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Book Chapter
Holder KK, Holder MT.  2007.  Phylogeography and Population Genetics. Biology and Conservation of {R}idley Sea Turtles. :107–118.
Holder MT, Sukumaran J, Brown RM.  2010.  Recent Developments in Bayesian Phylogenetics. Bayesian Modeling in Bioinformatics. :inpress.
Journal Article
Holder MT, Zwickl DJ, Dessimoz C.  2008.  Evaluating the Robustness of Phylogenetic Methods to Among-Site Variability in Substitution Processes. Philosophical Transactions of the Royal Society B: Biological Sciences. 363:4013-4012.
Alfaro ME, Holder MT.  2006.  The Posterior and the Prior in Bayesian Phylogenetics. Annual Review of Ecology, Evolution, and Systematics. 37:19-42.
Hillis DM, Holder MT.  2000.  Reconstructing the Tree of Life. New Technologies for the Life Sciences: A Trends Guide. Supplement to Trends Journals. :47-50.
Heath TA, Hedtke SM, Hillis DM.  2008.  Taxon sampling and the accuracy of phylogenetic analyses. Journal of Systematics and Evolution. 46:239-257.
Holder MT, Erdmann MV, Wilcox TP, Caldwell RL, Hillis DM.  1999.  Two living species of coelacanths? Proceedings of the National Academy of Sciences. 96:12616-12620.
Web Article