[{"date_published":"2017-01-01T00:00:00Z","oa_version":"Submitted Version","external_id":{"isi":["000393677300025"]},"ddc":["576"],"author":[{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","first_name":"Sebastian","last_name":"Novak"},{"full_name":"Kollár, Richard","first_name":"Richard","last_name":"Kollár"}],"publication":"Genetics","publist_id":"6188","issue":"1","publisher":"Genetics Society of America","doi":"10.1534/genetics.116.193946","file_date_updated":"2020-07-14T12:44:37Z","type":"journal_article","language":[{"iso":"eng"}],"article_processing_charge":"No","scopus_import":"1","publication_identifier":{"issn":["00166731"]},"date_updated":"2025-05-28T11:42:46Z","project":[{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"},{"call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"page":"367 - 374","quality_controlled":"1","year":"2017","date_created":"2018-12-11T11:50:31Z","volume":205,"isi":1,"file":[{"checksum":"7c8ab79cda1f92760bbbbe0f53175bfc","relation":"main_file","creator":"system","file_size":361500,"file_name":"IST-2016-727-v1+1_SFC_Genetics_final.pdf","date_updated":"2020-07-14T12:44:37Z","access_level":"open_access","file_id":"4833","content_type":"application/pdf","date_created":"2018-12-12T10:10:43Z"}],"department":[{"_id":"NiBa"}],"pubrep_id":"727","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1169","month":"01","oa":1,"title":"Spatial gene frequency waves under genotype dependent dispersal","publication_status":"published","has_accepted_license":"1","day":"01","citation":{"short":"S. Novak, R. Kollár, Genetics 205 (2017) 367–374.","ama":"Novak S, Kollár R. Spatial gene frequency waves under genotype dependent dispersal. <i>Genetics</i>. 2017;205(1):367-374. doi:<a href=\"https://doi.org/10.1534/genetics.116.193946\">10.1534/genetics.116.193946</a>","apa":"Novak, S., &#38; Kollár, R. (2017). Spatial gene frequency waves under genotype dependent dispersal. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.116.193946\">https://doi.org/10.1534/genetics.116.193946</a>","ista":"Novak S, Kollár R. 2017. Spatial gene frequency waves under genotype dependent dispersal. Genetics. 205(1), 367–374.","chicago":"Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype Dependent Dispersal.” <i>Genetics</i>. Genetics Society of America, 2017. <a href=\"https://doi.org/10.1534/genetics.116.193946\">https://doi.org/10.1534/genetics.116.193946</a>.","ieee":"S. Novak and R. Kollár, “Spatial gene frequency waves under genotype dependent dispersal,” <i>Genetics</i>, vol. 205, no. 1. Genetics Society of America, pp. 367–374, 2017.","mla":"Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype Dependent Dispersal.” <i>Genetics</i>, vol. 205, no. 1, Genetics Society of America, 2017, pp. 367–74, doi:<a href=\"https://doi.org/10.1534/genetics.116.193946\">10.1534/genetics.116.193946</a>."},"intvolume":"       205","ec_funded":1,"abstract":[{"lang":"eng","text":"Dispersal is a crucial factor in natural evolution, since it determines the habitat experienced by any population and defines the spatial scale of interactions between individuals. There is compelling evidence for systematic differences in dispersal characteristics within the same population, i.e., genotype-dependent dispersal. The consequences of genotype-dependent dispersal on other evolutionary phenomena, however, are poorly understood. In this article we investigate the effect of genotype-dependent dispersal on spatial gene frequency patterns, using a generalization of the classical diffusion model of selection and dispersal. Dispersal is characterized by the variance of dispersal (diffusion coefficient) and the mean displacement (directional advection term). We demonstrate that genotype-dependent dispersal may change the qualitative behavior of Fisher waves, which change from being “pulled” to being “pushed” wave fronts as the discrepancy in dispersal between genotypes increases. The speed of any wave is partitioned into components due to selection, genotype-dependent variance of dispersal, and genotype-dependent mean displacement. We apply our findings to wave fronts maintained by selection against heterozygotes. Furthermore, we identify a benefit of increased variance of dispersal, quantify its effect on the speed of the wave, and discuss the implications for the evolution of dispersal strategies."}],"status":"public"},{"abstract":[{"lang":"eng","text":"Variation in genotypes may be responsible for differences in dispersal rates, directional biases, and growth rates of individuals. These traits may favor certain genotypes and enhance their spatiotemporal spreading into areas occupied by the less advantageous genotypes. We study how these factors influence the speed of spreading in the case of two competing genotypes under the assumption that spatial variation of the total population is small compared to the spatial variation of the frequencies of the genotypes in the population. In that case, the dynamics of the frequency of one of the genotypes is approximately described by a generalized Fisher–Kolmogorov–Petrovskii–Piskunov (F–KPP) equation. This generalized F–KPP equation with (nonlinear) frequency-dependent diffusion and advection terms admits traveling wave solutions that characterize the invasion of the dominant genotype. Our existence results generalize the classical theory for traveling waves for the F–KPP with constant coefficients. Moreover, in the particular case of the quadratic (monostable) nonlinear growth–decay rate in the generalized F–KPP we study in detail the influence of the variance in diffusion and mean displacement rates of the two genotypes on the minimal wave propagation speed."}],"status":"public","ec_funded":1,"intvolume":"        79","citation":{"mla":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” <i>Bulletin of Mathematical Biology</i>, vol. 79, no. 3, Springer, 2017, pp. 525–59, doi:<a href=\"https://doi.org/10.1007/s11538-016-0244-3\">10.1007/s11538-016-0244-3</a>.","ieee":"R. Kollár and S. Novak, “Existence of traveling waves for the generalized F–KPP equation,” <i>Bulletin of Mathematical Biology</i>, vol. 79, no. 3. Springer, pp. 525–559, 2017.","ista":"Kollár R, Novak S. 2017. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 79(3), 525–559.","chicago":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” <i>Bulletin of Mathematical Biology</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s11538-016-0244-3\">https://doi.org/10.1007/s11538-016-0244-3</a>.","apa":"Kollár, R., &#38; Novak, S. (2017). Existence of traveling waves for the generalized F–KPP equation. <i>Bulletin of Mathematical Biology</i>. Springer. <a href=\"https://doi.org/10.1007/s11538-016-0244-3\">https://doi.org/10.1007/s11538-016-0244-3</a>","ama":"Kollár R, Novak S. Existence of traveling waves for the generalized F–KPP equation. <i>Bulletin of Mathematical Biology</i>. 2017;79(3):525-559. doi:<a href=\"https://doi.org/10.1007/s11538-016-0244-3\">10.1007/s11538-016-0244-3</a>","short":"R. Kollár, S. Novak, Bulletin of Mathematical Biology 79 (2017) 525–559."},"day":"01","oa":1,"title":"Existence of traveling waves for the generalized F–KPP equation","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1191","month":"03","department":[{"_id":"NiBa"}],"acknowledgement":"We thank Nick Barton, Katarína Bod’ová, and Sr\r\n-\r\ndan Sarikas for constructive feed-\r\nback and support. Furthermore, we would like to express our deep gratitude to the anonymous referees (one\r\nof whom, Jimmy Garnier, agreed to reveal his identity) and the editor Max Souza, for very helpful and\r\ndetailed comments and suggestions that significantly helped us to improve the manuscript. This project has\r\nreceived funding from the European Union’s Seventh Framework Programme for research, technological\r\ndevelopment and demonstration under Grant Agreement 618091 Speed of Adaptation in Population Genet-\r\nics and Evolutionary Computation (SAGE) and the European Research Council (ERC) Grant No. 250152\r\n(SN), from the Scientific Grant Agency of the Slovak Republic under the Grant 1/0459/13 and by the Slovak\r\nResearch and Development Agency under the Contract No. APVV-14-0378 (RK). RK would also like to\r\nthank IST Austria for its hospitality during the work on this project.","volume":79,"date_updated":"2025-05-28T11:42:46Z","project":[{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091"},{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"page":"525-559","quality_controlled":"1","year":"2017","date_created":"2018-12-11T11:50:38Z","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.00944"}],"type":"journal_article","language":[{"iso":"eng"}],"publisher":"Springer","doi":"10.1007/s11538-016-0244-3","author":[{"first_name":"Richard","full_name":"Kollár, Richard","last_name":"Kollár"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X","last_name":"Novak","full_name":"Novak, Sebastian","first_name":"Sebastian"}],"issue":"3","publication":"Bulletin of Mathematical Biology","publist_id":"6160","date_published":"2017-03-01T00:00:00Z","oa_version":"Preprint"},{"department":[{"_id":"NiBa"}],"_id":"1199","month":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","title":"How does epistasis influence the response to selection?","related_material":{"record":[{"status":"public","relation":"research_data","id":"9710"}]},"oa":1,"day":"01","intvolume":"       118","citation":{"ama":"Barton NH. How does epistasis influence the response to selection? <i>Heredity</i>. 2017;118:96-109. doi:<a href=\"https://doi.org/10.1038/hdy.2016.109\">10.1038/hdy.2016.109</a>","short":"N.H. Barton, Heredity 118 (2017) 96–109.","mla":"Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” <i>Heredity</i>, vol. 118, Nature Publishing Group, 2017, pp. 96–109, doi:<a href=\"https://doi.org/10.1038/hdy.2016.109\">10.1038/hdy.2016.109</a>.","ieee":"N. H. Barton, “How does epistasis influence the response to selection?,” <i>Heredity</i>, vol. 118. Nature Publishing Group, pp. 96–109, 2017.","ista":"Barton NH. 2017. How does epistasis influence the response to selection? Heredity. 118, 96–109.","chicago":"Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” <i>Heredity</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/hdy.2016.109\">https://doi.org/10.1038/hdy.2016.109</a>.","apa":"Barton, N. H. (2017). How does epistasis influence the response to selection? <i>Heredity</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/hdy.2016.109\">https://doi.org/10.1038/hdy.2016.109</a>"},"ec_funded":1,"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"}],"status":"public","date_published":"2017-01-01T00:00:00Z","external_id":{"isi":["000392229100011"]},"oa_version":"Submitted Version","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"publication":"Heredity","publist_id":"6151","publisher":"Nature Publishing Group","doi":"10.1038/hdy.2016.109","type":"journal_article","language":[{"iso":"eng"}],"article_processing_charge":"No","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5176114/","open_access":"1"}],"scopus_import":"1","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"date_updated":"2025-05-28T11:42:47Z","year":"2017","date_created":"2018-12-11T11:50:40Z","quality_controlled":"1","page":"96 - 109","isi":1,"volume":118},{"department":[{"_id":"NiBa"}],"date_published":"2016-01-01T00:00:00Z","oa_version":"None","author":[{"full_name":"Teitel, Zachary","first_name":"Zachary","last_name":"Teitel"},{"last_name":"Pickup","full_name":"Pickup, Melinda","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"},{"full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"last_name":"Barrett","full_name":"Barrett, Spencer","first_name":"Spencer"}],"issue":"1","publication":"Plant Biology","publist_id":"6110","publisher":"Wiley-Blackwell","month":"01","_id":"1224","doi":"10.1111/plb.12336","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publication_status":"published","language":[{"iso":"eng"}],"title":"The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant","day":"01","citation":{"mla":"Teitel, Zachary, et al. “The Dynamics of Resource Allocation and Costs of Reproduction in a Sexually Dimorphic, Wind-Pollinated Dioecious Plant.” <i>Plant Biology</i>, vol. 18, no. 1, Wiley-Blackwell, 2016, pp. 98–103, doi:<a href=\"https://doi.org/10.1111/plb.12336\">10.1111/plb.12336</a>.","ieee":"Z. Teitel, M. Pickup, D. Field, and S. Barrett, “The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant,” <i>Plant Biology</i>, vol. 18, no. 1. Wiley-Blackwell, pp. 98–103, 2016.","ista":"Teitel Z, Pickup M, Field D, Barrett S. 2016. The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant. Plant Biology. 