[{"status":"public","type":"journal_article","_id":"1074","department":[{"_id":"NiBa"}],"date_updated":"2023-09-20T12:00:56Z","intvolume":" 205","month":"03","main_file_link":[{"open_access":"1","url":"http://www.biorxiv.org/content/early/2016/09/23/076810"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"ec_funded":1,"volume":205,"issue":"3","related_material":{"record":[{"relation":"dissertation_contains","id":"200","status":"public"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00166731"]},"project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"title":"Inferring recent demography from isolation by distance of long shared sequence blocks","external_id":{"isi":["000395807200023"]},"article_processing_charge":"No","author":[{"full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682","last_name":"Ringbauer","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","first_name":"Harald"},{"first_name":"Graham","full_name":"Coop, Graham","last_name":"Coop"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"publist_id":"6307","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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.","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","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","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."},"oa":1,"quality_controlled":"1","publisher":"Genetics Society of America","date_created":"2018-12-11T11:50:00Z","date_published":"2017-03-01T00:00:00Z","doi":"10.1534/genetics.116.196220","page":"1335 - 1351","publication":"Genetics","day":"01","year":"2017","isi":1},{"publication_status":"published","publication_identifier":{"issn":["00143820"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":71,"issue":"4","abstract":[{"text":"Severe environmental change can drive a population extinct unless the population adapts in time to the new conditions (“evolutionary rescue”). How does biparental sexual reproduction influence the chances of population persistence compared to clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele model for adaptation in diploid species, where rescue is contingent on the establishment of the mutant homozygote. Reproduction can occur by random mating, selfing, or clonally. Random mating generates and destroys the rescue mutant; selfing is efficient at generating it but at the same time depletes the heterozygote, which can lead to a low mutant frequency in the standing genetic variation. Due to these (and other) antagonistic effects, we find a nontrivial dependence of population survival on the rate of sex/selfing, which is strongly influenced by the dominance coefficient of the mutation before and after the environmental change. Importantly, since mating with the wild‐type breaks the mutant homozygote up, a slow decay of the wild‐type population size can impede rescue in randomly mating populations.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"url":"http://biorxiv.org/content/early/2016/10/14/081042","open_access":"1"}],"scopus_import":"1","intvolume":" 71","month":"04","date_updated":"2023-09-20T12:10:32Z","department":[{"_id":"NiBa"}],"_id":"1063","type":"journal_article","status":"public","year":"2017","isi":1,"publication":"Evolution","day":"01","page":"845 - 858","date_created":"2018-12-11T11:49:57Z","date_published":"2017-04-01T00:00:00Z","doi":"10.1111/evo.13191","oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","citation":{"mla":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58, doi:10.1111/evo.13191.","apa":"Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13191","ama":"Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 2017;71(4):845-858. doi:10.1111/evo.13191","ieee":"H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,” Evolution, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.","short":"H. Uecker, Evolution 71 (2017) 845–858.","chicago":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13191.","ista":"Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 71(4), 845–858."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000398545200003"]},"article_processing_charge":"No","author":[{"orcid":"0000-0001-9435-2813","full_name":"Uecker, Hildegard","last_name":"Uecker","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","first_name":"Hildegard"}],"publist_id":"6327","title":"Evolutionary rescue in randomly mating, selfing, and clonal populations","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}]},{"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"title":"Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow","article_processing_charge":"No","external_id":{"isi":["000403014800005"],"pmid":["28419447"]},"publist_id":"6409","author":[{"last_name":"Sachdeva","full_name":"Sachdeva, Himani","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Sachdeva H, Barton NH. 2017. Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. 71(6), 1478–1493.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Divergence and Evolution of Assortative Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13252.","ieee":"H. Sachdeva and N. H. Barton, “Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow,” Evolution; International Journal of Organic Evolution, vol. 71, no. 6. Wiley-Blackwell, pp. 1478–1493, 2017.","short":"H. Sachdeva, N.H. Barton, Evolution; International Journal of Organic Evolution 71 (2017) 1478–1493.","ama":"Sachdeva H, Barton NH. Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. 2017;71(6):1478-1493. doi:10.1111/evo.13252","apa":"Sachdeva, H., & Barton, N. H. (2017). Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13252","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Divergence and Evolution of Assortative Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution; International Journal of Organic Evolution, vol. 71, no. 6, Wiley-Blackwell, 2017, pp. 1478–93, doi:10.1111/evo.13252."},"oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","date_created":"2018-12-11T11:49:34Z","doi":"10.1111/evo.13252","date_published":"2017-06-01T00:00:00Z","page":"1478 - 1493 ","publication":"Evolution; International Journal of Organic Evolution","day":"01","year":"2017","has_accepted_license":"1","isi":1,"pubrep_id":"977","status":"public","type":"journal_article","_id":"990","file_date_updated":"2020-07-14T12:48:18Z","department":[{"_id":"NiBa"}],"ddc":["576"],"date_updated":"2023-09-22T09:55:13Z","intvolume":" 71","month":"06","scopus_import":"1","pmid":1,"oa_version":"Submitted Version","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."