[{"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2050-084X"]},"year":"2017","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020"}],"month":"05","external_id":{"isi":["000404024800001"]},"oa_version":"Published Version","pubrep_id":"841","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"scopus_import":"1","ddc":["576"],"isi":1,"date_updated":"2025-07-10T12:01:50Z","citation":{"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,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 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.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.25192\">https://doi.org/10.7554/eLife.25192</a>.","ama":"Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature of epistasis in a canonical cis-regulatory element. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.25192\">10.7554/eLife.25192</a>","short":"M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).","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.","apa":"Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., &#38; Guet, C. C. (2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.25192\">https://doi.org/10.7554/eLife.25192</a>","mla":"Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” <i>ELife</i>, vol. 6, e25192, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.25192\">10.7554/eLife.25192</a>."},"oa":1,"date_created":"2018-12-11T11:49:23Z","file":[{"file_name":"IST-2017-841-v1+1_elife-25192-v2.pdf","file_id":"5306","date_updated":"2020-07-14T12:48:16Z","relation":"main_file","access_level":"open_access","file_size":2441529,"content_type":"application/pdf","date_created":"2018-12-12T10:17:49Z","creator":"system","checksum":"59cdd4400fb41280122d414fea971546"},{"file_id":"5307","date_updated":"2020-07-14T12:48:16Z","file_name":"IST-2017-841-v1+2_elife-25192-figures-v2.pdf","relation":"main_file","date_created":"2018-12-12T10:17:50Z","access_level":"open_access","file_size":3752660,"content_type":"application/pdf","checksum":"b69024880558b858eb8c5d47a92b6377","creator":"system"}],"day":"18","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","has_accepted_license":"1","fulldoi":"https://doi.org/10.7554/eLife.25192","publisher":"eLife Sciences Publications","file_date_updated":"2020-07-14T12:48:16Z","doi":"10.7554/eLife.25192","_id":"954","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"},{"_id":"NiBa"},{"_id":"JoBo"}],"ec_funded":1,"status":"public","publication":"eLife","article_number":"e25192","date_published":"2017-05-18T00:00:00Z","volume":6,"publication_status":"published","author":[{"last_name":"Lagator","full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato"},{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","orcid":"0000-0003-2361-3953","first_name":"Tiago"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"},{"first_name":"Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"article_processing_charge":"Yes","publist_id":"6460","intvolume":"         6","title":"On the mechanistic nature of epistasis in a canonical cis-regulatory element"},{"_id":"955","publisher":"Nature Publishing Group","doi":"10.1038/s41467-017-00238-8","file_date_updated":"2020-07-14T12:48:16Z","issue":"1","fulldoi":"https://doi.org/10.1038/s41467-017-00238-8","has_accepted_license":"1","day":"09","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"}],"quality_controlled":"1","publication_status":"published","author":[{"full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","last_name":"Friedlander","first_name":"Tamar"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"},{"last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper"}],"article_processing_charge":"Yes (in subscription journal)","publist_id":"6459","title":"Evolution of new regulatory functions on biophysically realistic fitness landscapes","intvolume":"         8","volume":8,"date_published":"2017-08-09T00:00:00Z","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"ec_funded":1,"status":"public","publication":"Nature Communications","article_number":"216","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"6071","relation":"dissertation_contains","status":"public"}]},"oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"scopus_import":"1","pubrep_id":"864","month":"08","external_id":{"isi":["000407198800005"]},"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","call_identifier":"FWF"}],"year":"2017","corr_author":"1","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2041-1723"]},"date_created":"2018-12-11T11:49:23Z","file":[{"relation":"main_file","file_id":"5064","date_updated":"2020-07-14T12:48:16Z","file_name":"IST-2017-864-v1+1_s41467-017-00238-8.pdf","checksum":"29a1b5db458048d3bd5c67e0e2a56818","creator":"system","date_created":"2018-12-12T10:14:14Z","access_level":"open_access","content_type":"application/pdf","file_size":998157},{"access_level":"open_access","content_type":"application/pdf","file_size":9715993,"date_created":"2018-12-12T10:14:15Z","creator":"system","checksum":"7b78401e52a576cf3e6bbf8d0abadc17","file_name":"IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf","date_updated":"2020-07-14T12:48:16Z","file_id":"5065","relation":"main_file"}],"citation":{"chicago":"Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-00238-8\">https://doi.org/10.1038/s41467-017-00238-8</a>.","ieee":"T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","mla":"Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” <i>Nature Communications</i>, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-00238-8\">10.1038/s41467-017-00238-8</a>.","apa":"Friedlander, T., Prizak, R., Barton, N. H., &#38; Tkačik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. <i>Nature Communications</i>. 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Tkačik, Nature Communications 8 (2017)."