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Edgcomb V, Orsi W, Bunge J, Jeon SO, Christen R, Leslin C, Holder M, Taylor GT, Suarez P, Varela R et al..  2011.  Protistan Microbial Observatory in the Cariaco Basin, Caribbean. I. Species richness and endemicity. ISME Journal. 5(8):1344-1356.
Alfaro ME, Holder MT.  2006.  The Posterior and the Prior in Bayesian Phylogenetics. Annual Review of Ecology, Evolution, and Systematics. 37:19-42.
Lewis PO, Holder MT, Holsinger KE.  2005.  Polytomies and Bayesian phylogenetic inference. Systematic Biology. 54:241–253.
Holder KK, Holder MT.  2007.  Phylogeography and Population Genetics. Biology and Conservation of {R}idley Sea Turtles. :107–118.
Holder MT, Lewis PO.  2003.  Phylogeny Estimation: Traditional and Bayesian Approaches. Nature Reviews Genetics. 43:275-284.
Siler CD, Oaks JR, Esselstyn JA, Diesmos AC, Brown RM.  2010.  Phylogeny and biogeography of Philippine bent-toed geckos (Gekkonidae: Cyrtodactylus) contradict a prevailing model of Pleistocene diversification. Molecular Phylogenetics and Evolution. ::inpress.
Wilcox TP, Zwickl DJ, Heath TA, Hillis DM.  2002.  Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Molecular Phylogenetics and Evolution. 25:361-71.
Matsui M, Tominaga A, Liu W, Khonsue W, Grismer LL, Diesmos AC, Das I, Sudin A, Yambun P, Yong H et al..  2010.  Phylogenetic relationships of Ansonia from Southeast Asia inferred from mitochondrial DNA sequences: Systematic and biogeographic implications (Anura: Bufonidae). Molecular Phylogenetics and Evolution. 54:561-570.
Evans NM, Holder MT, Barbeitos MS, Okamura B, Cartwright P.  2010.  The Phylogenetic Position of Myxozoa: Exploring Conflicting Signals in Phylogenomic and Ribosomal Data Sets. Molecular Biology and Evolution. 27:2733–2746.
Peterson TA, Holder MT.  2012.  Phylogenetic Assessment of Filoviruses: How Many Lineages of Marburvirus? Ecology and Evolution. 2(8):1826-1833.