecker and J. Hermisson, “The role of recombination in evolutionary rescue,” <i>Genetics</i>, vol. 202, no. 2. Genetics Society of America, pp. 721–732, 2016.","mla":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” <i>Genetics</i>, vol. 202, no. 2, Genetics Society of America, 2016, pp. 721–32, doi:<a href=\"https://doi.org/10.1534/genetics.115.180299\">10.1534/genetics.115.180299</a>.","apa":"Uecker, H., &#38; Hermisson, J. (2016). The role of recombination in evolutionary rescue. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.115.180299\">https://doi.org/10.1534/genetics.115.180299</a>","short":"H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732.","ista":"Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue. Genetics. 202(2), 721–732."},"quality_controlled":"1","volume":202,"biorxivid":1,"publisher":"Genetics Society of America","intvolume":"       202","month":"02"},{"date_published":"2015-11-06T00:00:00Z","month":"11","publisher":"Public Library of Science","citation":{"ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison &#38; for interacting TFBSs.” Public Library of Science, 2015.","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other Fitness Models for Comparison &#38; for Interacting TFBSs.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">https://doi.org/10.1371/journal.pgen.1005639.s001</a>.","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison &#38; for interacting TFBSs. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">10.1371/journal.pgen.1005639.s001</a>","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison &#38; for interacting TFBSs, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">10.1371/journal.pgen.1005639.s001</a>.","apa":"Tugrul, M., Paixao, T., Barton, N. H., &#38; Tkačik, G. (2015). Other fitness models for comparison &#38; for interacting TFBSs. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">https://doi.org/10.1371/journal.pgen.1005639.s001</a>","mla":"Tugrul, Murat, et al. <i>Other Fitness Models for Comparison &#38; for Interacting TFBSs</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">10.1371/journal.pgen.1005639.s001</a>."},"oa_version":"Published Version","article_processing_charge":"No","day":"06","author":[{"orcid":"0000-0002-8523-0758","last_name":"Tugrul","full_name":"Tugrul, Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","first_name":"Murat"},{"last_name":"Paixao","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","orcid":"0000-0003-2361-3953"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"_id":"9712","status":"public","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"type":"research_data_reference","title":"Other fitness models for comparison & for interacting TFBSs","date_created":"2021-07-23T12:00:37Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1666"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2015","date_updated":"2025-09-23T08:31:14Z","doi":"10.1371/journal.pgen.1005639.s001"},{"author":[{"orcid":"0000-0002-6873-2967","first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora","last_name":"Trubenova"},{"orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Novak","full_name":"Novak, Sebastian"},{"full_name":"Hager, Reinmar","last_name":"Hager","first_name":"Reinmar"}],"article_processing_charge":"No","day":"18","oa_version":"Published Version","citation":{"mla":"Trubenova, Barbora, et al. <i>Mathematical Inference of the Results</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">10.1371/journal.pone.0126907.s001</a>.","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Mathematical inference of the results. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">https://doi.org/10.1371/journal.pone.0126907.s001</a>","ista":"Trubenova B, Novak S, Hager R. 2015. Mathematical inference of the results, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">10.1371/journal.pone.0126907.s001</a>.","short":"B. Trubenova, S. Novak, R. Hager, (2015).","ama":"Trubenova B, Novak S, Hager R. Mathematical inference of the results. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">10.1371/journal.pone.0126907.s001</a>","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Mathematical Inference of the Results.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">https://doi.org/10.1371/journal.pone.0126907.s001</a>.","ieee":"B. Trubenova, S. Novak, and R. Hager, “Mathematical inference of the results.” Public Library of Science, 2015."},"publisher":"Public Library of Science","month":"05","date_published":"2015-05-18T00:00:00Z","doi":"10.1371/journal.pone.0126907.s001","date_updated":"2025-09-23T09:21:54Z","year":"2015","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-07-23T12:11:30Z","related_material":{"record":[{"id":"1809","status":"public","relation":"used_in_publication"}]},"type":"research_data_reference","title":"Mathematical inference of the results","department":[{"_id":"NiBa"}],"status":"public","_id":"9715"},{"article_processing_charge":"No","day":"18","author":[{"orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","last_name":"Trubenova","first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2519-824X","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","last_name":"Novak"},{"first_name":"Reinmar","last_name":"Hager","full_name":"Hager, Reinmar"}],"citation":{"apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Description of the agent based simulations. