{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"Authorea, Inc."}],"indexed":{"date-parts":[[2025,6,3]],"date-time":"2025-06-03T16:38:12Z","timestamp":1748968692278,"version":"3.41.0"},"posted":{"date-parts":[[2022,12,5]]},"group-title":"Preprints","reference-count":0,"publisher":"Wiley","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2022,12,5]]},"abstract":"<jats:p id=\"p1\">Next-generation sequencing of pooled samples (Pool-seq) is a popular\nmethod to assess genome-wide diversity patterns in natural and\nexperimental populations. However, Pool-seq is associated with specific\nsources of noise, such as unequal individual contributions.\nConsequently, using Pool-seq for the reconstruction of evolutionary\nhistory has remained underexplored. Here we describe a method to\nsimulate Pool-seq data, implemented in an Approximate Bayesian\nComputation (ABC) framework to infer demographic history under models\nwith two and four populations. By jointly modeling Pool-seq data,\ndemographic history and the effects of selection due to barrier loci, we\nobtain estimates of demographic history parameters accounting for\ntechnical errors associated with Pool-seq. Rather than simulating\ngenome-wide data, we perform ABC on subsets of loci, using relative\nsummary statistics and parameter estimates. Our simulation study results\nindicate Pool-seq data allows distinction between general scenarios of\necotype formation (single versus parallel origin), and to infer relevant\ndemographic parameters (e.g., effective sizes, split times). We\nexemplify the application of our method to Pool-seq data from the\nrocky-shore gastropod \\textit{Littorina saxatilis},\nsampled on a narrow geographical scale at two Swedish locations where\ntwo ecotypes (wave and crab) are found. Our model choice and parameter\nestimates show that ecotypes formed before colonization of the two\nlocations (i.e., single origin) and are maintained despite gene flow.\nThese results indicate that demographic modeling and inference can be\nsuccessful based on pool-sequencing using ABC, contributing to the\ndevelopment of suitable null models that allow for a better\nunderstanding of the genetic basis of divergent adaptation.<\/jats:p>","DOI":"10.22541\/au.167023671.11036754\/v1","type":"posted-content","created":{"date-parts":[[2022,12,5]],"date-time":"2022-12-05T10:38:57Z","timestamp":1670236737000},"source":"Crossref","is-referenced-by-count":1,"title":["Integrating Pool-seq uncertainties into demographic inference"],"prefix":"10.22541","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1728-0075","authenticated-orcid":true,"given":"Jo\u00e3o","family":"Carvalho","sequence":"first","affiliation":[{"name":"cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ci\u00eancias, Universidade de Lisboa, Campo Grande, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2964-020X","authenticated-orcid":true,"given":"Hernan","family":"Morales","sequence":"additional","affiliation":[{"name":"Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6635-685X","authenticated-orcid":true,"given":"Rui","family":"Faria","sequence":"additional","affiliation":[{"name":"CIBIO - Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, InBIO, Laborat\u00f3rio Associado, Universidade do Porto, Vair\u00e3o, Portugal"}]},{"given":"Roger","family":"Butlin","sequence":"additional","affiliation":[{"name":"Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, S10 2TN United Kingdom"}]},{"given":"Vitor","family":"Sousa","sequence":"additional","affiliation":[{"name":"cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ci\u00eancias, Universidade de Lisboa, Campo Grande, Portugal"}]}],"member":"311","container-title":[],"original-title":[],"deposited":{"date-parts":[[2022,12,5]],"date-time":"2022-12-05T10:38:58Z","timestamp":1670236738000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.authorea.com\/users\/562732\/articles\/610057-integrating-pool-seq-uncertainties-into-demographic-inference?commit=5921ce8f7fc13cf4bb8c91362fb870643c51b153"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,12,5]]},"references-count":0,"URL":"https:\/\/doi.org\/10.22541\/au.167023671.11036754\/v1","relation":{},"subject":[],"published":{"date-parts":[[2022,12,5]]},"subtype":"preprint"}}