{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T13:05:47Z","timestamp":1789477547459,"version":"build-2803163510"},"reference-count":34,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,8,22]],"date-time":"2026-08-22T00:00:00Z","timestamp":1787356800000},"content-version":"am","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DOB-1639014"],"award-info":[{"award-number":["DOB-1639014"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008524","name":"University of Montana","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008524","id-type":"DOI","asserted-by":"publisher"}]},{"name":"\u201cConGen\u201d population genetics analysis course"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>We introduce an updated and enhanced version of EASYPOP, a widely used population-genetics simulation program. The previous version (2.0.1), released in 2006, runs natively only in Windows or the old Apple PPC architecture. The new version (3.1) preserves EASYPOP\u2019s ease of installation and use and runs natively in Windows, Linux, Apple Silicon, and Apple Intel environments. For quick re-runs, it can now write simulation parameters to and read them from a configuration file, removing the need to retype input parameters before each run. It also adds genotype output options that facilitate temporal studies by sampling any generations of interest. We also introduce an R package, easypopr, that further automates running EASYPOP 3.1 using R commands to easily set up and rerun simulations with changes in parameters. easypopr provides tools to visualize the effects of different parameter choices (Ne, mutation models, migration rates, demographic scenarios, etc.) on summary statistics, including subpopulation mean heterozygosity (Hs), total metapopulation heterozygosity (HT), FIS, FST, and Ne estimates. Outputs from easypopr (and EASYPOP) are easily fed into snpR or other R packages for convenient, wide-ranging analysis to quantify the effects of demography on the power to detect genetic change, including integration with programs like NeEstimator and STRUCTURE. With these enhancements, available in executables for all common operating systems, EASYPOP 3.1 provides a streamlined approach for conducting forward-time genetic simulations across a wide range of scenarios.<\/jats:p>\n                  <jats:p>Multimedia abstract: We introduce EASYPOP 3.1, an enhanced version of the popular population genetics simulation program for teaching and research in ecology, evolution, and conservation biology. This software now runs on Windows, Linux, and both Apple Silicon and Intel Mac systems, while maintaining its easy installation process. Key improvements include the ability to save and load simulation settings for quicker reruns and new options for data collection (outputting genotypes) from each of multiple generations. Additionally, the new R package, easypopr, streamlines the simulation setup process and enables visualization of how different parameters impact genetic statistics. The outputs from EASYPOP and easypopr can be analyzed with the snpR package, making it easier to study the effects of demographic changes on genetic outcomes. With these updates, EASYPOP 3.1 is among the most accessible tools for forward-time genetic simulations of many genes (loci) in many individuals from each of many populations or metapopulation scenarios.<\/jats:p>","DOI":"10.1093\/jhered\/esag070","type":"journal-article","created":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T11:50:45Z","timestamp":1787313045000},"source":"Crossref","is-referenced-by-count":0,"title":["Population genetics simulations made easier: EASYPOP v3"],"prefix":"10.1093","author":[{"given":"Ted","family":"Cosart","sequence":"first","affiliation":[{"name":"Flathead Lake Biological Station, Division of Biological Sciences, University of Montana , Missoula, MT ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2408-9535","authenticated-orcid":false,"given":"William","family":"Hemstrom","sequence":"additional","affiliation":[{"name":"Department of Biology, Colorado State University , Fort Collins, CO ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3627-0769","authenticated-orcid":false,"given":"Jared","family":"Grummer","sequence":"additional","affiliation":[{"name":"Flathead Lake Biological Station, Division of Biological Sciences, University of Montana , Missoula, MT ,","place":["United States"]},{"name":"Wildlife Biology Program, University of Montana , Missoula, MT ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8697-0582","authenticated-orcid":false,"given":"Gordon","family":"Luikart","sequence":"additional","affiliation":[{"name":"Flathead Lake Biological Station, Division of Biological Sciences, University of Montana , Missoula, MT ,","place":["United States"]},{"name":"Wildlife Biology Program, University of Montana , Missoula, MT ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,8,22]]},"reference":[{"key":"2026091508261420700_ref1","doi-asserted-by":"publisher","DOI":"10.1093\/oso\/9780198856566.001.0001","volume-title":"Conservation