{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T00:15:04Z","timestamp":1784333704908,"version":"3.55.0"},"reference-count":76,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IOS 1137624\/0643606"],"award-info":[{"award-number":["IOS 1137624\/0643606"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006363","name":"National Geographic Society","doi-asserted-by":"publisher","award":["9023-11"],"award-info":[{"award-number":["9023-11"]}],"id":[{"id":"10.13039\/100006363","id-type":"DOI","asserted-by":"publisher"}]},{"name":"School of Arts & Sciences at the University of Rochester"}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"abstract":"<jats:p>Insular organisms often evolve predictable phenotypes, like flightlessness, extreme body sizes, or increased melanin deposition. The evolutionary forces and molecular targets mediating these patterns remain mostly unknown. Here we study the Chestnut-bellied Monarch (<jats:italic>Monarcha castaneiventris<\/jats:italic>) from the Solomon Islands, a complex of closely related subspecies in the early stages of speciation. On the large island of Makira <jats:italic>M<\/jats:italic>. <jats:italic>c<\/jats:italic>. <jats:italic>megarhynchus<\/jats:italic> has a chestnut belly, whereas on the small satellite islands of Ugi, and Santa Ana and Santa Catalina (SA\/SC) <jats:italic>M<\/jats:italic>. <jats:italic>c<\/jats:italic>. <jats:italic>ugiensis<\/jats:italic> is entirely iridescent blue-black (i.e., melanic). Melanism has likely evolved twice, as the Ugi and SA\/SC populations were established independently. To investigate the genetic basis of melanism on each island we generated whole genome sequence data from all three populations. Non-synonymous mutations at the <jats:italic>MC1R<\/jats:italic> pigmentation gene are associated with melanism on SA\/SC, while <jats:italic>ASIP<\/jats:italic>, an antagonistic ligand of <jats:italic>MC1R<\/jats:italic>, is associated with melanism on Ugi. Both genes show evidence of selective sweeps in traditional summary statistics and statistics derived from the ancestral recombination graph (ARG). Using the ARG in combination with machine learning, we inferred selection strength, timing of onset and allele frequency trajectories. <jats:italic>MC1R<\/jats:italic> shows evidence of a recent, strong, soft selective sweep. The region including <jats:italic>ASIP<\/jats:italic> shows more complex signatures; however, we find evidence for sweeps in mutations near <jats:italic>ASIP<\/jats:italic>, which are comparatively older than those on <jats:italic>MC1R<\/jats:italic> and have been under relatively strong selection. Overall, our study shows convergent melanism results from selective sweeps at independent molecular targets, evolving in taxa where coloration likely mediates reproductive isolation with the neighboring chestnut-bellied subspecies.<\/jats:p>","DOI":"10.1371\/journal.pgen.1010474","type":"journal-article","created":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T17:28:44Z","timestamp":1667323724000},"page":"e1010474","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":26,"title":["Selective sweeps on different pigmentation genes mediate convergent evolution of island melanism in two incipient bird species"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8408-8553","authenticated-orcid":true,"given":"Leonardo","family":"Campagna","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4567-6720","authenticated-orcid":true,"given":"Ziyi","family":"Mo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam","family":"Siepel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8437-5525","authenticated-orcid":true,"given":"J. Albert C.","family":"Uy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,11,1]]},"reference":[{"key":"pgen.1010474.ref001","volume-title":"Wonderful life: the Burgess Shale and the nature of history","author":"SJ Gould","year":"1990"},{"key":"pgen.1010474.ref002","doi-asserted-by":"crossref","first-page":"eaam5979","DOI":"10.1126\/science.aam5979","article-title":"Contingency and determinism in evolution: Replaying life\u2019s tape","volume":"362","author":"ZD Blount","year":"2018","journal-title":"Science"},{"key":"pgen.1010474.ref003","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1126\/science.1070315","article-title":"Unpredictable evolution in a 30-year study of Darwin\u2019s finches","volume":"296","author":"PR Grant","year":"2002","journal-title":"Science"},{"key":"pgen.1010474.ref004","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1126\/science.1232392","article-title":"Exceptional convergence on the macroevolutionary landscape in island lizard radiations","volume":"341","author":"DL Mahler","year":"2013","journal-title":"Science"},{"key":"pgen.1010474.ref005","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1007\/BF01237847","article-title":"The evolution of flightlessness: Is history important","volume":"8","author":"DA Roff","year":"1994","journal-title":"Evolutionary Ecology"},{"key":"pgen.1010474.ref006","doi-asserted-by":"crossref","first-page":"4765","DOI":"10.1073\/pnas.1522931113","article-title":"Predictable evolution toward flightlessness in volant island birds","volume":"113","author":"NA Wright","year":"2016","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"pgen.1010474.ref007","first-page":"1633","article-title":"A window on the genetics of evolution: MC1R and plumage colouration in birds","volume":"272","author":"NI Mundy","year":"2005","journal-title":"Proceedings of the Royal Society of London"},{"key":"pgen.1010474.ref008","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1016\/S0960-9822(01)00158-0","article-title":"The molecular basis of an avian plumage polymorphism in the wild: A melanocortin-1-receptor point mutation is perfectly associated with the melanic plumage morph of the bananaquit","volume":"11","author":"E Theron","year":"2001","journal-title":"Current Biology"},{"key":"pgen.1010474.ref009","first-page":"20160731","article-title":"Mutations in different pigmentation genes are associated with parallel melanism in island flycatchers","volume":"283","author":"JAC Uy","year":"2016","journal-title":"Proceedings of the Royal Society of London. Series B: Biological Sciences"},{"key":"pgen.1010474.ref010","doi-asserted-by":"crossref","first-page":"1348","DOI":"10.1111\/evo.14185","article-title":"Patterns of genetic divergence and demographic history shed light on island-mainland population dynamics and melanic plumage evolution in the White-winged Fairywren","volume":"75","author":"J Walsh","year":"2021","journal-title":"Evolution"},{"key":"pgen.1010474.ref011","volume-title":"Systematics and the origin of species","author":"E. Mayr","year":"1942"},{"key":"pgen.1010474.ref012","article-title":"The birds of northern Melanesia: speciation, ecology & biogeography","author":"E Mayr","year":"2001","journal-title":"Oxford University Press"},{"key":"pgen.1010474.ref013","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1111\/j.1558-5646.2008.00530.x","article-title":"Plumage and song differences mediate species recognition between incipient flycatcher species of the Solomon Islands","volume":"63","author":"JAC Uy","year":"2009","journal-title":"Evolution"},{"key":"pgen.1010474.ref014","doi-asserted-by":"crossref","first-page":"3760","DOI":"10.1111\/mec.14116","article-title":"Genomic evidence for convergent evolution of a key trait underlying divergence in island birds","volume":"26","author":"EA Cooper","year":"2017","journal-title":"Molecular Ecology"},{"key":"pgen.1010474.ref015","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1086\/600084","article-title":"Difference in plumage color used in species recognition between incipient species is linked to a single amino acid substitution in the melanocortin-1 receptor","volume":"174","author":"JAC Uy","year":"2009","journal-title":"The American Naturalist"},{"key":"pgen.1010474.ref016","doi-asserted-by":"crossref","first-page":"1499","DOI":"10.1007\/s00265-013-1492-y","article-title":"Variation in the temporal and spatial use of signals and its implications for multimodal communication","volume":"67","author":"JAC Uy","year":"2013","journal-title":"Behavioral Ecology and Sociobiology"},{"key":"pgen.1010474.ref017","doi-asserted-by":"crossref","first-page":"3831","DOI":"10.1111\/mec.14537","article-title":"Sex chromosomes and speciation in birds and other ZW systems","volume":"27","author":"DE Irwin","year":"2018","journal-title":"Molecular Ecology"},{"key":"pgen.1010474.ref018","doi-asserted-by":"crossref","first-page":"e1004342","DOI":"10.1371\/journal.pgen.1004342","article-title":"Genome-Wide Inference of Ancestral Recombination Graphs.","volume":"10","author":"MD Rasmussen","year":"2014","journal-title":"PLoS Genetics"},{"key":"pgen.1010474.ref019","doi-asserted-by":"crossref","first-page":"30554","DOI":"10.1073\/pnas.2015987117","article-title":"Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps","volume":"117","author":"HA Hejase","year":"2020","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"pgen.1010474.ref020","doi-asserted-by":"crossref","first-page":"msab332","DOI":"10.1093\/molbev\/msab332","article-title":"A Deep-Learning Approach for Inference of Selective Sweeps from the Ancestral Recombination Graph","volume":"39","author":"HA Hejase","year":"2022","journal-title":"Molecular Biology and Evolution"},{"key":"pgen.1010474.ref021","doi-asserted-by":"crossref","first-page":"1329","DOI":"10.1111\/j.0014-3820.2004.tb01711.x","article-title":"Ecological genetics of adaptive color polymorphism in pocket mice: geographic variation in selected and neutral genes","volume":"58","author":"HE Hoekstra","year":"2004","journal-title":"Evolution"},{"key":"pgen.1010474.ref022","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1086\/421051","article-title":"Genetic signatures of strong recent positive selection at the lactase gene","volume":"74","author":"T Bersaglieri","year":"2004","journal-title":"The American Journal of Human Genetics"},{"key":"pgen.1010474.ref023","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.1098\/rspb.2002.2020","article-title":"Houston. The sexual selection continuum","volume":"269","author":"H Kokko","year":"2002","journal-title":"Proceedings of the Royal Society of London. Series B: Biological Sciences."