}],"ec_funded":1,"volume":71,"issue":"6","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6329","checksum":"6d4c38cb1347fd43620d1736c6df5c79","creator":"dernst","file_size":625260,"date_updated":"2020-07-14T12:48:18Z","file_name":"2017_Evolution_Sachdeva_supplement.pdf","date_created":"2019-04-17T07:37:04Z"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6330","checksum":"f1d90dd8831b44baf49b4dd176f263af","date_updated":"2020-07-14T12:48:18Z","file_size":520110,"creator":"dernst","date_created":"2019-04-17T07:37:04Z","file_name":"2017_Evolution_Sachdeva_article.pdf"}],"publication_status":"published","publication_identifier":{"issn":["00143820"]}},{"citation":{"mla":"Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications, 2017, doi:10.7554/eLife.25192.","ama":"Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192","apa":"Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C. (2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192","ieee":"M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife, vol. 6. eLife Sciences Publications, 2017.","short":"M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).","chicago":"Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25192.","ista":"Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"Yes","external_id":{"isi":["000404024800001"]},"author":[{"first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato","last_name":"Lagator"},{"last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"publist_id":"6460","title":"On the mechanistic nature of epistasis in a canonical cis-regulatory element","article_number":"e25192","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer"}],"year":"2017","has_accepted_license":"1","isi":1,"publication":"eLife","day":"18","date_created":"2018-12-11T11:49:23Z","date_published":"2017-05-18T00:00:00Z","doi":"10.7554/eLife.25192","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","date_updated":"2023-09-22T10:01:17Z","ddc":["576"],"department":[{"_id":"CaGu"},{"_id":"NiBa"},{"_id":"JoBo"}],"file_date_updated":"2020-07-14T12:48:16Z","_id":"954","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"841","status":"public","publication_status":"published","publication_identifier":{"issn":["2050084X"]},"language":[{"iso":"eng"}],"file":[{"checksum":"59cdd4400fb41280122d414fea971546","file_id":"5306","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:17:49Z","file_name":"IST-2017-841-v1+1_elife-25192-v2.pdf","date_updated":"2020-07-14T12:48:16Z","file_size":2441529,"creator":"system"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5307","checksum":"b69024880558b858eb8c5d47a92b6377","creator":"system","file_size":3752660,"date_updated":"2020-07-14T12:48:16Z","file_name":"IST-2017-841-v1+2_elife-25192-figures-v2.pdf","date_created":"2018-12-12T10:17:50Z"}],"ec_funded":1,"volume":6,"abstract":[{"text":"Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites. Sign and magnitude of individual mutation effects are sufficient to predict the sign of epistasis and its environmental dependence. Thus, the thermodynamic model offers the correct null prediction for epistasis between mutations across DNA-binding sites. Our results indicate that a predictive theory for the effects of cis-regulatory mutations is possible from first principles, as long as the essential molecular mechanisms and the constraints these impose on a biological system are accounted for.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 6","month":"05"},{"publication_identifier":{"issn":["20411723"]},"publication_status":"published","file":[{"checksum":"29a1b5db458048d3bd5c67e0e2a56818","file_id":"5064","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2017-864-v1+1_s41467-017-00238-8.pdf","date_created":"2018-12-12T10:14:14Z","file_size":998157,"date_updated":"2020-07-14T12:48:16Z","creator":"system"},{"creator":"system","file_size":9715993,"date_updated":"2020-07-14T12:48:16Z","file_name":"IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf","date_created":"2018-12-12T10:14:15Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"7b78401e52a576cf3e6bbf8d0abadc17","file_id":"5065"}],"language":[{"iso":"eng"}],"issue":"1","volume":8,"related_material":{"record":[{"status":"public","id":"6071","relation":"dissertation_contains"}]},"ec_funded":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"}],"oa_version":"Published Version","scopus_import":"1","month":"08","intvolume":" 8","date_updated":"2023-09-22T10:00:49Z","ddc":["539","576"],"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:48:16Z","_id":"955","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"864","has_accepted_license":"1","isi":1,"year":"2017","day":"09","publication":"Nature Communications","date_published":"2017-08-09T00:00:00Z","doi":"10.1038/s41467-017-00238-8","date_created":"2018-12-11T11:49:23Z","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"citation":{"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","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).","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.","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.","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.","chicago":"Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Friedlander","full_name":"Friedlander, Tamar","first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Prizak","full_name":"Prizak, Roshan","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik"}],"publist_id":"6459","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000407198800005"]},"title":"Evolution of new regulatory functions on biophysically realistic fitness landscapes","article_number":"216","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}]},{"year":"2017","isi":1,"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","day":"31","date_created":"2018-12-11T11:49:23Z","doi":"10.1098/rspb.2016.2864","date_published":"2017-05-31T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Royal Society, The","citation":{"ieee":"D. Charlesworth, N. H. Barton, and B. Charlesworth, “The sources of adaptive evolution,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 284, no. 1855. Royal Society, The, 2017.","short":"D. Charlesworth, N.H. Barton, B. Charlesworth, Proceedings of the Royal Society of London Series B Biological Sciences 284 (2017).","apa":"Charlesworth, D., Barton, N. H., & Charlesworth, B. (2017). The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2016.2864","ama":"Charlesworth D, Barton NH, Charlesworth B. The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. 2017;284(1855). doi:10.1098/rspb.2016.2864","mla":"Charlesworth, Deborah, et al. “The Sources of Adaptive Evolution.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 284, no. 1855, 20162864, Royal Society, The, 2017, doi:10.1098/rspb.2016.2864.","ista":"Charlesworth D, Barton NH, Charlesworth B. 2017. The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. 284(1855), 20162864.","chicago":"Charlesworth, Deborah, Nicholas H Barton, and Brian Charlesworth. “The Sources of Adaptive Evolution.