and the genomics of populations","author":"Allendorf","year":"2022"},{"key":"2026091508261420700_ref2","doi-asserted-by":"publisher","DOI":"10.1111\/eva.13733","article-title":"What does effective population size tell us about loss of allelic variation?","volume":"17","author":"Allendorf","year":"2024","journal-title":"Evol Appl"},{"key":"2026091508261420700_ref3","doi-asserted-by":"publisher","first-page":"596","DOI":"10.1111\/1755-0998.13270","article-title":"MetaPopGen 2.0: a multilocus genetic simulator to model populations of large size","volume":"21","author":"Andrello","year":"2021","journal-title":"Mol Ecol Resour"},{"key":"2026091508261420700_ref4","doi-asserted-by":"publisher","first-page":"1661","DOI":"10.1111\/mec.12686","article-title":"Recent novel approaches for population genomics data analysis","volume":"23","author":"Andrews","year":"2014","journal-title":"Mol Ecol"},{"key":"2026091508261420700_ref5","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1093\/jhered\/92.3.301","article-title":"EASYPOP (version 1.7): a computer program for population genetics simulations","volume":"92","author":"Balloux","year":"2001","journal-title":"J Hered"},{"key":"2026091508261420700_ref6","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1093\/genetics\/160.2.741","article-title":"Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach","volume":"160","author":"Berthier","year":"2002","journal-title":"Genetics"},{"key":"2026091508261420700_ref7","volume-title":"Remotes: R package installation from remote repositories, including 'GitHub'. R package version 2.5.0.9000","author":"Cs\u00e1rdi","year":"2025"},{"key":"2026091508261420700_ref8","doi-asserted-by":"publisher","DOI":"10.1111\/ecog.06566","article-title":"CDMetaPOP 2: a multispecies, eco-evolutionary simulation framework for landscape demogenetics and connectivity","volume":"2023","author":"Day","year":"2023","journal-title":"Ecography"},{"key":"2026091508261420700_ref9","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1111\/1755-0998.12157","article-title":"NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data","volume":"14","author":"Do","year":"2014","journal-title":"Mol Ecol Resour"},{"key":"2026091508261420700_ref10","doi-asserted-by":"publisher","first-page":"2425","DOI":"10.1007\/s10592-010-0112-x","article-title":"Early detection of population fragmentation using linkage disequilibrium estimation of effective population size","volume":"11","author":"England","year":"2010","journal-title":"Conserv Genet"},{"key":"2026091508261420700_ref11","doi-asserted-by":"publisher","first-page":"2611","DOI":"10.1111\/j.1365-294X.2005.02553.x","article-title":"Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study","volume":"14","author":"Evanno","year":"2005","journal-title":"Mol Ecol"},{"key":"2026091508261420700_ref12","doi-asserted-by":"publisher","first-page":"1567","DOI":"10.1093\/genetics\/164.4.1567","article-title":"A Bayesian approach to mapping ancestry in a sample of individuals","volume":"164","author":"Falush","year":"2003","journal-title":"Genetics"},{"key":"2026091508261420700_ref13","volume-title":"PopG (4.03) [Computer software]","author":"Felsenstein","year":"2016"},{"key":"2026091508261420700_ref14","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1111\/j.1471-8286.2004.00828.x","article-title":"Hierfstat, a package for R to compute and test hierarchical F-statistics","volume":"5","author":"Goudet","year":"2005","journal-title":"Mol Ecol Notes"},{"key":"2026091508261420700_ref15","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.1111\/eva.12401","article-title":"Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 2. Separating the relative effects of gene flow and genetic drift","volume":"9","author":"Gracianne","year":"2016","journal-title":"Evol Appl"},{"key":"2026091508261420700_ref16","doi-asserted-by":"publisher","first-page":"552","DOI":"10.1111\/1755-0998.12968","article-title":"Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes","volume":"19","author":"Haller","year":"2019","journal-title":"Mol Ecol Resour"},{"key":"2026091508261420700_ref17","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msaf313","article-title":"SLiM 5: eco-evolutionary simulations across multiple chromosomes and full genomes","volume":"43","author":"Haller","year":"2026","journal-title":"Mol Biol Evol"},{"key":"2026091508261420700_ref18","doi-asserted-by":"publisher","first-page":"962","DOI":"10.1111\/1755-0998.13721","article-title":"snpR: user friendly population genomics for SNP data sets with categorical metadata","volume":"23","author":"Hemstrom","year":"2023","journal-title":"Mol Ecol Resour"},{"key":"2026091508261420700_ref19","doi-asserted-by":"publisher","first-page":"1403","DOI":"10.1093\/bioinformatics\/btn129","article-title":"adegenet: a R package for the multivariate analysis of genetic