[{"file":[{"file_size":8029982,"checksum":"0ba0bcd0bb8b18d84792136a4370df90","date_created":"2023-05-10T09:41:43Z","content_type":"text/csv","file_name":"Dataset_S1.csv","date_updated":"2023-05-10T09:41:43Z","relation":"main_file","access_level":"open_access","success":1,"creator":"gpuixeus","file_id":"12934"},{"relation":"main_file","success":1,"access_level":"open_access","file_id":"12935","creator":"gpuixeus","date_created":"2023-05-10T09:41:43Z","file_size":13667640,"checksum":"a62aa9a6d4904e0fdb699cf752640863","date_updated":"2023-05-10T09:41:43Z","file_name":"Dataset_S2.csv","content_type":"text/csv"},{"creator":"gpuixeus","file_id":"12936","relation":"main_file","access_level":"open_access","success":1,"content_type":"text/csv","file_name":"Dataset_S3.csv","date_updated":"2023-05-10T09:41:48Z","file_size":8369141,"checksum":"e20ea7f4f8a9bdf1b3849a44664ae58b","date_created":"2023-05-10T09:41:48Z"},{"creator":"gpuixeus","file_id":"12937","access_level":"open_access","success":1,"relation":"main_file","content_type":"text/csv","file_name":"Dataset_S4.csv","date_updated":"2023-05-10T09:41:50Z","file_size":19543247,"checksum":"f6156e5fc44446c907ddd0d7289d4cf8","date_created":"2023-05-10T09:41:50Z"},{"date_updated":"2023-05-11T12:50:18Z","content_type":"text/plain","file_name":"readme.txt","date_created":"2023-05-11T12:50:18Z","checksum":"ae9f54c77a1c42b666ae6c1dfd33ac86","file_size":4566,"file_id":"12944","creator":"gpuixeus","relation":"main_file","access_level":"open_access","success":1}],"ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14058"},{"id":"14077","relation":"used_in_publication","status":"public"}]},"doi":"10.15479/AT:ISTA:12933","day":"15","abstract":[{"text":"Datasets of the publication \"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster\".","lang":"eng"}],"oa":1,"date_updated":"2023-12-13T12:15:36Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2023","citation":{"ieee":"G. Puixeu Sala, “Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster.” Institute of Science and Technology Austria, 2023.","chicago":"Puixeu Sala, Gemma. “Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12933.","apa":"Puixeu Sala, G. (2023). Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12933","ama":"Puixeu Sala G. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. 2023. doi:10.15479/AT:ISTA:12933","ista":"Puixeu Sala G. 2023. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12933.","short":"G. Puixeu Sala, (2023).","mla":"Puixeu Sala, Gemma. Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12933."},"date_published":"2023-05-15T00:00:00Z","type":"research_data","publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-05-11T12:50:18Z","contributor":[{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","date_created":"2023-05-10T10:00:49Z","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"article_processing_charge":"No","month":"05","title":"Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","_id":"12933","has_accepted_license":"1","author":[{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","last_name":"Puixeu Sala","first_name":"Gemma"}]},{"oa":1,"abstract":[{"text":"The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and a non-genetic (environmental) component and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the trait values of the parents. Although the trait distribution across the whole population can be far from normal, the trait distributions within families are normally distributed with a variance-covariance matrix that is determined entirely by that in the ancestral population and the probabilities of identity determined by the pedigree. Moreover, conditioning on some of the trait values within the pedigree has predictable effects on the mean and variance within and between families. In previous work, Barton et al. (2017), we showed that when trait values are determined by the sum of a large number of Mendelian factors, each of small effect, one can justify the infinitesimal model as limit of Mendelian inheritance. It was also shown that under some forms of epistasis, trait values within a family are still normally distributed.","lang":"eng"}],"day":"13","doi":"10.15479/AT:ISTA:12949","type":"research_data","date_published":"2023-05-13T00:00:00Z","citation":{"mla":"Barton, Nicholas H. The Infinitesimal Model with Dominance. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12949.","short":"N.H. Barton, (2023).","ista":"Barton NH. 2023. The infinitesimal model with dominance, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12949.","ama":"Barton NH. The infinitesimal model with dominance. 2023. doi:10.15479/AT:ISTA:12949","apa":"Barton, N. H. (2023). The infinitesimal model with dominance. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12949","ieee":"N. H. Barton, “The infinitesimal model with dominance.” Institute of Science and Technology Austria, 2023.","chicago":"Barton, Nicholas H. “The Infinitesimal Model with Dominance.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12949."},"year":"2023","date_updated":"2025-05-28T11:57:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"relation":"used_in_publication","id":"14452","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["576"],"file":[{"date_updated":"2023-05-13T09:36:33Z","content_type":"application/octet-stream","file_name":"Neutral identities 16th Jan","date_created":"2023-05-13T09:36:33Z","file_size":13662,"checksum":"b0ce7d4b1ee7e7265430ceed36fc3336","file_id":"12950","creator":"nbarton","relation":"main_file","success":1,"access_level":"open_access"},{"creator":"nbarton","file_id":"12951","success":1,"access_level":"open_access","relation":"main_file","file_name":"p, zA, zD, N=30 neutral III","content_type":"application/octet-stream","date_updated":"2023-05-13T09:38:17Z","checksum":"ad5035ad4f7d3b150a252c79884f6a83","file_size":181619928,"date_created":"2023-05-13T09:38:17Z"},{"file_id":"12952","creator":"nbarton","access_level":"open_access","success":1,"relation":"main_file","date_updated":"2023-05-13T09:41:59Z","file_name":"p, zA, zD, N=30 neutral IV","content_type":"application/octet-stream","date_created":"2023-05-13T09:41:59Z","file_size":605902074,"checksum":"62182a1de796256edd6f4223704312ef"},{"access_level":"open_access","success":1,"relation":"main_file","creator":"nbarton","file_id":"12953","file_size":1018238746,"checksum":"af775dda5c4f6859cb1e5a81ec40a667","date_created":"2023-05-13T09:46:52Z","content_type":"application/octet-stream","file_name":"p, zA, zD, N=30 selected k=5","date_updated":"2023-05-13T09:46:52Z"},{"relation":"main_file","access_level":"open_access","success":1,"file_id":"12954","creator":"nbarton","date_created":"2023-05-13T09:42:05Z","checksum":"af26f3394c387d3ada14b434cd68b1e5","file_size":3197160,"date_updated":"2023-05-13T09:42:05Z","file_name":"Pairwise F N=30 neutral II","content_type":"application/octet-stream"},{"date_updated":"2023-05-13T09:42:06Z","file_name":"Pedigrees N=30 neutral II","content_type":"application/octet-stream","date_created":"2023-05-13T09:42:06Z","file_size":55492,"checksum":"d5da7dc0e7282dd48222e26d12e34220","file_id":"12955","creator":"nbarton","access_level":"open_access","success":1,"relation":"main_file"},{"date_updated":"2023-05-13T09:46:06Z","content_type":"application/octet-stream","file_name":"selected reps N=30 selected k=1,2 300 reps III","date_created":"2023-05-13T09:46:06Z","checksum":"00f386d80677590e29f6235d49cba58d","file_size":474003467,"file_id":"12956","creator":"nbarton","access_level":"open_access","success":1,"relation":"main_file"},{"file_name":"Algorithm for caclulating identities.nb","content_type":"application/octet-stream","date_updated":"2023-05-13T09:46:08Z","checksum":"658cef3eaea6136a4d24da4f074191d7","file_size":121209,"date_created":"2023-05-13T09:46:08Z","creator":"nbarton","file_id":"12957","success":1,"relation":"main_file","access_level":"open_access"},{"creator":"nbarton","file_id":"12958","success":1,"access_level":"open_access","relation":"main_file","file_name":"Infinitesimal with dominance.nb","content_type":"application/octet-stream","date_updated":"2023-05-13T09:46:08Z","file_size":1803898,"checksum":"db9b6dddd7a596d974e25f5e78f5c45c","date_created":"2023-05-13T09:46:08Z"},{"date_updated":"2023-05-16T04:09:08Z","content_type":"text/plain","file_name":"ReadMe.txt","date_created":"2023-05-16T04:09:08Z","checksum":"91f80a9fb58cae8eef2d8bf59fe30189","file_size":990,"file_id":"12967","creator":"nbarton","relation":"main_file","success":1,"access_level":"open_access"}],"title":"The infinitesimal model with dominance","month":"05","department":[{"_id":"NiBa"}],"project":[{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"article_processing_charge":"No","date_created":"2023-05-13T09:49:09Z","oa_version":"Published Version","author":[{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","_id":"12949","publisher":"Institute of Science and Technology Austria","keyword":["Quantitative genetics","infinitesimal model"],"contributor":[{"first_name":"Amandine","last_name":"Veber","contributor_type":"researcher"},{"first_name":"Alison","contributor_type":"researcher","last_name":"Etheridge"}],"file_date_updated":"2023-05-16T04:09:08Z"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-01-24T00:00:00Z","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"oa":1,"file":[{"file_id":"10659","creator":"oolusany","relation":"main_file","access_level":"open_access","date_updated":"2022-01-24T10:34:45Z","file_name":"rstb.2021.0010.pdf","content_type":"application/pdf","date_created":"2022-01-24T10:34:45Z","file_size":1845792,"checksum":"04ca9e2f0e344d680b947f2457df8d0a"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"url":"https://doi.org/10.1101/2021.08.05.455207","relation":"earlier_version"}],"record":[{"status":"public","id":"14711","relation":"dissertation_contains"}]},"has_accepted_license":"1","publication":"Philosophical Transactions of the Royal Society B","project":[{"_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","grant_number":"P32896","name":"Causes and consequences of population fragmentation"}],"oa_version":"Published Version","article_number":"20210010","month":"01","language":[{"iso":"eng"}],"year":"2022","citation":{"apa":"Sachdeva, H., Olusanya, O. O., & Barton, N. H. (2022). Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. The Royal Society. https://doi.org/10.1098/rstb.2021.0010","ama":"Sachdeva H, Olusanya OO, Barton NH. Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. 2022;377(1846). doi:10.1098/rstb.2021.0010","ieee":"H. Sachdeva, O. O. Olusanya, and N. H. Barton, “Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity,” Philosophical Transactions of the Royal Society B, vol. 377, no. 1846. The Royal Society, 2022.","chicago":"Sachdeva, Himani, Oluwafunmilola O Olusanya, and Nicholas H Barton. “Genetic Load and Extinction in Peripheral Populations: The Roles of Migration, Drift and Demographic Stochasticity.” Philosophical Transactions of the Royal Society B. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0010.","mla":"Sachdeva, Himani, et al. “Genetic Load and Extinction in Peripheral Populations: The Roles of Migration, Drift and Demographic Stochasticity.” Philosophical Transactions of the Royal Society B, vol. 377, no. 1846, 20210010, The Royal Society, 2022, doi:10.1098/rstb.2021.0010.","short":"H. Sachdeva, O.O. Olusanya, N.H. Barton, Philosophical Transactions of the Royal Society B 377 (2022).","ista":"Sachdeva H, Olusanya OO, Barton NH. 2022. Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. 377(1846), 20210010."},"date_updated":"2025-05-26T09:05:09Z","external_id":{"isi":["000745854300008"],"pmid":["35067097"]},"isi":1,"day":"24","doi":"10.1098/rstb.2021.0010","abstract":[{"lang":"eng","text":"We analyse how migration from a large mainland influences genetic load and population numbers on an island, in a scenario where fitness-affecting variants are unconditionally deleterious, and where numbers decline with increasing load. Our analysis shows that migration can have qualitatively different effects, depending on the total mutation target and fitness effects of deleterious variants. In particular, we find that populations exhibit a genetic Allee effect across a wide range of parameter combinations, when variants are partially recessive, cycling between low-load (large-population) and high-load (sink) states. Increased migration reduces load in the sink state (by increasing heterozygosity) but further inflates load in the large-population state (by hindering purging). We identify various critical parameter thresholds at which one or other stable state collapses, and discuss how these thresholds are influenced by the genetic versus demographic effects of migration. Our analysis is based on a ‘semi-deterministic’ analysis, which accounts for genetic drift but neglects demographic stochasticity. We also compare against simulations which account for both demographic stochasticity and drift. Our results clarify the importance of gene flow as a key determinant of extinction risk in peripheral populations, even in the absence of ecological gradients. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (part I)’."}],"volume":377,"acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) (grant no. P-32896B).","ddc":["576"],"pmid":1,"_id":"10658","issue":"1846","author":[{"first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani"},{"last_name":"Olusanya","first_name":"Oluwafunmilola O","full_name":"Olusanya, Oluwafunmilola O","orcid":"0000-0003-1971-8314","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_created":"2022-01-24T10:34:53Z","article_processing_charge":"No","publication_status":"published","intvolume":" 377","title":"Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity","quality_controlled":"1","file_date_updated":"2022-01-24T10:34:45Z","publisher":"The Royal Society","article_type":"original"},{"volume":11,"acknowledgement":"We thank Hande Acar, Nicholas H Barton, Rok Grah, Tiago Paixao, Maros Pleska, Anna Staron, and Murat Tugrul for insightful comments and input on the manuscript. This work was supported by: Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant number 216779/Z/19/Z) to ML; IPC Grant from IST Austria to ML and SS; European Research Council Funding Programme 7 (2007–2013, grant agreement number 648440) to JPB.","ddc":["576"],"year":"2022","citation":{"mla":"Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife, vol. 11, e64543, eLife Sciences Publications, 2022, doi:10.7554/eLife.64543.","short":"M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkačik, ELife 11 (2022).","ista":"Lagator M, Sarikas S, Steinrueck M, Toledo-Aparicio D, Bollback JP, Guet CC, Tkačik G. 2022. Predicting bacterial promoter function and evolution from random sequences. eLife. 11, e64543.","apa":"Lagator, M., Sarikas, S., Steinrueck, M., Toledo-Aparicio, D., Bollback, J. P., Guet, C. C., & Tkačik, G. (2022). Predicting bacterial promoter function and evolution from random sequences. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.64543","ama":"Lagator M, Sarikas S, Steinrueck M, et al. Predicting bacterial promoter function and evolution from random sequences. eLife. 2022;11. doi:10.7554/eLife.64543","chicago":"Lagator, Mato, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio, Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/eLife.64543.","ieee":"M. Lagator et al., “Predicting bacterial promoter function and evolution from random sequences,” eLife, vol. 11. eLife Sciences Publications, 2022."},"date_updated":"2023-08-02T14:09:02Z","external_id":{"pmid":["35080492"],"isi":["000751104400001"]},"isi":1,"day":"26","doi":"10.7554/eLife.64543","abstract":[{"lang":"eng","text":"Predicting function from sequence is a central problem of biology. Currently, this is possible only locally in a narrow mutational neighborhood around a wildtype sequence rather than globally from any sequence. Using random mutant libraries, we developed a biophysical model that accounts for multiple features of σ70 binding bacterial promoters to predict constitutive gene expression levels from any sequence. We experimentally and theoretically estimated that 10–20% of random sequences lead to expression and ~80% of non-expressing sequences are one mutation away from a functional promoter. The potential for generating expression from random sequences is so pervasive that selection acts against σ70-RNA polymerase binding sites even within inter-genic, promoter-containing regions. This pervasiveness of σ70-binding sites implies that emergence of promoters is not the limiting step in gene regulatory evolution. Ultimately, the inclusion of novel features of promoter function into a mechanistic model enabled not only more accurate predictions of gene expression levels, but also identified that promoters evolve more rapidly than previously thought."}],"ec_funded":1,"quality_controlled":"1","file_date_updated":"2022-02-07T07:14:09Z","publisher":"eLife Sciences Publications","article_type":"original","scopus_import":"1","pmid":1,"_id":"10736","author":[{"full_name":"Lagator, Mato","first_name":"Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"id":"35F0286E-F248-11E8-B48F-1D18A9856A87","full_name":"Sarikas, Srdjan","last_name":"Sarikas","first_name":"Srdjan"},{"full_name":"Steinrueck, Magdalena","last_name":"Steinrueck","first_name":"Magdalena"},{"full_name":"Toledo-Aparicio, David","last_name":"Toledo-Aparicio","first_name":"David"},{"first_name":"Jonathan P","last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper"}],"article_processing_charge":"No","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"NiBa"}],"date_created":"2022-02-06T23:01:32Z","publication_status":"published","intvolume":" 11","title":"Predicting bacterial promoter function and evolution from random sequences","file":[{"file_id":"10739","creator":"cchlebak","success":1,"access_level":"open_access","relation":"main_file","date_updated":"2022-02-07T07:14:09Z","file_name":"2022_ELife_Lagator.pdf","content_type":"application/pdf","date_created":"2022-02-07T07:14:09Z","file_size":5604343,"checksum":"decdcdf600ff51e9a9703b49ca114170"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-01-26T00:00:00Z","publication_identifier":{"eissn":["2050-084X"]},"oa":1,"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"eLife","project":[{"_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440"}],"oa_version":"Published Version","article_number":"e64543","month":"01"},{"volume":377,"acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) [FWF P-32896B].","ddc":["570"],"doi":"10.1098/rstb.2021.0009","day":"11","abstract":[{"lang":"eng","text":"A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a ‘fixed-state’ approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m−1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments.\r\nThis article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’."}],"date_updated":"2025-05-26T09:05:09Z","year":"2022","citation":{"apa":"Barton, N. H., & Olusanya, O. O. (2022). The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2021.0009","ama":"Barton NH, Olusanya OO. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 2022;377(1848). doi:10.1098/rstb.2021.0009","ieee":"N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing environment,” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1848. The Royal Society, 2022.","chicago":"Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a Metapopulation to a Changing Environment.” Philosophical Transactions of the Royal Society B: Biological Sciences. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0009.","mla":"Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation to a Changing Environment.” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1848, The Royal Society, 2022, doi:10.1098/rstb.2021.0009.","short":"N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","ista":"Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1848)."},"isi":1,"external_id":{"pmid":["35184588"],"isi":["000758140300001"]},"publisher":"The Royal Society","article_type":"original","quality_controlled":"1","file_date_updated":"2022-08-02T06:14:32Z","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"article_processing_charge":"No","date_created":"2022-02-21T16:08:10Z","title":"The response of a metapopulation to a changing environment","intvolume":" 377","_id":"10787","pmid":1,"scopus_import":"1","author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1971-8314","full_name":"Olusanya, Oluwafunmilola O","first_name":"Oluwafunmilola O","last_name":"Olusanya"}],"issue":"1848","file":[{"creator":"dernst","file_id":"11719","access_level":"open_access","success":1,"relation":"main_file","content_type":"application/pdf","file_name":"2022_PhilosophicalTransactionsRSB_Barton.pdf","date_updated":"2022-08-02T06:14:32Z","file_size":1349672,"checksum":"3b0243738f01bf3c07e0d7e8dc64f71d","date_created":"2022-08-02T06:14:32Z"}],"related_material":{"record":[{"status":"public","id":"14711","relation":"dissertation_contains"}]},"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-04-11T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"oa_version":"Published Version","project":[{"grant_number":"P32896","name":"Causes and consequences of population fragmentation","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"}],"month":"04","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","has_accepted_license":"1"},{"language":[{"iso":"eng"}],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}],"oa_version":"Published Version","month":"04","file":[{"file_name":"LenkaPhD_Official_PDFA.pdf","content_type":"application/pdf","date_updated":"2022-04-07T08:11:34Z","checksum":"e9609bc4e8f8e20146fc1125fd4f1bf7","file_size":11906472,"date_created":"2022-04-07T08:11:34Z","creator":"cchlebak","file_id":"11129","access_level":"open_access","relation":"main_file"},{"content_type":"application/x-zip-compressed","file_name":"LenkaPhD Official_source.zip","date_updated":"2022-04-07T08:11:51Z","checksum":"99d67040432fd07a225643a212ee8588","file_size":23036766,"date_created":"2022-04-07T08:11:51Z","creator":"cchlebak","file_id":"11130","access_level":"closed","relation":"source_file"}],"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-04-06T00:00:00Z","type":"dissertation","publication_identifier":{"isbn":["978-3-99078-016-9"],"issn":["2663-337X"]},"supervisor":[{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"page":"112","file_date_updated":"2022-04-07T08:11:51Z","publisher":"Institute of Science and Technology Austria","_id":"11128","author":[{"full_name":"Matejovicova, Lenka","first_name":"Lenka","last_name":"Matejovicova","id":"2DFDEC72-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","article_processing_charge":"No","date_created":"2022-04-07T08:19:54Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"alternative_title":["ISTA Thesis"],"title":"Genetic basis of flower colour as a model for adaptive evolution","ddc":["576","582"],"date_updated":"2023-06-23T06:26:41Z","citation":{"mla":"Matejovicova, Lenka. Genetic Basis of Flower Colour as a Model for Adaptive Evolution. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11128.","short":"L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022.","ista":"Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria.","ama":"Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution. 2022. doi:10.15479/at:ista:11128","apa":"Matejovicova, L. (2022). Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11128","ieee":"L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022.","chicago":"Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive Evolution.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11128."},"year":"2022","doi":"10.15479/at:ista:11128","degree_awarded":"PhD","day":"06","abstract":[{"lang":"eng","text":"Although we often see studies focusing on simple or even discrete traits in studies of colouration,\r\nthe variation of “appearance” phenotypes found in nature is often more complex, continuous\r\nand high-dimensional. Therefore, we developed automated methods suitable for large datasets\r\nof genomes and images, striving to account for their complex nature, while minimising human\r\nbias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in\r\nthe main fower colour regulating region. We study colour- and geography-related characteristics\r\nof the estimated haplotypes and how they connect to their relatedness. We show discrepancies\r\nfrom the expected fower colour distributions given the genotype and identify particular\r\nhaplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent parental type are much less variable than others.\r\nSecondly, we introduce our pipeline capable of processing tens of thousands of full fower\r\nimages without human interaction and summarising each image into a set of informative scores.\r\nWe show the compatibility of these machine-measured fower colour scores with the previously\r\nused manual scores and study impact of external efect on the resulting scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower images as opposed to discrete, manual scores and\r\ncompare it with the genotypic cline."}]},{"author":[{"last_name":"Surendranadh","first_name":"Parvathy","full_name":"Surendranadh, Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1771-714X","full_name":"Arathoon, Louise S","first_name":"Louise S","last_name":"Arathoon"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7354-8574","full_name":"Baskett, Carina","first_name":"Carina","last_name":"Baskett"},{"last_name":"Field","first_name":"David","full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pickup","first_name":"Melinda","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"_id":"11321","has_accepted_license":"1","month":"04","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_created":"2022-04-22T09:42:24Z","article_processing_charge":"No","file_date_updated":"2022-04-22T09:39:03Z","contributor":[{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","contributor_type":"project_member","first_name":"Louise S"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","last_name":"Baskett","contributor_type":"project_member","orcid":"0000-0002-7354-8574"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","contributor_type":"project_member","last_name":"Field","first_name":"David"},{"orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup","contributor_type":"project_member","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","contributor_type":"project_member","first_name":"Nicholas H"}],"publisher":"Institute of Science and Technology Austria","date_published":"2022-04-28T00:00:00Z","type":"research_data","date_updated":"2024-02-21T12:41:09Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2022","citation":{"ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, 10.15479/at:ista:11321.","mla":"Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11321.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2022).","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11321.","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2022.","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2022. doi:10.15479/at:ista:11321","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11321"},"abstract":[{"text":"Here are the research data underlying the publication \"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus\" Further information are summed up in the README document. ","lang":"eng"}],"oa":1,"doi":"10.15479/at:ista:11321","day":"28","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"11411"},{"relation":"earlier_version","id":"9192","status":"public"},{"relation":"earlier_version","id":"8254","status":"public"}]},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"file_id":"11326","creator":"larathoo","success":1,"relation":"main_file","access_level":"open_access","date_updated":"2022-04-22T09:39:03Z","content_type":"application/x-zip-compressed","file_name":"Data_Code.zip","date_created":"2022-04-22T09:39:03Z","checksum":"96c1b86cdf25481f2a52972fcc45ca7f","file_size":13260571}]},{"publication":"Evolution","has_accepted_license":"1","month":"05","oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"265B41B8-B435-11E9-9278-68D0E5697425","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","grant_number":"797747"}],"language":[{"iso":"eng"}],"date_published":"2022-05-01T00:00:00Z","type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"oa":1,"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"creator":"dernst","file_id":"11729","access_level":"open_access","success":1,"relation":"main_file","content_type":"application/pdf","file_name":"2022_Evolution_Freitas.pdf","date_updated":"2022-08-05T06:19:28Z","file_size":2855214,"checksum":"c27c025ae9afcf6c804d46a909775ee5","date_created":"2022-08-05T06:19:28Z"}],"author":[{"first_name":"Susana","last_name":"Freitas","full_name":"Freitas, Susana"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schwander, Tanja","last_name":"Schwander","first_name":"Tanja"},{"full_name":"Arakelyan, Marine","last_name":"Arakelyan","first_name":"Marine"},{"first_name":"Çetin","last_name":"Ilgaz","full_name":"Ilgaz, Çetin"},{"last_name":"Kumlutas","first_name":"Yusuf","full_name":"Kumlutas, Yusuf"},{"full_name":"Harris, David James","last_name":"Harris","first_name":"David James"},{"full_name":"Carretero, Miguel A.","first_name":"Miguel A.","last_name":"Carretero"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"issue":"5","pmid":1,"_id":"11334","scopus_import":"1","title":"Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization","intvolume":" 76","publication_status":"published","date_created":"2022-04-24T22:01:44Z","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"article_processing_charge":"No","file_date_updated":"2022-08-05T06:19:28Z","page":"899-914","ec_funded":1,"quality_controlled":"1","article_type":"original","publisher":"Wiley","isi":1,"external_id":{"isi":["000781632500001"],"pmid":["35323995"]},"date_updated":"2023-08-03T07:00:28Z","year":"2022","citation":{"short":"S. Freitas, A.M. Westram, T. Schwander, M. Arakelyan, Ç. Ilgaz, Y. Kumlutas, D.J. Harris, M.A. Carretero, R.K. Butlin, Evolution 76 (2022) 899–914.","mla":"Freitas, Susana, et al. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” Evolution, vol. 76, no. 5, Wiley, 2022, pp. 899–914, doi:10.1111/evo.14462.","ista":"Freitas S, Westram AM, Schwander T, Arakelyan M, Ilgaz Ç, Kumlutas Y, Harris DJ, Carretero MA, Butlin RK. 2022. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. 76(5), 899–914.","apa":"Freitas, S., Westram, A. M., Schwander, T., Arakelyan, M., Ilgaz, Ç., Kumlutas, Y., … Butlin, R. K. (2022). Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. Wiley. https://doi.org/10.1111/evo.14462","ama":"Freitas S, Westram AM, Schwander T, et al. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. 2022;76(5):899-914. doi:10.1111/evo.14462","chicago":"Freitas, Susana, Anja M Westram, Tanja Schwander, Marine Arakelyan, Çetin Ilgaz, Yusuf Kumlutas, David James Harris, Miguel A. Carretero, and Roger K. Butlin. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14462.","ieee":"S. Freitas et al., “Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization,” Evolution, vol. 76, no. 5. Wiley, pp. 899–914, 2022."},"abstract":[{"lang":"eng","text":"Hybridization is a common evolutionary process with multiple possible outcomes. In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic hybrid species. However, it is unknown whether the generation of parthenogenetic hybrids is a rare outcome of frequent hybridization between sexual species within a genus or the typical outcome of rare hybridization events. Darevskia is a genus of rock lizards with both hybrid parthenogenetic and sexual species. Using capture sequencing, we estimate phylogenetic relationships and gene flow among the sexual species, to determine how introgressive hybridization relates to the origins of parthenogenetic hybrids. We find evidence for widespread hybridization with gene flow, both between recently diverged species and deep branches. Surprisingly, we find no signal of gene flow between parental species of the parthenogenetic hybrids, suggesting that the parental pairs were either reproductively or geographically isolated early in their divergence. The generation of parthenogenetic hybrids in Darevskia is, then, a rare outcome of the total occurrence of hybridization within the genus, but the typical outcome when specific species pairs hybridize. Our results question the conventional view that parthenogenetic lineages are generated by hybridization in a window of divergence. Instead, they suggest that some lineages possess specific properties that underpin successful parthenogenetic reproduction."}],"doi":"10.1111/evo.14462","day":"01","ddc":["570"],"volume":76,"acknowledgement":"The authors thank A. van der Meijden and F. Ahmadzadeh for providing specimens and tissue samples, and A. Vardanyan, C. Corti, F. Jorge, and S. Drovetski for support during field work. The authors also thank S. Qiu for assistance with python scripting, S. Rocha for her support in BEAST analysis, and B. Wielstra for his comments on\r\na previous version of the manuscript. SF was funded by FCT grant SFRH/BD/81483/2011 (a PhD individual grant). AMW was funded by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 797747. TS acknowledges funding from the Swiss National Science Foundation (grants\r\nPP00P3_170627 and 31003A_182495). The work was carried out under financial support of the projects “Preserving Armenian biodiversity: Joint Portuguese – Armenian program for training in modern conservation biology” of Gulbenkian Foundation (Portugal) and PTDC/BIABEC/101256/2008 of Fundação para a Ciência e a Tecnologia (FCT, Portugal)."},{"page":"98","file_date_updated":"2023-05-20T22:30:03Z","publisher":"Institute of Science and Technology Austria","_id":"11388","author":[{"id":"43FE426A-F248-11E8-B48F-1D18A9856A87","full_name":"Belohlavy, Stefanie","orcid":"0000-0002-9849-498X","last_name":"Belohlavy","first_name":"Stefanie"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"date_created":"2022-05-16T16:49:18Z","article_processing_charge":"No","publication_status":"published","alternative_title":["ISTA Thesis"],"title":"The genetic basis of complex traits studied via analysis of evolve and resequence experiments","ddc":["576"],"citation":{"short":"S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022.","mla":"Belohlavy, Stefanie. The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11388.","ista":"Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria.","apa":"Belohlavy, S. (2022). The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11388","ama":"Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:10.15479/at:ista:11388","ieee":"S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022.","chicago":"Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11388."},"year":"2022","date_updated":"2023-08-29T06:41:51Z","day":"18","doi":"10.15479/at:ista:11388","degree_awarded":"PhD","abstract":[{"text":"In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work.","lang":"eng"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","oa_version":"Published Version","month":"05","file":[{"content_type":"application/pdf","file_name":"thesis_sb_final_pdfa.pdf","date_updated":"2023-05-20T22:30:03Z","file_size":8247240,"checksum":"4d75e6a619df7e8a9d6e840aee182380","embargo":"2023-05-19","date_created":"2022-05-19T13:03:13Z","creator":"sbelohla","file_id":"11398","relation":"main_file","access_level":"open_access"},{"date_created":"2022-05-19T13:07:47Z","embargo_to":"open_access","file_size":7094,"checksum":"7a5d8b6dd0ca00784f860075b0a7d8f0","date_updated":"2023-05-20T22:30:03Z","content_type":"application/x-zip-compressed","file_name":"thesis_sb_final.zip","access_level":"closed","relation":"source_file","file_id":"11399","creator":"sbelohla"}],"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"relation":"part_of_dissertation","id":"6713","status":"public"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"dissertation","date_published":"2022-05-18T00:00:00Z","publication_identifier":{"isbn":["978-3-99078-018-3"]},"oa":1,"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"}]},{"file_date_updated":"2022-05-26T12:48:21Z","quality_controlled":"1","article_type":"original","publisher":"Oxford University Press","author":[{"last_name":"Surendranadh","first_name":"Parvathy","full_name":"Surendranadh, Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","first_name":"Louise S","full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X"},{"first_name":"Carina","last_name":"Baskett","orcid":"0000-0002-7354-8574","full_name":"Baskett, Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Field","first_name":"David","full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"issue":"3","_id":"11411","pmid":1,"scopus_import":"1","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","intvolume":" 221","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"article_processing_charge":"No","date_created":"2022-05-26T13:44:50Z","ddc":["576"],"acknowledgement":"Part of this work was funded by Marie Curie COFUND Doctoral Fellowship and Austrian Science Fund FWF (grant P32166).\r\nWe thank the many volunteers and friends who have contributed to data collection in the field site over the years, in particular those who have managed field seasons: Barbora Trubenova, Maria Clara Melo, Tom Ellis, Eva Cereghetti, Lenka Matejovicova, Beatriz Pablo Carmona. Frederic Ferrer and Eva Salmerón Mateu have been immensely helpful with logistics at our informal field station, El Serrat de Planoles. We thank Sean Stankowski for technical help in\r\nproducing figure 1. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","volume":221,"isi":1,"external_id":{"pmid":["35639938"],"isi":["000803735800001"]},"date_updated":"2024-02-21T12:38:33Z","citation":{"chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Genetics. Oxford University Press, 2022. https://doi.org/10.1093/genetics/iyac083.","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus,” Genetics, vol. 221, no. 3. Oxford University Press, 2022.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. Oxford University Press. https://doi.org/10.1093/genetics/iyac083","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 2022;221(3). doi:10.1093/genetics/iyac083","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 221(3), iyac083.","mla":"Surendranadh, Parvathy, et al. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Genetics, vol. 221, no. 3, iyac083, Oxford University Press, 2022, doi:10.1093/genetics/iyac083.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, Genetics 221 (2022)."