},{"key":"pgen.1010474.ref024","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1210\/mend.12.4.0091","article-title":"A ligand-mimetic model for constitutive activation of the Melanocortin-1 Receptor","volume":"12","author":"D Lu","year":"1998","journal-title":"Molecular Endocrinology"},{"key":"pgen.1010474.ref025","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1093\/genetics\/150.3.1177","article-title":"Melanocortin Receptor 1 (MC1R) mutations and coat color in pigs.","volume":"150","author":"JMH Kijas","year":"1998","journal-title":"Genetics"},{"key":"pgen.1010474.ref026","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1007\/s003359900939","article-title":"Molecular and pharmacological characterization of dominant black coat color in sheep","volume":"10","author":"DI V\u00e5ge","year":"1999","journal-title":"Mammalian Genome"},{"key":"pgen.1010474.ref027","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1534\/genetics.107.077040","article-title":"Recessive black is allelic to the yellow plumage locus in Japanese Quail and associated with a frameshift deletion in the ASIP Gene","volume":"178","author":"T Hiragaki","year":"2008","journal-title":"Genetics"},{"key":"pgen.1010474.ref028","doi-asserted-by":"crossref","first-page":"e6435","DOI":"10.1371\/journal.pone.0006435","article-title":"Melanism in Peromyscus is caused by independent mutations in Agouti.","volume":"4","author":"EP Kingsley","year":"2009","journal-title":"PLoS ONE."},{"issue":"9","key":"pgen.1010474.ref029","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1016\/j.tree.2008.06.001","article-title":"Pleiotropy in the melanocortin system, coloration and behavioural syndromes","volume":"23","author":"AL Ducrest","year":"2008","journal-title":"Trends in Ecology & Evolution"},{"key":"pgen.1010474.ref030","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1534\/genetics.115.174912","article-title":"Soft shoulders ahead: spurious signatures of soft and partial selective sweeps result from linked hard sweeps","volume":"200","author":"DR Schrider","year":"2015","journal-title":"Genetics"},{"key":"pgen.1010474.ref031","first-page":"5039","article-title":"The probability of genetic parallelism and convergence in natural populations","volume":"279","author":"GL Conte","year":"2012","journal-title":"Proceedings of the Royal Society of London. Series B: Biological Sciences"},{"key":"pgen.1010474.ref032","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1642\/AUK-14-284.1","article-title":"Island size predicts the frequency of melanic birds in the color-polymorphic flycatcher Monarcha castaneiventris of the Solomon Islands","volume":"132","author":"JAC Uy","year":"2015","journal-title":"The Auk"},{"key":"pgen.1010474.ref033","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1111\/j.1600-048X.2010.05120.x","article-title":"Melanin-based coloration is related to parasite intensity and cellular immune response in an urban free living bird: the feral pigeon Columba livia","volume":"42","author":"L Jacquin","year":"2011","journal-title":"Journal of Avian Biology"},{"key":"pgen.1010474.ref034","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1086\/713386","article-title":"Rethinking Gloger\u2019s rule: climate, light environments, and color in a large family of tropical birds (Furnariidae).","volume":"197","author":"RS Marcondes","year":"2021","journal-title":"The American Naturalist"},{"key":"pgen.1010474.ref035","volume-title":"Speciation in birds","author":"T. Price","year":"2008"},{"key":"pgen.1010474.ref036","doi-asserted-by":"crossref","first-page":"1410","DOI":"10.1126\/science.1253226","article-title":"The genomic landscape underlying phenotypic integrity in the face of gene flow in crows","volume":"344","author":"JW Poelstra","year":"2014","journal-title":"Science"},{"key":"pgen.1010474.ref037","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1146\/annurev-ecolsys-110617-062646","article-title":"Behavioral isolation and incipient speciation in Birds","volume":"49","author":"JAC Uy","year":"2018","journal-title":"Annual Review of Ecology, Evolution and Systematics"},{"key":"pgen.1010474.ref038","doi-asserted-by":"crossref","first-page":"eabc0256","DOI":"10.1126\/science.abc0256","article-title":"Rapid speciation via the evolution of pre-mating isolation in the Iber\u00e1 Seedeater","volume":"371","author":"SP