[{"date_updated":"2025-09-22T08:01:07Z","publication_status":"published","ddc":["570"],"month":"01","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"language":[{"iso":"eng"}],"publication":"Genetics","_id":"1356","title":"Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”","scopus_import":"1","file":[{"creator":"system","file_id":"4687","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"IST-2017-769-v1+1_SewallWright1931.pdf","file_size":112674,"checksum":"3562b89c821a4be84edf2b6ebd870cf5","date_created":"2018-12-12T10:08:26Z","date_updated":"2020-07-14T12:44:46Z"}],"status":"public","external_id":{"isi":["000367718100002"]},"date_created":"2018-12-11T11:51:33Z","oa_version":"Submitted Version","publist_id":"5889","page":"3 - 4","volume":202,"isi":1,"year":"2016","quality_controlled":"1","day":"05","intvolume":"       202","date_published":"2016-01-05T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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>.","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>","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.","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.","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>"},"department":[{"_id":"NiBa"}],"issue":"1","publisher":"Genetics Society of America","pubrep_id":"769","article_processing_charge":"No","has_accepted_license":"1","corr_author":"1","file_date_updated":"2020-07-14T12:44:46Z","type":"journal_article","doi":"10.1534/genetics.115.184796","oa":1},{"external_id":{"isi":["000371596400001"]},"date_created":"2018-12-11T11:51:33Z","oa_version":"Submitted Version","page":"865 - 866","publist_id":"5888","year":"2016","isi":1,"volume":202,"ddc":["576"],"publication_status":"published","date_updated":"2025-09-22T07:56:18Z","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"month":"03","_id":"1357","language":[{"iso":"eng"}],"publication":"Genetics","scopus_import":"1","status":"public","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf","file_id":"5127","creator":"system","date_created":"2018-12-12T10:15:09Z","date_updated":"2020-07-14T12:44:46Z","checksum":"b2174bab2de1d1142900062a150f35c9","file_size":130779}],"title":"Richard Hudson and Norman Kaplan on the coalescent process","has_accepted_license":"1","corr_author":"1","type":"journal_article","file_date_updated":"2020-07-14T12:44:46Z","oa":1,"doi":"10.1534/genetics.116.187542","day":"01","quality_controlled":"1","date_published":"2016-03-01T00:00:00Z","intvolume":"       202","issue":"3","publisher":"Genetics Society of America","citation":{"short":"N.H. Barton, Genetics 202 (2016) 865–866.","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>","ista":"Barton NH. 2016. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 202(3), 865–866.","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>","ieee":"N. H. Barton, “Richard Hudson and Norman Kaplan on the coalescent process,” <i>Genetics</i>, vol. 202, no. 3. Genetics Society of America, pp. 865–866, 2016.","chicago":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.116.187542\">https://doi.org/10.1534/genetics.116.187542</a>.","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>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"NiBa"}],"article_processing_charge":"No","pubrep_id":"768"},{"corr_author":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/","open_access":"1"}],"pmid":1,"type":"journal_article","oa":1,"doi":"10.1073/pnas.1518830113","day":"19","quality_controlled":"1","date_published":"2016-04-19T00:00:00Z","intvolume":"       113","citation":{"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>.","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.","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>.","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>","ista":"Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 4422–4427.","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>","short":"T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"National Academy of Sciences","issue":"16","article_processing_charge":"No","date_created":"2018-12-11T11:51:34Z","external_id":{"pmid":["27044080"],"isi":["000374393800056"]},"oa_version":"Published Version","ec_funded":1,"abstract":[{"lang":"eng","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."}],"publist_id":"5886","page":"4422 - 4427","volume":113,"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152"},{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091"}],"isi":1,"year":"2016","date_updated":"2025-09-22T07:45:33Z","publication_status":"published","author":[{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"month":"04","_id":"1359","language":[{"iso":"eng"}],"publication":"PNAS","article_type":"original","title":"The effect of gene interactions on the long-term response to selection","status":"public","scopus_import":"1"},{"intvolume":"       117","date_published":"2016-06-01T00:00:00Z","quality_controlled":"1","day":"01","article_processing_charge":"No","citation":{"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>","short":"T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140.","mla":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” <i>Annals of Botany</i>, vol. 117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:<a href=\"https://doi.org/10.1093/aob/mcw043\">10.1093/aob/mcw043</a>.","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.","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.","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>.","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>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","issue":"7","corr_author":"1","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.","doi":"10.1093/aob/mcw043","type":"journal_article","author":[{"first_name":"Thomas","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis"},{"orcid":"0000-0002-4014-8478","first_name":"David","full_name":"Field, David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"}],"month":"06","date_updated":"2025-09-22T07:32:44Z","publication_status":"published","title":"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae","scopus_import":"1","status":"public","language":[{"iso":"eng"}],"publication":"Annals