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2017. https://doi.org/10.1098/rspb.2016.2864."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000405148800021"],"pmid":["28566483"]},"article_processing_charge":"No","publist_id":"6462","author":[{"full_name":"Charlesworth, Deborah","last_name":"Charlesworth","first_name":"Deborah"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Brian","full_name":"Charlesworth, Brian","last_name":"Charlesworth"}],"title":"The sources of adaptive evolution","article_number":"20162864","publication_status":"published","language":[{"iso":"eng"}],"volume":284,"issue":"1855","abstract":[{"lang":"eng","text":"The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed."}],"oa_version":"Submitted Version","pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454256/"}],"scopus_import":"1","intvolume":" 284","month":"05","date_updated":"2023-09-22T10:01:48Z","department":[{"_id":"NiBa"}],"_id":"953","type":"journal_article","status":"public"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Turelli M, Barton NH. 2017. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 115, 45–60.","chicago":"Turelli, Michael, and Nicholas H Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical Population Biology. Elsevier, 2017. https://doi.org/10.1016/j.tpb.2017.03.003.","apa":"Turelli, M., & Barton, N. H. (2017). Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2017.03.003","ama":"Turelli M, Barton NH. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 2017;115:45-60. doi:10.1016/j.tpb.2017.03.003","ieee":"M. Turelli and N. H. Barton, “Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti,” Theoretical Population Biology, vol. 115. Elsevier, pp. 45–60, 2017.","short":"M. Turelli, N.H. Barton, Theoretical Population Biology 115 (2017) 45–60.","mla":"Turelli, Michael, and Nicholas H. Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical Population Biology, vol. 115, Elsevier, 2017, pp. 45–60, doi:10.1016/j.tpb.2017.03.003."},"title":"Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti","external_id":{"pmid":["28411063"]},"article_processing_charge":"No","author":[{"last_name":"Turelli","full_name":"Turelli, Michael","first_name":"Michael"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"publist_id":"6463","oa":1,"quality_controlled":"1","publisher":"Elsevier","publication":"Theoretical Population Biology","day":"01","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:49:22Z","date_published":"2017-06-01T00:00:00Z","doi":"10.1016/j.tpb.2017.03.003","page":"45 - 60","_id":"952","pubrep_id":"972","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","ddc":["576"],"date_updated":"2023-09-22T10:02:21Z","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:48:16Z","pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"A novel strategy for controlling the spread of arboviral diseases such as dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressing Wolbachia. In general, Wolbachia transinfected into mosquitoes induce fitness costs through lower viability or fecundity. These maternally inherited bacteria also produce a frequency-dependent advantage for infected females by inducing cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected females mated to infected males. These competing effects, a frequency-dependent advantage and frequency-independent costs, produce bistable Wolbachia frequency dynamics. Above a threshold frequency, denoted pˆ, CI drives fitness-decreasing Wolbachia transinfections through local populations; but below pˆ, infection frequencies tend to decline to zero. If pˆ is not too high, CI also drives spatial spread once infections become established over sufficiently large areas. We illustrate how simple models provide testable predictions concerning the spatial and temporal dynamics of Wolbachia introductions, focusing on rate of spatial spread, the shape of spreading waves, and the conditions for initiating spread from local introductions. First, we consider the robustness of diffusion-based predictions to incorporating two important features of wMel-Aedes aegypti biology that may be inconsistent with the diffusion approximations, namely fast local dynamics induced by complete CI (i.e., all embryos produced from incompatible crosses die) and long-tailed, non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed dispersal changes wave-width predictions only slightly; but it can significantly reduce wave speed relative to the diffusion prediction; it also allows smaller local introductions to initiate spatial spread. Second, we use approximations for pˆ and dispersal distances to predict the outcome of 2013 releases of wMel-infected Aedes aegypti in Cairns, Australia, Third, we describe new data from Ae. aegypti populations near Cairns, Australia that demonstrate long-distance dispersal and provide an approximate lower bound on pˆ for wMel in northeastern Australia. Finally, we apply our analyses to produce operational guidelines for efficient transformation of vector populations over large areas. We demonstrate that even very slow spatial spread, on the order of 10-20 m/month (as predicted), can produce area-wide population transformation within a few years following initial releases covering about 20-30% of the target area."}],"intvolume":" 115","month":"06","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"checksum":"9aeff86fa7de69f7a15cf4fc60d57d01","file_id":"6327","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2017_TheoreticalPopulationBio_Turelli.pdf","date_created":"2019-04-17T06:39:45Z","creator":"dernst","file_size":2073856,"date_updated":"2020-07-14T12:48:16Z"}],"publication_status":"published","publication_identifier":{"issn":["00405809"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":115},{"abstract":[{"lang":"eng","text":"Dengue-suppressing Wolbachia strains are promising tools for arbovirus control, particularly as they have the potential to self-spread following local introductions. To test this, we followed the frequency of the transinfected Wolbachia strain wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated locations within the city in early 2013. Spatial spread was analysed graphically using interpolation and by fitting a statistical model describing the position and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and 0.52 km2), we observed slow but steady spatial spread, at about 100–200 m per year, roughly consistent with theoretical predictions. In contrast, the smallest release (0.11 km2) produced erratic temporal and spatial dynamics, with little evidence of spread after 2 years. This is consistent with the prediction concerning fitness-decreasing Wolbachia transinfections that a minimum release area is needed to achieve stable local establishment and spread in