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Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics, Public Library of Science, 10.1371/journal.pbio.2001894.s016.","mla":"Schmidt, Tom, et al. Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics. Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.s016.","ama":"Schmidt T, Barton NH, Rasic G, et al. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. 2017. doi:10.1371/journal.pbio.2001894.s016","ieee":"T. Schmidt et al., “Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics.” Public Library of Science, 2017.","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.s016.","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s016"}},{"abstract":[{"lang":"eng","text":"Assortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few-locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two-deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration-selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual-based simulations."}],"quality_controlled":"1","date_updated":"2025-07-10T12:02:04Z","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow","publication_status":"published","isi":1,"date_published":"2017-06-01T00:00:00Z","external_id":{"isi":["000403014800005"],"pmid":["28419447"]},"ec_funded":1,"publication_identifier":{"issn":["0014-3820"]},"corr_author":"1","publication":"Evolution; International Journal of Organic Evolution","pubrep_id":"977","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Sachdeva H, Barton NH. 2017. 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Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8.","apa":"Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8","short":"T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017).","ama":"Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00238-8","ieee":"T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","ista":"Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 8(1), 216.","mla":"Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8."},"publication":"Nature Communications","pubrep_id":"864","publication_identifier":{"issn":["2041-1723"]},"corr_author":"1","ec_funded":1,"date_updated":"2026-04-08T13:54:24Z","publication_status":"published","title":"Evolution of new regulatory functions on biophysically realistic fitness landscapes","project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"date_published":"2017-08-09T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"external_id":{"isi":["000407198800005"]},"quality_controlled":"1","abstract":[{"text":"Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.","lang":"eng"}]},{"_id":"1074","status":"public","oa_version":"Preprint","month":"03","oa":1,"volume":205,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"200"}]},"date_created":"2018-12-11T11:50:00Z","author":[{"id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","first_name":"Harald","last_name":"Ringbauer","full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682"},{"first_name":"Graham","last_name":"Coop","full_name":"Coop, Graham"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"main_file_link":[{"url":"http://www.biorxiv.org/content/early/2016/09/23/076810","open_access":"1"}],"intvolume":" 205","doi":"10.1534/genetics.116.196220","scopus_import":"1","department":[{"_id":"NiBa"}],"publist_id":"6307","article_processing_charge":"No","issue":"3","day":"01","publisher":"Genetics Society of America","page":"1335 - 1351","year":"2017","language":[{"iso":"eng"}],"ec_funded":1,"publication_identifier":{"issn":["0016-6731"]},"quality_controlled":"1","abstract":[{"lang":"eng","text":"Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite likelihood approach to fit these formulae. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the POPRES data set. We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance."}],"isi":1,"external_id":{"isi":["000395807200023"]},"date_published":"2017-03-01T00:00:00Z","title":"Inferring recent demography from isolation by distance of long shared sequence blocks","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication_status":"published","date_updated":"2026-04-08T14:06:35Z","type":"journal_article","publication":"Genetics","citation":{"chicago":"Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.196220.","apa":"Ringbauer, H., Coop, G., & Barton, N. H. (2017). Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.196220","short":"H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351.","ama":"Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 2017;205(3):1335-1351. doi:10.1534/genetics.116.196220","ieee":"H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from isolation by distance of long shared sequence blocks,” Genetics, vol. 205, no. 3. Genetics Society of America, pp. 1335–1351, 2017.","mla":"Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics, vol. 205, no. 3, Genetics Society of America, 2017, pp. 1335–51, doi:10.1534/genetics.116.196220.","ista":"Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"day":"01","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"has_accepted_license":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2017","page":"83","month":"02","oa":1,"oa_version":"Published Version","status":"public","_id":"6291","ddc":["570"],"file_date_updated":"2021-02-22T13:45:59Z","date_created":"2019-04-09T15:16:45Z","author":[{"id":"35F78294-F248-11E8-B48F-1D18A9856A87","first_name":"Pavel","last_name":"Payne","full_name":"Payne, Pavel","orcid":"0000-0002-2711-9453"}],"alternative_title":["ISTA Thesis"],"file":[{"file_name":"thesis_pavel_payne_final_w_signature_page.pdf","date_created":"2019-04-09T15:15:32Z","access_level":"closed","creator":"dernst","date_updated":"2020-07-14T12:47:27Z","file_id":"6292","file_size":3025175,"checksum":"a0fc5c26a89c0ea759947ffba87d0d8f","relation":"main_file","content_type":"application/pdf"},{"date_updated":"2021-02-22T13:45:59Z","success":1,"creator":"dernst","access_level":"open_access","file_name":"2017_Payne_Thesis.pdf","date_created":"2021-02-22T13:45:59Z","relation":"main_file","content_type":"application/pdf","checksum":"af531e921a7f64a9e0af4cd8783b2226","file_id":"9187","file_size":3111536}],"type":"dissertation","supervisor":[{"last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"},{"full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"short":"P. Payne, Bacterial Herd and Social Immunity to Phages, Institute of Science and Technology Austria, 2017.","apa":"Payne, P. (2017). Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","chicago":"Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute of Science and Technology Austria, 2017.","mla":"Payne, Pavel. Bacterial Herd and Social Immunity to Phages. Institute of Science and Technology Austria, 2017.","ista":"Payne P. 2017. Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","ieee":"P. Payne, “Bacterial herd and social immunity to phages,” Institute of Science and Technology Austria, 2017.","ama":"Payne P. Bacterial herd and social immunity to phages. 2017."},"publication_identifier":{"issn":["2663-337X"]},"corr_author":"1","date_published":"2017-02-01T00:00:00Z","date_updated":"2026-04-08T14:16:28Z","publication_status":"published","title":"Bacterial herd and social immunity to phages","degree_awarded":"PhD","abstract":[{"lang":"eng","text":"Bacteria and their pathogens – phages – are the most abundant living entities on Earth. Throughout their coevolution, bacteria have evolved multiple immune systems to overcome the ubiquitous threat from the phages. Although the molecu- lar details of these immune systems’ functions are relatively well understood, their epidemiological consequences for the phage-bacterial communities have been largely neglected. In this thesis we employed both experimental and theoretical methods to explore whether herd and social immunity may arise in bacterial popu- lations. Using our experimental system consisting of Escherichia coli strains with a CRISPR based immunity to the T7 phage we show that herd immunity arises in phage-bacterial communities and that it is accentuated when the populations are spatially structured. By fitting a mathematical model, we inferred expressions for the herd immunity threshold and the velocity of spread of a phage epidemic in partially resistant bacterial populations, which both depend on the bacterial growth rate, phage burst size and phage latent period. We also investigated the poten- tial for social immunity in Streptococcus thermophilus and its phage 2972 using a bioinformatic analysis of potentially coding short open reading frames with a signalling signature, encoded within the CRISPR associated genes. Subsequently, we tested one identified potentially signalling peptide and found that its addition to a phage-challenged culture increases probability of survival of bacteria two fold, although the results were only marginally significant. Together, these results demonstrate that the ubiquitous arms races between bacteria and phages have further consequences at the level of the population."}]},{"oa":1,"month":"06","status":"public","oa_version":"Published Version","_id":"1336","file_date_updated":"2020-07-14T12:44:44Z","ddc":["576"],"scopus_import":"1","doi":"10.1007/s00453-016-0212-1","intvolume":" 78","author":[{"last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"},{"first_name":"Jorge","last_name":"Pérez Heredia","full_name":"Pérez Heredia, Jorge"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora","full_name":"Trubenova, Barbora","last_name":"Trubenova","orcid":"0000-0002-6873-2967"}],"date_created":"2018-12-11T11:51:27Z","volume":78,"publisher":"Springer","day":"01","issue":"2","has_accepted_license":"1","article_processing_charge":"No","publist_id":"5931","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"language":[{"iso":"eng"}],"year":"2017","page":"681 - 713","publication_identifier":{"issn":["0178-4617"]},"ec_funded":1,"date_updated":"2026-04-16T09:55:33Z","title":"Towards a runtime comparison of natural and artificial