18(1), 98–103.","apa":"Teitel, Z., Pickup, M., Field, D., &#38; Barrett, S. (2016). The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant. <i>Plant Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/plb.12336\">https://doi.org/10.1111/plb.12336</a>","chicago":"Teitel, Zachary, Melinda Pickup, David Field, and Spencer Barrett. “The Dynamics of Resource Allocation and Costs of Reproduction in a Sexually Dimorphic, Wind-Pollinated Dioecious Plant.” <i>Plant Biology</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1111/plb.12336\">https://doi.org/10.1111/plb.12336</a>.","ama":"Teitel Z, Pickup M, Field D, Barrett S. The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant. <i>Plant Biology</i>. 2016;18(1):98-103. doi:<a href=\"https://doi.org/10.1111/plb.12336\">10.1111/plb.12336</a>","short":"Z. Teitel, M. Pickup, D. Field, S. Barrett, Plant Biology 18 (2016) 98–103."},"intvolume":"        18","scopus_import":1,"date_updated":"2021-01-12T06:49:12Z","year":"2016","date_created":"2018-12-11T11:50:48Z","page":"98 - 103","quality_controlled":"1","volume":18,"abstract":[{"lang":"eng","text":"Sexual dimorphism in resource allocation is expected to change during the life cycle of dioecious plants because of temporal differences between the sexes in reproductive investment. Given the potential for sex-specific differences in reproductive costs, resource availability may contribute to variation in reproductive allocation in females and males. Here, we used Rumex hastatulus, a dioecious, wind-pollinated annual plant, to investigate whether sexual dimorphism varies with life-history stage and nutrient availability, and determine whether allocation patterns differ depending on reproductive commitment. To examine if the costs of reproduction varied between the sexes, reproduction was either allowed or prevented through bud removal, and biomass allocation was measured at maturity. In a second experiment to assess variation in sexual dimorphism across the life cycle, and whether this varied with resource availability, plants were grown in high and low nutrients and allocation to roots, aboveground vegetative growth and reproduction were measured at three developmental stages. Males prevented from reproducing compensated with increased above- and belowground allocation to a much larger degree than females, suggesting that male reproductive costs reduce vegetative growth. The proportional allocation to roots, reproductive structures and aboveground vegetative growth varied between the sexes and among life-cycle stages, but not with nutrient treatment. Females allocated proportionally more resources to roots than males at peak flowering, but this pattern was reversed at reproductive maturity under low-nutrient conditions. Our study illustrates the importance of temporal dynamics in sex-specific resource allocation and provides support for high male reproductive costs in wind-pollinated plants."}],"status":"public"},{"scopus_import":"1","pmid":1,"article_processing_charge":"No","volume":202,"file":[{"file_name":"IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf","date_updated":"2020-07-14T12:45:00Z","access_level":"open_access","file_id":"5241","date_created":"2018-12-12T10:16:51Z","content_type":"application/pdf","checksum":"41c9b5d72e7fe4624dd22dfe622337d5","relation":"main_file","creator":"system","file_size":957466}],"quality_controlled":"1","page":"775 - 786","date_created":"2018-12-11T11:52:29Z","year":"2016","date_updated":"2025-05-28T11:42:48Z","project":[{"call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"publist_id":"5658","publication":"Genetics","issue":"2","ddc":["570"],"author":[{"first_name":"Konrad","full_name":"Lohse, Konrad","last_name":"Lohse"},{"full_name":"Chmelik, Martin","first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Simon","full_name":"Martin, Simon","last_name":"Martin"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"external_id":{"pmid":["26715666"]},"oa_version":"Preprint","date_published":"2016-02-01T00:00:00Z","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:00Z","type":"journal_article","doi":"10.1534/genetics.115.183814","publisher":"Genetics Society of America","intvolume":"       202","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>","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.","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>.","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>.","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."