[{"date_published":"2016-06-01T00:00:00Z","article_processing_charge":"No","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.","isi":1,"title":"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae","publist_id":"5828","volume":117,"month":"06","date_updated":"2025-09-22T07:32:44Z","quality_controlled":"1","external_id":{"isi":["000379733800004"]},"publisher":"Oxford University Press","citation":{"short":"T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140.","ista":"Ellis T, Field D. 2016. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. 117(7), 1133–1140.","mla":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” <i>Annals of Botany</i>, vol. 117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:<a href=\"https://doi.org/10.1093/aob/mcw043\">10.1093/aob/mcw043</a>.","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>","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>","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."},"scopus_import":"1","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."}],"oa_version":"None","status":"public","type":"journal_article","related_material":{"record":[{"id":"5550","relation":"popular_science","status":"public"}]},"date_created":"2018-12-11T11:51:42Z","year":"2016","intvolume":"       117","publication_status":"published","doi":"10.1093/aob/mcw043","language":[{"iso":"eng"}],"author":[{"first_name":"Thomas","last_name":"Ellis","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","full_name":"Ellis, Thomas"},{"full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field"}],"page":"1133 - 1140","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1382","issue":"7","department":[{"_id":"NiBa"}],"publication":"Annals of Botany","corr_author":"1","day":"01"},{"date_created":"2018-12-11T11:51:51Z","year":"2016","publication_status":"published","oa":1,"doi":"10.1111/mec.13685","file":[{"file_size":226137,"content_type":"application/pdf","date_updated":"2020-07-14T12:44:53Z","relation":"main_file","date_created":"2018-12-12T10:10:12Z","file_id":"4797","creator":"system","checksum":"ede7d0b8a471754f71f17e2b20f3135b","file_name":"IST-2017-772-v1+1_AbbotEtAl2016-3.pdf","access_level":"open_access"}],"intvolume":"        25","file_date_updated":"2020-07-14T12:44:53Z","pubrep_id":"772","ddc":["576"],"language":[{"iso":"eng"}],"author":[{"last_name":"Abbott","first_name":"Richard","full_name":"Abbott, Richard"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Jeffrey","last_name":"Good","full_name":"Good, Jeffrey"}],"page":"2325 - 2332","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1409","issue":"11","department":[{"_id":"NiBa"}],"publication":"Molecular Ecology","day":"08","title":"Genomics of hybridization and its evolutionary consequences","article_processing_charge":"No","date_published":"2016-06-08T00:00:00Z","isi":1,"volume":25,"publist_id":"5798","month":"06","external_id":{"isi":["000378941100001"]},"quality_controlled":"1","date_updated":"2025-09-18T14:30:06Z","publisher":"Wiley-Blackwell","scopus_import":"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.","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>","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>","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>.","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.","short":"R. Abbott, N.H. Barton, J. Good, Molecular Ecology 25 (2016) 2325–2332."},"oa_version":"Submitted Version","type":"journal_article","status":"public"},{"publist_id":"5787","volume":202,"isi":1,"arxiv":1,"date_published":"2016-04-06T00:00:00Z","article_processing_charge":"No","title":"A general approximation for the dynamics of quantitative traits","date_updated":"2025-09-18T14:22:05Z","quality_controlled":"1","external_id":{"arxiv":["1510.08344"],"isi":["000373959100022"]},"month":"04","oa_version":"Preprint","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"}],"citation":{"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>","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>.","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.","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>"},"scopus_import":"1","main_file_link":[{"url":"http://arxiv.org/abs/1510.08344","open_access":"1"}],"publisher":"Genetics Society of America","status":"public","type":"journal_article","year":"2016","date_created":"2018-12-11T11:51:55Z","author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","full_name":"Bod'ová, Katarína","first_name":"Katarína","last_name":"Bod'ová","orcid":"0000-0002-7214-0171"},{"last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"intvolume":"       202","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"name":"Information processing and computation in fish groups","grant_number":"RGP0065/2012","_id":"255008E4-B435-11E9-9278-68D0E5697425"}],"doi":"10.1534/genetics.115.184127","publication_status":"published","oa":1,"issue":"4","ec_funded":1,"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1420","page":"1523 - 1548","day":"06","publication":"Genetics","corr_author":"1"},{"author":[{"full_name":"Lohse, Konrad","first_name":"Konrad","last_name":"Lohse"},{"last_name":"Chmelik","first_name":"Martin","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Simon","last_name":"Martin","full_name":"Martin, Simon"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"language":[{"iso":"eng"}],"ddc":["570"],"pubrep_id":"561","file_date_updated":"2020-07-14T12:45:00Z","intvolume":"       