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">https://doi.org/10.1371/journal.pone.0126907.s003</a>","mla":"Trubenova, Barbora, et al. <i>Description of the Agent Based Simulations</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>.","short":"B. Trubenova, S. Novak, R. Hager, (2015).","ista":"Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>.","ama":"Trubenova B, Novak S, Hager R. Description of the agent based simulations. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of the Agent Based Simulations.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">https://doi.org/10.1371/journal.pone.0126907.s003</a>.","ieee":"B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.” Public Library of Science, 2015."},"oa_version":"Published Version","publisher":"Public Library of Science","date_published":"2015-05-18T00:00:00Z","month":"05","year":"2015","doi":"10.1371/journal.pone.0126907.s003","date_updated":"2025-09-23T09:21:54Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1809"}]},"date_created":"2021-08-05T12:55:20Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"NiBa"}],"type":"research_data_reference","title":"Description of the agent based simulations","_id":"9772","status":"public"},{"citation":{"chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>.","ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. 2015;10(5). doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>","ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” <i>PLoS One</i>, vol. 10, no. 5. Public Library of Science, 2015.","mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>, vol. 10, no. 5, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>.","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>","ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015)."},"has_accepted_license":"1","pubrep_id":"453","volume":10,"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","month":"05","publisher":"Public Library of Science","intvolume":"        10","related_material":{"record":[{"id":"9715","relation":"research_data","status":"public"},{"status":"public","relation":"research_data","id":"9772"}]},"oa":1,"publist_id":"5299","date_updated":"2025-09-23T09:21:54Z","corr_author":"1","_id":"1809","status":"public","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:45:17Z","ddc":["570","576"],"scopus_import":"1","issue":"5","oa_version":"Published Version","day":"18","author":[{"full_name":"Trubenova, Barbora","last_name":"Trubenova","first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967"},{"orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hager","full_name":"Hager, Reinmar","first_name":"Reinmar"}],"file":[{"file_size":2748982,"content_type":"application/pdf","date_created":"2018-12-12T10:09:07Z","date_updated":"2020-07-14T12:45:17Z","creator":"system","relation":"main_file","access_level":"open_access","file_id":"4730","file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf","checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743"}],"date_published":"2015-05-18T00:00:00Z","external_id":{"isi":["000354917300064"]},"publication":"PLoS One","abstract":[{"lang":"eng","text":"Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations."}],"date_created":"2018-12-11T11:54:07Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2015","doi":"10.1371/journal.pone.0126907","publication_status":"published","language":[{"iso":"eng"}],"isi":1,"title":"Indirect genetic effects and the dynamics of social interactions","type":"journal_article"},{"status":"public","_id":"1818","corr_author":"1","scopus_import":"1","department":[{"_id":"NiBa"}],"publist_id":"5288","oa":1,"date_updated":"2025-09-23T09:27:16Z","month":"05","intvolume":"       112","publisher":"National Academy of Sciences","volume":112,"quality_controlled":"1","citation":{"apa":"Polechova, J., &#38; Barton, N. H. (2015). Limits to adaptation along environmental gradients. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1421515112\">https://doi.org/10.1073/pnas.1421515112</a>","mla":"Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental Gradients.” <i>PNAS</i>, vol. 112, no. 20, National Academy of Sciences, 2015, pp. 6401–06, doi:<a href=\"https://doi.org/10.1073/pnas.1421515112\">10.1073/pnas.1421515112</a>.","ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406.","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","chicago":"Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental Gradients.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1421515112\">https://doi.org/10.1073/pnas.1421515112</a>.","ama":"Polechova J, Barton NH. Limits to adaptation along environmental gradients. <i>PNAS</i>. 2015;112(20):6401-6406. doi:<a href=\"https://doi.org/10.1073/pnas.1421515112\">10.1073/pnas.1421515112</a>","ieee":"J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,” <i>PNAS</i>, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015."