},"day":"01","has_accepted_license":"1","status":"public","abstract":[{"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.","lang":"eng"}],"ec_funded":1,"pubrep_id":"561","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.).","department":[{"_id":"KrCh"},{"_id":"NiBa"}],"oa":1,"title":"Efficient strategies for calculating blockwise likelihoods under the coalescent","publication_status":"published","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1518","month":"02"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":1,"project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"date_updated":"2021-01-12T06:52:07Z","year":"2016","date_created":"2018-12-11T11:53:08Z","page":"1 - 12","quality_controlled":"1","file":[{"date_created":"2018-12-12T10:11:12Z","content_type":"application/pdf","file_id":"4865","access_level":"open_access","date_updated":"2020-07-14T12:45:07Z","file_name":"IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf","file_size":1684043,"creator":"system","relation":"main_file","checksum":"6a65ba187994d4ad86c1c509e0ff482a"}],"volume":108,"date_published":"2016-04-01T00:00:00Z","oa_version":"Published Version","author":[{"full_name":"Kelleher, Jerome","first_name":"Jerome","last_name":"Kelleher"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"},{"last_name":"Véber","full_name":"Véber, Amandine","first_name":"Amandine"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"ddc":["576"],"publication":"Theoretical Population Biology","publist_id":"5524","publisher":"Academic Press","doi":"10.1016/j.tpb.2015.10.008","type":"journal_article","file_date_updated":"2020-07-14T12:45:07Z","language":[{"iso":"eng"}],"has_accepted_license":"1","day":"01","citation":{"short":"J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population Biology 108 (2016) 1–12.","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>","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>","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.","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>.","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.","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>."},"intvolume":"       108","ec_funded":1,"abstract":[{"lang":"eng","text":"Ancestral processes are fundamental to modern population genetics and spatial structure has been the subject of intense interest for many years. Despite this interest, almost nothing is known about the distribution of the locations of pedigree or genetic ancestors. Using both spatially continuous and stepping-stone models, we show that the distribution of pedigree ancestors approaches a travelling wave, for which we develop two alternative approximations. The speed and width of the wave are sensitive to the local details of the model. After a short time, genetic ancestors spread far more slowly than pedigree ancestors, ultimately diffusing out with radius ## rather than spreading at constant speed. In contrast to the wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the local details of the models."}],"status":"public","department":[{"_id":"NiBa"}],"pubrep_id":"465","month":"04","_id":"1631","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"Spread of pedigree versus genetic ancestry in spatially distributed populations","oa":1},{"file":[{"creator":"system","file_size":979026,"checksum":"a1896e39e4113f2711e46b435d5f3e69","relation":"main_file","date_updated":"2020-07-14T12:44:45Z","access_level":"open_access","date_created":"2018-12-12T10:16:27Z","file_id":"5214","content_type":"application/pdf","file_name":"IST-2016-650-v1+1_p1163-oliveto.pdf"}],"quality_controlled":"1","page":"1163 - 1170","year":"2016","date_created":"2018-12-11T11:51:31Z","date_updated":"2021-01-12T06:50:03Z","project":[{"call_identifier":"FP7","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"scopus_import":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:45Z","type":"conference","doi":"10.1145/2908812.2908909","publisher":"ACM","publication":"Proceedings of the Genetic and Evolutionary Computation Conference 2016 ","publist_id":"5900","ddc":["576"],"author":[{"full_name":"Oliveto, Pietro","first_name":"Pietro","last_name":"Oliveto"},{"last_name":"Paixao","full_name":"Paixao, Tiago","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heredia","full_name":"Heredia, Jorge","first_name":"Jorge"},{"first_name":"Dirk","full_name":"Sudholt, Dirk","last_name":"Sudholt"},{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","first_name":"Barbora","last_name":"Trubenova"}],"oa_version":"Published Version","conference":{"name":"GECCO: Genetic and evolutionary computation conference","start_date":"2016-07-20","location":"Denver, CO, USA","end_date":"2016-07-24"},"date_published":"2016-07-20T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"Crossing fitness valleys is one of the major obstacles to function optimization. In this paper we investigate how the structure of the fitness valley, namely its depth d and length ℓ, influence the runtime of different strategies for crossing these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis algorithm. While the (1+1) EA has to jump across the valley to a point of higher fitness because it does not accept decreasing moves, the non-elitist algorithms may cross the valley by accepting worsening moves. We show that while the runtime of the (1+1) EA algorithm depends critically on the length of the valley, the runtimes of the non-elitist algorithms depend crucially only on the depth of the valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of small length. Moreover, we show that both SSWM and Metropolis can also efficiently optimize a rugged function consisting of consecutive valleys."}],"ec_funded":1,"citation":{"mla":"Oliveto, Pietro, et al. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>, ACM, 2016, pp. 1163–70, doi:<a href=\"https://doi.org/10.1145/2908812.2908909\">10.1145/2908812.2908909</a>.","ieee":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism outperforms elitism for crossing fitness valleys,” in <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>, Denver, CO, USA, 2016, pp. 1163–1170.","ista":"Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. 