continuous habitats. Our graphical and likelihood analyses produced broadly consistent estimates of wave speed and wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental heterogeneity will affect large-scale Wolbachia transformations of urban mosquito populations. The persistence and spread of Wolbachia in release areas meeting minimum area requirements indicates the promise of successful large-scale population transfo"}],"oa_version":"Published Version","scopus_import":"1","month":"05","intvolume":" 15","publication_identifier":{"issn":["15449173"]},"publication_status":"published","file":[{"file_name":"IST-2017-843-v1+1_journal.pbio.2001894.pdf","date_created":"2018-12-12T10:08:30Z","creator":"system","file_size":5541206,"date_updated":"2020-07-14T12:48:16Z","file_id":"4691","checksum":"107d290bd1159ec77b734eb2824b01c8","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":15,"issue":"5","related_material":{"record":[{"id":"9856","status":"public","relation":"research_data"},{"relation":"research_data","id":"9857","status":"public"},{"relation":"research_data","status":"public","id":"9858"}]},"_id":"951","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"843","date_updated":"2023-09-22T10:02:52Z","ddc":["576"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:48:16Z","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"isi":1,"has_accepted_license":"1","year":"2017","day":"30","publication":"PLoS Biology","doi":"10.1371/journal.pbio.2001894","date_published":"2017-05-30T00:00:00Z","date_created":"2018-12-11T11:49:22Z","article_number":"e2001894","citation":{"ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 15(5), e2001894.","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.","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, PLoS Biology 15 (2017).","ieee":"T. Schmidt et al., “Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti,” PLoS Biology, vol. 15, no. 5. Public Library of Science, 2017.","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894","ama":"Schmidt T, Barton NH, Rasic G, et al. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 2017;15(5). doi:10.1371/journal.pbio.2001894","mla":"Schmidt, Tom, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS Biology, vol. 15, no. 5, e2001894, Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6464","author":[{"first_name":"Tom","last_name":"Schmidt","full_name":"Schmidt, Tom"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"first_name":"Gordana","last_name":"Rasic","full_name":"Rasic, Gordana"},{"last_name":"Turley","full_name":"Turley, Andrew","first_name":"Andrew"},{"first_name":"Brian","last_name":"Montgomery","full_name":"Montgomery, Brian"},{"last_name":"Iturbe Ormaetxe","full_name":"Iturbe Ormaetxe, Inaki","first_name":"Inaki"},{"full_name":"Cook, Peter","last_name":"Cook","first_name":"Peter"},{"first_name":"Peter","full_name":"Ryan, Peter","last_name":"Ryan"},{"last_name":"Ritchie","full_name":"Ritchie, Scott","first_name":"Scott"},{"first_name":"Ary","full_name":"Hoffmann, Ary","last_name":"Hoffmann"},{"first_name":"Scott","last_name":"O’Neill","full_name":"O’Neill, Scott"},{"first_name":"Michael","full_name":"Turelli, Michael","last_name":"Turelli"}],"external_id":{"isi":["000402520000012"]},"article_processing_charge":"No","title":"Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti"},{"_id":"9858","type":"research_data_reference","status":"public","date_updated":"2023-09-22T10:02:51Z","citation":{"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","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","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).","ieee":"T. Schmidt et al., “Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics.” Public Library of Science, 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.","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics, Public Library of Science, 10.1371/journal.pbio.2001894.s016."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Schmidt","full_name":"Schmidt, Tom","first_name":"Tom"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rasic, Gordana","last_name":"Rasic","first_name":"Gordana"},{"first_name":"Andrew","full_name":"Turley, Andrew","last_name":"Turley"},{"full_name":"Montgomery, Brian","last_name":"Montgomery","first_name":"Brian"},{"last_name":"Iturbe Ormaetxe","full_name":"Iturbe Ormaetxe, Inaki","first_name":"Inaki"},{"full_name":"Cook, Peter","last_name":"Cook","first_name":"Peter"},{"full_name":"Ryan, Peter","last_name":"Ryan","first_name":"Peter"},{"first_name":"Scott","full_name":"Ritchie, Scott","last_name":"Ritchie"},{"full_name":"Hoffmann, Ary","last_name":"Hoffmann","first_name":"Ary"},{"last_name":"O’Neill","full_name":"O’Neill, Scott","first_name":"Scott"},{"first_name":"Michael","last_name":"Turelli","full_name":"Turelli, Michael"}],"article_processing_charge":"No","department":[{"_id":"NiBa"}],"title":"Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics","oa_version":"Published Version","publisher":"Public Library of Science","month":"05","year":"2017","day":"30","doi":"10.1371/journal.pbio.2001894.s016","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"951"}]},"date_published":"2017-05-30T00:00:00Z","date_created":"2021-08-10T07:47:07Z"},{"citation":{"chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables.” Public Library of Science , 2017. https://doi.org/10.1371/journal.pbio.2001894.s015.","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting information concerning observed wMel frequencies and analyses of habitat variables, Public Library of Science , 10.1371/journal.pbio.2001894.s015.","mla":"Schmidt, Tom, et al. Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables. Public Library of Science , 2017, doi:10.1371/journal.pbio.2001894.s015.","ieee":"T. Schmidt et al., “Supporting information concerning observed wMel frequencies and analyses of habitat variables.” 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).","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Supporting information concerning observed wMel frequencies and analyses of habitat variables. 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Supporting information concerning observed wMel frequencies and analyses of habitat variables. 