},"oa":1,"isi":1,"date_updated":"2026-04-08T13:54:24Z","ddc":["539","576"]},{"article_processing_charge":"No","title":"Data for: Establishment in a new habitat by polygenic adaptation","date_created":"2021-08-09T13:18:55Z","author":[{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"citation":{"chicago":"Etheridge, Alison, and Nicholas H Barton. “Data for: Establishment in a New Habitat by Polygenic Adaptation.” Mendeley Data, 2017. <a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">https://doi.org/10.17632/nw68fxzjpm.1</a>.","ieee":"A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat by polygenic adaptation.” Mendeley Data, 2017.","ista":"Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by polygenic adaptation, Mendeley Data, <a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">10.17632/nw68fxzjpm.1</a>.","apa":"Etheridge, A., &#38; Barton, N. H. (2017). Data for: Establishment in a new habitat by polygenic adaptation. Mendeley Data. <a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">https://doi.org/10.17632/nw68fxzjpm.1</a>","mla":"Etheridge, Alison, and Nicholas H. Barton. <i>Data for: Establishment in a New Habitat by Polygenic Adaptation</i>. Mendeley Data, 2017, doi:<a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">10.17632/nw68fxzjpm.1</a>.","ama":"Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic adaptation. 2017. doi:<a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">10.17632/nw68fxzjpm.1</a>","short":"A. Etheridge, N.H. Barton, (2017)."},"oa":1,"date_published":"2017-12-29T00:00:00Z","date_updated":"2025-04-15T07:11:04Z","status":"public","department":[{"_id":"NiBa"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"564"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.17632/nw68fxzjpm.1"}],"oa_version":"Published Version","_id":"9842","publisher":"Mendeley Data","doi":"10.17632/nw68fxzjpm.1","month":"12","year":"2017","fulldoi":"https://doi.org/10.17632/nw68fxzjpm.1","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"29","abstract":[{"lang":"eng","text":"Mathematica notebooks used to generate figures."}],"type":"research_data_reference"},{"author":[{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle"}],"article_processing_charge":"No","title":"Supplementary Files for \"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W\"","file":[{"file_name":"Vicoso_Cohridella_Ndegeerella_Tsylvina_genome_assemblies.zip","date_updated":"2020-07-14T12:47:50Z","file_id":"7164","relation":"main_file","content_type":"application/zip","file_size":841375478,"access_level":"open_access","date_created":"2019-12-10T08:46:46Z","creator":"cfraisse","checksum":"3cae8a2e3cbf8703399b9c483aaba7f3"}],"date_created":"2019-12-09T23:03:03Z","citation":{"mla":"Fraisse, Christelle. <i>Supplementary Files for “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.”</i> Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7163\">10.15479/AT:ISTA:7163</a>.","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. <a href=\"https://doi.org/10.15479/AT:ISTA:7163\">https://doi.org/10.15479/AT:ISTA:7163</a>","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, <a href=\"https://doi.org/10.15479/AT:ISTA:7163\">10.15479/AT:ISTA:7163</a>.","ama":"Fraisse C. Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7163\">10.15479/AT:ISTA:7163</a>","short":"C. Fraisse, (2017).","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. <a href=\"https://doi.org/10.15479/AT:ISTA:7163\">https://doi.org/10.15479/AT:ISTA:7163</a>.","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."},"oa":1,"date_published":"2017-12-01T00:00:00Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"status":"public","date_updated":"2025-09-11T07:33:33Z","contributor":[{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","last_name":"Fraisse"},{"first_name":"Marion A L","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"}],"ddc":["576"],"related_material":{"record":[{"id":"614","relation":"research_paper","status":"public"}]},"oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"_id":"7163","month":"12","publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:7163","file_date_updated":"2020-07-14T12:47:50Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/AT:ISTA:7163","year":"2017","project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22"}],"day":"01","type":"research_data","abstract":[{"lang":"eng","text":"The de novo genome assemblies generated for this study, and the associated metadata."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","date_updated":"2025-09-10T11:11:52Z","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"related_material":{"record":[{"id":"696","relation":"used_in_publication","status":"public"}]},"article_processing_charge":"No","title":"Modelling and simulation details","date_created":"2021-08-09T14:02:34Z","author":[{"last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004","first_name":"Marta"},{"first_name":"Sebastian","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X","last_name":"Novak"},{"last_name":"Paixao","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","first_name":"Tiago"}],"citation":{"apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Modelling and simulation details. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s001\">https://doi.org/10.1371/journal.pcbi.1005609.s001</a>","mla":"Lukacisinova, Marta, et al. <i>Modelling and Simulation Details</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s001\">10.1371/journal.pcbi.1005609.s001</a>.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Modelling and simulation details, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s001\">10.1371/journal.pcbi.1005609.s001</a>.","ama":"Lukacisinova M, Novak S, Paixao T. Modelling and simulation details. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s001\">10.1371/journal.pcbi.1005609.s001</a>","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Modelling and Simulation Details.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s001\">https://doi.org/10.1371/journal.pcbi.1005609.s001</a>.","ieee":"M. Lukacisinova, S. Novak, and T. 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Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s002\">10.1371/journal.pcbi.1005609.s002</a>.","apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Extensions of the model. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s002\">https://doi.org/10.1371/journal.pcbi.1005609.s002</a>","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Extensions of the model, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s002\">10.1371/journal.pcbi.1005609.s002</a>.","ama":"Lukacisinova M, Novak S, Paixao T. Extensions of the model. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s002\">10.1371/journal.pcbi.1005609.s002</a>","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Extensions of the Model.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s002\">https://doi.org/10.1371/journal.pcbi.1005609.s002</a>.","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Extensions of the model.” Public Library of Science, 2017."},"date_published":"2017-07-18T00:00:00Z","year":"2017","fulldoi":"https://doi.org/10.1371/journal.pcbi.1005609.s002","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"18","type":"research_data_reference","abstract":[{"lang":"eng","text":"In this text, we discuss how a cost of resistance and the possibility of lethal mutations impact our model."}],"oa_version":"Published Version","_id":"9850","publisher":"Public Library of Science","doi":"10.1371/journal.pcbi.1005609.s002","month":"07"},{"month":"07","doi":"10.1371/journal.pcbi.1005609.s003","publisher":"Public Library of Science","_id":"9851","oa_version":"Published Version","type":"research_data_reference","abstract":[{"text":"Based on the intuitive derivation of the dynamics of SIM allele frequency pM in the main text, we present a heuristic prediction for the long-term SIM allele frequencies with χ > 1 stresses and compare it to numerical simulations.","lang":"eng"}],"day":"18","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","fulldoi":"https://doi.org/10.1371/journal.pcbi.1005609.s003","year":"2017","date_published":"2017-07-18T00:00:00Z","citation":{"short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","ama":"Lukacisinova M, Novak S, Paixao T. Heuristic prediction for multiple stresses. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s003\">10.1371/journal.pcbi.1005609.s003</a>","apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Heuristic prediction for multiple stresses. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s003\">https://doi.org/10.1371/journal.pcbi.1005609.s003</a>","mla":"Lukacisinova, Marta, et al. <i>Heuristic Prediction for Multiple Stresses</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s003\">10.1371/journal.pcbi.1005609.s003</a>.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Heuristic prediction for multiple stresses, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s003\">10.1371/journal.pcbi.1005609.s003</a>.","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Heuristic prediction for multiple stresses.” Public Library of Science, 2017.","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Heuristic Prediction for Multiple Stresses.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s003\">https://doi.org/10.1371/journal.pcbi.1005609.s003</a>."},"author":[{"last_name":"Lukacisinova","full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004","first_name":"Marta"},{"orcid":"0000-0002-2519-824X","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","first_name":"Sebastian"},{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","last_name":"Paixao","full_name":"Paixao, Tiago"}],"date_created":"2021-08-09T14:08:14Z","title":"Heuristic prediction for multiple stresses","article_processing_charge":"No","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"696"}]},"department":[{"_id":"ToBo"},{"_id":"CaGu"},{"_id":"NiBa"}],"date_updated":"2025-09-10T11:11:52Z","status":"public"},{"article_processing_charge":"No","date_created":"2021-08-09T14:11:40Z","title":"Resistance frequencies for different combination strategies","author":[{"full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisinova","orcid":"0000-0002-2519-8004","first_name":"Marta"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X","first_name":"Sebastian"},{"first_name":"Tiago","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","last_name":"Paixao"}],"citation":{"apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. 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Resistance frequencies for different combination strategies. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s004\">10.1371/journal.pcbi.1005609.s004</a>","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Resistance Frequencies for Different Combination Strategies.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s004\">https://doi.org/10.1371/journal.pcbi.1005609.s004</a>.","ieee":"M. Lukacisinova, S. Novak, and T. 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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).","ama":"Schmidt T, Barton NH, Rasic G, et al. Supporting Information concerning additional likelihood analyses and results. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001894.s014\">10.1371/journal.pbio.2001894.s014</a>","mla":"Schmidt, Tom, et al. <i>Supporting Information Concerning Additional Likelihood Analyses and Results</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001894.s014\">10.1371/journal.pbio.2001894.s014</a>.","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. 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Schmidt <i>et al.</i>, “Supporting Information concerning additional likelihood analyses and results.” Public Library of Science, 2017.","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. <a href=\"https://doi.org/10.1371/journal.pbio.2001894.s014\">https://doi.org/10.1371/journal.pbio.2001894.s014</a>."},"date_published":"2017-05-30T00:00:00Z"},{"day":"30","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","fulldoi":"https://doi.org/10.1371/journal.pbio.2001894.s016","year":"2017","month":"05","publisher":"Public Library of Science","doi":"10.1371/journal.pbio.2001894.s016","oa_version":"Published Version","_id":"9858","related_material":{"record":[{"status":"public","id":"951","relation":"used_in_publication"}]},"department":[{"_id":"NiBa"}],"date_updated":"2025-07-10T12:01:48Z","status":"public","citation":{"ieee":"T. Schmidt <i>et al.</i>, “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. <a href=\"https://doi.org/10.1371/journal.pbio.2001894.s016\">https://doi.org/10.1371/journal.pbio.2001894.s016</a>.","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).","ama":"Schmidt T, Barton NH, Rasic G, et al. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001894.s016\">10.1371/journal.pbio.2001894.s016</a>","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. <a href=\"https://doi.org/10.1371/journal.pbio.2001894.s016\">https://doi.org/10.1371/journal.pbio.2001894.s016</a>","mla":"Schmidt, Tom, et al. <i>Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001894.s016\">10.1371/journal.pbio.2001894.s016</a>.","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. 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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.","lang":"eng"}],"day":"01","quality_controlled":"1","issue":"6","fulldoi":"https://doi.org/10.1111/evo.13252","has_accepted_license":"1","file_date_updated":"2020-07-14T12:48:18Z","doi":"10.1111/evo.13252","publisher":"Wiley-Blackwell","_id":"990","language":[{"iso":"eng"}],"ec_funded":1,"department":[{"_id":"NiBa"}],"publication":"Evolution; International Journal of Organic Evolution","page":"1478 - 1493 ","status":"public","volume":71,"date_published":"2017-06-01T00:00:00Z","pmid":1,"publication_status":"published","author":[{"first_name":"Himani","full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"title":"Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow","intvolume":"        71","publist_id":"6409","article_processing_charge":"No","type":"journal_article","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0014-3820"]},"project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"year":"2017","month":"06","external_id":{"isi":["000403014800005"],"pmid":["28419447"]},"scopus_import":"1","pubrep_id":"977","oa_version":"Submitted Version","ddc":["576"],"isi":1,"date_updated":"2025-07-10T12:02:04Z","oa":1,"citation":{"ieee":"H. Sachdeva and N. H. Barton, “Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow,” <i>Evolution; International Journal of Organic Evolution</i>, vol. 71, no. 6. Wiley-Blackwell, pp. 1478–1493, 2017.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Divergence and Evolution of Assortative Mating in a Polygenic Trait Model of Speciation with Gene Flow.” <i>Evolution; International Journal of Organic Evolution</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/evo.13252\">https://doi.org/10.1111/evo.13252</a>.","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. <i>Evolution; International Journal of Organic Evolution</i>. 2017;71(6):1478-1493. doi:<a href=\"https://doi.org/10.1111/evo.13252\">10.1111/evo.13252</a>","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.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Divergence and Evolution of Assortative Mating in a Polygenic Trait Model of Speciation with Gene Flow.” <i>Evolution; International Journal of Organic Evolution</i>, vol. 71, no. 6, Wiley-Blackwell, 2017, pp. 1478–93, doi:<a href=\"https://doi.org/10.1111/evo.13252\">10.1111/evo.13252</a>.","apa":"Sachdeva, H., &#38; Barton, N. H. (2017). Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. <i>Evolution; International Journal of Organic Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/evo.13252\">https://doi.org/10.1111/evo.13252</a>"},"file":[{"creator":"dernst","checksum":"6d4c38cb1347fd43620d1736c6df5c79","access_level":"open_access","file_size":625260,"content_type":"application/pdf","date_created":"2019-04-17T07:37:04Z","relation":"main_file","file_name":"2017_Evolution_Sachdeva_supplement.pdf","date_updated":"2020-07-14T12:48:18Z","file_id":"6329"},{"access_level":"open_access","file_size":520110,"content_type":"application/pdf","date_created":"2019-04-17T07:37:04Z","creator":"dernst","checksum":"f1d90dd8831b44baf49b4dd176f263af","file_name":"2017_Evolution_Sachdeva_article.pdf","date_updated":"2020-07-14T12:48:18Z","file_id":"6330","relation":"main_file"}],"date_created":"2018-12-11T11:49:34Z"},{"publisher":"Public Library of Science","doi":"10.1371/journal.pbio.2001894","file_date_updated":"2020-07-14T12:48:16Z","_id":"951","day":"30","abstract":[{"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","lang":"eng"}],"quality_controlled":"1","fulldoi":"https://doi.org/10.1371/journal.pbio.2001894","issue":"5","has_accepted_license":"1","volume":15,"date_published":"2017-05-30T00:00:00Z","publication_status":"published","author":[{"full_name":"Schmidt, Tom","last_name":"Schmidt","first_name":"Tom"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"first_name":"Gordana","last_name":"Rasic","full_name":"Rasic, Gordana"},{"first_name":"Andrew","full_name":"Turley, Andrew","last_name":"Turley"},{"first_name":"Brian","last_name":"Montgomery","full_name":"Montgomery, Brian"},{"last_name":"Iturbe Ormaetxe","full_name":"Iturbe Ormaetxe, Inaki","first_name":"Inaki"},{"first_name":"Peter","full_name":"Cook, Peter","last_name":"Cook"},{"first_name":"Peter","last_name":"Ryan","full_name":"Ryan, Peter"},{"last_name":"Ritchie","full_name":"Ritchie, Scott","first_name":"Scott"},{"first_name":"Ary","last_name":"Hoffmann","full_name":"Hoffmann, Ary"},{"full_name":"O’Neill, Scott","last_name":"O’Neill","first_name":"Scott"},{"first_name":"Michael","last_name":"Turelli","full_name":"Turelli, Michael"}],"article_processing_charge":"No","publist_id":"6464","title":"Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti","intvolume":"        15","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"9856","relation":"research_data"},{"relation":"research_data","id":"9858","status":"public"},{"id":"9857","relation":"research_data","status":"public"}]},"department":[{"_id":"NiBa"}],"status":"public","publication":"PLoS Biology","article_number":"e2001894","month":"05","external_id":{"isi":["000402520000012"]},"oa_version":"Published Version","pubrep_id":"843","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"scopus_import":"1","type":"journal_article","publication_identifier":{"issn":["1544-9173"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","citation":{"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.” <i>PLoS Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pbio.2001894\">https://doi.org/10.1371/journal.pbio.2001894</a>.","ieee":"T. Schmidt <i>et al.