Literature Cited

[1]Charles E. Antoniak. Mixtures of Dirichlet processes with applications to Bayesian nonparametric problems. Annals of Statistics, 2(6):1152–1174, 1974.
[2]E. T. Bell. Exponential numbers. American Mathematical Monthly, 41:411–419, 1934.
[3]David Bryant, Remco Bouckaert, Joseph Felsenstein, Noah A. Rosenberg, and Arindam Roychoudhury. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Molecular Biology and Evolution, 29(8):1917–1932, 2012. doi:10.1093/molbev/mss086.
[4]Thomas S Ferguson. A Bayesian Analysis of Some Nonparametric Problems. The Annals of Statistics, 1(2):209–230, March 1973.
[5]Peter J. Green, Krzysztof Łatuszyński, Marcelo Pereyra, and Christian P. Robert. Bayesian computation: a summary of the current state, and samples backwards and forwards. Statistics and Computing, 25(4):835–862, 2015. URL: https://doi.org/10.1007/s11222-015-9574-5, doi:10.1007/s11222-015-9574-5.
[6]Michael J. Hickerson, Eli A. Stahl, and H. A. Lessios. Test for simultaneous divergence using approximate Bayesian computation. Evolution, 60(12):2435–2453, 2006.
[7]Michael J. Hickerson, Graham N. Stone, Konrad Lohse, Terrence. C. Demos, Xiaoou Xie, Cedric Landerer, and Naoki Takebayashi. Recommendations for using msbayes to incorporate uncertainty in selecting an ABC model prior: a response to Oaks et al. Evolution, 68(1):284–294, 2014. URL: http://doi.wiley.com/10.1111/evo.12241, doi:10.1111/evo.12241.
[8]Wen Huang, Naoki Takebayashi, Yan Qi, and Michael J. Hickerson. MTML-msBayes: approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity. BMC Bioinformatics, 12:1, 2011. doi:10.1186/1471-2105-12-1.
[9]Thomas. H. Jukes and Charles. R. Cantor. Evolution of protein molecules. In H. N. Munro, editor, Mammalian Protein Metabolism, volume III, chapter 24, pages 21–132. Academic Press, New York, 1969.
[10]J. F. C. Kingman. The coalescent. Stochastic processes and their applications, 13:235–248, 1982.
[11]Jean‐Michel Marin, Natesh S. Pillai, Christian P. Robert, and Judith Rousseau. Relevant statistics for bayesian model choice. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 76(5):833–859, 2013. URL: https://rss.onlinelibrary.wiley.com/doi/abs/10.1111/rssb.12056, arXiv:https://rss.onlinelibrary.wiley.com/doi/pdf/10.1111/rssb.12056, doi:10.1111/rssb.12056.
[12]R. M. Neal. Markov chain sampling methods for Dirichlet process mixture models. Journal of Computational and Graphical Statistics, 9:249–265, 2000.
[13]Jamie R. Oaks. An improved approximate-bayesian model-choice method for estimating shared evolutionary history. BMC Evolutionary Biology, 14:150, 2014. URL: http://www.biomedcentral.com/1471-2148/14/150/abstract, doi:10.1186/1471-2148-14-150.
[14]Jamie R. Oaks. Full Bayesian comparative phylogeography from genomic data. bioRxiv, 2018. URL: https://www.biorxiv.org/content/early/2018/05/17/324525, arXiv:https://www.biorxiv.org/content/early/2018/05/17/324525.full.pdf, doi:10.1101/324525.
[15]Jamie R. Oaks, Kerry A. Cobb, Vladimir N. Minin, and Adam D. Leaché. Marginal likelihoods in phylogenetics: a review of methods and applications. arXiv:1805.04072 [q-bio.PE], 2018. URL: https://arxiv.org/abs/1805.04072.
[16]Jamie R. Oaks, Charles W. Linkem, and Jeet Sukumaran. Implications of uniformly distributed, empirically informed priors for phylogeographical model selection: a reply to hickerson et al. Evolution, 68():3607–3617, 2014. URL: http://onlinelibrary.wiley.com/doi/10.1111/evo.12523/abstract, doi:10.1111/evo.12523.
[17]Jamie R. Oaks, Jeet Sukumaran, Jacob A. Esselstyn, Charles W. Linkem, Cameron D. Siler, Mark T. Holder, and Rafe M. Brown. Evidence for climate-driven diversification? a caution for interpreting ABC inferences of simultaneous historical events. Evolution, 67(4):991–1010, 2013. doi:10.1111/j.1558-5646.2012.01840.x.
[18]Christian P Robert, Jean-Marie Cornuet, Jean-Michel Marin, and Natesh S Pillai. Lack of confidence in approximate Bayesian computation model choice. Proceedings of the National Academy of Sciences, 108(37):15112–15117, September 2011.
[19]Cameron D. Siler, Jamie R. Oaks, Kerry Cobb, Ota Hidetoshi, and Rafe M. Brown. Critically endangered island endemic or peripheral population of a widespread species? conservation genetics of Kikuchi’s gecko and the global challenge of protecting peripheral oceanic island endemic vertebrates. Diversity and Distributions, 20:756–772, 2014. doi:10.1111/ddi.12169.
[20]Cameron D. Siler, Jamie R. Oaks, Luke J. Welton, Charles W. Linkem, John Swab, Arvin C. Diesmos, and Rafe M. Brown. Did geckos ride the Palawan raft to the Philippines? Journal of Biogeography, 39:1217–1234, 2012. doi:10.1111/j.1365-2699.2011.02680.x.
[21]Simon Tavaré. Some probabilistic and statistical problems in the analysis of DNA sequences. American Mathematical Society: Lectures on Mathematics in the Life Sciences, 17:57–86, 1986.