evolution","project":[{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091"}],"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2017-06-01T00:00:00Z","external_id":{"isi":["000400379500013"]},"isi":1,"abstract":[{"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 the runtimes of EAs 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 occurrences of new mutations is much longer than the time it takes for a mutated genotype to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a stochastic process evolving one genotype by means of mutation and selection between the resident and the mutated genotype. The probability of accepting the mutated genotype then depends on the change in fitness. We study this process, SSWM, from an algorithmic perspective, quantifying its expected optimisation time for various parameters and investigating differences to a similar evolutionary algorithm, the well-known (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.","lang":"eng"}],"quality_controlled":"1","file":[{"access_level":"open_access","creator":"system","date_updated":"2020-07-14T12:44:44Z","file_name":"IST-2016-658-v1+1_s00453-016-0212-1.pdf","date_created":"2018-12-12T10:10:19Z","checksum":"7873f665a0c598ac747c908f34cb14b9","relation":"main_file","content_type":"application/pdf","file_id":"4805","file_size":710206}],"type":"journal_article","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"apa":"Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. Algorithmica. Springer. https://doi.org/10.1007/s00453-016-0212-1","chicago":"Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica. Springer, 2017. https://doi.org/10.1007/s00453-016-0212-1.","short":"T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713.","ama":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 2017;78(2):681-713. doi:10.1007/s00453-016-0212-1","ieee":"T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” Algorithmica, vol. 78, no. 2. Springer, pp. 681–713, 2017.","ista":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713.","mla":"Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica, vol. 78, no. 2, Springer, 2017, pp. 681–713, doi:10.1007/s00453-016-0212-1."},"publication":"Algorithmica","pubrep_id":"658"},{"oa":1,"month":"07","status":"public","oa_version":"Published Version","_id":"696","ddc":["576"],"file_date_updated":"2020-07-14T12:47:46Z","article_number":"e1005609","scopus_import":"1","doi":"10.1371/journal.pcbi.1005609","intvolume":" 13","author":[{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta","last_name":"Lukacisinova","full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Novak, Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X"},{"orcid":"0000-0003-2361-3953","last_name":"Paixao","full_name":"Paixao, Tiago","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:47:58Z","related_material":{"record":[{"id":"9849","relation":"research_data","status":"public"},{"relation":"research_data","id":"9850","status":"public"},{"id":"9851","relation":"research_data","status":"public"},{"id":"9852","relation":"research_data","status":"public"},{"relation":"dissertation_contains","id":"6263","status":"public"}]},"volume":13,"article_type":"original","publisher":"Public Library of Science","day":"18","issue":"7","has_accepted_license":"1","article_processing_charge":"No","publist_id":"7004","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"language":[{"iso":"eng"}],"year":"2017","publication_identifier":{"issn":["1553-734X"]},"corr_author":"1","ec_funded":1,"date_updated":"2026-05-27T22:31:02Z","publication_status":"published","title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","project":[{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000406619800014"]},"isi":1,"date_published":"2017-07-18T00:00:00Z","abstract":[{"text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy.","lang":"eng"}],"quality_controlled":"1","file":[{"file_size":3775716,"file_id":"5117","relation":"main_file","content_type":"application/pdf","checksum":"9143c290fa6458ed2563bff4b295554a","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","date_created":"2018-12-12T10:15:01Z","date_updated":"2020-07-14T12:47:46Z","access_level":"open_access","creator":"system"}],"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609.","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” PLoS Computational Biology, vol. 13, no. 7. Public Library of Science, 2017.","ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 2017;13(7). doi:10.1371/journal.pcbi.1005609"},"publication":"PLoS Computational Biology","pubrep_id":"894"},{"isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2016-12-27T00:00:00Z","external_id":{"isi":["000392120100008"]},"publication_status":"published","title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","date_updated":"2025-09-22T09:55:10Z","quality_controlled":"1","abstract":[{"text":"Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate "grey zone" of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation.","lang":"eng"}],"file":[{"access_level":"open_access","creator":"system","date_updated":"2020-07-14T12:44:36Z","date_created":"2018-12-12T10:15:42Z","file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","checksum":"2bab63b068a9840efd532b9ae583f9bb","content_type":"application/pdf","relation":"main_file","file_id":"5164","file_size":2494348}],"acknowledgement":"European Research Council (ERC) https://erc.europa.eu/ (grant number ERC grant 232971). PopPhyl project. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/ (grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch) Center for high-performance computing of the SIB Swiss Institute of Bioinformatics and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité.","type":"journal_article","citation":{"mla":"Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” PLoS Biology, vol. 14, no. 12, e2000234, Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 14(12), e2000234.","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Shedding light on the grey zone of speciation along a continuum of genomic divergence,” PLoS Biology, vol. 14, no. 12. Public Library of Science, 2016.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 2016;14(12). doi:10.1371/journal.pbio.2000234","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016).","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” PLoS Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pubrep_id":"742","publication":"PLoS Biology","month":"12","oa":1,"article_number":"e2000234","_id":"1158","ddc":["576"],"file_date_updated":"2020-07-14T12:44:36Z","oa_version":"Published Version","status":"public","intvolume":" 14","doi":"10.1371/journal.pbio.2000234","scopus_import":"1","volume":14,"date_created":"2018-12-11T11:50:28Z","related_material":{"record":[{"status":"public","id":"9862","relation":"research_data"},{"status":"public","relation":"research_data","id":"9863"}]},"author":[{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"},{"last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"full_name":"Romiguier, Jonathan","last_name":"Romiguier","first_name":"Jonathan"},{"first_name":"Youann","last_name":"Anciaux","full_name":"Anciaux, Youann"},{"last_name":"Galtier","full_name":"Galtier, Nicolas","first_name":"Nicolas"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}],"day":"27","issue":"12","publisher":"Public Library of Science","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publist_id":"6200","article_processing_charge":"No","has_accepted_license":"1","year":"2016","language":[{"iso":"eng"}]},{"article_number":"38840","file_date_updated":"2020-07-14T12:44:37Z","_id":"1172","ddc":["576"],"oa_version":"Published Version","status":"public","month":"12","oa":1,"volume":6,"date_created":"2018-12-11T11:50:32Z","author":[{"last_name":"Sachdeva","full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani"},{"full_name":"Barma, Mustansir","last_name":"Barma","first_name":"Mustansir"},{"last_name":"Rao","full_name":"Rao, Madan","first_name":"Madan"}],"intvolume":" 6","doi":"10.1038/srep38840","scopus_import":"1","department":[{"_id":"NiBa"}],"publist_id":"6183","article_processing_charge":"No","has_accepted_license":"1","day":"19","publisher":"Nature Publishing Group","year":"2016","language":[{"iso":"eng"}],"abstract":[{"text":"A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner-this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging.","lang":"eng"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2016-12-19T00:00:00Z","external_id":{"isi":["000389885900001"]},"publication_status":"published","title":"Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae","date_updated":"2025-09-22T09:49:53Z","type":"journal_article","acknowledgement":"H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund Thattai for critical discussions and suggestions.","file":[{"file_size":760967,"file_id":"4977","content_type":"application/pdf","relation":"main_file","checksum":"cb378732da885ea4959ec5b845fb6e52","date_created":"2018-12-12T10:12:56Z","file_name":"IST-2017-737-v1+1_srep38840.pdf","date_updated":"2020-07-14T12:44:37Z","creator":"system","access_level":"open_access"}],"pubrep_id":"737","publication":"Scientific Reports","citation":{"short":"H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).","apa":"Sachdeva, H., Barma, M., & Rao, M. (2016). Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep38840","chicago":"Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep38840.","mla":"Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific Reports, vol. 6, 38840, Nature Publishing Group, 2016, doi:10.1038/srep38840.","ista":"Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.","ama":"Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 2016;6. doi:10.1038/srep38840","ieee":"H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae,” Scientific Reports, vol. 6. 