{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T13:45:04Z","timestamp":1789479904609,"version":"build-2803163510"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2018,9,15]],"date-time":"2018-09-15T00:00:00Z","timestamp":1536969600000},"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":["DBI 1308885"],"award-info":[{"award-number":["DBI 1308885"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DEB 1656004"],"award-info":[{"award-number":["DEB 1656004"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,5,1]]},"DOI":"10.1093\/sysbio\/syy063","type":"journal-article","created":{"date-parts":[[2018,9,13]],"date-time":"2018-09-13T15:11:38Z","timestamp":1536851498000},"page":"371-395","source":"Crossref","is-referenced-by-count":51,"title":["Full Bayesian Comparative Phylogeography from Genomic Data"],"prefix":"10.1093","volume":"68","author":[{"given":"Jamie R","family":"Oaks","sequence":"first","affiliation":[{"name":"Department of Biological Sciences & Museum of Natural History, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,9,15]]},"reference":[{"key":"2019041810125691000_B1","doi-asserted-by":"crossref","first-page":"1152","DOI":"10.1214\/aos\/1176342871","article-title":"Mixtures of Dirichlet processes with applications to Bayesian nonparametric problems","volume":"2","author":"Antoniak","year":"1974","journal-title":"Ann. Stat."},{"key":"2019041810125691000_B2","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1080\/00029890.1934.11987615","article-title":"Exponential numbers","volume":"41","author":"Bell","year":"1934","journal-title":"Am. Math. Mon."},{"key":"2019041810125691000_B3","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1080\/10618600.1998.10474787","article-title":"General methods for monitoring convergence of iterative simulations","volume":"7","author":"Brooks","year":"1998","journal-title":"J. Comput. Graph. Stat."},{"key":"2019041810125691000_B4","doi-asserted-by":"crossref","first-page":"1917","DOI":"10.1093\/molbev\/mss086","article-title":"Inferring species trees directly from biallelic genetic markers: Bypassing gene trees in a full coalescent analysis","volume":"29","author":"Bryant","year":"2012","journal-title":"Mol. Biol. Evol."},{"key":"2019041810125691000_B5","doi-asserted-by":"crossref","first-page":"3317","DOI":"10.1093\/bioinformatics\/btu530","article-title":"Quartet inference from SNP data under the coalescent model","volume":"30","author":"Chifman","year":"2014","journal-title":"Bioinformatics"},{"key":"2019041810125691000_B6","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1080\/01621459.1995.10476550","article-title":"Bayesian density estimation and inference using mixtures","volume":"90","author":"Escobar","year":"1995","journal-title":"J. Am. Stat. Assoc."},{"key":"2019041810125691000_B7","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1146\/annurev.ge.22.120188.002513","article-title":"Phylogenies from molecular sequences: inference and reliability","volume":"22","author":"Felsenstein","year":"1988","journal-title":"Ann. Rev. Genet."},{"key":"2019041810125691000_B8","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1214\/aos\/1176342360","article-title":"A Bayesian analysis of some nonparametric problems","volume":"1","author":"Ferguson","year":"1973","journal-title":"Ann. Stat."},{"key":"2019041810125691000_B9","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1080\/10618600.2015.1044092","article-title":"A practical sequential stopping rule for high-dimensional Markov chain Monte Carlo","volume":"25","author":"Gong","year":"2016","journal-title":"J. Comput. Graph. Stat."},{"key":"2019041810125691000_B10","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1093\/biomet\/82.4.711","article-title":"Reversible jump Markov chain Monte Carlo computation and Bayesian model determination","volume":"82","author":"Green","year":"1995","journal-title":"Biometrika"},{"key":"2019041810125691000_B11","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1007\/s11222-015-9574-5","article-title":"Bayesian computation: a summary of the current state, and samples backwards and forwards","volume":"25","author":"Green","year":"2015","journal-title":"Stat. Comput."