2017. doi:10.1371/journal.pbio.2001894.s015"},"date_updated":"2023-09-22T10:02:51Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"last_name":"Schmidt","full_name":"Schmidt, Tom","first_name":"Tom"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"first_name":"Gordana","full_name":"Rasic, Gordana","last_name":"Rasic"},{"first_name":"Andrew","last_name":"Turley","full_name":"Turley, Andrew"},{"first_name":"Brian","last_name":"Montgomery","full_name":"Montgomery, Brian"},{"first_name":"Inaki","last_name":"Iturbe Ormaetxe","full_name":"Iturbe Ormaetxe, Inaki"},{"first_name":"Peter","full_name":"Cook, Peter","last_name":"Cook"},{"first_name":"Peter","full_name":"Ryan, Peter","last_name":"Ryan"},{"first_name":"Scott","full_name":"Ritchie, Scott","last_name":"Ritchie"},{"first_name":"Ary","last_name":"Hoffmann","full_name":"Hoffmann, Ary"},{"first_name":"Scott","last_name":"O’Neill","full_name":"O’Neill, Scott"},{"full_name":"Turelli, Michael","last_name":"Turelli","first_name":"Michael"}],"department":[{"_id":"NiBa"}],"title":"Supporting information concerning observed wMel frequencies and analyses of habitat variables","_id":"9857","type":"research_data_reference","status":"public","year":"2017","day":"30","date_created":"2021-08-10T07:41:52Z","date_published":"2017-05-30T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"951"}]},"doi":"10.1371/journal.pbio.2001894.s015","oa_version":"Published Version","publisher":"Public Library of Science ","month":"05"},{"status":"public","type":"research_data_reference","_id":"9856","title":"Supporting Information concerning additional likelihood analyses and results","department":[{"_id":"NiBa"}],"author":[{"full_name":"Schmidt, Tom","last_name":"Schmidt","first_name":"Tom"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"last_name":"Rasic","full_name":"Rasic, Gordana","first_name":"Gordana"},{"last_name":"Turley","full_name":"Turley, Andrew","first_name":"Andrew"},{"last_name":"Montgomery","full_name":"Montgomery, Brian","first_name":"Brian"},{"full_name":"Iturbe Ormaetxe, Inaki","last_name":"Iturbe Ormaetxe","first_name":"Inaki"},{"last_name":"Cook","full_name":"Cook, Peter","first_name":"Peter"},{"last_name":"Ryan","full_name":"Ryan, Peter","first_name":"Peter"},{"last_name":"Ritchie","full_name":"Ritchie, Scott","first_name":"Scott"},{"last_name":"Hoffmann","full_name":"Hoffmann, Ary","first_name":"Ary"},{"first_name":"Scott","full_name":"O’Neill, Scott","last_name":"O’Neill"},{"first_name":"Michael","last_name":"Turelli","full_name":"Turelli, Michael"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Additional Likelihood Analyses and Results.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.s014.","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting Information concerning additional likelihood analyses and results, Public Library of Science, 10.1371/journal.pbio.2001894.s014.","mla":"Schmidt, Tom, et al. Supporting Information Concerning Additional Likelihood Analyses and Results. Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.s014.","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Supporting Information concerning additional likelihood analyses and results. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s014","ama":"Schmidt T, Barton NH, Rasic G, et al. Supporting Information concerning additional likelihood analyses and results. 2017. doi:10.1371/journal.pbio.2001894.s014","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).","ieee":"T. Schmidt et al., “Supporting Information concerning additional likelihood analyses and results.” Public Library of Science, 2017."},"date_updated":"2023-09-22T10:02:51Z","month":"05","publisher":"Public Library of Science","oa_version":"Published Version","doi":"10.1371/journal.pbio.2001894.s014","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"951"}]},"date_published":"2017-05-30T00:00:00Z","date_created":"2021-08-10T07:36:04Z","day":"30","year":"2017"},{"external_id":{"isi":["000412232600019"]},"article_processing_charge":"No","publist_id":"6533","author":[{"orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"title":"When does frequency-independent selection maintain genetic variation?","citation":{"ama":"Novak S, Barton NH. When does frequency-independent selection maintain genetic variation? Genetics. 2017;207(2):653-668. doi:10.1534/genetics.117.300129","apa":"Novak, S., & Barton, N. H. (2017). When does frequency-independent selection maintain genetic variation? Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300129","ieee":"S. Novak and N. H. Barton, “When does frequency-independent selection maintain genetic variation?,” Genetics, vol. 207, no. 2. Genetics Society of America, pp. 653–668, 2017.","short":"S. Novak, N.H. Barton, Genetics 207 (2017) 653–668.","mla":"Novak, Sebastian, and Nicholas H. Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” Genetics, vol. 207, no. 2, Genetics Society of America, 2017, pp. 653–68, doi:10.1534/genetics.117.300129.","ista":"Novak S, Barton NH. 2017. When does frequency-independent selection maintain genetic variation? Genetics. 207(2), 653–668.","chicago":"Novak, Sebastian, and Nicholas H Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.117.300129."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091"}],"page":"653 - 668","date_created":"2018-12-11T11:49:09Z","doi":"10.1534/genetics.117.300129","date_published":"2017-10-01T00:00:00Z","year":"2017","isi":1,"has_accepted_license":"1","publication":"Genetics","day":"01","oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","file_date_updated":"2020-07-14T12:48:15Z","department":[{"_id":"NiBa"}],"date_updated":"2023-09-26T15:49:15Z","ddc":["576"],"type":"journal_article","pubrep_id":"974","status":"public","_id":"910","ec_funded":1,"issue":"2","volume":207,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"5264","checksum":"f7c32dabf52e6d9e709d9203761e39fd","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-974-v1+1_manuscript.pdf","date_created":"2018-12-12T10:17:12Z","creator":"system","file_size":494268,"date_updated":"2020-07-14T12:48:15Z"}],"scopus_import":"1","intvolume":" 207","month":"10","abstract":[{"text":"Frequency-independent selection is generally considered as a force that acts to reduce the genetic variation in evolving populations, yet rigorous arguments for this idea are scarce. When selection fluctuates in time, it is unclear whether frequency-independent selection may maintain genetic polymorphism without invoking additional mechanisms. We show that constant frequency-independent selection with arbitrary epistasis on a well-mixed haploid population eliminates genetic variation if we assume linkage equilibrium between alleles. To this end, we introduce the notion of frequency-independent selection at the level of alleles, which is sufficient to prove our claim and contains the notion of frequency-independent selection on haploids. When selection and recombination are weak but of the same order, there may be strong linkage disequilibrium; numerical calculations show that stable equilibria are highly unlikely. Using the example of a diallelic two-locus model, we then demonstrate that frequency-independent selection that fluctuates in time can maintain stable polymorphism if linkage disequilibrium changes its sign periodically. We put our findings in the context of results from the existing literature and point out those scenarios in which the possible role of frequency-independent selection in maintaining genetic variation remains unclear.