of Botany","_id":"1382","oa_version":"None","related_material":{"record":[{"relation":"popular_science","id":"5550","status":"public"}]},"date_created":"2018-12-11T11:51:42Z","external_id":{"isi":["000379733800004"]},"isi":1,"volume":117,"year":"2016","publist_id":"5828","page":"1133 - 1140","abstract":[{"text":"Background and aims Angiosperms display remarkable diversity in flower colour, implying that transitions between pigmentation phenotypes must have been common. Despite progress in understanding transitions between anthocyanin (blue, purple, pink or red) and unpigmented (white) flowers, little is known about the evolutionary patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented flowers. This study investigates the relative rates of evolutionary transitions between different combinations of yellow- and anthocyanin-pigmentation phenotypes in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on anthocyanin and yellow floral pigmentation for 369 species across the tribe. We then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative methods to estimate transition rates among pigmentation phenotypes across the phylogeny. Key Results In contrast to previous studies we found a bias towards transitions involving a gain in pigmentation, although transitions to phenotypes with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite the dominance of yellow and anthocyanin-pigmented taxa, transitions between these phenotypes are constrained to move through a white intermediate stage, whereas transitions to double-pigmentation are very rare. The most abundant transitions are between anthocyanin-pigmented and unpigmented flowers, and similarly the most abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented flowers. Conclusions Our findings show that pigment evolution is limited by the presence of other floral pigments. This interaction between anthocyanin and yellow pigments constrains the breadth of potential floral diversity observed in nature. In particular, they suggest that selection has repeatedly acted to promote the spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore, the correlation between transition rates and polymorphism suggests that the forces causing and maintaining variance in the short term reflect evolutionary processes on longer time scales.","lang":"eng"}]},{"type":"journal_article","file_date_updated":"2020-07-14T12:44:53Z","doi":"10.1111/mec.13685","oa":1,"has_accepted_license":"1","issue":"11","publisher":"Wiley-Blackwell","citation":{"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>","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>.","ista":"Abbott R, Barton NH, Good J. 2016. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 25(11), 2325–2332.","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>.","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>","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."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"NiBa"}],"pubrep_id":"772","article_processing_charge":"No","quality_controlled":"1","day":"08","intvolume":"        25","date_published":"2016-06-08T00:00:00Z","page":"2325 - 2332","publist_id":"5798","year":"2016","volume":25,"isi":1,"date_created":"2018-12-11T11:51:51Z","external_id":{"isi":["000378941100001"]},"oa_version":"Submitted Version","publication":"Molecular Ecology","language":[{"iso":"eng"}],"_id":"1409","status":"public","file":[{"date_created":"2018-12-12T10:10:12Z","date_updated":"2020-07-14T12:44:53Z","file_size":226137,"checksum":"ede7d0b8a471754f71f17e2b20f3135b","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-772-v1+1_AbbotEtAl2016-3.pdf","file_id":"4797","creator":"system"}],"scopus_import":"1","title":"Genomics of hybridization and its evolutionary consequences","publication_status":"published","date_updated":"2025-09-18T14:30:06Z","ddc":["576"],"author":[{"last_name":"Abbott","first_name":"Richard","full_name":"Abbott, Richard"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Good","full_name":"Good, Jeffrey","first_name":"Jeffrey"}],"month":"06"},{"publication_status":"published","date_updated":"2025-09-18T14:22:05Z","author":[{"first_name":"Katarína","orcid":"0000-0002-7214-0171","full_name":"Bod'ová, Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bod'ová"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"month":"04","language":[{"iso":"eng"}],"publication":"Genetics","_id":"1420","scopus_import":"1","status":"public","title":"A general approximation for the dynamics of quantitative traits","date_created":"2018-12-11T11:51:55Z","external_id":{"isi":["000373959100022"],"arxiv":["1510.08344"]},"oa_version":"Preprint","page":"1523 - 1548","publist_id":"5787","abstract":[{"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. ","lang":"eng"}],"ec_funded":1,"year":"2016","volume":202,"isi":1,"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"},{"grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","arxiv":1,"day":"06","intvolume":"       202","date_published":"2016-04-06T00:00:00Z","issue":"4","publisher":"Genetics Society of