markers","volume":"24","author":"Jombart","year":"2008","journal-title":"Bioinformatics"},{"key":"2026091508261420700_ref20","doi-asserted-by":"publisher","DOI":"10.1002\/ecs2.2567","article-title":"Evaluating the popularity of R in ecology","volume":"10","author":"Lai","year":"2019","journal-title":"Ecosphere"},{"key":"2026091508261420700_ref21","doi-asserted-by":"publisher","DOI":"10.1111\/ele.14461","article-title":"Multinational evaluation of genetic diversity indicators for the Kunming-Montreal Global Biodiversity Framework","volume":"27","author":"Mastretta-Yanes","year":"2024","journal-title":"Ecol Lett"},{"key":"2026091508261420700_ref22","doi-asserted-by":"publisher","first-page":"1745","DOI":"10.1111\/1755-0998.13372","article-title":"SimBit: a high performance, flexible and easy-to-use population genetic simulator","volume":"21","author":"Matthey-Doret","year":"2021","journal-title":"Mol Ecol Resour"},{"key":"2026091508261420700_ref23","doi-asserted-by":"publisher","first-page":"1378","DOI":"10.1111\/1755-0998.12673","article-title":"gesp: a computer program for modelling genetic effective population size, inbreeding and divergence in substructured populations","volume":"17","author":"Olsson","year":"2017","journal-title":"Mol Ecol Resour"},{"key":"2026091508261420700_ref24","doi-asserted-by":"publisher","first-page":"945","DOI":"10.1093\/genetics\/155.2.945","article-title":"Population structure and the Bayesian inference of population history","volume":"155","author":"Pritchard","year":"2000","journal-title":"Genetics"},{"key":"2026091508261420700_ref25","doi-asserted-by":"publisher","first-page":"1334","DOI":"10.1111\/1755-0998.13804","article-title":"Variance effective population size is affected by census size in sub-structured populations","volume":"23","author":"Ryman","year":"2023","journal-title":"Mol Ecol Resour"},{"key":"2026091508261420700_ref26","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.13893","article-title":"Genomics and conservation: guidance from training to analyses and applications","volume":"24","author":"Schiebelhut","year":"2024","journal-title":"Mol Ecol Resour"},{"key":"2026091508261420700_ref27","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1093\/jhered\/esab019","article-title":"Big data in conservation genomics: boosting skills, hedging bets, and staying current in the field","volume":"112","author":"Schweizer","year":"2021","journal-title":"J Hered"},{"key":"2026091508261420700_ref28","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1093\/genetics\/121.2.379","article-title":"A generalized approach for estimating effective population size from temporal changes in allele frequency","volume":"121","author":"Waples","year":"1989","journal-title":"Genetics"},{"key":"2026091508261420700_ref29","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1111\/j.1755-0998.2010.02876.x","article-title":"Spatial-temporal stratifications in natural populations and how they affect understanding and estimation of effective population size","volume":"10","author":"Waples","year":"2010","journal-title":"Mol Ecol Resour"},{"key":"2026091508261420700_ref30","doi-asserted-by":"publisher","DOI":"10.1111\/eva.13695","article-title":"The Ne\/N ratio in applied conservation","volume":"17","author":"Waples","year":"2024","journal-title":"Evol Appl"},{"key":"2026091508261420700_ref31","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1111\/j.1752-4571.2009.00104.x","article-title":"Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution","volume":"3","author":"Waples","year":"2010","journal-title":"Evol Appl"},{"key":"2026091508261420700_ref1w","doi-asserted-by":"publisher","volume-title":"Genetics","DOI":"10.1534\/genetics.111.132233"},{"key":"2026091508261420700_ref32","first-page":"439","article-title":"Gametic disequilibrium analysis as a means of identifying mixtures of salmon populations","volume":"7","author":"Waples","year":"1990","journal-title":"Am Fish Soc Symp"},{"key":"2026091508261420700_ref33","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.14081","article-title":"Cgsim: an R package for simulation of population genetics for conservation and management applications","volume":"25","author":"Zimmerman","year":"2025","journal-title":"Mol Ecol Resour"}],"container-title":["Journal of Heredity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jhered\/advance-article-pdf\/doi\/10.1093\/jhered\/esag070\/70763793\/esag070.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jhered\/advance-article-pdf\/doi\/10.1093\/jhered\/esag070\/70763793\/esag070.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T12:26:21Z","timestamp":1789475181000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jhered\/advance-article\/doi\/10.1093\/jhered\/esag070\/8768674"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,22]]},"references-count":34,"URL":"https:\/\/doi.org\/10.1093\/jhered\/esag070","relation":{},"ISSN":["0022-1503","1465-7333"],"issn-type":[{"value":"0022-1503","type":"print"},{"value":"1465-7333","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,22]]},"article-number":"esag070"}}