},"page":"6401 - 6406","ec_funded":1,"article_processing_charge":"No","publication_status":"published","type":"journal_article","title":"Limits to adaptation along environmental gradients","project":[{"call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:54:11Z","doi":"10.1073/pnas.1421515112","year":"2015","publication":"PNAS","external_id":{"isi":["000354729500058"],"pmid":["25941385"]},"date_published":"2015-05-19T00:00:00Z","abstract":[{"lang":"eng","text":"Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, &quot;swamping&quot; by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible."}],"oa_version":"Submitted Version","pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/"}],"issue":"20","author":[{"full_name":"Polechova, Jitka","last_name":"Polechova","first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"day":"19"},{"abstract":[{"lang":"eng","text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs –an important problem of interest in evolutionary biology– more efficiently than the classical simulation method. We specify the property in linear temporal logics. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights."}],"external_id":{"arxiv":["1410.7704"]},"date_published":"2015-04-01T00:00:00Z","author":[{"orcid":"0000-0001-8180-0904","last_name":"Giacobbe","full_name":"Giacobbe, Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","first_name":"Mirco"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gupta","full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2361-3953","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","last_name":"Paixao"},{"last_name":"Petrov","full_name":"Petrov, Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana","orcid":"0000-0002-9041-0905"}],"day":"01","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.7704"}],"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"},{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"type":"conference","title":"Model checking gene regulatory networks","language":[{"iso":"eng"}],"series_title":"Lecture Notes in Computer Science","publication_status":"published","doi":"10.1007/978-3-662-46681-0_47","acknowledgement":"SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2 148797.\r\n","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2015-04-11","location":"London, United Kingdom","end_date":"2015-04-18"},"date_created":"2018-12-11T11:54:16Z","alternative_title":["LNCS"],"intvolume":"      9035","publisher":"Springer","month":"04","page":"469 - 483","article_processing_charge":"No","ec_funded":1,"volume":9035,"quality_controlled":"1","citation":{"chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.” Lecture Notes in Computer Science. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">https://doi.org/10.1007/978-3-662-46681-0_47</a>.","ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking gene regulatory networks. 2015;9035:469-483. doi:<a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">10.1007/978-3-662-46681-0_47</a>","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking gene regulatory networks,” vol. 9035. Springer, pp. 469–483, 2015.","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., &#38; Petrov, T. (2015). Model checking gene regulatory networks. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">https://doi.org/10.1007/978-3-662-46681-0_47</a>","mla":"Giacobbe, Mirco, et al. <i>Model Checking Gene Regulatory Networks</i>. Vol. 9035, Springer, 2015, pp. 469–83, doi:<a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">10.1007/978-3-662-46681-0_47</a>.","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, 9035 (2015) 469–483.","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model checking gene regulatory networks. 9035, 469–483."},"arxiv":1,"scopus_import":"1","department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"status":"public","_id":"1835","date_updated":"2025-07-10T11:50:42Z","publist_id":"5267","oa":1,"related_material":{"record":[{"id":"1351","relation":"later_version","status":"public"}]}},{"publisher":"Elsevier","intvolume":"       372","month":"05","article_processing_charge":"No","ec_funded":1,"page":"54 - 64","has_accepted_license":"1","citation":{"short":"S. Novak, S. Cremer, Journal of Theoretical Biology 372 (2015) 54–64.","ista":"Novak S, Cremer S. 2015. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. 372(5), 54–64.","apa":"Novak, S., &#38; Cremer, S. (2015). Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2015.02.018\">https://doi.org/10.1016/j.jtbi.2015.02.018</a>","mla":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” <i>Journal of Theoretical Biology</i>, vol. 372, no. 5, Elsevier, 2015, pp. 54–64, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.02.018\">10.1016/j.jtbi.2015.02.018</a>.","ieee":"S. Novak and S. Cremer, “Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates,” <i>Journal of Theoretical Biology</i>, vol. 372, no. 5. Elsevier, pp. 54–64, 2015.","chicago":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” <i>Journal of Theoretical Biology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jtbi.2015.02.018\">https://doi.org/10.1016/j.jtbi.2015.02.018</a>.","ama":"Novak S, Cremer S. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. <i>Journal of Theoretical Biology</i>. 2015;372(5):54-64. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.02.018\">10.1016/j.jtbi.2015.02.018</a>"},"quality_controlled":"1","pubrep_id":"329","volume":372,"ddc":["576"],"file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"NiBa"},{"_id":"SyCr"}],"scopus_import":"1","_id":"1850","corr_author":"1","status":"public","date_updated":"2025-09-23T08:54:35Z","oa":1,"publist_id":"5251","abstract":[{"text":"Entomopathogenic fungi are potent biocontrol agents that are widely used against insect pests, many of which are social insects. Nevertheless, theoretical investigations of their particular life history are scarce. We develop a model that takes into account the main distinguishing features between traditionally studied diseases and obligate killing pathogens, like the (biocontrol-relevant) insect-pathogenic fungi Metarhizium and Beauveria. First, obligate killing entomopathogenic fungi produce new infectious particles (conidiospores) only after host death and not yet on the living host. Second, the killing rates of entomopathogenic fungi depend strongly on the initial exposure dosage, thus we explicitly consider the pathogen load of individual hosts. Further, we make the model applicable not only to solitary host species, but also to group living species by incorporating social interactions between hosts, like the collective disease defences of insect societies. Our results identify the optimal killing rate for the pathogen that minimises its invasion threshold. Furthermore, we find that the rate of contact between hosts has an ambivalent effect: dense interaction networks between individuals are considered to facilitate disease outbreaks because of increased pathogen transmission. In social insects, this is compensated by their collective disease defences, i.e., social immunity. For the type of pathogens considered here, we show that even without social immunity, high contact rates between live individuals dilute the pathogen in the host colony and hence can reduce individual pathogen loads below disease-causing levels.","lang":"eng"}],"date_published":"2015-05-07T00:00:00Z","external_id":{"isi":["000353311700006"]},"file":[{"date_created":"2018-12-12T10:18:07Z","content_type":"application/pdf","file_size":1546914,"creator":"system","date_updated":"2020-07-14T12:45:19Z","file_name":"IST-2015-329-v1+1_manuscript.pdf","file_id":"5326","access_level":"open_access","relation":"main_file","checksum":"3c0dcacc900bc45cc65a453dfda4ca43"}],"publication":"Journal of Theoretical Biology","day":"07","author":[{"orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"}],"issue":"5","oa_version":"Submitted Version","isi":1,"language":[{"iso":"eng"}],"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"type":"journal_article","title":"Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates","publication_status":"published","year":"2015","doi":"10.1016/j.jtbi.2015.02.018","date_created":"2018-12-11T11:54:21Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"page":"1015 - 1026","article_processing_charge":"No","ec_funded":1,"quality_controlled":"1","volume":69,"has_accepted_license":"1","citation":{"ama":"Priklopil T, Kisdi E, Gyllenberg M. Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. <i>Evolution</i>. 2015;69(4):1015-1026. doi:<a href=\"https://doi.org/10.1111/evo.12618\">10.1111/evo.12618</a>","chicago":"Priklopil, Tadeas, Eva Kisdi, and Mats Gyllenberg. “Evolutionarily Stable Mating Decisions for Sequentially Searching Females and the Stability of Reproductive Isolation by Assortative Mating.” <i>Evolution</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/evo.12618\">https://doi.org/10.1111/evo.12618</a>.","ieee":"T. Priklopil, E. Kisdi, and M. Gyllenberg, “Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating,” <i>Evolution</i>, vol. 69, no. 4. Wiley, pp. 1015–1026, 2015.","apa":"Priklopil, T., Kisdi, E., &#38; Gyllenberg, M. (2015). Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.12618\">https://doi.org/10.1111/evo.12618</a>","mla":"Priklopil, Tadeas, et al. “Evolutionarily Stable Mating Decisions for Sequentially Searching Females and the Stability of Reproductive Isolation by Assortative Mating.” <i>Evolution</i>, vol. 69, no. 4, Wiley, 2015, pp. 1015–26, doi:<a href=\"https://doi.org/10.1111/evo.12618\">10.1111/evo.12618</a>.","ista":"Priklopil T, Kisdi E, Gyllenberg M. 2015. Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. 69(4), 1015–1026.","short":"T. Priklopil, E. Kisdi, M. Gyllenberg, Evolution 69 (2015) 1015–1026."},"intvolume":"        69","publisher":"Wiley","month":"02","date_updated":"2025-09-22T14:27:30Z","publist_id":"5249","oa":1,"scopus_import":"1","ddc":["570"],"department":[{"_id":"NiBa"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:19Z","status":"public","corr_author":"1","_id":"1851","author":[{"last_name":"Priklopil","full_name":"Priklopil, Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas"},{"full_name":"Kisdi, Eva","last_name":"Kisdi","first_name":"Eva"},{"first_name":"Mats","full_name":"Gyllenberg, Mats","last_name":"Gyllenberg"}],"day":"09","oa_version":"Submitted Version","pmid":1,"issue":"4","abstract":[{"lang":"eng","text":"We consider mating strategies for females who search for males sequentially during a season of limited length. We show that the best strategy rejects a given male type if encountered before a time-threshold but accepts him after. For frequency-independent benefits, we obtain the optimal time-thresholds explicitly for both discrete and continuous