America","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"citation":{"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>","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>.","ista":"Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548.","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>.","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>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","corr_author":"1","type":"journal_article","main_file_link":[{"url":"http://arxiv.org/abs/1510.08344","open_access":"1"}],"doi":"10.1534/genetics.115.184127","oa":1},{"date_updated":"2025-09-22T09:17:06Z","publication_status":"published","author":[{"full_name":"Uecker, Hildegard","first_name":"Hildegard","orcid":"0000-0001-9435-2813","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","last_name":"Uecker"},{"last_name":"Hermisson","first_name":"Joachim","full_name":"Hermisson, Joachim"}],"month":"02","language":[{"iso":"eng"}],"publication":"Genetics","_id":"1241","title":"The role of recombination in evolutionary rescue","status":"public","scopus_import":"1","date_created":"2018-12-11T11:50:54Z","external_id":{"isi":["000371304600028"]},"oa_version":"Preprint","publist_id":"6091","page":"721 - 732","abstract":[{"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.","lang":"eng"}],"ec_funded":1,"volume":202,"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152"},{"_id":"25B67606-B435-11E9-9278-68D0E5697425","name":"Evolutionary rescue"}],"isi":1,"year":"2016","quality_controlled":"1","day":"01","intvolume":"       202","date_published":"2016-02-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"NiBa"}],"citation":{"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>.","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>.","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>","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.","ista":"Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue. Genetics. 202(2), 721–732.","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>","short":"H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732."},"issue":"2","publisher":"Genetics Society of America","article_processing_charge":"No","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).","type":"journal_article","main_file_link":[{"open_access":"1","url":"http://biorxiv.org/content/early/2015/07/06/022020.abstract"}],"doi":"10.1534/genetics.115.180299","oa":1},{"date_created":"2018-12-11T11:52:29Z","external_id":{"pmid":["26715666"],"isi":["000371304600032"]},"oa_version":"Preprint","publist_id":"5658","page":"775 - 786","abstract":[{"lang":"eng","text":"The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proved difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has a simple, recursive form, the size of such likelihood calculations explodes quickly with the number of individuals and applications of this framework have so far been mainly limited to small samples (pairs and triplets) for which the GF can be written by hand. Here we investigate several strategies for exploiting the inherent symmetries of the coalescent. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes that allows likelihood calculations from nontrivial samples. Using this strategy, we automated blockwise likelihood calculations for a general set of demographic scenarios in Mathematica. These histories may involve population size changes, continuous migration, discrete divergence, and admixture between multiple populations. To give a concrete example, we calculate the likelihood for a model of isolation with migration (IM), assuming two diploid samples without phase and outgroup information. We demonstrate the new inference scheme with an analysis of two individual butterfly genomes from the sister species Heliconius melpomene rosina and H. cydno."}],"ec_funded":1,"project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"isi":1,"volume":202,"year":"2016","date_updated":"2025-09-18T11:09:34Z","publication_status":"published","ddc":["570"],"month":"02","author":[{"full_name":"Lohse, Konrad","first_name":"Konrad","last_name":"Lohse"},{"full_name":"Chmelik, Martin","first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Martin","full_name":"Martin, Simon","first_name":"Simon"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"publication":"Genetics","_id":"1518","title":"Efficient strategies for calculating blockwise likelihoods under the coalescent","status":"public","file":[{"date_created":"2018-12-12T10:16:51Z","date_updated":"2020-07-14T12:45:00Z","checksum":"41c9b5d72e7fe4624dd22dfe622337d5","file_size":957466,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf","file_id":"5241","creator":"system"}],"scopus_import":"1","article_type":"original","has_accepted_license":"1","acknowledgement":"We thank Lynsey Bunnefeld for discussions throughout the project and Joshua Schraiber and one anonymous reviewer\r\nfor constructive comments on an earlier version of this manuscript. This work was supported by funding from the\r\nUnited Kingdom Natural Environment Research Council (to K.L.) (NE/I020288/1) and a grant from the European\r\nResearch Council (250152) (to N.H.B.).","file_date_updated":"2020-07-14T12:45:00Z","type":"journal_article","pmid":1,"doi":"10.1534/genetics.115.183814","oa":1,"quality_controlled":"1","day":"01","intvolume":"       202","date_published":"2016-02-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"short":"K. Lohse, M. Chmelik, S. Martin, N.H. Barton, Genetics 202 (2016) 775–786.","ama":"Lohse K, Chmelik M, Martin S, Barton NH. Efficient strategies for calculating blockwise likelihoods under the coalescent. <i>Genetics</i>. 2016;202(2):775-786. doi:<a href=\"https://doi.org/10.1534/genetics.115.183814\">10.1534/genetics.115.183814</a>","chicago":"Lohse, Konrad, Martin Chmelik, Simon Martin, and Nicholas H Barton. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.115.183814\">https://doi.org/10.1534/genetics.115.183814</a>.","apa":"Lohse, K., Chmelik, M., Martin, S., &#38; Barton, N. H. (2016). Efficient strategies for calculating blockwise likelihoods under the coalescent. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.115.183814\">https://doi.org/10.1534/genetics.115.183814</a>","ieee":"K. Lohse, M. Chmelik, S. Martin, and N. H. Barton, “Efficient strategies for calculating blockwise likelihoods under the coalescent,” <i>Genetics</i>, vol. 202, no. 2. Genetics Society of America, pp. 775–786, 2016.","ista":"Lohse K, Chmelik M, Martin S, Barton NH. 2016. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 202(2), 775–786.","mla":"Lohse, Konrad, et al. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” <i>Genetics</i>, vol. 202, no. 2, Genetics Society of America, 2016, pp. 775–86, doi:<a href=\"https://doi.org/10.1534/genetics.115.183814\">10.1534/genetics.115.183814</a>."},"department":[{"_id":"KrCh"},{"_id":"NiBa"}],"publisher":"Genetics Society of America","issue":"2","pubrep_id":"561","article_processing_charge":"No"},{"file_date_updated":"2020-07-14T12:45:07Z","type":"journal_article","doi":"10.1016/j.tpb.2015.10.008","oa":1,"license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","corr_author":"1","citation":{"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.","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>","ieee":"J. Kelleher, A. Etheridge, A. Véber, and N. H. Barton, “Spread of pedigree versus genetic ancestry in spatially distributed populations,” <i>Theoretical Population Biology</i>, vol. 108. Academic Press, pp. 1–12, 2016.","chicago":"Kelleher, Jerome, Alison Etheridge, Amandine Véber, and Nicholas H Barton. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” <i>Theoretical Population Biology</i>. Academic Press, 2016. <a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">https://doi.org/10.1016/j.tpb.2015.10.008</a>.","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>","short":"J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population Biology 108 (2016) 1–12."},"department":[{"_id":"NiBa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Academic Press","pubrep_id":"465","article_processing_charge":"No","quality_controlled":"1","day":"01","intvolume":"       108","date_published":"2016-04-01T00:00:00Z","publist_id":"5524","page":"1 - 12","abstract":[{"text":"Ancestral processes are fundamental to modern population genetics and spatial structure has been the subject of intense interest for many years. Despite this interest, almost nothing is known about the distribution of the locations of pedigree or genetic ancestors. Using both spatially continuous and stepping-stone models, we show that the distribution of pedigree ancestors approaches a travelling wave, for which we develop two alternative approximations. The speed and width of the wave are sensitive to the local details of the model. After a short time, genetic ancestors spread far more slowly than pedigree ancestors, ultimately diffusing out with radius ## rather than spreading at constant speed. In contrast to the wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the local details of the models.","lang":"eng"}],"ec_funded":1,"isi":1,"project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"volume":108,"year":"2016","date_created":"2018-12-11T11:53:08Z","external_id":{"isi":["000372560000001"]},"oa_version":"Published Version","publication":"Theoretical Population Biology","language":[{"iso":"eng"}],"_id":"1631","title":"Spread of pedigree versus genetic ancestry in spatially distributed populations","file":[{"checksum":"6a65ba187994d4ad86c1c509e0ff482a","file_size":1684043,"date_created":"2018-12-12T10:11:12Z","date_updated":"2020-07-14T12:45:07Z","creator":"system","file_id":"4865","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf"}],"scopus_import":"1","status":"public","date_updated":"2025-09-18T10:51:58Z","publication_status":"published","ddc":["576"],"month":"04","author":[{"last_name":"Kelleher","full_name":"Kelleher, Jerome","first_name":"Jerome"},{"first_name":"Alison","full_name":"Etheridge, Alison","last_name":"Etheridge"},{"last_name":"Véber","full_name":"Véber, Amandine","first_name":"Amandine"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}]},{"publisher":"Dryad","_id":"9710","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Barton, Nicholas H. <i>Data from: How Does Epistasis Influence the Response to Selection?</i> Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>.","ista":"Barton NH. 2016. Data from: How does epistasis influence the response to selection?, Dryad, <a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>.","ieee":"N. H. Barton, “Data from: How does epistasis influence the response to selection?” Dryad, 2016.","chicago":"Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response to Selection?” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>.","apa":"Barton, N. H. (2016). Data from: How does epistasis influence the response to selection? Dryad. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>","ama":"Barton NH. Data from: How does epistasis influence the response to selection? 2016. doi:<a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>","short":"N.H. Barton, (2016)."},"department":[{"_id":"NiBa"}],"status":"public","article_processing_charge":"No","title":"Data from: How does epistasis influence the response to selection?","date_updated":"2025-04-15T07:11:02Z","day":"23","month":"09","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"date_published":"2016-09-23T00:00:00Z","type":"research_data_reference","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.s5s7r"}],"abstract":[{"lang":"eng","text":"Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects."}],"doi":"10.5061/dryad.s5s7r","oa":1,"year":"2016","related_material":{"record":[{"status":"public","id":"1199","relation":"used_in_publication"}]},"date_created":"2021-07-23T11:45:47Z","oa_version":"Published Version"},{"file":[{"access_level":"open_access","content_type":"application/zip","relation":"main_file","file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip","creator":"system","file_id":"5594","date_created":"2018-12-12T13:02:27Z","date_updated":"2020-07-14T12:47:00Z","file_size":4468543,"checksum":"950f85b80427d357bfeff09608ba02e9"}],"status":"public","article_processing_charge":"No","title":"Flower colour data and phylogeny (NEXUS) files","datarep_id":"34","publisher":"Institute of Science and Technology Austria","citation":{"short":"T. Ellis, D. Field, (2016).","ama":"Ellis T, Field D. Flower colour data and phylogeny (NEXUS) files. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>","ista":"Ellis T, Field D. 2016. Flower colour data and phylogeny (NEXUS) files, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>.","chicago":"Ellis, Thomas, and David Field. “Flower Colour Data and Phylogeny (NEXUS) Files.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:34\">https://doi.org/10.15479/AT:ISTA:34</a>.","apa":"Ellis, T., &#38; Field, D. (2016). Flower colour data and phylogeny (NEXUS) files. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:34\">https://doi.org/10.15479/AT:ISTA:34</a>","ieee":"T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute of Science and Technology Austria, 2016.","mla":"Ellis, Thomas, and David Field. <i>Flower Colour Data and Phylogeny (NEXUS) Files</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>."},"_id":"5550","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"date_published":"2016-02-19T00:00:00Z","month":"02","author":[{"last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","first_name":"Thomas"},{"orcid":"0000-0002-4014-8478","first_name":"David","full_name":"Field, David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"}],"ddc":["576"],"day":"19","date_updated":"2025-09-22T07:32:43Z","oa":1,"year":"2016","doi":"10.15479/AT:ISTA:34","abstract":[{"text":"We collected flower colour information on species in the tribe Antirrhineae from taxonomic literature. We also retreived molecular data from GenBank for as many of these species as possible to estimate phylogenetic relationships among these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny.\r\n\r\nFor full details of the methods see:\r\nEllis TJ and Field DL \"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)","lang":"eng"}],"type":"research_data","file_date_updated":"2020-07-14T12:47:00Z","publist_id":"5828","oa_version":"Published Version","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"research_paper","id":"1382"}]},"date_created":"2018-12-12T12:31:29Z","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"license":"https://creativecommons.org/publicdomain/zero/1.0/"},{"month":"12","author":[{"last_name":"Roux","full_name":"Roux, Camille","first_name":"Camille"},{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"last_name":"Romiguier","full_name":"Romiguier, Jonathan","first_name":"Jonathan"},{"last_name":"Anciaux","full_name":"Anciaux, Youann","first_name":"Youann"},{"last_name":"Galtier","first_name":"Nicolas","full_name":"Galtier, Nicolas"},{"last_name":"Bierne","full_name":"Bierne, Nicolas","first_name":"Nicolas"}],"date_updated":"2025-09-22T09:55:08Z","day":"27","article_processing_charge":"No","status":"public","title":"Simulation study to test the robustness of ABC in face of recent times of divergence","publisher":"Public Library of Science","_id":"9862","citation":{"short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation study to test the robustness of ABC in face of recent times of divergence. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Simulation study to test the robustness of ABC in face of recent times of divergence. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Simulation study to test the robustness of ABC in face of recent times of divergence.” Public Library of Science, 2016.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation study to test the robustness of ABC in face of recent times of divergence, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>.","mla":"Roux, Camille, et al. <i>Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"oa_version":"Published Version","date_created":"2021-08-10T08:20:17Z","related_material":{"record":[{"status":"public","id":"1158","relation":"used_in_publication"}]},"doi":"10.1371/journal.pbio.2000234.s016","year":"2016","type":"research_data_reference"},{"month":"12","author":[{"first_name":"Camille","full_name":"Roux, Camille","last_name":"Roux"},{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"first_name":"Jonathan","full_name":"Romiguier, Jonathan","last_name":"Romiguier"},{"first_name":"Youann","full_name":"Anciaux, Youann","last_name":"Anciaux"},{"last_name":"Galtier","full_name":"Galtier, Nicolas","first_name":"Nicolas"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}],"day":"27","date_updated":"2025-09-22T09:55:09Z","title":"Accessions of surveyed individuals, geographic locations and summary statistics","status":"public","article_processing_charge":"No","_id":"9863","citation":{"ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions of surveyed individuals, geographic locations and summary statistics. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","mla":"Roux, Camille, et al. <i>Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions of surveyed individuals, geographic locations and summary statistics, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Accessions of surveyed individuals, geographic locations and summary statistics. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Accessions of surveyed individuals, geographic locations and summary statistics.” Public Library of Science, 2016.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>."