\r\n","lang":"eng"}],"oa_version":"Submitted Version"},{"article_number":"1486","project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Fraisse C, Picard MAL, Vicoso B. 2017. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. 8(1), 1486.","chicago":"Fraisse, Christelle, Marion A L Picard, and Beatriz Vicoso. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01663-5.","ama":"Fraisse C, Picard MAL, Vicoso B. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01663-5","apa":"Fraisse, C., Picard, M. A. L., & Vicoso, B. (2017). The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01663-5","short":"C. Fraisse, M.A.L. Picard, B. Vicoso, Nature Communications 8 (2017).","ieee":"C. Fraisse, M. A. L. Picard, and B. Vicoso, “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","mla":"Fraisse, Christelle, et al. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Nature Communications, vol. 8, no. 1, 1486, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01663-5."},"title":"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W","publist_id":"7190","author":[{"last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Picard","full_name":"Picard, Marion A","orcid":"0000-0002-8101-2518","first_name":"Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"article_processing_charge":"No","external_id":{"pmid":["29133797"]},"quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"day":"01","publication":"Nature Communications","has_accepted_license":"1","year":"2017","date_published":"2017-12-01T00:00:00Z","doi":"10.1038/s41467-017-01663-5","date_created":"2018-12-11T11:47:30Z","_id":"614","status":"public","pubrep_id":"910","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570","576"],"date_updated":"2024-02-21T13:47:47Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:20Z","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Moths and butterflies (Lepidoptera) usually have a pair of differentiated WZ sex chromosomes. However, in most lineages outside of the division Ditrysia, as well as in the sister order Trichoptera, females lack a W chromosome. The W is therefore thought to have been acquired secondarily. Here we compare the genomes of three Lepidoptera species (one Dytrisia and two non-Dytrisia) to test three models accounting for the origin of the W: (1) a Z-autosome fusion; (2) a sex chromosome turnover; and (3) a non-canonical mechanism (e.g., through the recruitment of a B chromosome). We show that the gene content of the Z is highly conserved across Lepidoptera (rejecting a sex chromosome turnover) and that very few genes moved onto the Z in the common ancestor of the Ditrysia (arguing against a Z-autosome fusion). Our comparative genomics analysis therefore supports the secondary acquisition of the Lepidoptera W by a non-canonical mechanism, and it confirms the extreme stability of well-differentiated sex chromosomes.","lang":"eng"}],"month":"12","intvolume":" 8","scopus_import":1,"file":[{"date_updated":"2020-07-14T12:47:20Z","file_size":1201520,"creator":"dernst","date_created":"2020-03-03T15:55:50Z","file_name":"2017_NatureComm_Fraisse.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"4da2651303c8afc2f7fc419be42a2433","file_id":"7562"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["20411723"]},"publication_status":"published","related_material":{"record":[{"status":"public","id":"7163","relation":"popular_science"}]},"volume":8,"issue":"1"},{"month":"12","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The de novo genome assemblies generated for this study, and the associated metadata."}],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"614"}]},"doi":"10.15479/AT:ISTA:7163","date_published":"2017-12-01T00:00:00Z","date_created":"2019-12-09T23:03:03Z","contributor":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075"},{"last_name":"Picard","orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A L"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"day":"01","file":[{"date_updated":"2020-07-14T12:47:50Z","file_size":841375478,"creator":"cfraisse","date_created":"2019-12-10T08:46:46Z","file_name":"Vicoso_Cohridella_Ndegeerella_Tsylvina_genome_assemblies.zip","content_type":"application/zip","access_level":"open_access","relation":"main_file","checksum":"3cae8a2e3cbf8703399b9c483aaba7f3","file_id":"7164"}],"has_accepted_license":"1","year":"2017","project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"status":"public","type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"7163","file_date_updated":"2020-07-14T12:47:50Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"title":"Supplementary Files for \"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W\"","author":[{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"}],"article_processing_charge":"No","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Fraisse C. Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” 2017. doi:10.15479/AT:ISTA:7163","apa":"Fraisse, C. (2017). Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7163","ieee":"C. Fraisse, “Supplementary Files for ‘The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.’” Institute of Science and Technology Austria, 2017.","short":"C. Fraisse, (2017).","mla":"Fraisse, Christelle. Supplementary Files for “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:7163.","ista":"Fraisse C. 2017. Supplementary Files for ‘The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7163.","chicago":"Fraisse, Christelle. “Supplementary Files for ‘The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.’” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:7163."},"date_updated":"2024-02-21T13:47:47Z"},{"citation":{"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.","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","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","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisinova","full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004"},{"orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"},{"last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"}],"publist_id":"7004","title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","article_number":"e1005609","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"year":"2017","has_accepted_license":"1","publication":"PLoS Computational