2016. When non-elitism outperforms elitism for crossing fitness valleys. Proceedings of the Genetic and Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation conference, 1163–1170.","chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” In <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>, 1163–70. ACM, 2016. <a href=\"https://doi.org/10.1145/2908812.2908909\">https://doi.org/10.1145/2908812.2908909</a>.","apa":"Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., &#38; Trubenova, B. (2016). When non-elitism outperforms elitism for crossing fitness valleys. In <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i> (pp. 1163–1170). Denver, CO, USA: ACM. <a href=\"https://doi.org/10.1145/2908812.2908909\">https://doi.org/10.1145/2908812.2908909</a>","ama":"Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. When non-elitism outperforms elitism for crossing fitness valleys. In: <i>Proceedings of the Genetic and Evolutionary Computation Conference 2016 </i>. ACM; 2016:1163-1170. doi:<a href=\"https://doi.org/10.1145/2908812.2908909\">10.1145/2908812.2908909</a>","short":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, B. Trubenova, in:, Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–1170."},"day":"20","has_accepted_license":"1","oa":1,"title":"When non-elitism outperforms elitism for crossing fitness valleys","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"07","_id":"1349","pubrep_id":"650","department":[{"_id":"NiBa"},{"_id":"CaGu"}]},{"scopus_import":1,"quality_controlled":"1","page":"3 - 4","date_created":"2018-12-11T11:51:33Z","year":"2016","date_updated":"2021-01-12T06:50:07Z","volume":202,"file":[{"checksum":"3562b89c821a4be84edf2b6ebd870cf5","relation":"main_file","creator":"system","file_size":112674,"file_name":"IST-2017-769-v1+1_SewallWright1931.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:46Z","date_created":"2018-12-12T10:08:26Z","file_id":"4687","content_type":"application/pdf"}],"oa_version":"Submitted Version","date_published":"2016-01-05T00:00:00Z","publication":"Genetics","issue":"1","publist_id":"5889","ddc":["570"],"author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"doi":"10.1534/genetics.115.184796","publisher":"Genetics Society of America","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:46Z","type":"journal_article","day":"05","has_accepted_license":"1","citation":{"ama":"Barton NH. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” <i>Genetics</i>. 2016;202(1):3-4. doi:<a href=\"https://doi.org/10.1534/genetics.115.184796\">10.1534/genetics.115.184796</a>","short":"N.H. Barton, Genetics 202 (2016) 3–4.","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>.","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>.","ista":"Barton NH. 2016. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”. Genetics. 202(1), 3–4.","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>"},"intvolume":"       202","status":"public","department":[{"_id":"NiBa"}],"pubrep_id":"769","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1356","month":"01","oa":1,"title":"Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”","publication_status":"published"},{"pubrep_id":"768","department":[{"_id":"NiBa"}],"title":"Richard Hudson and Norman Kaplan on the coalescent process","oa":1,"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1357","month":"03","intvolume":"       202","citation":{"chicago":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.116.187542\">https://doi.org/10.1534/genetics.116.187542</a>.","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.","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>.","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>"},"has_accepted_license":"1","day":"01","status":"public","ddc":["576"],"author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"issue":"3","publication":"Genetics","publist_id":"5888","date_published":"2016-03-01T00:00:00Z","oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:44:46Z","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Genetics Society of America","doi":"10.1534/genetics.116.187542","scopus_import":1,"volume":202,"file":[{"file_size":130779,"creator":"system","relation":"main_file","checksum":"b2174bab2de1d1142900062a150f35c9","file_id":"5127","date_created":"2018-12-12T10:15:09Z","content_type":"application/pdf","date_updated":"2020-07-14T12:44:46Z","access_level":"open_access","file_name":"IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf"}],"date_updated":"2021-01-12T06:50:07Z","quality_controlled":"1","page":"865 - 866","date_created":"2018-12-11T11:51:33Z","year":"2016"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":1,"date_updated":"2023-09-07T12:53:49Z","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","year":"2016","date_created":"2018-12-11T11:51:34Z","volume":7,"file":[{"access_level":"open_access","date_updated":"2020-07-14T12:44:46Z","date_created":"2018-12-12T10:12:01Z","content_type":"application/pdf","file_id":"4919","file_name":"IST-2016-627-v1+1_ncomms12307.pdf","creator":"system","file_size":861805,"checksum":"fe3f3a1526d180b29fe691ab11435b78","relation":"main_file"},{"file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","date_updated":"2020-07-14T12:44:46Z","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:12:02Z","file_id":"4920","checksum":"164864a1a675f3ad80e9917c27aba07f","relation":"main_file","creator":"system","file_size":1084703}],"date_published":"2016-08-04T00:00:00Z","oa_version":"Published Version","ddc":["576"],"author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar","full_name":"Friedlander, Tamar","last_name":"Friedlander"},{"last_name":"Prizak","first_name":"Roshan","full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H"},{"first_name":"Gasper","full_name":"Tkacik, Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"publication":"Nature Communications","publist_id":"5887","publisher":"Nature Publishing Group","doi":"10.1038/ncomms12307","file_date_updated":"2020-07-14T12:44:46Z","type":"journal_article","language":[{"iso":"eng"}],"has_accepted_license":"1","day":"04","citation":{"short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).","ama":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>","chicago":"Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>.","ista":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307.","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>","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.","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>."