Turbek","year":"2021","journal-title":"Science"},{"key":"pgen.1010474.ref039","doi-asserted-by":"crossref","first-page":"1019","DOI":"10.1038\/s41467-021-21340-y","article-title":"Asymmetric introgression reveals the genetic architecture of a plumage trait.","volume":"12","author":"GA Semenov","year":"2021","journal-title":"Nature Communications"},{"key":"pgen.1010474.ref040","doi-asserted-by":"crossref","first-page":"160805","DOI":"10.1098\/rsos.160805","article-title":"A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird","volume":"15","author":"YX Bourgeois","year":"2017","journal-title":"Royal Society Open Science"},{"key":"pgen.1010474.ref041","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"pgen.1010474.ref042","doi-asserted-by":"crossref","first-page":"2669","DOI":"10.1093\/bioinformatics\/btt476","article-title":"The MaSuRCA genome assembler","volume":"29","author":"AV Zimin","year":"2013","journal-title":"Bioinformatics"},{"key":"pgen.1010474.ref043","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"A Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"pgen.1010474.ref044","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs","volume":"31","author":"FA Sim\u00e3o","year":"2015","journal-title":"Bioinformatics"},{"key":"pgen.1010474.ref045","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1093\/bioinformatics\/btq102","article-title":"Genome-wide synteny through highly sensitive sequence alignment: Satsuma","volume":"26","author":"MG Grabherr","year":"2010","journal-title":"Bioinformatics"},{"key":"pgen.1010474.ref046","doi-asserted-by":"crossref","first-page":"9451","DOI":"10.1073\/pnas.1921046117","article-title":"RepeatModeler2 for automated genomic discovery of transposable element families","volume":"117","author":"JM Flynn","year":"2020","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"pgen.1010474.ref047","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1101\/gr.6743907","article-title":"MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes","volume":"18","author":"BL Cantarel","year":"2007","journal-title":"Genome Research"},{"key":"pgen.1010474.ref048","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1186\/s13104-016-1900-2","article-title":"AdapterRemoval v2: rapid adapter trimming, identification, and read merging.","volume":"9","author":"M Schubert","year":"2016","journal-title":"BMC Research Notes"},{"key":"pgen.1010474.ref049","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"B Langmead","year":"2012","journal-title":"Nature Methods"},{"key":"pgen.1010474.ref050","article-title":"Genomics in the Cloud: Using Docker, GATK, and WDL in Terra","author":"GA Van der Auwera","year":"2020","journal-title":"O\u2019Reilly Media, Incorporated"},{"key":"pgen.1010474.ref051","doi-asserted-by":"crossref","first-page":"2678","DOI":"10.1093\/bioinformatics\/bts503","article-title":"Qualimap: evaluating next-generation sequencing alignment data","volume":"28","author":"F Garc\u00eda-Alcalde","year":"2012","journal-title":"Bioinformatics"},{"key":"pgen.1010474.ref052","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"P Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"pgen.1010474.ref053","volume-title":"R: A Language and Environment for Statistical Computing","author":"R Core Team","year":"2021"},{"key":"pgen.1010474.ref054","doi-asserted-by":"crossref","first-page":"3326","DOI":"10.1093\/bioinformatics\/bts606","article-title":"A high-performance computing toolset for relatedness and principal component analysis of SNP data","volume":"28","author":"X Zheng","year":"2012","journal-title":"Bioinformatics"},{"key":"pgen.1010474.ref055","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model-based estimation of ancestry in unrelated individuals","volume":"19","author":"DH Alexander","year":"2009","journal-title":"Genome Research"},{"key":"pgen.1010474.ref056","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: A tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"S Purcell","year":"2007","journal-title":"The American Journal of Human Genetics"},{"key":"pgen.1010474.ref057","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant graphics for data analysis","author":"H. Wickham","year":"2016"},{"key":"pgen.1010474.ref058","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"A. Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"pgen.1010474.ref059","doi-asserted-by":"crossref","first-page":"e1005004","DOI":"10.1371\/journal.pgen.1005004","article-title":"Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps","volume":"11","author":"NR Garud","year":"2015","journal-title":"PLoS Genetics"},{"key":"pgen.1010474.ref060","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1111\/2041-210X.12410","article-title":"popart: full-feature software for haplotype network construction","volume":"6","author":"JW Leigh","year":"2015","journal-title":"Methods in Ecology and Evolution"},{"key":"pgen.1010474.ref061","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1093\/oxfordjournals.molbev.a026036","article-title":"Median-joining networks for inferring intraspecific phylogenies","volume":"16","author":"HJ Bandelt","year":"1999","journal-title":"Molecular Biology and Evolution"},{"key":"pgen.1010474.ref062","doi-asserted-by":"crossref","first-page":"e129","DOI":"10.1093\/nar\/gkt371","article-title":"Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads\u2014a baiting and iterative mapping approach","volume":"41","author":"C Hahn","year":"2013","journal-title":"Nucleic Acids Research"},{"key":"pgen.1010474.ref063","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1093\/bioinformatics\/bts199","article-title":"Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data","volume":"28","author":"M Kearse","year":"2012","journal-title":"Bioinformatics"},{"key":"pgen.1010474.ref064","article-title":"Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species","volume":"270","author":"PDN Hebert","year":"2003","journal-title":"Proceedings of the Royal Society of London. Series B: Biological Sciences."},{"key":"pgen.1010474.ref065","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1038\/ng.937","article-title":"Bayesian inference of ancient human demography from individual genome sequences","volume":"43","author":"I Gronau","year":"2011","journal-title":"Nature Genetics"},{"key":"pgen.1010474.ref066","first-page":"7","article-title":"CODA: Convergence Diagnosis and Output Analysis for MCMC.","volume":"6","author":"M Plummer","year":"2006","journal-title":"R News"},{"key":"pgen.1010474.ref067","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1101\/gr.204669.116","article-title":"Direct estimate of the rate of germline mutation in a bird","volume":"26","author":"L Smeds","year":"2016","journal-title":"Genome Res"},{"key":"pgen.1010474.ref068","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1038\/nmeth.2848","article-title":"Efficient multivariate linear mixed model algorithms for genome-wide association studies","volume":"11","author":"X Zhou","year":"2014","journal-title":"Nature Methods"},{"key":"pgen.1010474.ref069","doi-asserted-by":"crossref","first-page":"731","DOI":"10.21105\/joss.00731","article-title":"qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots","volume":"3","author":"SD Turner","year":"2018","journal-title":"Journal of Open Source Software"},{"key":"pgen.1010474.ref070","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1086\/521987","article-title":"Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering","volume":"81","author":"SR Browning","year":"2007","journal-title":"Am J Hum Genet"},{"key":"pgen.1010474.ref071","article-title":"vegan: Community Ecology Package.","author":"J Oksanen","year":"2019","journal-title":"R package version 2.5\u20136"},{"key":"pgen.1010474.ref072","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1111\/j.2041-210X.2011.00169.x","article-title":"phytools: an R package for phylogenetic comparative biology (and other things): phytools: R package.","volume":"3","author":"LJ Revell","year":"2012","journal-title":"Methods in Ecology and Evolution"},{"key":"pgen.1010474.ref073","doi-asserted-by":"crossref","first-page":"e1004842","DOI":"10.1371\/journal.pcbi.1004842","article-title":"Efficient coalescent simulation and genealogical analysis for large sample sizes","volume":"12","author":"J Kelleher","year":"2016","journal-title":"PLoS Computational Biology"},{"key":"pgen.1010474.ref074","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1093\/molbev\/msy228","article-title":"SLiM 3: Forward Genetic Simulations Beyond the Wright\u2013Fisher Model. Hernandez R, editor","volume":"36","author":"BC Haller","year":"2019","journal-title":"Molecular Biology and Evolution"},{"key":"pgen.1010474.ref075","doi-asserted-by":"crossref","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":"BC Haller","year":"2019","journal-title":"Molecular Ecology Resources"},{"key":"pgen.1010474.ref076","first-page":"1050","article-title":"Dropout as a bayesian approximation: Representing model uncertainty in deep learning","author":"Y Gal","year":"2016","journal-title":"In international conference on machine learning. Proceedings of Machine Learning Research"}],"container-title":["PLOS Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1010474","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T17:29:49Z","timestamp":1667323789000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1010474"}},"subtitle":[],"editor":[{"given":"Nicolas","family":"Bierne","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,11,1]]},"references-count":76,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2022,11,1]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1010474","relation":{},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,1]]}}}