</i>, “Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti,” <i>PLoS Biology</i>, vol. 15, no. 5. Public Library of Science, 2017.","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.","mla":"Schmidt, Tom, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” <i>PLoS Biology</i>, vol. 15, no. 5, e2001894, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001894\">10.1371/journal.pbio.2001894</a>.","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. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2001894\">https://doi.org/10.1371/journal.pbio.2001894</a>","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).","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. <i>PLoS Biology</i>. 2017;15(5). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001894\">10.1371/journal.pbio.2001894</a>"},"oa":1,"file":[{"date_updated":"2020-07-14T12:48:16Z","file_id":"4691","file_name":"IST-2017-843-v1+1_journal.pbio.2001894.pdf","relation":"main_file","date_created":"2018-12-12T10:08:30Z","access_level":"open_access","file_size":5541206,"content_type":"application/pdf","checksum":"107d290bd1159ec77b734eb2824b01c8","creator":"system"}],"date_created":"2018-12-11T11:49:22Z","ddc":["576"],"isi":1,"date_updated":"2026-07-06T13:53:54Z"},{"related_material":{"record":[{"relation":"used_in_publication","id":"951","status":"public"}]},"department":[{"_id":"NiBa"}],"status":"public","date_updated":"2026-07-06T13:53:55Z","citation":{"mla":"Schmidt, Tom, et al. <i>Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001894.s015\">10.1371/journal.pbio.2001894.s015</a>.","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. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2001894.s015\">https://doi.org/10.1371/journal.pbio.2001894.s015</a>","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, <a href=\"https://doi.org/10.1371/journal.pbio.2001894.s015\">10.1371/journal.pbio.2001894.s015</a>.","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).","ama":"Schmidt T, Barton NH, Rasic G, et al. Supporting information concerning observed wMel frequencies and analyses of habitat variables. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2001894.s015\">10.1371/journal.pbio.2001894.s015</a>","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. <a href=\"https://doi.org/10.1371/journal.pbio.2001894.s015\">https://doi.org/10.1371/journal.pbio.2001894.s015</a>.","ieee":"T. Schmidt <i>et al.</i>, “Supporting information concerning observed wMel frequencies and analyses of habitat variables.” Public Library of Science, 2017."},"date_published":"2017-05-30T00:00:00Z","author":[{"full_name":"Schmidt, Tom","last_name":"Schmidt","first_name":"Tom"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"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"},{"first_name":"Inaki","full_name":"Iturbe Ormaetxe, Inaki","last_name":"Iturbe Ormaetxe"},{"first_name":"Peter","full_name":"Cook, Peter","last_name":"Cook"},{"first_name":"Peter","last_name":"Ryan","full_name":"Ryan, Peter"},{"full_name":"Ritchie, Scott","last_name":"Ritchie","first_name":"Scott"},{"last_name":"Hoffmann","full_name":"Hoffmann, Ary","first_name":"Ary"},{"last_name":"O’Neill","full_name":"O’Neill, Scott","first_name":"Scott"},{"last_name":"Turelli","full_name":"Turelli, Michael","first_name":"Michael"}],"article_processing_charge":"No","title":"Supporting information concerning observed wMel frequencies and analyses of habitat variables","date_created":"2021-08-10T07:41:52Z","day":"30","type":"research_data_reference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1371/journal.pbio.2001894.s015","year":"2017","month":"05","publisher":"Public Library of Science","doi":"10.1371/journal.pbio.2001894.s015","oa_version":"Published Version","_id":"9857"},{"oa":1,"citation":{"apa":"Charlesworth, D., Barton, N. H., &#38; Charlesworth, B. (2017). The sources of adaptive evolution. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rspb.2016.2864\">https://doi.org/10.1098/rspb.2016.2864</a>","mla":"Charlesworth, Deborah, et al. “The Sources of Adaptive Evolution.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 284, no. 1855, 20162864, Royal Society, 2017, doi:<a href=\"https://doi.org/10.1098/rspb.2016.2864\">10.1098/rspb.2016.2864</a>.","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.","ama":"Charlesworth D, Barton NH, Charlesworth B. The sources of adaptive evolution. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2017;284(1855). doi:<a href=\"https://doi.org/10.1098/rspb.2016.2864\">10.1098/rspb.2016.2864</a>","short":"D. Charlesworth, N.H. Barton, B. Charlesworth, Proceedings of the Royal Society of London Series B Biological Sciences 284 (2017).","chicago":"Charlesworth, Deborah, Nicholas H Barton, and Brian Charlesworth. “The Sources of Adaptive Evolution.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, 2017. <a href=\"https://doi.org/10.1098/rspb.2016.2864\">https://doi.org/10.1098/rspb.2016.2864</a>.","ieee":"D. Charlesworth, N. H. Barton, and B. Charlesworth, “The sources of adaptive evolution,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 284, no. 1855. Royal Society, 2017."},"date_created":"2018-12-11T11:49:23Z","date_updated":"2026-08-12T06:26:59Z","isi":1,"external_id":{"pmid":["28566483"],"isi":["000405148800021"]},"month":"05","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454256/","open_access":"1"}],"scopus_import":"1","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","year":"2017","date_published":"2017-05-31T00:00:00Z","volume":284,"pmid":1,"intvolume":"       284","title":"The sources of adaptive evolution","publist_id":"6462","article_processing_charge":"No","publication_status":"published","author":[{"full_name":"Charlesworth, Deborah","last_name":"Charlesworth","first_name":"Deborah"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"}],"language":[{"iso":"eng"}],"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","article_number":"20162864","status":"public","department":[{"_id":"NiBa"}],"doi":"10.1098/rspb.2016.2864","publisher":"Royal Society","_id":"953","quality_controlled":"1","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."