},"intvolume":"         7","ec_funded":1,"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."}],"article_number":"12307","status":"public","department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"pubrep_id":"627","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"08","_id":"1358","title":"Intrinsic limits to gene regulation by global crosstalk","oa":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6071"}]},"publication_status":"published"},{"intvolume":"       113","citation":{"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.","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>.","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.","mla":"Paixao, Tiago, and Nicholas H. Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” <i>PNAS</i>, vol. 113, no. 16, National Academy of Sciences, 2016, pp. 4422–27, doi:<a href=\"https://doi.org/10.1073/pnas.1518830113\">10.1073/pnas.1518830113</a>.","short":"T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427.","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>"},"day":"19","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."}],"status":"public","ec_funded":1,"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"article_type":"original","oa":1,"title":"The effect of gene interactions on the long-term response to selection","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1359","month":"04","scopus_import":1,"pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/"}],"article_processing_charge":"No","volume":113,"date_updated":"2021-01-12T06:50:08Z","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"}],"page":"4422 - 4427","quality_controlled":"1","year":"2016","date_created":"2018-12-11T11:51:34Z","author":[{"last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953"},{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"issue":"16","publist_id":"5886","publication":"PNAS","date_published":"2016-04-19T00:00:00Z","external_id":{"pmid":["27044080"]},"oa_version":"Published Version","type":"journal_article","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","doi":"10.1073/pnas.1518830113"},{"type":"journal_article","title":"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5550"}]},"publication_status":"published","language":[{"iso":"eng"}],"publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1382","doi":"10.1093/aob/mcw043","month":"06","author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","first_name":"Thomas","full_name":"Ellis, Thomas","last_name":"Ellis"},{"last_name":"Field","first_name":"David","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"}],"publication":"Annals of Botany","publist_id":"5828","issue":"7","date_published":"2016-06-01T00:00:00Z","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.","department":[{"_id":"NiBa"}],"oa_version":"None","volume":117,"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."}],"status":"public","date_updated":"2024-02-21T13:49:53Z","quality_controlled":"1","page":"1133 - 1140","year":"2016","date_created":"2018-12-11T11:51:42Z","scopus_import":1,"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.","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.","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>","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."},"intvolume":"       117","day":"1"},{"file":[{"date_updated":"2020-07-14T12:44:48Z","access_level":"open_access","file_id":"5106","content_type":"application/pdf","date_created":"2018-12-12T10:14:51Z","file_name":"IST-2016-526-v1+1_Ellis_signed_thesis.pdf","creator":"system","file_size":11928241,"checksum":"a89b17ff27cf92c9a15f6b3d46bd7e53","relation":"main_file"}],"date_updated":"2024-02-21T13:51:39Z","page":"130","year":"2016","date_created":"2018-12-11T11:51:47Z","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","file_date_updated":"2020-07-14T12:44:48Z","type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:TH_526 ","ddc":["576"],"author":[{"last_name":"Ellis","full_name":"Ellis, Thomas","first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254"}],"publist_id":"5809","date_published":"2016-02-18T00:00:00Z","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"}],"status":"public","degree_awarded":"PhD","citation":{"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.","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.","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>","chicago":"Ellis, Thomas. “The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">https://doi.org/10.15479/AT:ISTA:TH_526 </a>.","ama":"Ellis T. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">10.15479/AT:ISTA:TH_526 </a>","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."},"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"has_accepted_license":"1","day":"18","title":"The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone","oa":1,"related_material":{"record":[{"status":"public","relation":"popular_science","id":"5553"},{"status":"public","relation":"popular_science","id":"5551"},{"id":"5552","relation":"popular_science","status":"public"}]},"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"02","_id":"1398","alternative_title":["ISTA Thesis"],"pubrep_id":"526","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. ","department":[{"_id":"NiBa"}]},{"ddc":["576"],"author":[{"last_name":"Abbott","full_name":"Abbott, Richard","first_name":"Richard"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Good","first_name":"Jeffrey","full_name":"Good, Jeffrey"}],"publication":"Molecular Ecology","publist_id":"5798","issue":"11","date_published":"2016-06-08T00:00:00Z","oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:44:53Z","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Wiley-Blackwell","doi":"10.1111/mec.13685","scopus_import":1,"volume":25,"file":[{"checksum":"ede7d0b8a471754f71f17e2b20f3135b","relation":"main_file","creator":"system","file_size":226137,"file_name":"IST-2017-772-v1+1_AbbotEtAl2016-3.