},"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"1158","relation":"used_in_publication"}]},"date_created":"2021-08-10T08:22:52Z","year":"2016","doi":"10.1371/journal.pbio.2000234.s017","type":"research_data_reference"},{"related_material":{"record":[{"relation":"used_in_publication","id":"1077","status":"public"}]},"date_created":"2021-08-10T08:29:47Z","oa_version":"Published Version","type":"research_data_reference","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.4315652.v1"}],"abstract":[{"text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.","lang":"eng"}],"doi":"10.6084/m9.figshare.4315652.v1","year":"2016","oa":1,"date_updated":"2025-07-10T11:49:59Z","day":"14","author":[{"orcid":"0000-0002-5837-2793","first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"},{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","last_name":"de Vladar","full_name":"de Vladar, Harold","first_name":"Harold","orcid":"0000-0002-5985-7653"},{"last_name":"Włodarski","first_name":"Tomasz","full_name":"Włodarski, Tomasz"},{"first_name":"Jonathan P","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback"}],"month":"12","date_published":"2016-12-14T00:00:00Z","publisher":"The Royal Society","_id":"9864","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Fernandes Redondo, Rodrigo A., et al. <i>Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family</i>. The Royal Society, 2016, doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family, The Royal Society, <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2016). Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. The Royal Society. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>.","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.” The Royal Society, 2016.","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016)."},"status":"public","article_processing_charge":"No","title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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>","short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).","mla":"Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>, vol. 7, 12307, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>.","apa":"Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., &#38; Tkačik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>","chicago":"Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>.","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.","ista":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307."},"department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"Nature Publishing Group","article_processing_charge":"No","pubrep_id":"627","quality_controlled":"1","day":"04","intvolume":"         7","date_published":"2016-08-04T00:00:00Z","file_date_updated":"2020-07-14T12:44:46Z","type":"journal_article","doi":"10.1038/ncomms12307","oa":1,"article_number":"12307","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","corr_author":"1","publication":"Nature Communications","language":[{"iso":"eng"}],"_id":"1358","title":"Intrinsic limits to gene regulation by global crosstalk","status":"public","file":[{"file_name":"IST-2016-627-v1+1_ncomms12307.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"4919","creator":"system","date_updated":"2020-07-14T12:44:46Z","date_created":"2018-12-12T10:12:01Z","checksum":"fe3f3a1526d180b29fe691ab11435b78","file_size":861805},{"date_created":"2018-12-12T10:12:02Z","date_updated":"2020-07-14T12:44:46Z","file_size":1084703,"checksum":"164864a1a675f3ad80e9917c27aba07f","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","creator":"system","file_id":"4920"}],"scopus_import":"1","date_updated":"2026-04-08T13:54:24Z","publication_status":"published","ddc":["576"],"author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","last_name":"Friedlander","full_name":"Friedlander, Tamar","first_name":"Tamar"},{"full_name":"Prizak, Roshan","first_name":"Roshan","last_name":"Prizak","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6220-2052","first_name":"Calin C","full_name":"Guet, Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper"}],"month":"08","publist_id":"5887","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."}],"ec_funded":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"volume":7,"isi":1,"year":"2016","external_id":{"isi":["000380858400001"]},"related_material":{"record":[{"id":"6071","relation":"dissertation_contains","status":"public"}]},"date_created":"2018-12-11T11:51:34Z","oa_version":"Published Version"},{"day":"18","date_published":"2016-02-18T00:00:00Z","OA_place":"publisher","alternative_title":["ISTA Thesis"],"department":[{"_id":"NiBa"},{"_id":"GradSch"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"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>.","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.","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>.","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>","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>","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."},"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"pubrep_id":"526","has_accepted_license":"1","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. ","corr_author":"1","file_date_updated":"2025-07-03T06:24:39Z","type":"dissertation","oa":1,"doi":"10.15479/AT:ISTA:TH_526 ","ddc":["576"],"date_updated":"2026-04-09T10:52:07Z","publication_status":"published","author":[{"full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","first_name":"Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"}],"month":"02","_id":"1398","language":[{"iso":"eng"}],"title":"The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone","status":"public","file":[{"creator":"dernst","file_id":"19957","file_name":"2016_Thesis_Ellis_noSignatures.