Biology","day":"18","date_created":"2018-12-11T11:47:58Z","date_published":"2017-07-18T00:00:00Z","doi":"10.1371/journal.pcbi.1005609","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","date_updated":"2024-03-27T23:30:28Z","ddc":["576"],"department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:47:46Z","_id":"696","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","pubrep_id":"894","status":"public","publication_status":"published","publication_identifier":{"issn":["1553734X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5117","checksum":"9143c290fa6458ed2563bff4b295554a","file_size":3775716,"date_updated":"2020-07-14T12:47:46Z","creator":"system","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","date_created":"2018-12-12T10:15:01Z"}],"ec_funded":1,"issue":"7","volume":13,"related_material":{"record":[{"status":"public","id":"9849","relation":"research_data"},{"status":"public","id":"9850","relation":"research_data"},{"id":"9851","status":"public","relation":"research_data"},{"relation":"research_data","id":"9852","status":"public"},{"status":"public","id":"6263","relation":"dissertation_contains"}]},"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 13","month":"07"},{"year":"2016","has_accepted_license":"1","publication":"Scientific Reports","day":"19","date_created":"2018-12-11T11:50:32Z","doi":"10.1038/srep38840","date_published":"2016-12-19T00:00:00Z","acknowledgement":"H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund Thattai for critical discussions and suggestions.","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","citation":{"ista":"Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.","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.","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","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","short":"H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).","ieee":"H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani","last_name":"Sachdeva"},{"first_name":"Mustansir","full_name":"Barma, Mustansir","last_name":"Barma"},{"last_name":"Rao","full_name":"Rao, Madan","first_name":"Madan"}],"publist_id":"6183","title":"Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae","article_number":"38840","publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"cb378732da885ea4959ec5b845fb6e52","file_id":"4977","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:12:56Z","file_name":"IST-2017-737-v1+1_srep38840.pdf","creator":"system","date_updated":"2020-07-14T12:44:37Z","file_size":760967}],"volume":6,"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 6","month":"12","date_updated":"2021-01-12T06:48:50Z","ddc":["576"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:37Z","_id":"1172","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"737","status":"public"},{"scopus_import":1,"intvolume":" 34","month":"10","abstract":[{"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. ","lang":"eng"}],"oa_version":"Submitted Version","ec_funded":1,"issue":"1","volume":34,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:16:35Z","file_name":"IST-2017-770-v1+1_FranssenEtAl_nofigs-1.pdf","date_updated":"2020-07-14T12:44:38Z","file_size":295274,"creator":"system","checksum":"1e78d3aaffcb40dc8b02b7b4666019e0","file_id":"5223","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"file_name":"IST-2017-770-v1+2_Fig1.pdf","date_created":"2018-12-12T10:16:36Z","creator":"system","file_size":10902625,"date_updated":"2020-07-14T12:44:38Z","file_id":"5224","checksum":"e13171843283774404c936c581b4543e","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"file_name":"IST-2017-770-v1+3_Fig2.pdf","date_created":"2018-12-12T10:16:37Z","creator":"system","file_size":21437,"date_updated":"2020-07-14T12:44:38Z","checksum":"63bc6e6e61f347594d8c00c37f874a0b","file_id":"5225","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"file_name":"IST-2017-770-v1+4_Fig3.pdf","date_created":"2018-12-12T10:16:38Z","file_size":1172194,"date_updated":"2020-07-14T12:44:38Z","creator":"system","file_id":"5226","checksum":"da87cc7c78808837f22a3dae1c8397f9","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"date_updated":"2020-07-14T12:44:38Z","file_size":50045,"creator":"system","date_created":"2018-12-12T10:16:38Z","file_name":"IST-2017-770-v1+5_Fig4.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5227","checksum":"e47b2a0c32142f423b3100150c0294f8"},{"date_updated":"2020-07-14T12:44:38Z","file_size":50705,"creator":"system","date_created":"2018-12-12T10:16:39Z","file_name":"IST-2017-770-v1+6_Fig5.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5228","checksum":"a5a7d6b32e7e17d35d337d7ec2a9f6c9"}],"type":"journal_article","pubrep_id":"770","status":"public","_id":"1195","file_date_updated":"2020-07-14T12:44:38Z","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:49:00Z","ddc":["576"],"oa":1,"publisher":"Oxford University Press","quality_controlled":"1","acknowledgement":"The authors thank all members of the Institute of Population\r\nGenetics for discussion and support on the project and par-\r\nticularly N. 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”.","page":"174 - 184","date_created":"2018-12-11T11:50:39Z","date_published":"2016-10-03T00:00:00Z","doi":"10.1093/molbev/msw210","year":"2016","has_accepted_license":"1","publication":"Molecular Biology and Evolution","day":"03","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"author":[{"first_name":"Susan","full_name":"Franssen, Susan","last_name":"Franssen"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"last_name":"Schlötterer","full_name":"Schlötterer, Christian","first_name":"Christian"}],"publist_id":"6155","title":"Reconstruction of haplotype-blocks selected during experimental evolution.","citation":{"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.","ista":"Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 34(1), 174–184.","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.","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","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","short":"S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution 34 (2016) 174–184.","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"_id":"1224","status":"public","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"Z. Teitel, M. Pickup, D. Field, S. Barrett, Plant Biology 18 (2016) 98–103.","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","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","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.","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."