202","file":[{"date_updated":"2020-07-14T12:45:00Z","relation":"main_file","content_type":"application/pdf","file_size":957466,"file_id":"5241","date_created":"2018-12-12T10:16:51Z","file_name":"IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf","access_level":"open_access","creator":"system","checksum":"41c9b5d72e7fe4624dd22dfe622337d5"}],"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"doi":"10.1534/genetics.115.183814","oa":1,"publication_status":"published","year":"2016","article_type":"original","date_created":"2018-12-11T11:52:29Z","day":"01","publication":"Genetics","pmid":1,"department":[{"_id":"KrCh"},{"_id":"NiBa"}],"ec_funded":1,"issue":"2","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1518","has_accepted_license":"1","page":"775 - 786","date_updated":"2025-09-18T11:09:34Z","quality_controlled":"1","external_id":{"isi":["000371304600032"],"pmid":["26715666"]},"month":"02","publist_id":"5658","volume":202,"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.).","isi":1,"article_processing_charge":"No","date_published":"2016-02-01T00:00:00Z","title":"Efficient strategies for calculating blockwise likelihoods under the coalescent","status":"public","type":"journal_article","oa_version":"Preprint","scopus_import":"1","citation":{"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.","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>","ista":"Lohse K, Chmelik M, Martin S, Barton NH. 2016. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 202(2), 775–786.","short":"K. Lohse, M. Chmelik, S. Martin, N.H. Barton, Genetics 202 (2016) 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>."},"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."}],"publisher":"Genetics Society of America"},{"file_date_updated":"2020-07-14T12:45:07Z","pubrep_id":"465","ddc":["576"],"language":[{"iso":"eng"}],"author":[{"full_name":"Kelleher, Jerome","last_name":"Kelleher","first_name":"Jerome"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"},{"full_name":"Véber, Amandine","last_name":"Véber","first_name":"Amandine"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"oa":1,"publication_status":"published","doi":"10.1016/j.tpb.2015.10.008","file":[{"checksum":"6a65ba187994d4ad86c1c509e0ff482a","creator":"system","file_name":"IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf","access_level":"open_access","date_created":"2018-12-12T10:11:12Z","file_id":"4865","file_size":1684043,"date_updated":"2020-07-14T12:45:07Z","relation":"main_file","content_type":"application/pdf"}],"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"intvolume":"       108","year":"2016","date_created":"2018-12-11T11:53:08Z","day":"01","corr_author":"1","publication":"Theoretical Population Biology","_id":"1631","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"department":[{"_id":"NiBa"}],"page":"1 - 12","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","external_id":{"isi":["000372560000001"]},"quality_controlled":"1","date_updated":"2025-09-18T10:51:58Z","month":"04","volume":108,"publist_id":"5524","title":"Spread of pedigree versus genetic ancestry in spatially distributed populations","date_published":"2016-04-01T00:00:00Z","article_processing_charge":"No","isi":1,"type":"journal_article","status":"public","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"}],"citation":{"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.","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.","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>.","chicago":"Kelleher, Jerome, Alison Etheridge, Amandine Véber, and Nicholas H Barton. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” <i>Theoretical Population Biology</i>. Academic Press, 2016. <a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">https://doi.org/10.1016/j.tpb.2015.10.008</a>.","apa":"Kelleher, J., Etheridge, A., Véber, A., &#38; Barton, N. H. (2016). Spread of pedigree versus genetic ancestry in spatially distributed populations. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">https://doi.org/10.1016/j.tpb.2015.10.008</a>"},"scopus_import":"1","oa_version":"Published Version","publisher":"Academic Press"},{"department":[{"_id":"NiBa"}],"_id":"5550","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","abstract":[{"lang":"eng","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)"}],"citation":{"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>","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>.","mla":"Ellis, Thomas, and David Field. <i>Flower Colour Data and Phylogeny (NEXUS) Files</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>.","short":"T. Ellis, D. Field, (2016).","ista":"Ellis T, Field D. 2016. Flower colour data and phylogeny (NEXUS) files, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>.","ieee":"T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute of Science and Technology Austria, 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>"},"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"related_material":{"record":[{"status":"public","relation":"research_paper","id":"1382"}]},"day":"19","type":"research_data","status":"public","year":"2016","publist_id":"5828","datarep_id":"34","date_created":"2018-12-12T12:31:29Z","title":"Flower colour data and phylogeny (NEXUS) files","date_published":"2016-02-19T00:00:00Z","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:00Z","author":[{"orcid":"0000-0002-8511-0254","first_name":"Thomas","last_name":"Ellis","full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478"}],"date_updated":"2025-09-22T07:32:43Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","ddc":["576"],"file":[{"file_size":4468543,"relation":"main_file","content_type":"application/zip","date_updated":"2020-07-14T12:47:00Z","date_created":"2018-12-12T13:02:27Z","file_id":"5594","checksum":"950f85b80427d357bfeff09608ba02e9","creator":"system","file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip","access_level":"open_access"}],"month":"02","doi":"10.15479/AT:ISTA:34","oa":1},{"status":"public","type":"research_data_reference","day":"23","related_material":{"record":[{"id":"1199","relation":"used_in_publication","status":"public"}]},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.s5s7r","open_access":"1"}],"publisher":"Dryad","citation":{"short":"N.H. Barton, (2016).","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>.","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>.","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>","ieee":"N. H. Barton, “Data from: How does epistasis influence the response to selection?” Dryad, 2016."},"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","_id":"9710","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"NiBa"}],"oa":1,"doi":"10.5061/dryad.s5s7r","month":"09","date_updated":"2025-04-15T07:11:02Z","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"date_published":"2016-09-23T00:00:00Z","article_processing_charge":"No","title":"Data from: How does epistasis influence the response to selection?","date_created":"2021-07-23T11:45:47Z","year":"2016"},{"related_material":{"record":[{"id":"1158","relation":"used_in_publication","status":"public"}]},"day":"27","type":"research_data_reference","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9862","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"citation":{"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>","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>.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","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>.","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.","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>"},"oa_version":"Published Version","publisher":"Public Library of Science","author":[{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"},{"full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle"},{"full_name":"Romiguier, Jonathan","first_name":"Jonathan","last_name":"Romiguier"},{"first_name":"Youann","last_name":"Anciaux","full_name":"Anciaux, Youann"},{"last_name":"Galtier","first_name":"Nicolas","full_name":"Galtier, Nicolas"},{"full_name":"Bierne, Nicolas","first_name":"Nicolas","last_name":"Bierne"}],"date_updated":"2025-09-22T09:55:08Z","doi":"10.1371/journal.pbio.2000234.s016","month":"12","year":"2016","title":"Simulation study to test the robustness of ABC in face of recent times of divergence","date_created":"2021-08-10T08:20:17Z","article_processing_charge":"No"},{"title":"Accessions of surveyed individuals, geographic locations and summary statistics","date_created":"2021-08-10T08:22:52Z","article_processing_charge":"No","year":"2016","doi":"10.1371/journal.pbio.2000234.s017","month":"12","date_updated":"2025-09-22T09:55:09Z","author":[{"full_name":"Roux, Camille","first_name":"Camille","last_name":"Roux"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075"},{"first_name":"Jonathan","last_name":"Romiguier","full_name":"Romiguier, Jonathan"},{"full_name":"Anciaux, Youann","first_name":"Youann","last_name":"Anciaux"},{"last_name":"Galtier","first_name":"Nicolas","full_name":"Galtier, Nicolas"},{"first_name":"Nicolas","last_name":"Bierne","full_name":"Bierne, Nicolas"}],"publisher":"Public Library of Science","_id":"9863","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"citation":{"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>.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","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>","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>.","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>","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."},"oa_version":"Published Version","type":"research_data_reference","status":"public","related_material":{"record":[{"relation":"used_in_publication","id":"1158","status":"public"}]},"day":"27"},{"status":"public","type":"research_data_reference","day":"14","related_material":{"record":[{"id":"1077","relation":"used_in_publication","status":"public"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.4315652.v1"}],"publisher":"The Royal Society","citation":{"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>","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>.","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>","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).","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>.","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>."