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Barghi for helpful comments on earlier versions of\r\nthe manuscript. This work was supported by the European\r\nResearch Council (ERC) grants “ArchAdapt” and “250152”.","file":[{"file_size":295274,"file_id":"5223","checksum":"1e78d3aaffcb40dc8b02b7b4666019e0","content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T10:16:35Z","file_name":"IST-2017-770-v1+1_FranssenEtAl_nofigs-1.pdf","creator":"system","access_level":"open_access","date_updated":"2020-07-14T12:44:38Z"},{"file_size":10902625,"file_id":"5224","content_type":"application/pdf","relation":"main_file","checksum":"e13171843283774404c936c581b4543e","date_created":"2018-12-12T10:16:36Z","file_name":"IST-2017-770-v1+2_Fig1.pdf","date_updated":"2020-07-14T12:44:38Z","creator":"system","access_level":"open_access"},{"file_size":21437,"file_id":"5225","content_type":"application/pdf","relation":"main_file","checksum":"63bc6e6e61f347594d8c00c37f874a0b","date_created":"2018-12-12T10:16:37Z","file_name":"IST-2017-770-v1+3_Fig2.pdf","date_updated":"2020-07-14T12:44:38Z","creator":"system","access_level":"open_access"},{"date_updated":"2020-07-14T12:44:38Z","creator":"system","access_level":"open_access","file_name":"IST-2017-770-v1+4_Fig3.pdf","date_created":"2018-12-12T10:16:38Z","relation":"main_file","content_type":"application/pdf","checksum":"da87cc7c78808837f22a3dae1c8397f9","file_size":1172194,"file_id":"5226"},{"access_level":"open_access","creator":"system","date_updated":"2020-07-14T12:44:38Z","date_created":"2018-12-12T10:16:38Z","file_name":"IST-2017-770-v1+5_Fig4.pdf","checksum":"e47b2a0c32142f423b3100150c0294f8","content_type":"application/pdf","relation":"main_file","file_size":50045,"file_id":"5227"},{"file_size":50705,"file_id":"5228","checksum":"a5a7d6b32e7e17d35d337d7ec2a9f6c9","relation":"main_file","content_type":"application/pdf","file_name":"IST-2017-770-v1+6_Fig5.pdf","date_created":"2018-12-12T10:16:39Z","access_level":"open_access","creator":"system","date_updated":"2020-07-14T12:44:38Z"}],"publication":"Molecular Biology and Evolution","pubrep_id":"770","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"mla":"Franssen, Susan, et al. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology and Evolution, vol. 34, no. 1, Oxford University Press, 2016, pp. 174–84, doi:10.1093/molbev/msw210.","ista":"Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 34(1), 174–184.","ama":"Franssen S, Barton NH, Schlötterer C. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 2016;34(1):174-184. doi:10.1093/molbev/msw210","ieee":"S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks selected during experimental evolution.,” Molecular Biology and Evolution, vol. 34, no. 1. Oxford University Press, pp. 174–184, 2016.","short":"S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution 34 (2016) 174–184.","apa":"Franssen, S., Barton, N. H., & Schlötterer, C. (2016). Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msw210","chicago":"Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msw210."},"ec_funded":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (Pool-Seq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpretation of selection signatures in most Evolve and Resequencing studies remains challenging. To facilitate the characterization of selection targets, we propose a new approach that reconstructs selected haplotypes from replicated time series, using Pool-Seq data. We identify selected haplotypes through the correlated frequencies of alleles carried by them. Computer simulations indicate that selected haplotype-blocks of several Mb can be reconstructed with high confidence and low error rates, even when allele frequencies change only by 20% across three replicates. Applying this method to real data from D. melanogaster populations adapting to a hot environment, we identify a selected haplotype-block of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations by experimental haplotyping, demonstrating the power and accuracy of our haplotype reconstruction from Pool-Seq data. We propose that the combination of allele frequency estimates with haplotype information will provide the key to understanding the dynamics of adaptive alleles. "}],"isi":1,"external_id":{"isi":["000396772000009"]},"date_published":"2016-10-03T00:00:00Z","date_updated":"2025-09-22T09:43:41Z","title":"Reconstruction of haplotype-blocks selected during experimental evolution.","publication_status":"published","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"publication":"Plant Biology","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"short":"Z. Teitel, M. Pickup, D. Field, S. Barrett, Plant Biology 18 (2016) 98–103.","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.” Plant Biology. Wiley-Blackwell, 2016. https://doi.org/10.1111/plb.12336.","apa":"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. Wiley-Blackwell. https://doi.org/10.1111/plb.12336","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.","mla":"Teitel, Zachary, et al. “The Dynamics of Resource Allocation and Costs of Reproduction in a Sexually Dimorphic, Wind-Pollinated Dioecious Plant.” Plant Biology, vol. 18, no. 1, Wiley-Blackwell, 2016, pp. 98–103, doi:10.1111/plb.12336.","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,” Plant Biology, vol. 18, no. 1. Wiley-Blackwell, pp. 98–103, 2016.","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. Plant Biology. 