}],"day":"31","fulldoi":"https://doi.org/10.1098/rspb.2016.2864","issue":"1855"},{"date_created":"2018-12-11T11:50:01Z","file":[{"relation":"main_file","date_updated":"2019-01-18T09:14:02Z","file_id":"5843","file_name":"2017_JRSI_Redondo.pdf","creator":"dernst","date_created":"2019-01-18T09:14:02Z","success":1,"file_size":1092015,"content_type":"application/pdf","access_level":"open_access"}],"citation":{"short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. <i>Journal of the Royal Society Interface</i>. 2017;14(126). doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 14(126), 20160139.","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. <i>Journal of the Royal Society Interface</i>. Royal Society. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>","mla":"Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126, 20160139, Royal Society, 2017, doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>.","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family,” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126. Royal Society, 2017.","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” <i>Journal of the Royal Society Interface</i>. Royal Society, 2017. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>."},"oa":1,"date_updated":"2026-08-27T12:09:33Z","isi":1,"ddc":["570"],"oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"scopus_import":"1","external_id":{"isi":["000393380400001"]},"month":"01","year":"2017","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7"},{"_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer"}],"publication_identifier":{"issn":["1742-5689"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publist_id":"6303","article_processing_charge":"Yes (in subscription journal)","intvolume":"        14","title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","publication_status":"published","author":[{"orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","last_name":"Fernandes Redondo","full_name":"Fernandes Redondo, Rodrigo A","first_name":"Rodrigo A"},{"full_name":"Vladar, Harold","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","last_name":"Vladar","first_name":"Harold"},{"first_name":"Tomasz","last_name":"Włodarski","full_name":"Włodarski, Tomasz"},{"last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"}],"date_published":"2017-01-04T00:00:00Z","volume":14,"status":"public","publication":"Journal of the Royal Society Interface","article_number":"20160139","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"ec_funded":1,"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"9864","relation":"research_data"}]},"_id":"1077","publisher":"Royal Society","doi":"10.1098/rsif.2016.0139","file_date_updated":"2019-01-18T09:14:02Z","fulldoi":"https://doi.org/10.1098/rsif.2016.0139","issue":"126","has_accepted_license":"1","quality_controlled":"1","day":"04","abstract":[{"text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the fX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.","lang":"eng"}]},{"fulldoi":"https://doi.org/10.1371/journal.pcbi.1005609","issue":"7","has_accepted_license":"1","day":"18","abstract":[{"text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy.","lang":"eng"}],"quality_controlled":"1","_id":"696","publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:47:46Z","doi":"10.1371/journal.pcbi.1005609","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"ec_funded":1,"status":"public","publication":"PLoS Computational Biology","article_number":"e1005609","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"research_data","id":"9849","status":"public"},{"status":"public","relation":"research_data","id":"9850"},{"id":"9851","relation":"research_data","status":"public"},{"status":"public","relation":"research_data","id":"9852"},{"id":"6263","relation":"dissertation_contains","status":"public"}]},"author":[{"first_name":"Marta","orcid":"0000-0002-2519-8004","last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta"},{"first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X","last_name":"Novak","full_name":"Novak, Sebastian"},{"first_name":"Tiago","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publist_id":"7004","article_processing_charge":"No","intvolume":"        13","title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","date_published":"2017-07-18T00:00:00Z","volume":13,"project":[{"call_identifier":"FP7","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"year":"2017","corr_author":"1","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["1553-734X"]},"oa_version":"Published Version","scopus_import":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"pubrep_id":"894","month":"07","external_id":{"isi":["000406619800014"]},"article_type":"original","isi":1,"date_updated":"2026-09-28T22:31:01Z","ddc":["576"],"date_created":"2018-12-11T11:47:58Z","file":[{"date_updated":"2020-07-14T12:47:46Z","file_id":"5117","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","relation":"main_file","date_created":"2018-12-12T10:15:01Z","file_size":3775716,"content_type":"application/pdf","access_level":"open_access","checksum":"9143c290fa6458ed2563bff4b295554a","creator":"system"}],"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.","apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>.","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. 2017;13(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>.","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” <i>PLoS Computational Biology</i>, vol. 13, no. 7. Public Library of Science, 2017."},"oa":1},{"fulldoi":"https://doi.org/10.1371/journal.pbio.2000234","has_accepted_license":"1","issue":"12","quality_controlled":"1","day":"27","abstract":[{"lang":"eng","text":"Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate &quot;grey zone&quot; of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation."}],"_id":"1158","publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:44:36Z","doi":"10.1371/journal.pbio.2000234","status":"public","publication":"PLoS Biology","article_number":"e2000234","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"9862","relation":"research_data","status":"public"},{"status":"public","relation":"research_data","id":"9863"}]},"article_processing_charge":"No","publist_id":"6200","acknowledgement":"European Research Council (ERC) https://erc.europa.eu/ (grant number ERC grant 232971). PopPhyl project. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/ (grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch) Center for high-performance computing of the SIB Swiss Institute of Bioinformatics and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité.","intvolume":"        14","title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","author":[{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"},{"first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Romiguier, Jonathan","last_name":"Romiguier","first_name":"Jonathan"},{"full_name":"Anciaux, Youann","last_name":"Anciaux","first_name":"Youann"},{"last_name":"Galtier","full_name":"Galtier, Nicolas","first_name":"Nicolas"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"publication_status":"published","date_published":"2016-12-27T00:00:00Z","volume":14,"year":"2016","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","oa_version":"Published Version","pubrep_id":"742","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"scopus_import":"1","external_id":{"isi":["000392120100008"]},"month":"12","date_updated":"2025-09-22T09:55:10Z","isi":1,"ddc":["576"],"date_created":"2018-12-11T11:50:28Z","file":[{"relation":"main_file","file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","file_id":"5164","date_updated":"2020-07-14T12:44:36Z","creator":"system","checksum":"2bab63b068a9840efd532b9ae583f9bb","file_size":2494348,"content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:15:42Z"}],"citation":{"chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” <i>PLoS Biology</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234\">https://doi.org/10.1371/journal.pbio.2000234</a>.","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Shedding light on the grey zone of speciation along a continuum of genomic divergence,” <i>PLoS Biology</i>, vol. 14, no. 12. Public Library of Science, 2016.","mla":"Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” <i>PLoS Biology</i>, vol. 14, no. 12, e2000234, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234\">10.1371/journal.pbio.2000234</a>.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Shedding light on the grey zone of speciation along a continuum of genomic divergence. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234\">https://doi.org/10.1371/journal.pbio.2000234</a>","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 14(12), e2000234.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016).","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light on the grey zone of speciation along a continuum of genomic divergence. <i>PLoS Biology</i>. 2016;14(12). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234\">10.1371/journal.pbio.2000234</a>"},"oa":1},{"_id":"1172","publisher":"Nature Publishing Group","doi":"10.1038/srep38840","file_date_updated":"2020-07-14T12:44:37Z","fulldoi":"https://doi.org/10.1038/srep38840","has_accepted_license":"1","day":"19","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."}],"quality_controlled":"1","author":[{"last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani","first_name":"Himani"},{"first_name":"Mustansir","last_name":"Barma","full_name":"Barma, Mustansir"},{"first_name":"Madan","full_name":"Rao, Madan","last_name":"Rao"}],"publication_status":"published","article_processing_charge":"No","publist_id":"6183","acknowledgement":"H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund Thattai for critical discussions and suggestions.","title":"Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae","intvolume":"         6","date_published":"2016-12-19T00:00:00Z","volume":6,"department":[{"_id":"NiBa"}],"status":"public","publication":"Scientific Reports","article_number":"38840","language":[{"iso":"eng"}],"oa_version":"Published Version","pubrep_id":"737","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"scopus_import":"1","month":"12","external_id":{"isi":["000389885900001"]},"year":"2016","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:32Z","file":[{"date_created":"2018-12-12T10:12:56Z","content_type":"application/pdf","file_size":760967,"access_level":"open_access","checksum":"cb378732da885ea4959ec5b845fb6e52","creator":"system","date_updated":"2020-07-14T12:44:37Z","file_id":"4977","file_name":"IST-2017-737-v1+1_srep38840.pdf","relation":"main_file"}],"citation":{"mla":"Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” <i>Scientific Reports</i>, vol. 6, 38840, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep38840\">10.1038/srep38840</a>.","apa":"Sachdeva, H., Barma, M., &#38; Rao, M. (2016). Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep38840\">https://doi.org/10.1038/srep38840</a>","ista":"Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.","ama":"Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep38840\">10.1038/srep38840</a>","short":"H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).","chicago":"Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep38840\">https://doi.org/10.1038/srep38840</a>.","ieee":"H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016."},"oa":1,"isi":1,"date_updated":"2025-09-22T09:49:53Z","ddc":["576"]},{"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"ec_funded":1,"status":"public","page":"174 - 184","publication":"Molecular Biology and Evolution","date_published":"2016-10-03T00:00:00Z","volume":34,"author":[{"full_name":"Franssen, Susan","last_name":"Franssen","first_name":"Susan"},{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"last_name":"Schlötterer","full_name":"Schlötterer, Christian","first_name":"Christian"}],"publication_status":"published","article_processing_charge":"No","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”.","publist_id":"6155","intvolume":"        34","title":"Reconstruction of haplotype-blocks selected during experimental evolution.","day":"03","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"}],"quality_controlled":"1","has_accepted_license":"1","fulldoi":"https://doi.org/10.1093/molbev/msw210","issue":"1","publisher":"Oxford University Press","doi":"10.1093/molbev/msw210","file_date_updated":"2020-07-14T12:44:38Z","_id":"1195","ddc":["576"],"isi":1,"date_updated":"2025-09-22T09:43:41Z","citation":{"short":"S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution 34 (2016) 174–184.","ama":"Franssen S, Barton NH, Schlötterer C. Reconstruction of haplotype-blocks selected during experimental evolution. <i>Molecular Biology and Evolution</i>. 