},{"key":"2019041810125691000_B12","doi-asserted-by":"crossref","first-page":"e895","DOI":"10.7717\/peerj.895","article-title":"Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species","volume":"3","author":"Harvey","year":"2015","journal-title":"PeerJ"},{"key":"2019041810125691000_B13","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1093\/biomet\/57.1.97","article-title":"Monte Carlo sampling methods using Markov chains and their applications","volume":"57","author":"Hastings","year":"1970","journal-title":"Biometrika"},{"key":"2019041810125691000_B14","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1093\/molbev\/msr255","article-title":"A Dirichlet process prior for estimating lineage-specific substitution rates","volume":"29","author":"Heath","year":"2011","journal-title":"Mol. Biol. Evol."},{"key":"2019041810125691000_B15","doi-asserted-by":"crossref","first-page":"2435","DOI":"10.1111\/j.0014-3820.2006.tb01880.x","article-title":"Test for simultaneous divergence using approximate Bayesian computation","volume":"60","author":"Hickerson","year":"2006","journal-title":"Evolution"},{"key":"2019041810125691000_B16","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1111\/evo.12241","article-title":"Recommendations for using msbayes to incorporate uncertainty in selecting an ABC model prior: a response to Oaks et al.","volume":"68","author":"Hickerson","year":"2014","journal-title":"Evolution"},{"key":"2019041810125691000_B17","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-12-1","article-title":"MTML-msBayes: Approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity","volume":"12","author":"Huang","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2019041810125691000_B18","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1080\/10635150490522629","article-title":"Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models","volume":"53","author":"Huelsenbeck","year":"2004","journal-title":"Syst. Biol."},{"key":"2019041810125691000_B19","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1109\/MCSE.2007.55","article-title":"Matplotlib: A 2D graphics environment","volume":"9","author":"Hunter","year":"2007","journal-title":"Comput. Sci. Eng."},{"key":"2019041810125691000_B20","first-page":"21","article-title":"Evolution of protein molecules","author":"Jukes","year":"1969"},{"key":"2019041810125691000_B21","doi-asserted-by":"crossref","DOI":"10.1101\/188623","article-title":"Minor allele frequency thresholds strongly affect population structure inference with genomic datasets","author":"Linck","year":"2017"},{"key":"2019041810125691000_B22","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1111\/rssb.12056","article-title":"Relevant statistics for bayesian model choice","volume":"76","author":"Marin","year":"2013","journal-title":"J. R. Stat. Soc. B"},{"key":"2019041810125691000_B23","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1063\/1.1699114","article-title":"Equation of state calculations by fast computing machines","volume":"21","author":"Metropolis","year":"1953","journal-title":"J. Chem. Phys."},{"key":"2019041810125691000_B24","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1080\/10618600.2000.10474879","article-title":"Markov chain sampling methods for Dirichlet process mixture models","volume":"9","author":"Neal","year":"2000","journal-title":"J. Comput. Graph. Stat."},{"key":"2019041810125691000_B25","doi-asserted-by":"crossref","first-page":"5269","DOI":"10.1073\/pnas.76.10.5269","article-title":"Mathematical model for studying genetic variation in terms of restriction endonucleases","volume":"76","author":"Nei","year":"1979","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2019041810125691000_B26","doi-asserted-by":"crossref","first-page":"885","DOI":"10.1093\/genetics\/158.2.885","article-title":"Distinguishing migration from isolation: a Markov chain Monte Carlo approach","volume":"158","author":"Nielsen","year":"2001","journal-title":"Genetics"},{"key":"2019041810125691000_B27","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1186\/1471-2148-14-150","article-title":"An improved approximate-bayesian model-choice method for estimating shared evolutionary history","volume":"14","author":"Oaks","year":"2014","journal-title":"BMC Evol. Biol."