2016;18(1):98-103. doi:10.1111/plb.12336"},"type":"journal_article","quality_controlled":"1","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."}],"date_updated":"2025-09-22T09:31:49Z","title":"The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant","publication_status":"published","date_published":"2016-01-01T00:00:00Z","isi":1,"external_id":{"isi":["000369975700011"]},"page":"98 - 103","language":[{"iso":"eng"}],"year":"2016","publist_id":"6110","article_processing_charge":"No","department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","day":"01","issue":"1","author":[{"last_name":"Teitel","full_name":"Teitel, Zachary","first_name":"Zachary"},{"first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda","last_name":"Pickup"},{"last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"first_name":"Spencer","last_name":"Barrett","full_name":"Barrett, Spencer"}],"date_created":"2018-12-11T11:50:48Z","volume":18,"scopus_import":"1","doi":"10.1111/plb.12336","intvolume":" 18","oa_version":"None","status":"public","_id":"1224","month":"01"},{"ec_funded":1,"title":"When non-elitism outperforms elitism for crossing fitness valleys","publication_status":"published","project":[{"grant_number":"618091","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"date_updated":"2025-09-22T08:13:19Z","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000382659200147"]},"date_published":"2016-07-20T00:00:00Z","abstract":[{"text":"Crossing fitness valleys is one of the major obstacles to function optimization. In this paper we investigate how the structure of the fitness valley, namely its depth d and length ℓ, influence the runtime of different strategies for crossing these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis algorithm. While the (1+1) EA has to jump across the valley to a point of higher fitness because it does not accept decreasing moves, the non-elitist algorithms may cross the valley by accepting worsening moves. We show that while the runtime of the (1+1) EA algorithm depends critically on the length of the valley, the runtimes of the non-elitist algorithms depend crucially only on the depth of the valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of small length. Moreover, we show that both SSWM and Metropolis can also efficiently optimize a rugged function consisting of consecutive valleys.","lang":"eng"}],"quality_controlled":"1","file":[{"file_id":"5214","file_size":979026,"content_type":"application/pdf","relation":"main_file","checksum":"a1896e39e4113f2711e46b435d5f3e69","date_created":"2018-12-12T10:16:27Z","file_name":"IST-2016-650-v1+1_p1163-oliveto.pdf","date_updated":"2020-07-14T12:44:45Z","access_level":"open_access","creator":"system"}],"type":"conference","conference":{"name":"GECCO: Genetic and evolutionary computation conference","end_date":"2016-07-24","start_date":"2016-07-20","location":"Denver, CO, USA"},"citation":{"apa":"Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., & Trubenova, B. (2016). When non-elitism outperforms elitism for crossing fitness valleys. In Proceedings of the Genetic and Evolutionary Computation Conference 2016 (pp. 1163–1170). Denver, CO, USA: ACM. https://doi.org/10.1145/2908812.2908909","chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” In Proceedings of the Genetic and Evolutionary Computation Conference 2016 , 1163–70. ACM, 2016. https://doi.org/10.1145/2908812.2908909.","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.","ama":"Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. When non-elitism outperforms elitism for crossing fitness valleys. In: Proceedings of the Genetic and Evolutionary Computation Conference 2016 . ACM; 2016:1163-1170. doi:10.1145/2908812.2908909","ieee":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism outperforms elitism for crossing fitness valleys,” in Proceedings of the Genetic and Evolutionary Computation Conference 2016 , 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.","mla":"Oliveto, Pietro, et al. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–70, doi:10.1145/2908812.2908909."