},"year":"2022","abstract":[{"text":"Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium, which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use 2 types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1,000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity.","lang":"eng"}],"doi":"10.1093/genetics/iyac083","day":"01","language":[{"iso":"eng"}],"publication":"Genetics","has_accepted_license":"1","month":"07","article_number":"iyac083","acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Submitted Version","project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"status":"public","id":"14651","relation":"dissertation_contains"},{"status":"public","relation":"research_data","id":"11321"},{"status":"public","id":"9192","relation":"research_data"}]},"file":[{"file_id":"11412","creator":"larathoo","access_level":"open_access","success":1,"relation":"main_file","date_updated":"2022-05-26T12:48:15Z","file_name":"Manuscript.pdf","content_type":"application/pdf","date_created":"2022-05-26T12:48:15Z","checksum":"cc2d56deb608bd53c5cc02f03a875107","file_size":885374},{"file_id":"11413","creator":"larathoo","access_level":"open_access","relation":"main_file","success":1,"date_updated":"2022-05-26T12:48:21Z","content_type":"application/pdf","file_name":"SupplementalMaterial.pdf","date_created":"2022-05-26T12:48:21Z","checksum":"693742595b6c7ed809423be01460d083","file_size":1401704}],"date_published":"2022-07-01T00:00:00Z","type":"journal_article","oa":1,"publication_identifier":{"eissn":["1943-2631"]}},{"file":[{"file_id":"11455","creator":"dernst","access_level":"open_access","relation":"main_file","success":1,"date_updated":"2022-06-20T07:51:32Z","content_type":"application/pdf","file_name":"2022_BulletinMathBiology_Saona.pdf","date_created":"2022-06-20T07:51:32Z","file_size":463025,"checksum":"05a1fe7d10914a00c2bca9b447993a65"}],"status":"public","related_material":{"link":[{"url":"https://doi.org/10.1007/s11538-022-01118-z","relation":"erratum"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-06-17T00:00:00Z","publication_identifier":{"eissn":["1522-9602"],"issn":["0092-8240"]},"oa":1,"keyword":["Computational Theory and Mathematics","General Agricultural and Biological Sciences","Pharmacology","General Environmental Science","General Biochemistry","Genetics and Molecular Biology","General Mathematics","Immunology","General Neuroscience"],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Bulletin of Mathematical Biology","project":[{"name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"I05127","name":"Evolutionary analysis of gene regulation","_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f"}],"oa_version":"Published Version","article_number":"74","month":"06","volume":84,"acknowledgement":"We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful discussions. Open access funding provided by Austrian Science Fund (FWF). Partially supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund (I5127-B) grants to FAK.","ddc":["510","570"],"citation":{"chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical Biology. Springer Nature, 2022. https://doi.org/10.1007/s11538-022-01029-z.","ieee":"R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” Bulletin of Mathematical Biology, vol. 84, no. 8. Springer Nature, 2022.","apa":"Saona Urmeneta, R. J., Kondrashov, F., & Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. Springer Nature. https://doi.org/10.1007/s11538-022-01029-z","ama":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 2022;84(8). doi:10.1007/s11538-022-01029-z","ista":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 84(8), 74.","mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical Biology, vol. 84, no. 8, 74, Springer Nature, 2022, doi:10.1007/s11538-022-01029-z.","short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022)."},"year":"2022","date_updated":"2023-08-03T07:20:53Z","external_id":{"isi":["000812509800001"]},"isi":1,"day":"17","doi":"10.1007/s11538-022-01029-z","abstract":[{"text":"Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks.","lang":"eng"}],"quality_controlled":"1","ec_funded":1,"file_date_updated":"2022-06-20T07:51:32Z","publisher":"Springer Nature","article_type":"original","scopus_import":"1","_id":"11447","issue":"8","author":[{"id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","last_name":"Saona Urmeneta","first_name":"Raimundo J","full_name":"Saona Urmeneta, Raimundo J","orcid":"0000-0001-5103-038X"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"orcid":"0000-0002-6246-1465","full_name":"Khudiakova, Kseniia","first_name":"Kseniia","last_name":"Khudiakova","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"article_processing_charge":"Yes (via OA deal)","date_created":"2022-06-17T16:16:15Z","publication_status":"published","intvolume":" 84","title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions"},{"publication_status":"published","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_created":"2022-07-08T11:41:56Z","title":"Inversions and parallel evolution","intvolume":" 377","_id":"11546","scopus_import":"1","author":[{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"issue":"1856","publisher":"Royal Society of London","article_type":"original","quality_controlled":"1","file_date_updated":"2023-02-02T08:20:29Z","doi":"10.1098/rstb.2021.0203","day":"01","abstract":[{"text":"Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions.","lang":"eng"}],"date_updated":"2023-08-03T11:55:42Z","citation":{"ama":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 2022;377(1856). doi:10.1098/rstb.2021.0203","apa":"Westram, A. M., Faria, R., Johannesson, K., Butlin, R., & Barton, N. H. (2022). Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. Royal Society of London. https://doi.org/10.1098/rstb.2021.0203","ieee":"A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions and parallel evolution,” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1856. Royal Society of London, 2022.","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas H Barton. “Inversions and Parallel Evolution.” Philosophical Transactions of the Royal Society B: Biological Sciences. Royal Society of London, 2022. https://doi.org/10.1098/rstb.2021.0203.","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","mla":"Westram, Anja M., et al. “Inversions and Parallel Evolution.” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1856, 20210203, Royal Society of London, 2022, doi:10.1098/rstb.2021.0203.","ista":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1856), 20210203."},"year":"2022","isi":1,"external_id":{"isi":["000812317300005"]},"acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","volume":377,"ddc":["570"],"oa_version":"Published Version","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"The maintenance of alternative adaptive peaks in snapdragons"}],"month":"08","article_number":"20210203","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","has_accepted_license":"1","language":[{"iso":"eng"}],"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-08-01T00:00:00Z","type":"journal_article","file":[{"date_created":"2023-02-02T08:20:29Z","checksum":"49f69428f3dcf5ce3ff281f7d199e9df","file_size":920304,"date_updated":"2023-02-02T08:20:29Z","content_type":"application/pdf","file_name":"2022_PhilosophicalTransactionsB_Westram.pdf","success":1,"relation":"main_file","access_level":"open_access","file_id":"12479","creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public"},{"publication":"Molecular Ecology Resources","has_accepted_license":"1","oa_version":"Published Version","project":[{"grant_number":"704172","name":"Rate of Adaptation in Changing Environment","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"month":"11","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"date_published":"2022-11-01T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["1755-0998"],"issn":["1755-098X"]},"oa":1,"file":[{"content_type":"application/pdf","file_name":"2022_MolecularEcologyRes_Szep.pdf","date_updated":"2023-02-02T08:11:23Z","checksum":"3102e203e77b884bffffdbe8e548da88","file_size":6431779,"date_created":"2023-02-02T08:11:23Z","creator":"dernst","file_id":"12477","access_level":"open_access","success":1,"relation":"main_file"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11640","scopus_import":"1","author":[{"id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Eniko","first_name":"Eniko","last_name":"Szep"},{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora","last_name":"Trubenova","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora"},{"full_name":"Csilléry, Katalin","last_name":"Csilléry","first_name":"Katalin"}],"issue":"8","publication_status":"published","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"NiBa"}],"date_created":"2022-07-24T22:01:43Z","title":"Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size","intvolume":" 22","page":"2941-2955","quality_controlled":"1","ec_funded":1,"file_date_updated":"2023-02-02T08:11:23Z","publisher":"Wiley","article_type":"original","date_updated":"2023-08-03T12:11:01Z","year":"2022","citation":{"ama":"Szep E, Trubenova B, Csilléry K. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Molecular Ecology Resources. 2022;22(8):2941-2955. doi:10.1111/1755-0998.13676","apa":"Szep, E., Trubenova, B., & Csilléry, K. (2022). Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13676","ieee":"E. Szep, B. Trubenova, and K. Csilléry, “Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size,” Molecular Ecology Resources, vol. 22, no. 8. Wiley, pp. 2941–2955, 2022.","chicago":"Szep, Eniko, Barbora Trubenova, and Katalin Csilléry. “Using GridCoal to Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.” Molecular Ecology Resources. Wiley, 2022. https://doi.org/10.1111/1755-0998.13676.","short":"E. Szep, B. Trubenova, K. Csilléry, Molecular Ecology Resources 22 (2022) 2941–2955.","mla":"Szep, Eniko, et al. “Using GridCoal to Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.” Molecular Ecology Resources, vol. 22, no. 8, Wiley, 2022, pp. 2941–55, doi:10.1111/1755-0998.13676.","ista":"Szep E, Trubenova B, Csilléry K. 2022. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Molecular Ecology Resources. 22(8), 2941–2955."