},"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"}],"oa_version":"Published Version","_id":"9864","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"oa":1,"doi":"10.6084/m9.figshare.4315652.v1","month":"12","author":[{"full_name":"Fernandes Redondo, Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5837-2793","last_name":"Fernandes Redondo","first_name":"Rodrigo A"},{"orcid":"0000-0002-5985-7653","first_name":"Harold","last_name":"de Vladar","full_name":"de Vladar, Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tomasz","last_name":"Włodarski","full_name":"Włodarski, Tomasz"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612"}],"date_updated":"2025-07-10T11:49:59Z","article_processing_charge":"No","date_published":"2016-12-14T00:00:00Z","title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","date_created":"2021-08-10T08:29:47Z","year":"2016"},{"date_updated":"2026-07-29T11:27:43Z","month":"07","publist_id":"6235","article_processing_charge":"No","date_published":"2016-07-01T00:00:00Z","title":"Evolutionary proccesses in variable emvironments","related_material":{"record":[{"id":"2023","relation":"part_of_dissertation","status":"public"}]},"status":"public","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"doi_confirm":"1","abstract":[{"text":"Natural environments are never constant but subject to spatial and temporal change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial to understand the\r\nimpact of environmental variation on evolutionary processes. In this thesis, I present\r\nthree topics that share the common theme of environmental variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst, I show how a temporally fluctuating environment gives rise to second-order\r\nselection on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations are adapted to their environment, mutation rates are minimized. I argue\r\nthat a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly subjected to diverse environmental challenges, and I outline implications of\r\nthe presented results to antibiotic treatment strategies.\r\nSecond, I discuss my work on the evolution of dispersal. Besides reproducing\r\nknown results about the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes in dispersal type frequencies as a source for selection for increased\r\npropensities to disperse. This concept contains effects of relatedness that are known\r\nto promote dispersal, and I explain how it identifies other forces selecting for dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances of phenotypic traits under multivariate stabilizing\r\nselection. For the case of constant environments, I generalize known formulae of\r\nequilibrium variances to multiple traits and discuss how the genetic variance of a focal\r\ntrait is influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary work aiming at including environmental fluctuations in the form of moving\r\ntrait optima into the model.","lang":"eng"}],"citation":{"ama":"Novak S. Evolutionary proccesses in variable emvironments. 2016.","ieee":"S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of Science and Technology Austria, 2016.","mla":"Novak, Sebastian. <i>Evolutionary Proccesses in Variable Emvironments</i>. Institute of Science and Technology Austria, 2016.","short":"S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of Science and Technology Austria, 2016.","ista":"Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria.","apa":"Novak, S. (2016). <i>Evolutionary proccesses in variable emvironments</i>. Institute of Science and Technology Austria.","chicago":"Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute of Science and Technology Austria, 2016."},"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"ddc":["576"],"author":[{"last_name":"Novak","first_name":"Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"}],"file_date_updated":"2021-02-22T13:42:47Z","degree_awarded":"PhD","oa":1,"publication_status":"published","file":[{"file_size":3564901,"relation":"main_file","date_updated":"2019-08-13T09:01:00Z","content_type":"application/pdf","date_created":"2019-08-13T09:01:00Z","file_id":"6811","creator":"dernst","checksum":"81dcc838dfcf7aa0b1a27ecf4fe2da4e","access_level":"closed","file_name":"Novak_thesis.pdf"},{"content_type":"application/pdf","date_updated":"2021-02-22T13:42:47Z","relation":"main_file","file_size":2814384,"file_name":"2016_Novak_Thesis.pdf","access_level":"open_access","checksum":"30808d2f7ca920e09f63a95cdc49bffd","creator":"dernst","success":1,"file_id":"9186","date_created":"2021-02-22T13:42:47Z"}],"year":"2016","alternative_title":["ISTA Thesis"],"date_created":"2018-12-11T11:50:17Z","day":"01","OA_place":"publisher","corr_author":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"1125","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"supervisor":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"has_accepted_license":"1","page":"124"},{"status":"public","doi_confirm":"1","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","related_material":{"record":[{"status":"public","id":"5554","relation":"research_data"},{"status":"public","relation":"part_of_dissertation","id":"1666"}]},"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","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."}],"citation":{"ama":"Tugrul M. Evolution of transcriptional regulatory sequences. 2016.","ieee":"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.","short":"M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of Science and Technology Austria, 2016.","ista":"Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria.","apa":"Tugrul, M. (2016). <i>Evolution of transcriptional regulatory sequences</i>. Institute of Science and Technology Austria.","chicago":"Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute of Science and Technology Austria, 2016."