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:53Z","content_type":"application/pdf","date_created":"2018-12-12T10:10:12Z","file_id":"4797"}],"date_updated":"2021-01-12T06:50:33Z","quality_controlled":"1","page":"2325 - 2332","date_created":"2018-12-11T11:51:51Z","year":"2016","pubrep_id":"772","department":[{"_id":"NiBa"}],"title":"Genomics of hybridization and its evolutionary consequences","oa":1,"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"06","_id":"1409","intvolume":"        25","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.","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.","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>"},"has_accepted_license":"1","day":"08","status":"public"},{"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"publication_status":"published","title":"A general approximation for the dynamics of quantitative traits","oa":1,"_id":"1420","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       202","citation":{"short":"K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.","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>","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>.","ista":"Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548.","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>","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.","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>."},"day":"06","abstract":[{"lang":"eng","text":"Selection, mutation, and random drift affect the dynamics of allele frequencies and consequently of quantitative traits. While the macroscopic dynamics of quantitative traits can be measured, the underlying allele frequencies are typically unobserved. Can we understand how the macroscopic observables evolve without following these microscopic processes? This problem has been studied previously by analogy with statistical mechanics: the allele frequency distribution at each time point is approximated by the stationary form, which maximizes entropy. We explore the limitations of this method when mutation is small (4Nμ &lt; 1) so that populations are typically close to fixation, and we extend the theory in this regime to account for changes in mutation strength. We consider a single diallelic locus either under directional selection or with overdominance and then generalize to multiple unlinked biallelic loci with unequal effects. We find that the maximum-entropy approximation is remarkably accurate, even when mutation and selection change rapidly. "}],"status":"public","ec_funded":1,"author":[{"last_name":"Bod'ová","first_name":"Katarína","full_name":"Bod'ová, Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","first_name":"Gasper"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"issue":"4","publist_id":"5787","publication":"Genetics","date_published":"2016-04-06T00:00:00Z","oa_version":"Preprint","external_id":{"arxiv":["1510.08344"]},"type":"journal_article","arxiv":1,"language":[{"iso":"eng"}],"publisher":"Genetics Society of America","doi":"10.1534/genetics.115.184127","main_file_link":[{"url":"http://arxiv.org/abs/1510.08344","open_access":"1"}],"scopus_import":"1","article_processing_charge":"No","volume":202,"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"name":"Information processing and computation in fish groups","grant_number":"RGP0065/2012","_id":"255008E4-B435-11E9-9278-68D0E5697425"}],"date_updated":"2025-05-28T11:42:47Z","date_created":"2018-12-11T11:51:55Z","year":"2016","quality_controlled":"1","page":"1523 - 1548"},{"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>","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>","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>.","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>.","ieee":"T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute of Science and Technology Austria, 2016."},"day":"19","has_accepted_license":"1","article_processing_charge":"No","tmp":{"short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"status":"public","file":[{"file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip","content_type":"application/zip","file_id":"5594","date_created":"2018-12-12T13:02:27Z","access_level":"open_access","date_updated":"2020-07-14T12:47:00Z","relation":"main_file","checksum":"950f85b80427d357bfeff09608ba02e9","file_size":4468543,"creator":"system"}],"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)"}],"date_created":"2018-12-12T12:31:29Z","year":"2016","date_updated":"2024-02-21T13:49:54Z","publist_id":"5828","author":[{"last_name":"Ellis","full_name":"Ellis, Thomas","first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David","first_name":"David","last_name":"Field"}],"ddc":["576"],"oa_version":"Published Version","department":[{"_id":"NiBa"}],"date_published":"2016-02-19T00:00:00Z","oa":1,"title":"Flower colour data and phylogeny (NEXUS) files","related_material":{"record":[{"status":"public","relation":"research_paper","id":"1382"}]},"type":"research_data","file_date_updated":"2020-07-14T12:47:00Z","datarep_id":"34","_id":"5550","doi":"10.15479/AT:ISTA:34","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria"},{"abstract":[{"lang":"eng","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."}],"file":[{"content_type":"application/zip","file_id":"5640","date_created":"2018-12-12T13:05:12Z","access_level":"open_access","date_updated":"2020-07-14T12:47:01Z","file_name":"IST-2016-35-v1+1_array_data.zip","file_size":32775,"creator":"system","relation":"main_file","checksum":"aa3eb85d52b110cd192aa23147c4d4f3"}],"contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"status":"public","date_updated":"2024-02-21T13:51:27Z","year":"2016","date_created":"2018-12-12T12:31:29Z","citation":{"short":"T. Ellis, (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>","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>.","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>.","ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016.","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>."