2016;34(1):174-184. doi:<a href=\"https://doi.org/10.1093/molbev/msw210\">10.1093/molbev/msw210</a>","ista":"Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks selected during experimental evolution. Molecular Biology and Evolution. 34(1), 174–184.","apa":"Franssen, S., Barton, N. H., &#38; Schlötterer, C. (2016). Reconstruction of haplotype-blocks selected during experimental evolution. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msw210\">https://doi.org/10.1093/molbev/msw210</a>","mla":"Franssen, Susan, et al. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” <i>Molecular Biology and Evolution</i>, vol. 34, no. 1, Oxford University Press, 2016, pp. 174–84, doi:<a href=\"https://doi.org/10.1093/molbev/msw210\">10.1093/molbev/msw210</a>.","ieee":"S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks selected during experimental evolution.,” <i>Molecular Biology and Evolution</i>, vol. 34, no. 1. Oxford University Press, pp. 174–184, 2016.","chicago":"Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction of Haplotype-Blocks Selected during Experimental Evolution.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/molbev/msw210\">https://doi.org/10.1093/molbev/msw210</a>."},"oa":1,"date_created":"2018-12-11T11:50:39Z","file":[{"file_name":"IST-2017-770-v1+1_FranssenEtAl_nofigs-1.pdf","date_updated":"2020-07-14T12:44:38Z","file_id":"5223","relation":"main_file","access_level":"open_access","file_size":295274,"content_type":"application/pdf","date_created":"2018-12-12T10:16:35Z","creator":"system","checksum":"1e78d3aaffcb40dc8b02b7b4666019e0"},{"date_created":"2018-12-12T10:16:36Z","access_level":"open_access","file_size":10902625,"content_type":"application/pdf","checksum":"e13171843283774404c936c581b4543e","creator":"system","file_id":"5224","date_updated":"2020-07-14T12:44:38Z","file_name":"IST-2017-770-v1+2_Fig1.pdf","relation":"main_file"},{"relation":"main_file","file_name":"IST-2017-770-v1+3_Fig2.pdf","file_id":"5225","date_updated":"2020-07-14T12:44:38Z","creator":"system","checksum":"63bc6e6e61f347594d8c00c37f874a0b","access_level":"open_access","content_type":"application/pdf","file_size":21437,"date_created":"2018-12-12T10:16:37Z"},{"checksum":"da87cc7c78808837f22a3dae1c8397f9","creator":"system","date_created":"2018-12-12T10:16:38Z","file_size":1172194,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5226","date_updated":"2020-07-14T12:44:38Z","file_name":"IST-2017-770-v1+4_Fig3.pdf"},{"relation":"main_file","file_id":"5227","date_updated":"2020-07-14T12:44:38Z","file_name":"IST-2017-770-v1+5_Fig4.pdf","checksum":"e47b2a0c32142f423b3100150c0294f8","creator":"system","date_created":"2018-12-12T10:16:38Z","access_level":"open_access","content_type":"application/pdf","file_size":50045},{"file_name":"IST-2017-770-v1+6_Fig5.pdf","file_id":"5228","date_updated":"2020-07-14T12:44:38Z","relation":"main_file","file_size":50705,"content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:16:39Z","creator":"system","checksum":"a5a7d6b32e7e17d35d337d7ec2a9f6c9"}],"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"year":"2016","month":"10","external_id":{"isi":["000396772000009"]},"oa_version":"Submitted Version","pubrep_id":"770","scopus_import":"1"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","year":"2016","external_id":{"isi":["000369975700011"]},"month":"01","oa_version":"None","scopus_import":"1","date_updated":"2025-09-22T09:31:49Z","isi":1,"citation":{"apa":"Teitel, Z., Pickup, M., Field, D., &#38; Barrett, S. (2016). The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant. <i>Plant Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/plb.12336\">https://doi.org/10.1111/plb.12336</a>","mla":"Teitel, Zachary, et al. “The Dynamics of Resource Allocation and Costs of Reproduction in a Sexually Dimorphic, Wind-Pollinated Dioecious Plant.” <i>Plant Biology</i>, vol. 18, no. 1, Wiley-Blackwell, 2016, pp. 98–103, doi:<a href=\"https://doi.org/10.1111/plb.12336\">10.1111/plb.12336</a>.","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.","ama":"Teitel Z, Pickup M, Field D, Barrett S. The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant. <i>Plant Biology</i>. 2016;18(1):98-103. doi:<a href=\"https://doi.org/10.1111/plb.12336\">10.1111/plb.12336</a>","short":"Z. Teitel, M. Pickup, D. Field, S. Barrett, Plant Biology 18 (2016) 98–103.","chicago":"Teitel, Zachary, Melinda Pickup, David Field, and Spencer Barrett. “The Dynamics of Resource Allocation and Costs of Reproduction in a Sexually Dimorphic, Wind-Pollinated Dioecious Plant.” <i>Plant Biology</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1111/plb.12336\">https://doi.org/10.1111/plb.12336</a>.","ieee":"Z. Teitel, M. Pickup, D. Field, and S. Barrett, “The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant,” <i>Plant Biology</i>, vol. 18, no. 1. Wiley-Blackwell, pp. 98–103, 2016."},"date_created":"2018-12-11T11:50:48Z","quality_controlled":"1","day":"01","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"}],"fulldoi":"https://doi.org/10.1111/plb.12336","issue":"1","publisher":"Wiley-Blackwell","doi":"10.1111/plb.12336","_id":"1224","language":[{"iso":"eng"}],"status":"public","page":"98 - 103","publication":"Plant Biology","department":[{"_id":"NiBa"}],"date_published":"2016-01-01T00:00:00Z","volume":18,"publist_id":"6110","article_processing_charge":"No","intvolume":"        18","title":"The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant","author":[{"full_name":"Teitel, Zachary","last_name":"Teitel","first_name":"Zachary"},{"orcid":"0000-0001-6118-0541","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda","first_name":"Melinda"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field","first_name":"David"},{"full_name":"Barrett, Spencer","last_name":"Barrett","first_name":"Spencer"}],"publication_status":"published"}]