},"month":"07","date_updated":"2026-07-29T11:31:14Z","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.","article_processing_charge":"No","date_published":"2016-07-01T00:00:00Z","title":"Evolution of transcriptional regulatory sequences","publist_id":"6229","OA_place":"publisher","corr_author":"1","day":"01","has_accepted_license":"1","supervisor":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"}],"page":"89","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"_id":"1131","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"content_type":"application/pdf","date_updated":"2019-08-13T08:53:52Z","relation":"main_file","file_size":3695257,"file_id":"6810","date_created":"2019-08-13T08:53:52Z","file_name":"Tugrul_thesis_w_signature_page.pdf","access_level":"closed","creator":"dernst","checksum":"66cb61a59943e4fb7447c6a86be5ef51"},{"creator":"dernst","checksum":"293e388d70563760f6b24c3e66283dda","file_name":"2016_Tugrul_Thesis.pdf","access_level":"open_access","date_created":"2021-02-22T11:45:20Z","success":1,"file_id":"9182","file_size":3880811,"relation":"main_file","date_updated":"2021-02-22T11:45:20Z","content_type":"application/pdf"}],"publication_status":"published","oa":1,"author":[{"id":"37C323C6-F248-11E8-B48F-1D18A9856A87","full_name":"Tugrul, Murat","first_name":"Murat","last_name":"Tugrul","orcid":"0000-0002-8523-0758"}],"language":[{"iso":"eng"}],"ddc":["576"],"degree_awarded":"PhD","file_date_updated":"2021-02-22T11:45:20Z","alternative_title":["ISTA Thesis"],"date_created":"2018-12-11T11:50:19Z","year":"2016"},{"datarep_id":"43","year":"2016","date_published":"2016-05-12T00:00:00Z","article_processing_charge":"No","date_created":"2018-12-12T12:31:30Z","title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","author":[{"orcid":"0000-0002-8523-0758","first_name":"Murat","last_name":"Tugrul","full_name":"Tugrul, Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-07-29T11:31:13Z","file_date_updated":"2020-07-14T12:47:01Z","file":[{"relation":"main_file","content_type":"application/zip","date_updated":"2020-07-14T12:47:01Z","file_size":1123495,"file_id":"5626","date_created":"2018-12-12T13:03:08Z","access_level":"open_access","file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip","creator":"system","checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2"}],"doi":"10.15479/AT:ISTA:43","month":"05","oa":1,"oa_version":"Published Version","keyword":["RNAP binding","de novo promoter evolution","lac promoter"],"abstract":[{"text":"The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution.","lang":"eng"}],"citation":{"mla":"Tugrul, Murat. <i>Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>.","short":"M. Tugrul, (2016).","ista":"Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>.","apa":"Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:43\">https://doi.org/10.15479/AT:ISTA:43</a>","chicago":"Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:43\">https://doi.org/10.15479/AT:ISTA:43</a>.","ama":"Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016."},"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"_id":"5554","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"publisher":"Institute of Science and Technology Austria","day":"12","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1131"}]},"contributor":[{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Magdalena","last_name":"Steinrück"},{"id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Fabienne","last_name":"Jesse"}],"status":"public","type":"research_data"},{"status":"public","publication_identifier":{"issn":["2663-337X"]},"doi_confirm":"1","type":"dissertation","related_material":{"record":[{"id":"5553","relation":"part_of_dissertation","status":"public"},{"id":"5551","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"5552","relation":"part_of_dissertation"}]},"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"citation":{"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>","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.","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.","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>"},"month":"02","date_updated":"2026-07-30T14:56:14Z","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. ","date_published":"2016-02-18T00:00:00Z","article_processing_charge":"No","title":"The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone","publist_id":"5809","OA_place":"publisher","corr_author":"1","day":"18","has_accepted_license":"1","supervisor":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"page":"130","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"1398","doi":"10.15479/AT:ISTA:TH_526 ","file":[{"file_size":7590862,"relation":"main_file","date_updated":"2025-07-03T06:24:17Z","content_type":"application/pdf","date_created":"2025-07-03T06:24:17Z","file_id":"19957","creator":"dernst","checksum":"f0f7c260e19ec1416824b165afe2d5fd","access_level":"open_access","file_name":"2016_Thesis_Ellis_noSignatures.pdf"},{"file_size":11928241,"content_type":"application/pdf","date_updated":"2025-07-03T06:24:39Z","relation":"main_file","checksum":"a89b17ff27cf92c9a15f6b3d46bd7e53","creator":"system","access_level":"closed","file_name":"IST-2016-526-v1+1_Ellis_signed_thesis.pdf","date_created":"2018-12-12T10:14:51Z","file_id":"5106"}],"publication_status":"published","oa":1,"author":[{"last_name":"Ellis","first_name":"Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","full_name":"Ellis, Thomas"}],"ddc":["576"],"language":[{"iso":"eng"}],"pubrep_id":"526","degree_awarded":"PhD","file_date_updated":"2025-07-03T06:24:39Z","alternative_title":["ISTA