},"date_updated":"2021-01-12T06:49:12Z","department":[{"_id":"NiBa"}],"title":"The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant","publist_id":"6110","author":[{"first_name":"Zachary","full_name":"Teitel, Zachary","last_name":"Teitel"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup"},{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field"},{"last_name":"Barrett","full_name":"Barrett, Spencer","first_name":"Spencer"}],"oa_version":"None","abstract":[{"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.","lang":"eng"}],"month":"01","intvolume":" 18","scopus_import":1,"quality_controlled":"1","publisher":"Wiley-Blackwell","day":"01","publication":"Plant Biology","language":[{"iso":"eng"}],"publication_status":"published","year":"2016","date_published":"2016-01-01T00:00:00Z","issue":"1","volume":18,"doi":"10.1111/plb.12336","date_created":"2018-12-11T11:50:48Z","page":"98 - 103"},{"publisher":"Genetics Society of America","quality_controlled":"1","oa":1,"acknowledgement":"This work was made possible by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for the United Nations Educational, Scientific, and Cultural Organization and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria) and European Research Council grant 250152 (to Nick Barton).","page":"721 - 732","date_published":"2016-02-01T00:00:00Z","doi":"10.1534/genetics.115.180299","date_created":"2018-12-11T11:50:54Z","year":"2016","day":"01","publication":"Genetics","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"name":"L'OREAL Fellowship","_id":"25B67606-B435-11E9-9278-68D0E5697425"}],"publist_id":"6091","author":[{"id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","first_name":"Hildegard","orcid":"0000-0001-9435-2813","full_name":"Uecker, Hildegard","last_name":"Uecker"},{"first_name":"Joachim","full_name":"Hermisson, Joachim","last_name":"Hermisson"}],"title":"The role of recombination in evolutionary rescue","citation":{"chicago":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.180299.","ista":"Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue. Genetics. 202(2), 721–732.","mla":"Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary Rescue.” Genetics, vol. 202, no. 2, Genetics Society of America, 2016, pp. 721–32, doi:10.1534/genetics.115.180299.","ieee":"H. Uecker and J. Hermisson, “The role of recombination in evolutionary rescue,” Genetics, vol. 202, no. 2. Genetics Society of America, pp. 721–732, 2016.","short":"H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732.","ama":"Uecker H, Hermisson J. The role of recombination in evolutionary rescue. Genetics. 2016;202(2):721-732. doi:10.1534/genetics.115.180299","apa":"Uecker, H., & Hermisson, J. (2016). The role of recombination in evolutionary rescue. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.180299"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://biorxiv.org/content/early/2015/07/06/022020.abstract"}],"month":"02","intvolume":" 202","abstract":[{"lang":"eng","text":"How likely is it that a population escapes extinction through adaptive evolution? The answer to this question is of great relevance in conservation biology, where we aim at species’ rescue and the maintenance of biodiversity, and in agriculture and medicine, where we seek to hamper the emergence of pesticide or drug resistance. By reshuffling the genome, recombination has two antagonistic effects on the probability of evolutionary rescue: It generates and it breaks up favorable gene combinations. Which of the two effects prevails depends on the fitness effects of mutations and on the impact of stochasticity on the allele frequencies. In this article, we analyze a mathematical model for rescue after a sudden environmental change when adaptation is contingent on mutations at two loci. The analysis reveals a complex nonlinear dependence of population survival on recombination. We moreover find that, counterintuitively, a fast eradication of the wild type can promote rescue in the presence of recombination. The model also shows that two-step rescue is not unlikely to happen and can even be more likely than single-step rescue (where adaptation relies on a single mutation), depending on the circumstances."}],"oa_version":"Preprint","volume":202,"issue":"2","ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1241","department":[{"_id":"NiBa"}],"date_updated":"2023-02-21T10:24:19Z"},{"year":"2016","has_accepted_license":"1","publication":"Proceedings of the Genetic and Evolutionary Computation Conference 2016 ","day":"20","page":"1163 - 1170","date_created":"2018-12-11T11:51:31Z","date_published":"2016-07-20T00:00:00Z","doi":"10.1145/2908812.2908909","oa":1,"publisher":"ACM","quality_controlled":"1","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","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.","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.","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.","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 Proceedings of the Genetic and Evolutionary Computation Conference 2016 , 1163–70. ACM, 2016. https://doi.org/10.1145/2908812.2908909."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Oliveto, Pietro","last_name":"Oliveto","first_name":"Pietro"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao"},{"first_name":"Jorge","full_name":"Heredia, Jorge","last_name":"Heredia"},{"last_name":"Sudholt","full_name":"Sudholt, Dirk","first_name":"Dirk"},{"last_name":"Trubenova","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora"}],"publist_id":"5900","title":"When non-elitism outperforms elitism for crossing fitness valleys","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":979026,"date_updated":"2020-07-14T12:44:45Z","file_name":"IST-2016-650-v1+1_p1163-oliveto.pdf","date_created":"2018-12-12T10:16:27Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5214","checksum":"a1896e39e4113f2711e46b435d5f3e69"}],"ec_funded":1,"abstract":[{"text":"Crossing fitness valleys is one of the major obstacles to function optimization. In this paper we investigate how the structure of the fitness valley, namely its depth d and length ℓ, influence the runtime of different strategies for crossing these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis algorithm. While the (1+1) EA has to jump across the valley to a point of higher fitness because it does not accept decreasing moves, the non-elitist algorithms may cross the valley by accepting worsening moves. We show that while the runtime of the (1+1) EA algorithm depends critically on the length of the valley, the runtimes of the non-elitist algorithms depend crucially only on the depth of the valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of small length. Moreover, we show that both SSWM and Metropolis can also efficiently optimize a rugged function consisting of consecutive valleys.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"07","date_updated":"2021-01-12T06:50:03Z","ddc":["576"],"department":[{"_id":"NiBa"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:44:45Z","_id":"1349","conference":{"start_date":"2016-07-20","end_date":"2016-07-24","location":"Denver, CO, USA","name":"GECCO: Genetic and evolutionary computation conference"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","pubrep_id":"650","status":"public"}]