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pubrep_id":"650","publication":"Proceedings of the Genetic and Evolutionary Computation Conference 2016 ","oa":1,"month":"07","ddc":["576"],"_id":"1349","file_date_updated":"2020-07-14T12:44:45Z","oa_version":"Published Version","status":"public","doi":"10.1145/2908812.2908909","scopus_import":"1","author":[{"full_name":"Oliveto, Pietro","last_name":"Oliveto","first_name":"Pietro"},{"orcid":"0000-0003-2361-3953","last_name":"Paixao","full_name":"Paixao, Tiago","first_name":"Tiago","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","first_name":"Barbora","full_name":"Trubenova, Barbora","last_name":"Trubenova","orcid":"0000-0002-6873-2967"}],"date_created":"2018-12-11T11:51:31Z","publisher":"ACM","day":"20","publist_id":"5900","article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"year":"2016","language":[{"iso":"eng"}],"page":"1163 - 1170"},{"type":"journal_article","file":[{"date_updated":"2020-07-14T12:44:46Z","creator":"system","access_level":"open_access","date_created":"2018-12-12T10:08:26Z","file_name":"IST-2017-769-v1+1_SewallWright1931.pdf","content_type":"application/pdf","relation":"main_file","checksum":"3562b89c821a4be84edf2b6ebd870cf5","file_id":"4687","file_size":112674}],"pubrep_id":"769","publication":"Genetics","citation":{"ama":"Barton NH. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” Genetics. 2016;202(1):3-4. doi:10.1534/genetics.115.184796","ieee":"N. H. Barton, “Sewall Wright on evolution in Mendelian populations and the ‘Shifting Balance,’” Genetics, vol. 202, no. 1. Genetics Society of America, pp. 3–4, 2016.","ista":"Barton NH. 2016. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”. Genetics. 202(1), 3–4.","mla":"Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” Genetics, vol. 202, no. 1, Genetics Society of America, 2016, pp. 3–4, doi:10.1534/genetics.115.184796.","apa":"Barton, N. H. (2016). Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184796","chicago":"Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184796.","short":"N.H. Barton, Genetics 202 (2016) 3–4."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","quality_controlled":"1","isi":1,"external_id":{"isi":["000367718100002"]},"date_published":"2016-01-05T00:00:00Z","publication_status":"published","title":"Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”","date_updated":"2025-09-22T08:01:07Z","department":[{"_id":"NiBa"}],"article_processing_charge":"No","publist_id":"5889","has_accepted_license":"1","day":"05","issue":"1","publisher":"Genetics Society of America","page":"3 - 4","year":"2016","language":[{"iso":"eng"}],"ddc":["570"],"_id":"1356","file_date_updated":"2020-07-14T12:44:46Z","oa_version":"Submitted Version","status":"public","month":"01","oa":1,"volume":202,"date_created":"2018-12-11T11:51:33Z","author":[{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"intvolume":" 202","doi":"10.1534/genetics.115.184796","scopus_import":"1"},{"corr_author":"1","isi":1,"date_published":"2016-03-01T00:00:00Z","external_id":{"isi":["000371596400001"]},"date_updated":"2025-09-22T07:56:18Z","title":"Richard Hudson and Norman Kaplan on the coalescent process","publication_status":"published","quality_controlled":"1","file":[{"date_created":"2018-12-12T10:15:09Z","file_name":"IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf","date_updated":"2020-07-14T12:44:46Z","access_level":"open_access","creator":"system","file_size":130779,"file_id":"5127","content_type":"application/pdf","relation":"main_file","checksum":"b2174bab2de1d1142900062a150f35c9"}],"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"short":"N.H. Barton, Genetics 202 (2016) 865–866.","apa":"Barton, N. H. (2016). Richard Hudson and Norman Kaplan on the coalescent process. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.187542","chicago":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.116.187542.","mla":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” Genetics, vol. 202, no. 3, Genetics Society of America, 2016, pp. 865–66, doi:10.1534/genetics.116.187542.","ista":"Barton NH. 2016. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 202(3), 865–866.","ama":"Barton NH. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 2016;202(3):865-866. doi:10.1534/genetics.116.187542","ieee":"N. H. Barton, “Richard Hudson and Norman Kaplan on the coalescent process,” Genetics, vol. 202, no. 3. Genetics Society of America, pp. 865–866, 2016."},"publication":"Genetics","pubrep_id":"768","month":"03","oa":1,"oa_version":"Submitted Version","status":"public","_id":"1357","ddc":["576"],"file_date_updated":"2020-07-14T12:44:46Z","intvolume":" 202","scopus_import":"1","doi":"10.1534/genetics.116.187542","date_created":"2018-12-11T11:51:33Z","volume":202,"author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"issue":"3","day":"01","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"has_accepted_license":"1","publist_id":"5888","article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2016","page":"865 - 866"},{"article_processing_charge":"No","publist_id":"5886","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"National Academy of Sciences","article_type":"original","day":"19","issue":"16","page":"4422 - 4427","language":[{"iso":"eng"}],"year":"2016","status":"public","oa_version":"Published Version","_id":"1359","oa":1,"month":"04","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/"}],"author":[{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","last_name":"Paixao"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:51:34Z","volume":113,"scopus_import":"1","doi":"10.1073/pnas.1518830113","intvolume":" 113","type":"journal_article","publication":"PNAS","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"short":"T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427.","chicago":"Paixao, Tiago, and Nicholas H Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1518830113.","apa":"Paixao, T., & Barton, N. H. (2016). The effect of gene interactions on the long-term response to selection. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1518830113","ista":"Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 4422–4427.","mla":"Paixao, Tiago, and Nicholas H. Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” PNAS, vol. 113, no. 16, National Academy of Sciences, 2016, pp. 4422–27, doi:10.1073/pnas.1518830113.","ama":"Paixao T, Barton NH. The effect of gene interactions on the long-term response to selection. PNAS. 2016;113(16):4422-4427. doi:10.1073/pnas.1518830113","ieee":"T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term response to selection,” PNAS, vol. 113, no. 16. National Academy of Sciences, pp. 4422–4427, 2016."},"pmid":1,"ec_funded":1,"corr_author":"1","abstract":[{"lang":"eng","text":"The role of gene interactions in the evolutionary process has long\r\nbeen controversial. Although some argue that they are not of\r\nimportance, because most variation is additive, others claim that\r\ntheir effect in the long term can be substantial. Here, we focus on\r\nthe long-term effects of genetic interactions under directional\r\nselection assuming no mutation or dominance, and that epistasis is\r\nsymmetrical overall. We ask by how much the mean of a complex\r\ntrait can be increased by selection and analyze two extreme\r\nregimes, in which either drift or selection dominate the dynamics\r\nof allele frequencies. In both scenarios, epistatic interactions affect\r\nthe long-term response to selection by modulating the additive\r\ngenetic variance. When drift dominates, we extend Robertson\r\n’\r\ns\r\n[Robertson A (1960)\r\nProc R Soc Lond B Biol Sci\r\n153(951):234\r\n−\r\n249]\r\nargument to show that, for any form of epistasis, the total response\r\nof a haploid population is proportional to the initial total genotypic\r\nvariance. In contrast, the total response of a diploid population is\r\nincreased by epistasis, for a given initial genotypic variance. When\r\nselection dominates, we show that the total selection response can\r\nonly be increased by epistasis when s\r\nome initially deleterious alleles\r\nbecome favored as the genetic background changes. We find a sim-\r\nple approximation for this effect and show that, in this regime, it is\r\nthe structure of the genotype - phenotype map that matters and not\r\nthe variance components of the population."}],"quality_controlled":"1","date_updated":"2025-09-22T07:45:33Z","title":"The effect of gene interactions on the long-term response to selection","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091"}],"publication_status":"published","isi":1,"date_published":"2016-04-19T00:00:00Z","external_id":{"pmid":["27044080"],"isi":["000374393800056"]}},{"page":"1133 - 1140","year":"2016","language":[{"iso":"eng"}],"publist_id":"5828","article_processing_charge":"No","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","day":"01","issue":"7","author":[{"full_name":"Ellis, Thomas","last_name":"Ellis","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","last_name":"Field","full_name":"Field, David"}],"volume":117,"related_material":{"record":[{"id":"5550","relation":"popular_science","status":"public"}]},"date_created":"2018-12-11T11:51:42Z","doi":"10.1093/aob/mcw043","scopus_import":"1","intvolume":" 117","_id":"1382","status":"public","oa_version":"None","month":"06","publication":"Annals of Botany","citation":{"short":"T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140.","chicago":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany. Oxford University Press, 2016. https://doi.org/10.1093/aob/mcw043.","apa":"Ellis, T., & Field, D. (2016). Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. Oxford University Press. https://doi.org/10.1093/aob/mcw043","mla":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany, vol. 117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:10.1093/aob/mcw043.","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.","ama":"Ellis T, Field D. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. 2016;117(7):1133-1140. doi:10.1093/aob/mcw043","ieee":"T. Ellis and D. Field, “Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae,” Annals of Botany, vol. 117, no. 7. Oxford University Press, pp. 1133–1140, 2016."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","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.","quality_controlled":"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."}],"publication_status":"published","title":"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae","date_updated":"2025-09-22T07:32:44Z","isi":1,"external_id":{"isi":["000379733800004"]},"date_published":"2016-06-01T00:00:00Z","corr_author":"1"}]