Thesis"],"date_created":"2018-12-11T11:51:47Z","year":"2016"},{"article_processing_charge":"No","date_published":"2016-02-19T00:00:00Z","date_created":"2018-12-12T12:31:30Z","title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","datarep_id":"37","year":"2016","doi":"10.15479/AT:ISTA:37","month":"02","file":[{"access_level":"open_access","file_name":"IST-2016-37-v1+1_paternity_archive.zip","creator":"system","checksum":"4ae751b1fa4897fa216241f975a57313","file_id":"5620","date_created":"2018-12-12T13:03:02Z","content_type":"application/zip","relation":"main_file","date_updated":"2020-07-14T12:47:01Z","file_size":132808}],"oa":1,"date_updated":"2026-07-30T14:56:13Z","author":[{"full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","last_name":"Field","first_name":"David"},{"first_name":"Thomas","last_name":"Ellis","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","full_name":"Ellis, Thomas"}],"ddc":["576"],"file_date_updated":"2020-07-14T12:47:01Z","has_accepted_license":"1","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"citation":{"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>.","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>","ista":"Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>.","short":"D. Field, T. Ellis, (2016).","mla":"Field, David, and Thomas Ellis. <i>Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>.","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.","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>"},"keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"],"department":[{"_id":"NiBa"}],"_id":"5553","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","type":"research_data","day":"19","related_material":{"record":[{"status":"public","id":"1398","relation":"dissertation_contains"}]},"contributor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_manager","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}]},{"related_material":{"record":[{"status":"public","id":"1398","relation":"dissertation_contains"}]},"contributor":[{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"day":"19","type":"research_data","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5551","department":[{"_id":"NiBa"}],"citation":{"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>","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>.","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>.","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>.","short":"T. Ellis, (2016).","ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016.","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>"},"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","publisher":"Institute of Science and Technology Austria","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:01Z","date_updated":"2026-07-30T14:56:13Z","author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","full_name":"Ellis, Thomas","last_name":"Ellis","first_name":"Thomas","orcid":"0000-0002-8511-0254"}],"oa":1,"file":[{"date_updated":"2020-07-14T12:47:01Z","relation":"main_file","content_type":"application/zip","file_size":32775,"file_id":"5640","date_created":"2018-12-12T13:05:12Z","file_name":"IST-2016-35-v1+1_array_data.zip","access_level":"open_access","checksum":"aa3eb85d52b110cd192aa23147c4d4f3","creator":"system"}],"doi":"10.15479/AT:ISTA:35","month":"02","year":"2016","datarep_id":"35","title":"Data on pollinator observations and offpsring phenotypes","date_created":"2018-12-12T12:31:29Z","article_processing_charge":"No","date_published":"2016-02-19T00:00:00Z"},{"abstract":[{"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.","lang":"eng"}],"citation":{"mla":"Ellis, Thomas. <i>Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.</i> Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>.","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>.","short":"T. Ellis, (2016).","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>.","ama":"Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>","ieee":"T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.” Institute of Science and Technology Austria, 2016."},"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5552","department":[{"_id":"NiBa"}],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","day":"19","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1398"}]},"contributor":[{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"status":"public","type":"research_data","datarep_id":"36","year":"2016","article_processing_charge":"No","date_published":"2016-02-19T00:00:00Z","title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.","date_created":"2018-12-12T12:31:30Z","date_updated":"2026-07-30T14:56:13Z","author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","full_name":"Ellis, Thomas","first_name":"Thomas","last_name":"Ellis","orcid":"0000-0002-8511-0254"}],"file_date_updated":"2020-07-14T12:47:01Z","oa":1,"month":"02","file":[{"date_created":"2018-12-12T13:03:07Z","file_id":"5625","checksum":"cbc61b523d4d475a04a737d50dc470ef","creator":"system","access_level":"open_access","file_name":"IST-2016-36-v1+1_tag_assay_archive.zip","file_size":44905,"relation":"main_file","content_type":"application/zip","date_updated":"2020-07-14T12:47:01Z"}],"doi":"10.15479/AT:ISTA:36"},{"publist_id":"5768","title":"First steps towards a runtime comparison of natural and artificial evolution","date_published":"2015-07-11T00:00:00Z","article_processing_charge":"No","arxiv":1,"isi":1,"external_id":{"arxiv":["1504.06260"],"isi":["000358795700182"]},"quality_controlled":"1","date_updated":"2025-09-23T08:50:33Z","month":"07","citation":{"mla":"Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i>, ACM, 2015, pp. 1455–62, doi:<a href=\"https://doi.org/10.1145/2739480.2754758\">10.1145/2739480.2754758</a>.","short":"T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–1462.","ista":"Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a runtime comparison of natural and artificial evolution. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and evolutionary computation conference, 1455–1462.","apa":"Paixao, T., Sudholt, D., Heredia, J., &#38; Trubenova, B. (2015). First steps towards a runtime comparison of natural and artificial evolution. In <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i> (pp. 1455–1462). Madrid, Spain: ACM. <a href=\"https://doi.org/10.1145/2739480.2754758\">https://doi.org/10.1145/2739480.2754758</a>","chicago":"Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i>, 1455–62. ACM, 2015. <a href=\"https://doi.org/10.1145/2739480.2754758\">https://doi.org/10.1145/2739480.2754758</a>.","ama":"Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime comparison of natural and artificial evolution. In: <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i>. ACM; 2015:1455-1462. doi:<a href=\"https://doi.org/10.1145/2739480.2754758\">10.1145/2739480.2754758</a>","ieee":"T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards a runtime comparison of natural and artificial evolution,” in <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i>, Madrid, Spain, 2015, pp. 1455–1462."},"scopus_import":"1","abstract":[{"lang":"eng","text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse their runtime on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrence of new mutations is much longer than the time it takes for a new beneficial mutation to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a (1+1)-type process where the probability of accepting a new genotype (improvements or worsenings) depends on the change in fitness. We present an initial runtime analysis of SSWM, quantifying its performance for various parameters and investigating differences to the (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient."}],"oa_version":"Preprint","publisher":"ACM","main_file_link":[{"url":"http://arxiv.org/abs/1504.06260","open_access":"1"}],"type":"conference","status":"public","year":"2015","date_created":"2018-12-11T11:51:58Z","language":[{"iso":"eng"}],"author":[{"first_name":"Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"full_name":"Sudholt, Dirk","first_name":"Dirk","last_name":"Sudholt"},{"first_name":"Jorge","last_name":"Heredia","full_name":"Heredia, Jorge"},{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora","first_name":"Barbora","last_name":"Trubenova","orcid":"0000-0002-6873-2967"}],"publication_status":"published","oa":1,"doi":"10.1145/2739480.2754758","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091"}],"_id":"1430","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","conference":{"start_date":"2015-07-11","end_date":"2015-07-15","name":"GECCO: Genetic and evolutionary computation conference","location":"Madrid, Spain"},"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"ec_funded":1,"page":"1455 - 1462","day":"11","publication":"Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation"},{"year":"2015","date_created":"2018-12-11T11:52:29Z","pubrep_id":"560","file_date_updated":"2020-07-14T12:45:00Z","author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Servedio, Maria","first_name":"Maria","last_name":"Servedio"}],"language":[{"iso":"eng"}],"ddc":["570"],"file":[{"file_id":"4822","date_created":"2018-12-12T10:10:34Z","file_name":"IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf","access_level":"open_access","checksum":"fd8d23f476bc194419929b72ca265c02","creator":"system","relation":"main_file","date_updated":"2020-07-14T12:45:00Z","content_type":"application/pdf","file_size":188872},{"file_size":577415,"relation":"main_file","date_updated":"2020-07-14T12:45:00Z","content_type":"application/pdf","creator":"system","checksum":"b774911e70044641d556e258efcb52ef","access_level":"open_access","file_name":"IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf","date_created":"2018-12-12T10:10:35Z","file_id":"4823"}],"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"doi":"10.1111/evo.12641","publication_status":"published","oa":1,"intvolume":"        69","issue":"5","department":[{"_id":"NiBa"}],"ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1519","page":"1101 - 1112","has_accepted_license":"1","day":"19","corr_author":"1","publication":"Evolution","volume":69,"publist_id":"5656","title":"The interpretation of selection coefficients","isi":1,"article_processing_charge":"No","date_published":"2015-03-19T00:00:00Z","external_id":{"isi":["000354561600001"]},"quality_controlled":"1","date_updated":"2025-09-23T13:53:01Z","month":"03","oa_version":"Submitted Version","citation":{"ieee":"N. H. Barton and M. Servedio, “The interpretation of selection coefficients,” <i>Evolution</i>, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015.","ama":"Barton NH, Servedio M. The interpretation of selection coefficients. <i>Evolution</i>. 2015;69(5):1101-1112. doi:<a href=\"https://doi.org/10.1111/evo.12641\">10.1111/evo.12641</a>","apa":"Barton, N. H., &#38; Servedio, M. (2015). The interpretation of selection coefficients. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.12641\">https://doi.org/10.1111/evo.12641</a>","chicago":"Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection Coefficients.” <i>Evolution</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/evo.12641\">https://doi.org/10.1111/evo.12641</a>.","mla":"Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.” <i>Evolution</i>, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:<a href=\"https://doi.org/10.1111/evo.12641\">10.1111/evo.12641</a>.","ista":"Barton NH, Servedio M. 2015. The interpretation of selection coefficients. Evolution. 