[{"author":[{"last_name":"Schmidt","first_name":"Tom","full_name":"Schmidt, Tom"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"last_name":"Rasic","first_name":"Gordana","full_name":"Rasic, Gordana"},{"last_name":"Turley","first_name":"Andrew","full_name":"Turley, Andrew"},{"first_name":"Brian","last_name":"Montgomery","full_name":"Montgomery, Brian"},{"full_name":"Iturbe Ormaetxe, Inaki","last_name":"Iturbe Ormaetxe","first_name":"Inaki"},{"full_name":"Cook, Peter","last_name":"Cook","first_name":"Peter"},{"full_name":"Ryan, Peter","last_name":"Ryan","first_name":"Peter"},{"last_name":"Ritchie","first_name":"Scott","full_name":"Ritchie, Scott"},{"full_name":"Hoffmann, Ary","first_name":"Ary","last_name":"Hoffmann"},{"first_name":"Scott","last_name":"O’Neill","full_name":"O’Neill, Scott"},{"full_name":"Turelli, Michael","first_name":"Michael","last_name":"Turelli"}],"date_created":"2021-08-10T07:36:04Z","doi":"10.1371/journal.pbio.2001894.s014","oa_version":"Published Version","title":"Supporting Information concerning additional likelihood analyses and results","type":"research_data_reference","publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","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. Supporting Information concerning additional likelihood analyses and results, Public Library of Science, 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","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.","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.","ieee":"T. Schmidt et al., “Supporting Information concerning additional likelihood analyses and results.” Public Library of Science, 2017.","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","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)."},"date_published":"2017-05-30T00:00:00Z","month":"05","article_processing_charge":"No","department":[{"_id":"NiBa"}],"_id":"9856","related_material":{"record":[{"relation":"used_in_publication","id":"951","status":"public"}]},"day":"30","date_updated":"2023-09-22T10:02:51Z","year":"2017"},{"scopus_import":"1","external_id":{"isi":["000412232600019"]},"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","abstract":[{"lang":"eng","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"}],"file":[{"content_type":"application/pdf","file_id":"5264","file_name":"IST-2018-974-v1+1_manuscript.pdf","date_created":"2018-12-12T10:17:12Z","date_updated":"2020-07-14T12:48:15Z","checksum":"f7c32dabf52e6d9e709d9203761e39fd","creator":"system","file_size":494268,"access_level":"open_access","relation":"main_file"}],"has_accepted_license":"1","page":"653 - 668","quality_controlled":"1","oa_version":"Submitted Version","publisher":"Genetics Society of America","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"When does frequency-independent selection maintain genetic variation?","issue":"2","ec_funded":1,"date_created":"2018-12-11T11:49:09Z","oa":1,"ddc":["576"],"day":"01","date_updated":"2023-09-26T15:49:15Z","year":"2017","month":"10","date_published":"2017-10-01T00:00:00Z","_id":"910","department":[{"_id":"NiBa"}],"isi":1,"pubrep_id":"974","publication_status":"published","status":"public","type":"journal_article","volume":207,"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","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.","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.","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.","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","short":"S. Novak, N.H. Barton, Genetics 207 (2017) 653–668."},"author":[{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Novak","full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"file_date_updated":"2020-07-14T12:48:15Z","publist_id":"6533","language":[{"iso":"eng"}],"intvolume":" 207","doi":"10.1534/genetics.117.300129","publication":"Genetics"},{"has_accepted_license":"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"}],"file":[{"date_created":"2020-03-03T15:55:50Z","file_name":"2017_NatureComm_Fraisse.pdf","content_type":"application/pdf","file_id":"7562","creator":"dernst","checksum":"4da2651303c8afc2f7fc419be42a2433","date_updated":"2020-07-14T12:47:20Z","access_level":"open_access","relation":"main_file","file_size":1201520}],"project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22"}],"article_processing_charge":"No","license":"https://creativecommons.org/licenses/by/4.0/","scopus_import":1,"external_id":{"pmid":["29133797"]},"pmid":1,"date_created":"2018-12-11T11:47:30Z","oa":1,"ddc":["570","576"],"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Nature Publishing Group","title":"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W","quality_controlled":"1","oa_version":"Published Version","issue":"1","month":"12","date_published":"2017-12-01T00:00:00Z","article_number":"1486","_id":"614","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"day":"01","related_material":{"record":[{"status":"public","id":"7163","relation":"popular_science"}]},"year":"2017","date_updated":"2024-02-21T13:47:47Z","publist_id":"7190","author":[{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"full_name":"Picard, Marion