},{"key":"2019041810125691000_B28","doi-asserted-by":"crossref","first-page":"3607","DOI":"10.1111\/evo.12523","article-title":"Implications of uniformly distributed, empirically informed priors for phylogeographical model selection: a reply to hickerson et al.","volume":"68","author":"Oaks","year":"2014","journal-title":"Evolution"},{"key":"2019041810125691000_B29","doi-asserted-by":"crossref","DOI":"10.1101\/395434","article-title":"The comparative biogeography of geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago","author":"Oaks","year":"2018"},{"key":"2019041810125691000_B30","first-page":"991","article-title":"Evidence for climate-driven diversification?","volume":"67","author":"Oaks","year":"2013","journal-title":"a caution for interpreting ABC inferences of simultaneous historical events. Evolution"},{"key":"2019041810125691000_B31","doi-asserted-by":"crossref","first-page":"8018","DOI":"10.1073\/pnas.1601069113","article-title":"Toward a paradigm shift in comparative phylogeography driven by trait-based hypotheses","volume":"113","author":"Papadopoulou","year":"2016","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2019041810125691000_B32","author":"Rambaut","year":"2014"},{"key":"2019041810125691000_B33","doi-asserted-by":"crossref","first-page":"1645","DOI":"10.1093\/genetics\/164.4.1645","article-title":"Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci","volume":"164","author":"Rannala","year":"2003","journal-title":"Genetics"},{"key":"2019041810125691000_B34","doi-asserted-by":"crossref","first-page":"15112","DOI":"10.1073\/pnas.1102900108","article-title":"Lack of confidence in approximate Bayesian computation model choice","volume":"108","author":"Robert","year":"2011","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2019041810125691000_B35","first-page":"756","article-title":"Critically endangered island endemic or peripheral population of a widespread species?","volume":"20","author":"Siler","year":"2014","journal-title":"conservation genetics of Kikuchi\u2019s gecko and the global challenge of protecting peripheral oceanic island endemic vertebrates. Divers. Distrib."},{"key":"2019041810125691000_B36","doi-asserted-by":"crossref","first-page":"1217","DOI":"10.1111\/j.1365-2699.2011.02680.x","article-title":"Did geckos ride the Palawan raft to the Philippines?","volume":"39","author":"Siler","year":"2012","journal-title":"J. Biogeogr."},{"key":"2019041810125691000_B37","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1093\/genetics\/123.3.585","article-title":"Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.","volume":"123","author":"Tajima","year":"1989","journal-title":"Genetics"},{"key":"2019041810125691000_B38","first-page":"57","article-title":"Some probabilistic and statistical problems in the analysis of DNA sequences","volume-title":"Some mathematical questions in biology: DNA sequence analysis. Providence","author":"Tavar\u00e9","year":"1986"},{"key":"2019041810125691000_B39","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1016\/0040-5809(75)90020-9","article-title":"On the number of segregating sites in genetical models without recombination","volume":"7","author":"Watterson","year":"1975","journal-title":"Theor. Popul. Biol."},{"key":"2019041810125691000_B40","doi-asserted-by":"crossref","DOI":"10.1007\/978-0-387-98141-3","article-title":"ggplot2: Elegant graphics for data analysis","author":"Wickham","year":"2009"},{"key":"2019041810125691000_B41","author":"Wilke","year":"2018"}],"container-title":["Systematic Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/sysbio\/article-pdf\/68\/3\/371\/28483318\/syy063.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,10]],"date-time":"2024-07-10T05:00:51Z","timestamp":1720587651000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/sysbio\/article\/68\/3\/371\/5098295"}},"subtitle":[],"editor":[{"given":"Laura","family":"Kubatko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,9,15]]},"references-count":41,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2018,9,15]]},"published-print":{"date-parts":[[2019,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/sysbio\/syy063","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/324525","asserted-by":"object"}]},"ISSN":["1063-5157","1076-836X"],"issn-type":[{"value":"1063-5157","type":"print"},{"value":"1076-836X","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,5]]},"published":{"date-parts":[[2018,9,15]]}}}