69(5), 1101–1112.","short":"N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112."},"abstract":[{"lang":"eng","text":"Evolutionary biologists have an array of powerful theoretical techniques that can accurately predict changes in the genetic composition of populations. Changes in gene frequencies and genetic associations between loci can be tracked as they respond to a wide variety of evolutionary forces. However, it is often less clear how to decompose these various forces into components that accurately reflect the underlying biology. Here, we present several issues that arise in the definition and interpretation of selection and selection coefficients, focusing on insights gained through the examination of selection coefficients in multilocus notation. Using this notation, we discuss how its flexibility-which allows different biological units to be identified as targets of selection-is reflected in the interpretation of the coefficients that the notation generates. In many situations, it can be difficult to agree on whether loci can be considered to be under &quot;direct&quot; versus &quot;indirect&quot; selection, or to quantify this selection. We present arguments for what the terms direct and indirect selection might best encompass, considering a range of issues, from viability and sexual selection to kin selection. We show how multilocus notation can discriminate between direct and indirect selection, and describe when it can do so."}],"scopus_import":"1","publisher":"Wiley","type":"journal_article","status":"public"},{"publication_identifier":{"eissn":["2073-4336"]},"type":"journal_article","status":"public","oa_version":"Published Version","abstract":[{"lang":"eng","text":"In many social situations, individuals endeavor to find the single best possible partner, but are constrained to evaluate the candidates in sequence. Examples include the search for mates, economic partnerships, or any other long-term ties where the choice to interact involves two parties. Surprisingly, however, previous theoretical work on mutual choice problems focuses on finding equilibrium solutions, while ignoring the evolutionary dynamics of decisions. Empirically, this may be of high importance, as some equilibrium solutions can never be reached unless the population undergoes radical changes and a sufficient number of individuals change their decisions simultaneously. To address this question, we apply a mutual choice sequential search problem in an evolutionary game-theoretical model that allows one to find solutions that are favored by evolution. As an example, we study the influence of sequential search on the evolutionary dynamics of cooperation. For this, we focus on the classic snowdrift game and the prisoner’s dilemma game."}],"citation":{"ieee":"T. Priklopil and K. Chatterjee, “Evolution of decisions in population games with sequentially searching individuals,” <i>Games</i>, vol. 6, no. 4. MDPI, pp. 413–437, 2015.","ama":"Priklopil T, Chatterjee K. Evolution of decisions in population games with sequentially searching individuals. <i>Games</i>. 2015;6(4):413-437. doi:<a href=\"https://doi.org/10.3390/g6040413\">10.3390/g6040413</a>","apa":"Priklopil, T., &#38; Chatterjee, K. (2015). Evolution of decisions in population games with sequentially searching individuals. <i>Games</i>. MDPI. <a href=\"https://doi.org/10.3390/g6040413\">https://doi.org/10.3390/g6040413</a>","chicago":"Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population Games with Sequentially Searching Individuals.” <i>Games</i>. MDPI, 2015. <a href=\"https://doi.org/10.3390/g6040413\">https://doi.org/10.3390/g6040413</a>.","mla":"Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population Games with Sequentially Searching Individuals.” <i>Games</i>, vol. 6, no. 4, MDPI, 2015, pp. 413–37, doi:<a href=\"https://doi.org/10.3390/g6040413\">10.3390/g6040413</a>.","ista":"Priklopil T, Chatterjee K. 2015. Evolution of decisions in population games with sequentially searching individuals. Games. 6(4), 413–437.","short":"T. Priklopil, K. Chatterjee, Games 6 (2015) 413–437."},"scopus_import":"1","publisher":"MDPI","date_updated":"2025-04-15T06:50:21Z","quality_controlled":"1","month":"09","volume":6,"publist_id":"5467","title":"Evolution of decisions in population games with sequentially searching individuals","date_published":"2015-09-29T00:00:00Z","article_processing_charge":"No","day":"29","corr_author":"1","publication":"Games","issue":"4","department":[{"_id":"NiBa"},{"_id":"KrCh"}],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1681","page":"413 - 437","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pubrep_id":"448","file_date_updated":"2020-07-14T12:45:12Z","author":[{"last_name":"Priklopil","first_name":"Tadeas","full_name":"Priklopil, Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"ddc":["000"],"file":[{"relation":"main_file","date_updated":"2020-07-14T12:45:12Z","content_type":"application/pdf","file_size":518832,"file_id":"4959","date_created":"2018-12-12T10:12:41Z","access_level":"open_access","file_name":"IST-2016-448-v1+1_games-06-00413.pdf","checksum":"912e1acbaf201100f447a43e4d5958bd","creator":"system"}],"doi":"10.3390/g6040413","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"publication_status":"published","oa":1,"intvolume":"         6","year":"2015","date_created":"2018-12-11T11:53:26Z","article_type":"original"}]