},"tmp":{"short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"article_processing_charge":"No","has_accepted_license":"1","day":"19","file_date_updated":"2020-07-14T12:47:01Z","type":"research_data","oa":1,"title":"Data on pollinator observations and offpsring phenotypes","related_material":{"record":[{"status":"public","relation":"research_paper","id":"1398"}]},"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5551","doi":"10.15479/AT:ISTA:35","month":"02","datarep_id":"35","author":[{"first_name":"Thomas","full_name":"Ellis, Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254"}],"date_published":"2016-02-19T00:00:00Z","department":[{"_id":"NiBa"}],"oa_version":"Published Version"},{"article_processing_charge":"No","has_accepted_license":"1","day":"19","citation":{"short":"T. Ellis, (2016).","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>","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>.","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>","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>.","ieee":"T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.” Institute of Science and Technology Austria, 2016."},"date_updated":"2024-02-21T13:51:40Z","year":"2016","date_created":"2018-12-12T12:31:30Z","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"}],"file":[{"file_size":44905,"creator":"system","relation":"main_file","checksum":"cbc61b523d4d475a04a737d50dc470ef","file_id":"5625","content_type":"application/zip","date_created":"2018-12-12T13:03:07Z","date_updated":"2020-07-14T12:47:01Z","access_level":"open_access","file_name":"IST-2016-36-v1+1_tag_assay_archive.zip"}],"contributor":[{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"status":"public","date_published":"2016-02-19T00:00:00Z","department":[{"_id":"NiBa"}],"oa_version":"Published Version","author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","last_name":"Ellis","first_name":"Thomas","full_name":"Ellis, Thomas"}],"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","datarep_id":"36","_id":"5552","doi":"10.15479/AT:ISTA:36","month":"02","file_date_updated":"2020-07-14T12:47:01Z","type":"research_data","oa":1,"related_material":{"record":[{"id":"1398","relation":"research_paper","status":"public"}]},"title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data."},{"keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"],"citation":{"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>.","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>","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.","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>.","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>"},"day":"19","tmp":{"short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"article_processing_charge":"No","has_accepted_license":"1","status":"public","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."}],"file":[{"access_level":"open_access","date_updated":"2020-07-14T12:47:01Z","content_type":"application/zip","file_id":"5620","date_created":"2018-12-12T13:03:02Z","file_name":"IST-2016-37-v1+1_paternity_archive.zip","creator":"system","file_size":132808,"checksum":"4ae751b1fa4897fa216241f975a57313","relation":"main_file"}],"contributor":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_manager","orcid":"0000-0002-8548-5240"}],"date_created":"2018-12-12T12:31:30Z","year":"2016","date_updated":"2024-02-21T13:51:14Z","ddc":["576"],"author":[{"last_name":"Field","full_name":"Field, David","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","last_name":"Ellis","first_name":"Thomas","full_name":"Ellis, Thomas"}],"oa_version":"Published Version","date_published":"2016-02-19T00:00:00Z","department":[{"_id":"NiBa"}],"oa":1,"related_material":{"record":[{"status":"public","relation":"research_paper","id":"1398"}]},"title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","file_date_updated":"2020-07-14T12:47:01Z","type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","datarep_id":"37","_id":"5553","month":"02","doi":"10.15479/AT:ISTA:37","publisher":"Institute of Science and Technology Austria"},{"author":[{"last_name":"Tugrul","full_name":"Tugrul, Murat","first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8523-0758"}],"oa_version":"Published Version","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"date_published":"2016-05-12T00:00:00Z","oa":1,"title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","related_material":{"record":[{"id":"1131","relation":"used_in_publication","status":"public"}]},"type":"research_data","file_date_updated":"2020-07-14T12:47:01Z","datarep_id":"43","_id":"5554","doi":"10.15479/AT:ISTA:43","month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","keyword":["RNAP binding","de novo promoter evolution","lac promoter"],"citation":{"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>","short":"M. Tugrul, (2016).","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016.","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>.","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>."},"day":"12","has_accepted_license":"1","article_processing_charge":"No","tmp":{"short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"status":"public","contributor":[{"first_name":"Magdalena","last_name":"Steinrück","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher"},{"id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Fabienne","last_name":"Jesse"}],"file":[{"file_id":"5626","content_type":"application/zip","date_created":"2018-12-12T13:03:08Z","date_updated":"2020-07-14T12:47:01Z","access_level":"open_access","file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip","file_size":1123495,"creator":"system","relation":"main_file","checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2"}],"abstract":[{"lang":"eng","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."}],"year":"2016","date_created":"2018-12-12T12:31:30Z","date_updated":"2024-02-21T13:50:34Z"}]