{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T14:03:33Z","timestamp":1774879413319,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2019,6,20]],"date-time":"2019-06-20T00:00:00Z","timestamp":1560988800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Grant-in-Aid for Japan Society for the Promotion of Science"},{"DOI":"10.13039\/501100001691","name":"JSPS","doi-asserted-by":"publisher","award":["17J09326"],"award-info":[{"award-number":["17J09326"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"name":"JSPS KAKENHI","award":["15H01465"],"award-info":[{"award-number":["15H01465"]}]},{"name":"JSPS KAKENHI","award":["25134701"],"award-info":[{"award-number":["25134701"]}]},{"name":"JSPS KAKENHI","award":["25870190"],"award-info":[{"award-number":["25870190"]}]},{"name":"JSPS KAKENHI","award":["16H01532"],"award-info":[{"award-number":["16H01532"]}]},{"name":"Human Genome Center"},{"DOI":"10.13039\/501100004721","name":"The University of Tokyo","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100004721","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Evolve and resequence (E&amp;R) experiments show promise in capturing real-time evolution at genome-wide scales, enabling the assessment of allele frequency changes SNPs in evolving populations and thus the estimation of population genetic parameters in the Wright\u2013Fisher model (WF) that quantify the selection on SNPs. Currently, these analyses face two key difficulties: the numerous SNPs in E&amp;R data and the frequent unreliability of estimates. Hence, a methodology for efficiently estimating WF parameters is needed to understand the evolutionary processes that shape genomes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed a novel method for estimating WF parameters (EMWER), by applying an expectation maximization algorithm to the Kolmogorov forward equation associated with the WF model diffusion approximation. EMWER was used to infer the effective population size, selection coefficients and dominance parameters from E&amp;R data. Of the methods examined, EMWER was the most efficient method for selection strength estimation in multi-core computing environments, estimating both selection and dominance with accurate confidence intervals. We applied EMWER to E&amp;R data from experimental Drosophila populations adapting to thermally fluctuating environments and found a common selection affecting allele frequency of many SNPs within the cosmopolitan In(3R)P inversion. Furthermore, this application indicated that many of beneficial alleles in this experiment are dominant.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Our C++ implementation of \u2018EMWER\u2019 is available at https:\/\/github.com\/kojikoji\/EMWER.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz498","type":"journal-article","created":{"date-parts":[[2019,6,13]],"date-time":"2019-06-13T03:14:18Z","timestamp":1560395658000},"page":"221-231","source":"Crossref","is-referenced-by-count":8,"title":["Estimation of population genetic parameters using an EM algorithm and sequence data from experimental evolution populations"],"prefix":"10.1093","volume":"36","author":[{"given":"Yasuhiro","family":"Kojima","sequence":"first","affiliation":[{"name":"Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa , Chiba 1277-8561, Japan"}]},{"given":"Hirotaka","family":"Matsumoto","sequence":"additional","affiliation":[{"name":"Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN , Wako, Saitama 351-0198, Japan"}]},{"given":"Hisanori","family":"Kiryu","sequence":"additional","affiliation":[{"name":"Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa , Chiba 1277-8561, Japan"}]}],"member":"286","published-online":{"date-parts":[[2019,6,20]]},"reference":[{"key":"2023013109504732500_btz498-B1","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1534\/genetics.110.124560","article-title":"Inferences about the distribution of dominance drawn from yeast gene knockout data","volume":"187","author":"Agrawal","year":"2011","journal-title":"Genetics"},{"key":"2023013109504732500_btz498-B2","author":"Agresti","year":"2002"},{"key":"2023013109504732500_btz498-B3","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1016\/j.tig.2014.09.010","article-title":"Thinking too positive? 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Edinb."},{"key":"2023013109504732500_btz498-B8","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1111\/1755-0998.12280","article-title":"WFABC: a Wright\u2013Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data","volume":"15","author":"Foll","year":"2015","journal-title":"Mol. Ecol. Resources"},{"key":"2023013109504732500_btz498-B9","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1534\/genetics.110.114397","article-title":"The next generation of molecular markers from massively parallel sequencing of pooled DNA samples","volume":"186","author":"Futschik","year":"2010","journal-title":"Genetics"},{"key":"2023013109504732500_btz498-B11","doi-asserted-by":"crossref","first-page":"2750","DOI":"10.1038\/s41467-018-05281-7","article-title":"Gene expression drives the evolution of dominance","volume":"9","author":"Huber","year":"2018","journal-title":"Nat. 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