},"isi":1,"external_id":{"isi":["000825873600001"]},"doi":"10.1111/1755-0998.13676","day":"01","abstract":[{"lang":"eng","text":"Spatially explicit population genetic models have long been developed, yet have rarely been used to test hypotheses about the spatial distribution of genetic diversity or the genetic divergence between populations. Here, we use spatially explicit coalescence simulations to explore the properties of the island and the two-dimensional stepping stone models under a wide range of scenarios with spatio-temporal variation in deme size. We avoid the simulation of genetic data, using the fact that under the studied models, summary statistics of genetic diversity and divergence can be approximated from coalescence times. We perform the simulations using gridCoal, a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change arbitrarily across space and time, as well as migration rates between individual demes. We identify different factors that can cause a deviation from theoretical expectations, such as the simulation time in comparison to the effective deme size and the spatio-temporal autocorrelation across the grid. Our results highlight that FST, a measure of the strength of population structure, principally depends on recent demography, which makes it robust to temporal variation in deme size. In contrast, the amount of genetic diversity is dependent on the distant past when Ne is large, therefore longer run times are needed to estimate Ne than FST. Finally, we illustrate the use of gridCoal on a real-world example, the range expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using different degrees of spatio-temporal variation in deme size."}],"volume":22,"acknowledgement":"ES was supported by an IST studentship provided by IST Austria. BT was funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Independent Fellowship (704172, RACE). This project received further funding awarded to KC from the Swiss National Science Foundation (SNSF CRSK-3_190288) and the Swiss Federal Research Institute WSL. We thank Nick Barton for many invaluable discussions and his comments on the thesis chapter and this manuscript. We thank Peter Ralph and Jerome Kelleher for useful discussions and Bisschop Gertjan for comments on this manuscript. We thank Fortunat Joos for providing us with the raw data from the LPX-Bern model for silver fir, and Willy Tinner for helpful insights about the demographic history of silver fir. We also thank the editor Alana Alexander for useful comments and advice on the manuscript. Open access funding provided by Eidgenossische Technische Hochschule Zurich.","ddc":["570"]},{"ddc":["570"],"status":"public","related_material":{"record":[{"id":"10604","relation":"used_in_publication","status":"public"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"url":"https://doi.org/10.25338/B81931","open_access":"1"}],"acknowledgement":"Bill and Melinda Gates Foundation, Award: OPP1180815","type":"research_data_reference","date_published":"2022-01-06T00:00:00Z","citation":{"ista":"Turelli M, Barton NH. 2022. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control, Dryad, 10.25338/B81931.","short":"M. Turelli, N.H. Barton, (2022).","mla":"Turelli, Michael, and Nicholas H. Barton. Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control. Dryad, 2022, doi:10.25338/B81931.","ieee":"M. Turelli and N. H. Barton, “Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control.” Dryad, 2022.","chicago":"Turelli, Michael, and Nicholas H Barton. “Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control.” Dryad, 2022. https://doi.org/10.25338/B81931.","ama":"Turelli M, Barton NH. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. 2022. doi:10.25338/B81931","apa":"Turelli, M., & Barton, N. H. (2022). Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. Dryad. https://doi.org/10.25338/B81931"},"year":"2022","date_updated":"2023-08-02T13:50:08Z","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"oa":1,"abstract":[{"lang":"eng","text":"Maternally inherited Wolbachia transinfections are being introduced into natural mosquito populations to reduce the transmission of dengue, Zika and other arboviruses. Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive advantage to infected females that can spread transinfections within and among populations. However, because transinfections generally reduce host fitness, they tend to spread within populations only after their frequency exceeds a critical threshold. This produces bistability with stable equilibrium frequencies at both 0 and 1, analogous to the bistability produced by underdominance between alleles or karyotypes and by population dynamics under Allee effects. Here, we analyze how stochastic frequency variation produced by finite population size can facilitate the local spread of variants with bistable dynamics into areas where invasion is unexpected from deterministic models. Our exemplar is the establishment of wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small community in far north Queensland, Australia. In 2011, wMel was stably introduced into Gordonvale, separated from PE by barriers to Ae. aegypti dispersal. After nearly six years during which wMel was observed only at low frequencies in PE, corresponding to an apparent equilibrium between immigration and selection, wMel rose to fixation by 2018. Using analytic approximations and statistical analyses, we demonstrate that the observed fixation of wMel at PE is consistent with both stochastic transition past an unstable threshold frequency and deterministic transformation produced by steady immigration at a rate just above the threshold required for deterministic invasion. The indeterminacy results from a delicate balance of parameters needed to produce the delayed transition observed. Our analyses suggest that once Wolbachia transinfections are established locally through systematic introductions, stochastic “threshold crossing” is likely to only minimally enhance spatial spread, providing a local ratchet that slightly – but systematically – aids area-wide transformation of disease-vector populations in heterogeneous landscapes."}],"day":"06","doi":"10.25338/B81931","keyword":["Biological sciences"],"publisher":"Dryad","author":[{"full_name":"Turelli, Michael","last_name":"Turelli","first_name":"Michael"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","_id":"11686","month":"01","title":"Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control","date_created":"2022-07-29T06:45:41Z","department":[{"_id":"NiBa"}],"article_processing_charge":"No","oa_version":"Published Version"},{"publisher":"Proceedings of the National Academy of Sciences","article_type":"original","quality_controlled":"1","file_date_updated":"2022-08-01T10:58:28Z","date_created":"2022-07-31T22:01:47Z","article_processing_charge":"No","department":[{"_id":"NiBa"}],"publication_status":"published","intvolume":" 119","title":"The \"New Synthesis\"","scopus_import":"1","_id":"11702","pmid":1,"issue":"30","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"acknowledgement":"I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions and comments.","volume":119,"ddc":["570"],"day":"18","doi":"10.1073/pnas.2122147119","abstract":[{"lang":"eng","text":"When Mendel’s work was rediscovered in 1900, and extended to establish classical genetics, it was initially seen in opposition to Darwin’s theory of evolution by natural selection on continuous variation, as represented by the biometric research program that was the foundation of quantitative genetics. As Fisher, Haldane, and Wright established a century ago, Mendelian inheritance is exactly what is needed for natural selection to work efficiently. Yet, the synthesis remains unfinished. We do not understand why sexual reproduction and a fair meiosis predominate in eukaryotes, or how far these are responsible for their diversity and complexity. Moreover, although quantitative geneticists have long known that adaptive variation is highly polygenic, and that this is essential for efficient selection, this is only now becoming appreciated by molecular biologists—and we still do not have a good framework for understanding polygenic variation or diffuse function."}],"year":"2022","citation":{"mla":"Barton, Nicholas H. “The ‘New Synthesis.’” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 30, e2122147119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2122147119.","short":"N.H. Barton, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ista":"Barton NH. 2022. The ‘New Synthesis’. Proceedings of the National Academy of Sciences of the United States of America. 119(30), e2122147119.","apa":"Barton, N. H. (2022). The “New Synthesis.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2122147119","ama":"Barton NH. The “New Synthesis.” Proceedings of the National Academy of Sciences of the United States of America. 2022;119(30). doi:10.1073/pnas.2122147119","chicago":"Barton, Nicholas H. “The ‘New Synthesis.’” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2122147119.","ieee":"N. H. Barton, “The ‘New Synthesis,’” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 30. Proceedings of the National Academy of Sciences, 2022."},"date_updated":"2022-08-01T11:00:25Z","external_id":{"pmid":["35858408"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","article_number":"e2122147119","month":"07","has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","file":[{"file_size":848511,"checksum":"06c866196a8957f0c37b8a121771c885","date_created":"2022-08-01T10:58:28Z","file_name":"2022_PNAS_Barton.pdf","content_type":"application/pdf","date_updated":"2022-08-01T10:58:28Z","access_level":"open_access","relation":"main_file","success":1,"creator":"dernst","file_id":"11716"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-07-18T00:00:00Z"},{"oa":1,"abstract":[{"lang":"eng","text":"Chromosomal inversions have been shown to play a major role in local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence."}],"day":"28","doi":"10.5061/DRYAD.M905QFV4B","type":"research_data_reference","date_published":"2022-07-28T00:00:00Z","year":"2022","citation":{"ista":"Koch E, Ravinet M, Westram AM, Jonannesson K, Butlin R. 2022. Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution, Dryad, 10.5061/DRYAD.M905QFV4B.","short":"E. Koch, M. Ravinet, A.M. Westram, K. Jonannesson, R. Butlin, (2022).","mla":"Koch, Eva, et al. Data from: Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Ecotype Evolution. Dryad, 2022, doi:10.5061/DRYAD.M905QFV4B.","ieee":"E. Koch, M. Ravinet, A. M. Westram, K. Jonannesson, and R. Butlin, “Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution.” Dryad, 2022.","chicago":"Koch, Eva, Mark Ravinet, Anja M Westram, Kerstin Jonannesson, and Roger Butlin. “Data from: Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Ecotype Evolution.” Dryad, 2022. https://doi.org/10.5061/DRYAD.M905QFV4B.","apa":"Koch, E., Ravinet, M., Westram, A. M., Jonannesson, K., & Butlin, R. (2022). Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. Dryad. https://doi.org/10.5061/DRYAD.M905QFV4B","ama":"Koch E, Ravinet M, Westram AM, Jonannesson K, Butlin R. Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. 2022. doi:10.5061/DRYAD.M905QFV4B"},"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"date_updated":"2023-08-04T09:42:10Z","status":"public","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"12247"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.m905qfv4b"}],"title":"Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution","month":"07","article_processing_charge":"No","date_created":"2023-05-23T16:33:12Z","department":[{"_id":"NiBa"}],"oa_version":"Published Version","author":[{"full_name":"Koch, Eva","first_name":"Eva","last_name":"Koch"},{"full_name":"Ravinet, Mark","first_name":"Mark","last_name":"Ravinet"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram"},{"full_name":"Jonannesson, Kerstin","last_name":"Jonannesson","first_name":"Kerstin"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"}],"_id":"13066","publisher":"Dryad"},{"oa":1,"publication_identifier":{"eissn":["2056-3744"]},"type":"journal_article","date_published":"2022-02-01T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"status":"public","id":"11686","relation":"research_data"}]},"file":[{"date_updated":"2022-07-29T06:59:10Z","file_name":"2022_EvolutionLetters_Turelli.pdf","content_type":"application/pdf","date_created":"2022-07-29T06:59:10Z","file_size":2435185,"checksum":"7e9a37e3b65b480cd7014a6a4a7e460a","file_id":"11689","creator":"dernst","access_level":"open_access","relation":"main_file","success":1}],"month":"02","oa_version":"Published Version","has_accepted_license":"1","publication":"Evolution Letters","keyword":["genetics","ecology","evolution","behavior and systematics"],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Maternally inherited Wolbachia transinfections are being introduced into natural mosquito populations to reduce the transmission of dengue, Zika, and other arboviruses. Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive advantage to infected females that can spread transinfections within and among populations. However, because transinfections generally reduce host fitness, they tend to spread within populations only after their frequency exceeds a critical threshold. This produces bistability with stable equilibrium frequencies at both 0 and 1, analogous to the bistability produced by underdominance between alleles or karyotypes and by population dynamics under Allee effects. Here, we analyze how stochastic frequency variation produced by finite population size can facilitate the local spread of variants with bistable dynamics into areas where invasion is unexpected from deterministic models. Our exemplar is the establishment of wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small community in far north Queensland, Australia. In 2011, wMel was stably introduced into Gordonvale, separated from PE by barriers to A. aegypti dispersal. After nearly 6 years during which wMel was observed only at low frequencies in PE, corresponding to an apparent equilibrium between immigration and selection, wMel rose to fixation by 2018. Using analytic approximations and statistical analyses, we demonstrate that the observed fixation of wMel at PE is consistent with both stochastic transition past an unstable threshold frequency and deterministic transformation produced by steady immigration at a rate just above the threshold required for deterministic invasion. The indeterminacy results from a delicate balance of parameters needed to produce the delayed transition observed. Our analyses suggest that once Wolbachia transinfections are established locally through systematic introductions, stochastic “threshold crossing” is likely to only minimally enhance spatial spread, providing a local ratchet that slightly—but systematically—aids area-wide transformation of disease-vector populations in heterogeneous landscapes."}],"day":"01","doi":"10.1002/evl3.270","external_id":{"isi":["000754412600008"]},"isi":1,"year":"2022","citation":{"chicago":"Turelli, Michael, and Nicholas H Barton. “Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” Evolution Letters. Wiley, 2022. https://doi.org/10.1002/evl3.270.","ieee":"M. Turelli and N. H. Barton, “Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control,” Evolution Letters, vol. 6, no. 1. Wiley, pp. 92–105, 2022.","apa":"Turelli, M., & Barton, N. H. (2022). Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control. Evolution Letters. Wiley. https://doi.org/10.1002/evl3.270","ama":"Turelli M, Barton NH. Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control. Evolution Letters. 2022;6(1):92-105. doi:10.1002/evl3.270","ista":"Turelli M, Barton NH. 2022. Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control. Evolution Letters. 6(1), 92–105.","short":"M. Turelli, N.H. Barton, Evolution Letters 6 (2022) 92–105.","mla":"Turelli, Michael, and Nicholas H. Barton. “Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” Evolution Letters, vol. 6, no. 1, Wiley, 2022, pp. 92–105, doi:10.1002/evl3.270."},"date_updated":"2023-08-02T13:50:09Z","ddc":["570"],"volume":6,"acknowledgement":"We thank S. O'Neill, C. Simmons, and the World Mosquito Project for providing access to unpublished data. S. Ritchie provided valuable insights into Aedes aegypti biology and the literature describing A. aegypti populations near Cairns. We thank B. Cooper for help with the figures and D. Shropshire, S. O'Neill, S. Ritchie, A. Hoffmann, B. Cooper, and members of the Cooper lab for comments on an earlier draft. Comments from three reviewers greatly improved our presentation.","intvolume":" 6","title":"Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control","department":[{"_id":"NiBa"}],"date_created":"2022-01-09T09:45:17Z","article_processing_charge":"No","publication_status":"published","issue":"1","author":[{"full_name":"Turelli, Michael","first_name":"Michael","last_name":"Turelli"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"_id":"10604","article_type":"original","publisher":"Wiley","file_date_updated":"2022-07-29T06:59:10Z","quality_controlled":"1","page":"92-105"},{"abstract":[{"text":"Sexual antagonism is a common hypothesis for driving the evolution of sex chromosomes, whereby recombination suppression is favored between sexually antagonistic loci and the sex-determining locus to maintain beneficial combinations of alleles. This results in the formation of a sex-determining region. Chromosomal inversions may contribute to recombination suppression but their precise role in sex chromosome evolution remains unclear. Because local adaptation is frequently facilitated through the suppression of recombination between adaptive loci by chromosomal inversions, there is potential for inversions that cover sex-determining regions to be involved in local adaptation as well, particularly if habitat variation creates environment-dependent sexual antagonism. With these processes in mind, we investigated sex determination in a well-studied example of local adaptation within a species: the intertidal snail, Littorina saxatilis. Using SNP data from a Swedish hybrid zone, we find novel evidence for a female-heterogametic sex determination system that is restricted to one ecotype. Our results suggest that four putative chromosomal inversions, two previously described and two newly discovered, span the putative sex chromosome pair. We determine their differing associations with sex, which suggest distinct strata of differing ages. The same inversions are found in the second ecotype but do not show any sex association. The striking disparity in inversion-sex associations between ecotypes that are connected by gene flow across a habitat transition that is just a few meters wide indicates a difference in selective regime that has produced a distinct barrier to the spread of the newly discovered sex-determining region between ecotypes. Such sex chromosome-environment interactions have not previously been uncovered in L. saxatilis and are known in few other organisms. A combination of both sex-specific selection and divergent natural selection is required to explain these highly unusual patterns.","lang":"eng"}],"day":"01","doi":"10.1002/evl3.295","external_id":{"isi":["000839621100001"]},"isi":1,"year":"2022","citation":{"ama":"Hearn KE, Koch EL, Stankowski S, et al. Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution Letters. 2022;6(5):358-374. doi:10.1002/evl3.295","apa":"Hearn, K. E., Koch, E. L., Stankowski, S., Butlin, R. K., Faria, R., Johannesson, K., & Westram, A. M. (2022). Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution Letters. Oxford Academic. https://doi.org/10.1002/evl3.295","ieee":"K. E. Hearn et al., “Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis,” Evolution Letters, vol. 6, no. 5. Oxford Academic, pp. 358–374, 2022.","chicago":"Hearn, Katherine E., Eva L. Koch, Sean Stankowski, Roger K. Butlin, Rui Faria, Kerstin Johannesson, and Anja M Westram. “Differing Associations between Sex Determination and Sex-Linked Inversions in Two Ecotypes of Littorina Saxatilis.” Evolution Letters. Oxford Academic, 2022. https://doi.org/10.1002/evl3.295.","short":"K.E. Hearn, E.L. Koch, S. Stankowski, R.K. Butlin, R. Faria, K. Johannesson, A.M. Westram, Evolution Letters 6 (2022) 358–374.","mla":"Hearn, Katherine E., et al. “Differing Associations between Sex Determination and Sex-Linked Inversions in Two Ecotypes of Littorina Saxatilis.” Evolution Letters, vol. 6, no. 5, Oxford Academic, 2022, pp. 358–74, doi:10.1002/evl3.295.","ista":"Hearn KE, Koch EL, Stankowski S, Butlin RK, Faria R, Johannesson K, Westram AM. 2022. Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution Letters. 6(5), 358–374."},"date_updated":"2023-08-03T13:18:17Z","ddc":["570"],"acknowledgement":"We thank A. Wright and four anonymous reviewers for valuable comments on an earlier draft of this manuscript and all members of the Littorina group for helpful discussions. This work was supported by a European Research Council grant to RKB and by a Natural Environment Research Council studentship to KEH through the ACCE doctoral training program. KJ acknowledges support from the Swedish Science Research Council VR (Vetenskaprådet) (2017-03798). RF was supported by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao Emprego Científico) contract (2020.00275.CEECIND).","volume":6,"intvolume":" 6","title":"Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis","department":[{"_id":"NiBa"}],"date_created":"2022-08-28T22:02:02Z","article_processing_charge":"Yes","publication_status":"published","issue":"5","author":[{"last_name":"Hearn","first_name":"Katherine E.","full_name":"Hearn, Katherine E."},{"full_name":"Koch, Eva L.","last_name":"Koch","first_name":"Eva L."},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"}],"scopus_import":"1","_id":"12001","article_type":"original","publisher":"Oxford Academic","file_date_updated":"2023-02-27T07:17:42Z","quality_controlled":"1","page":"358-374","oa":1,"publication_identifier":{"eissn":["2056-3744"]},"type":"journal_article","date_published":"2022-10-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"date_updated":"2023-02-27T07:17:42Z","content_type":"application/pdf","file_name":"2022_EvolutionLetters_Hearn.pdf","date_created":"2023-02-27T07:17:42Z","checksum":"2dcd06186a11b7d1be4cddc6b189f8fb","file_size":2368965,"file_id":"12686","creator":"dernst","success":1,"access_level":"open_access","relation":"main_file"}],"month":"10","oa_version":"Published Version","has_accepted_license":"1","publication":"Evolution Letters","language":[{"iso":"eng"}]},{"publication_status":"published","article_processing_charge":"No","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"date_created":"2022-09-11T22:01:55Z","title":"Accumulation and maintenance of information in evolution","intvolume":" 119","pmid":1,"_id":"12081","scopus_import":"1","author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal","first_name":"Michal","last_name":"Hledik"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","orcid":"1","full_name":"Tkačik, Gašper"}],"issue":"36","publisher":"Proceedings of the National Academy of Sciences","article_type":"original","ec_funded":1,"quality_controlled":"1","file_date_updated":"2022-09-12T08:08:12Z","doi":"10.1073/pnas.2123152119","day":"29","abstract":[{"lang":"eng","text":"Selection accumulates information in the genome—it guides stochastically evolving populations toward states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright–Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation, and recombination. Finally, the cost of maintaining information depends on how it is encoded: Specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap."}],"date_updated":"2025-06-30T13:21:05Z","citation":{"ista":"Hledik M, Barton NH, Tkačik G. 2022. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 119(36), e2123152119.","short":"M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences 119 (2022).","mla":"Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences, vol. 119, no. 36, e2123152119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2123152119.","chicago":"Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2123152119.","ieee":"M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information in evolution,” Proceedings of the National Academy of Sciences, vol. 119, no. 36. Proceedings of the National Academy of Sciences, 2022.","ama":"Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 2022;119(36). doi:10.1073/pnas.2123152119","apa":"Hledik, M., Barton, N. H., & Tkačik, G. (2022). Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2123152119"},"year":"2022","isi":1,"external_id":{"isi":["000889278400014"],"pmid":["36037343"]},"acknowledgement":"We thank Ksenia Khudiakova, Wiktor Młynarski, Sean Stankowski, and two anonymous reviewers for discussions and comments on the manuscript. G.T. and M.H. acknowledge funding from the Human Frontier Science Program Grant RGP0032/2018. N.B. acknowledges funding from ERC Grant 250152 “Information and Evolution.”","volume":119,"ddc":["570"],"oa_version":"Published Version","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"}],"month":"08","article_number":"e2123152119","publication":"Proceedings of the National Academy of Sciences","has_accepted_license":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-08-29T00:00:00Z","type":"journal_article","file":[{"relation":"main_file","access_level":"open_access","success":1,"creator":"dernst","file_id":"12091","checksum":"6dec51f6567da9039982a571508a8e4d","file_size":2165752,"date_created":"2022-09-12T08:08:12Z","content_type":"application/pdf","file_name":"2022_PNAS_Hledik.pdf","date_updated":"2022-09-12T08:08:12Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"15020"}]}},{"publisher":"eLife Sciences Publications","article_type":"original","quality_controlled":"1","file_date_updated":"2023-01-24T12:21:32Z","department":[{"_id":"NiBa"}],"date_created":"2023-01-12T12:09:00Z","article_processing_charge":"No","publication_status":"published","intvolume":" 11","title":"Polygenic adaptation after a sudden change in environment","scopus_import":"1","_id":"12157","author":[{"id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b","full_name":"Hayward, Laura","first_name":"Laura","last_name":"Hayward"},{"full_name":"Sella, Guy","last_name":"Sella","first_name":"Guy"}],"volume":11,"acknowledgement":"We thank Guy Amster, Jeremy Berg, Nick Barton, Yuval Simons and Molly Przeworski for many helpful discussions, and Jeremy Berg, Graham Coop, Joachim Hermisson, Guillaume Martin, Will Milligan, Peter Ralph, Yuval Simons, Leo Speidel and Molly Przeworski for comments on the manuscript.\r\nNational Institutes of Health GM115889 Laura Katharine Hayward Guy Sella \r\nNational Institutes of Health GM121372 Laura Katharine Hayward","ddc":["570"],"day":"26","doi":"10.7554/elife.66697","abstract":[{"text":"Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood. Here, we model this process analytically, in the plausible setting of a highly polygenic, quantitative trait that experiences a sudden shift in the fitness optimum. We show how the mean phenotype changes over time, depending on the effect sizes of loci that contribute to variance in the trait, and characterize the allele dynamics at these loci. Notably, we describe the two phases of the allele dynamics: The first is a rapid phase, in which directional selection introduces small frequency differences between alleles whose effects are aligned with or opposed to the shift, ultimately leading to small differences in their probability of fixation during a second, longer phase, governed by stabilizing selection. As we discuss, key results should hold in more general settings and have important implications for efforts to identify the genetic basis of adaptation in humans and other species.","lang":"eng"}],"citation":{"chicago":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/elife.66697.","ieee":"L. Hayward and G. Sella, “Polygenic adaptation after a sudden change in environment,” eLife, vol. 11. eLife Sciences Publications, 2022.","apa":"Hayward, L., & Sella, G. (2022). Polygenic adaptation after a sudden change in environment. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.66697","ama":"Hayward L, Sella G. Polygenic adaptation after a sudden change in environment. eLife. 2022;11. doi:10.7554/elife.66697","ista":"Hayward L, Sella G. 2022. Polygenic adaptation after a sudden change in environment. eLife. 11, 66697.","short":"L. Hayward, G. Sella, ELife 11 (2022).","mla":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” ELife, vol. 11, 66697, eLife Sciences Publications, 2022, doi:10.7554/elife.66697."},"year":"2022","date_updated":"2023-08-04T09:04:58Z","external_id":{"isi":["000890735600001"]},"isi":1,"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"language":[{"iso":"eng"}],"oa_version":"Published Version","article_number":"66697","month":"09","has_accepted_license":"1","publication":"eLife","file":[{"creator":"dernst","file_id":"12363","access_level":"open_access","success":1,"relation":"main_file","file_name":"2022_eLife_Hayward.pdf","content_type":"application/pdf","date_updated":"2023-01-24T12:21:32Z","checksum":"28de155b231ac1c8d4501c98b2fb359a","file_size":18935612,"date_created":"2023-01-24T12:21:32Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_identifier":{"eissn":["2050-084X"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-09-26T00:00:00Z"}]