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"f0f7c260e19ec1416824b165afe2d5fd","file_size":7590862,"date_updated":"2025-07-03T06:24:17Z","date_created":"2025-07-03T06:24:17Z"},{"checksum":"a89b17ff27cf92c9a15f6b3d46bd7e53","file_size":11928241,"date_created":"2018-12-12T10:14:51Z","date_updated":"2025-07-03T06:24:39Z","file_id":"5106","creator":"system","relation":"main_file","access_level":"closed","content_type":"application/pdf","file_name":"IST-2016-526-v1+1_Ellis_signed_thesis.pdf"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"5553"},{"relation":"dissertation_contains","id":"5551","status":"public"},{"status":"public","id":"5552","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:51:47Z","oa_version":"Published Version","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"}],"publist_id":"5809","page":"130","year":"2016"},{"contributor":[{"contributor_type":"project_manager","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"],"related_material":{"record":[{"relation":"part_of_dissertation","id":"1398","status":"public"}]},"has_accepted_license":"1","date_created":"2018-12-12T12:31:30Z","doi":"10.15479/AT:ISTA:37","year":"2016","oa":1,"type":"research_data","file_date_updated":"2020-07-14T12:47:01Z","abstract":[{"lang":"eng","text":"Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset.\r\n\r\nOther data were retreived from an online database of this population at www.antspec.org."}],"month":"02","author":[{"full_name":"Field, David","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field"},{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","first_name":"Thomas","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"}],"date_published":"2016-02-19T00:00:00Z","date_updated":"2026-04-09T10:52:06Z","ddc":["576"],"day":"19","article_processing_charge":"No","file":[{"file_size":132808,"checksum":"4ae751b1fa4897fa216241f975a57313","date_updated":"2020-07-14T12:47:01Z","date_created":"2018-12-12T13:03:02Z","creator":"system","file_id":"5620","file_name":"IST-2016-37-v1+1_paternity_archive.zip","content_type":"application/zip","access_level":"open_access","relation":"main_file"}],"status":"public","title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","datarep_id":"37","publisher":"Institute of Science and Technology Austria","_id":"5553","citation":{"short":"D. Field, T. Ellis, (2016).","ama":"Field D, Ellis T. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>","ista":"Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>.","chicago":"Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:37\">https://doi.org/10.15479/AT:ISTA:37</a>.","ieee":"D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012.” Institute of Science and Technology Austria, 2016.","apa":"Field, D., &#38; Ellis, T. (2016). Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:37\">https://doi.org/10.15479/AT:ISTA:37</a>","mla":"Field, David, and Thomas Ellis. <i>Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}]},{"doi":"10.15479/AT:ISTA:35","oa":1,"year":"2016","type":"research_data","file_date_updated":"2020-07-14T12:47:01Z","abstract":[{"text":"Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid.","lang":"eng"}],"oa_version":"Published Version","contributor":[{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"has_accepted_license":"1","related_material":{"record":[{"id":"1398","relation":"part_of_dissertation","status":"public"}]},"date_created":"2018-12-12T12:31:29Z","status":"public","file":[{"access_level":"open_access","content_type":"application/zip","relation":"main_file","file_name":"IST-2016-35-v1+1_array_data.zip","creator":"system","file_id":"5640","date_created":"2018-12-12T13:05:12Z","date_updated":"2020-07-14T12:47:01Z","file_size":32775,"checksum":"aa3eb85d52b110cd192aa23147c4d4f3"}],"article_processing_charge":"No","title":"Data on pollinator observations and offpsring phenotypes","datarep_id":"35","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"_id":"5551","citation":{"mla":"Ellis, Thomas. <i>Data on Pollinator Observations and Offpsring Phenotypes</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>.","chicago":"Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:35\">https://doi.org/10.15479/AT:ISTA:35</a>.","ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016.","apa":"Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:35\">https://doi.org/10.15479/AT:ISTA:35</a>","ista":"Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>.","ama":"Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>","short":"T. Ellis, (2016)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Ellis, Thomas","first_name":"Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis"}],"month":"02","date_published":"2016-02-19T00:00:00Z","date_updated":"2026-04-09T10:52:07Z","day":"19"},{"contributor":[{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"oa_version":"Published Version","related_material":{"record":[{"id":"1398","relation":"part_of_dissertation","status":"public"}]},"date_created":"2018-12-12T12:31:30Z","has_accepted_license":"1","oa":1,"year":"2016","doi":"10.15479/AT:ISTA:36","abstract":[{"lang":"eng","text":"Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016).\r\n\r\nSnapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012.\r\n\r\nAlso included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation."}],"type":"research_data","file_date_updated":"2020-07-14T12:47:01Z","date_published":"2016-02-19T00:00:00Z","author":[{"full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","first_name":"Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"}],"month":"02","day":"19","date_updated":"2026-04-09T10:52:07Z","article_processing_charge":"No","status":"public","file":[{"file_name":"IST-2016-36-v1+1_tag_assay_archive.zip","relation":"main_file","access_level":"open_access","content_type":"application/zip","file_id":"5625","creator":"system","date_updated":"2020-07-14T12:47:01Z","date_created":"2018-12-12T13:03:07Z","file_size":44905,"checksum":"cbc61b523d4d475a04a737d50dc470ef"}],"title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.","datarep_id":"36","publisher":"Institute of Science and Technology Austria","_id":"5552","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>","short":"T. Ellis, (2016).","mla":"Ellis, Thomas. <i>Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.