distributions of males, and allow for mistakes being made in assessing the correct male type. When the benefits are indirect (genes for the offspring) and the population is under frequency-dependent ecological selection, the benefits depend on the mating strategy of other females as well. This case is particularly relevant to speciation models that seek to explore the stability of reproductive isolation by assortative mating under frequency-dependent ecological selection. We show that the indirect benefits are to be quantified by the reproductive values of couples, and describe how the evolutionarily stable time-thresholds can be found. We conclude with an example based on the Levene model, in which we analyze the evolutionarily stable assortative mating strategies and the strength of reproductive isolation provided by them."}],"publication":"Evolution","file":[{"file_size":967214,"content_type":"application/pdf","date_created":"2020-05-15T09:05:34Z","date_updated":"2020-07-14T12:45:19Z","creator":"dernst","access_level":"open_access","relation":"main_file","file_name":"2015_Evolution_Priklopil.pdf","file_id":"7855","checksum":"1e8be0b1d7598a78cd2623d8ee8e7798"}],"date_published":"2015-02-09T00:00:00Z","external_id":{"pmid":["25662095"],"isi":["000353236000014"]},"doi":"10.1111/evo.12618","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"year":"2015","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:54:21Z","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating","type":"journal_article","isi":1,"language":[{"iso":"eng"}],"publication_status":"published","article_type":"original"},{"publist_id":"5213","oa":1,"date_updated":"2025-09-23T07:53:52Z","status":"public","_id":"1883","arxiv":1,"scopus_import":"1","department":[{"_id":"NiBa"}],"volume":91,"quality_controlled":"1","citation":{"mla":"Keller-Schmidt, Stephanie, et al. “Anomalous Scaling in an Age-Dependent Branching Model.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 91, no. 2, 022803, American Institute of Physics, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevE.91.022803\">10.1103/PhysRevE.91.022803</a>.","apa":"Keller-Schmidt, S., Tugrul, M., Eguíluz, V., Hernandez Garcia, E., &#38; Klemm, K. (2015). Anomalous scaling in an age-dependent branching model. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.91.022803\">https://doi.org/10.1103/PhysRevE.91.022803</a>","short":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, K. Klemm, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","ista":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. 2015. Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(2), 022803.","ama":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. Anomalous scaling in an age-dependent branching model. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2015;91(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.91.022803\">10.1103/PhysRevE.91.022803</a>","chicago":"Keller-Schmidt, Stephanie, Murat Tugrul, Víctor Eguíluz, Emilio Hernandez Garcia, and Konstantin Klemm. “Anomalous Scaling in an Age-Dependent Branching Model.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2015. <a href=\"https://doi.org/10.1103/PhysRevE.91.022803\">https://doi.org/10.1103/PhysRevE.91.022803</a>.","ieee":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, and K. Klemm, “Anomalous scaling in an age-dependent branching model,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 91, no. 2. American Institute of Physics, 2015."},"article_processing_charge":"No","month":"02","intvolume":"        91","publisher":"American Institute of Physics","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:54:31Z","doi":"10.1103/PhysRevE.91.022803","year":"2015","article_number":"022803","publication_status":"published","article_type":"original","type":"journal_article","title":"Anomalous scaling in an age-dependent branching model","isi":1,"language":[{"iso":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1012.3298"}],"issue":"2","author":[{"first_name":"Stephanie","full_name":"Keller-Schmidt, Stephanie","last_name":"Keller-Schmidt"},{"orcid":"0000-0002-8523-0758","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","first_name":"Murat","last_name":"Tugrul","full_name":"Tugrul, Murat"},{"full_name":"Eguíluz, Víctor","last_name":"Eguíluz","first_name":"Víctor"},{"first_name":"Emilio","last_name":"Hernandez Garcia","full_name":"Hernandez Garcia, Emilio"},{"last_name":"Klemm","full_name":"Klemm, Konstantin","first_name":"Konstantin"}],"day":"02","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","external_id":{"arxiv":["1012.3298"],"isi":["000349860900006"]},"date_published":"2015-02-02T00:00:00Z","abstract":[{"lang":"eng","text":"We introduce a one-parametric family of tree growth models, in which branching probabilities decrease with branch age τ as τ-α. Depending on the exponent α, the scaling of tree depth with tree size n displays a transition between the logarithmic scaling of random trees and an algebraic growth. At the transition (α=1) tree depth grows as (logn)2. This anomalous scaling is in good agreement with the trend observed in evolution of biological species, thus providing a theoretical support for age-dependent speciation and associating it to the occurrence of a critical point.\r\n"}]}]