A","orcid":"0000-0002-8101-2518","first_name":"Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"file_date_updated":"2020-07-14T12:47:20Z","doi":"10.1038/s41467-017-01663-5","publication":"Nature Communications","publication_identifier":{"issn":["20411723"]},"intvolume":" 8","language":[{"iso":"eng"}],"status":"public","volume":8,"type":"journal_article","publication_status":"published","pubrep_id":"910","citation":{"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","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.","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.","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.","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.","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)."},"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)"}},{"year":"2017","date_updated":"2024-02-21T13:47:47Z","day":"01","related_material":{"record":[{"id":"614","relation":"research_paper","status":"public"}]},"has_accepted_license":"1","file":[{"date_created":"2019-12-10T08:46:46Z","file_name":"Vicoso_Cohridella_Ndegeerella_Tsylvina_genome_assemblies.zip","file_id":"7164","content_type":"application/zip","date_updated":"2020-07-14T12:47:50Z","checksum":"3cae8a2e3cbf8703399b9c483aaba7f3","creator":"cfraisse","file_size":841375478,"access_level":"open_access","relation":"main_file"}],"abstract":[{"text":"The de novo genome assemblies generated for this study, and the associated metadata.","lang":"eng"}],"_id":"7163","project":[{"grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety"}],"article_processing_charge":"No","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"month":"12","date_published":"2017-12-01T00:00:00Z","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)"},"citation":{"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.","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.","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.","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","short":"C. Fraisse, (2017).","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."},"contributor":[{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"first_name":"Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard","orcid":"0000-0002-8101-2518"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"status":"public","publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","title":"Supplementary Files for \"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W\"","oa_version":"Published Version","doi":"10.15479/AT:ISTA:7163","oa":1,"ddc":["576"],"date_created":"2019-12-09T23:03:03Z","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075"}],"file_date_updated":"2020-07-14T12:47:50Z"},{"project":[{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"file":[{"date_updated":"2020-07-14T12:47:46Z","creator":"system","checksum":"9143c290fa6458ed2563bff4b295554a","file_size":3775716,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5117","date_created":"2018-12-12T10:15:01Z","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf"}],"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"}],"has_accepted_license":"1","scopus_import":1,"date_created":"2018-12-11T11:47:58Z","ec_funded":1,"ddc":["576"],"article_type":"original","oa":1,"quality_controlled":"1","oa_version":"Published Version","title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Public Library of Science","issue":"7","article_number":"e1005609","date_published":"2017-07-18T00:00:00Z","month":"07","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"_id":"696","related_material":{"record":[{"relation":"research_data","id":"9849","status":"public"},{"id":"9850","relation":"research_data","status":"public"},{"status":"public","id":"9851","relation":"research_data"},{"status":"public","id":"9852","relation":"research_data"},{"relation":"dissertation_contains","id":"6263","status":"public"}]},"day":"18","date_updated":"2024-03-18T23:30:29Z","year":"2017","file_date_updated":"2020-07-14T12:47:46Z","author":[{"full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta","last_name":"Lukacisinova"},{"full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak"},{"orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","last_name":"Paixao","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7004","intvolume":" 13","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553734X"]},"publication":"PLoS Computational Biology","doi":"10.1371/journal.pcbi.1005609","publication_status":"published","pubrep_id":"894","volume":13,"type":"journal_article","status":"public","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)"},"citation":{"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.","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","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.","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.","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","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017)."}}]