</i> Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>.","ista":"Ellis T. 2016. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data., Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>.","apa":"Ellis, T. (2016). Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:36\">https://doi.org/10.15479/AT:ISTA:36</a>","chicago":"Ellis, Thomas. “Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:36\">https://doi.org/10.15479/AT:ISTA:36</a>.","ieee":"T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.” Institute of Science and Technology Austria, 2016."},"department":[{"_id":"NiBa"}]},{"year":"2016","abstract":[{"lang":"eng","text":"Evolution of gene regulation is important for phenotypic evolution and diversity. Sequence-specific binding of regulatory proteins is one of the key regulatory mechanisms determining gene expression. Although there has been intense interest in evolution of regulatory binding sites in the last decades, a theoretical understanding is far from being complete. In this thesis, I aim at a better understanding of the evolution of transcriptional regulatory binding sequences by using biophysical and population genetic models.\r\nIn the first part of the thesis, I discuss how to formulate the evolutionary dynamics of binding se- quences in a single isolated binding site and in promoter/enhancer regions. I develop a theoretical framework bridging between a thermodynamical model for transcription and a mutation-selection-drift model for monomorphic populations. I mainly address the typical evolutionary rates, and how they de- pend on biophysical parameters (e.g. binding length and specificity) and population genetic parameters (e.g. population size and selection strength).\r\nIn the second part of the thesis, I analyse empirical data for a better evolutionary and biophysical understanding of sequence-specific binding of bacterial RNA polymerase. First, I infer selection on regulatory and non-regulatory binding sites of RNA polymerase in the E. coli K12 genome. Second, I infer the chemical potential of RNA polymerase, an important but unknown physical parameter defining the threshold energy for strong binding. Furthermore, I try to understand the relation between the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial isolates by constructing a simple but biophysically motivated gene expression model. Lastly, I lay out a statistical framework to predict adaptive point mutations in de novo promoter evolution in a selection experiment."}],"page":"89","publist_id":"6229","oa_version":"Published Version","date_created":"2018-12-11T11:50:19Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"5554"},{"status":"public","id":"1666","relation":"part_of_dissertation"}]},"file":[{"content_type":"application/pdf","access_level":"closed","relation":"main_file","file_name":"Tugrul_thesis_w_signature_page.pdf","creator":"dernst","file_id":"6810","date_created":"2019-08-13T08:53:52Z","date_updated":"2019-08-13T08:53:52Z","file_size":3695257,"checksum":"66cb61a59943e4fb7447c6a86be5ef51"},{"date_updated":"2021-02-22T11:45:20Z","date_created":"2021-02-22T11:45:20Z","success":1,"file_size":3880811,"checksum":"293e388d70563760f6b24c3e66283dda","file_name":"2016_Tugrul_Thesis.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","creator":"dernst","file_id":"9182"}],"status":"public","title":"Evolution of transcriptional regulatory sequences","_id":"1131","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-8523-0758","first_name":"Murat","full_name":"Tugrul, Murat","last_name":"Tugrul","id":"37C323C6-F248-11E8-B48F-1D18A9856A87"}],"month":"07","ddc":["576"],"publication_status":"published","date_updated":"2026-04-09T10:52:40Z","oa":1,"type":"dissertation","file_date_updated":"2021-02-22T11:45:20Z","corr_author":"1","acknowledgement":"This PhD thesis may not have been completed without the help and care I received from some peo- ple during my PhD life. I am especially grateful to Tiago Paixao, Gasper Tkacik, Nick Barton, not only for their scientific advices but also for their patience and support. I thank Calin Guet and Jonathan Bollback for allowing me to “play around” in their labs and get some experience on experimental evolution. I thank Magdalena Steinrueck and Fabienne Jesse for collaborating and sharing their experimental data with me. I thank Johannes Jaeger for reviewing my thesis. I thank all members of Barton group (aka bartonians) for their feedback, and all workers of IST Austria for making the best working conditions. Lastly, I thank two special women, Nejla Sag ̆lam and Setenay Dog ̆an, for their continuous support and encouragement. I truly had a great chance of having right people around me.","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"citation":{"ama":"Tugrul M. Evolution of transcriptional regulatory sequences. 2016.","short":"M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of Science and Technology Austria, 2016.","mla":"Tugrul, Murat. <i>Evolution of Transcriptional Regulatory Sequences</i>. Institute of Science and Technology Austria, 2016.","ista":"Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria.","chicago":"Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute of Science and Technology Austria, 2016.","apa":"Tugrul, M. (2016). <i>Evolution of transcriptional regulatory sequences</i>. Institute of Science and Technology Austria.","ieee":"M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute of Science and Technology Austria, 2016."},"department":[{"_id":"NiBa"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","date_published":"2016-07-01T00:00:00Z","OA_place":"publisher","day":"01"}]