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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.
Holder MT, Lewis PO, Swofford DL.  2010.  The Akaike Information Criterion Will Not Choose the No Common Mechanism Model. Systematic Biology. 59(4):477-485.
Holder MT, Lewis PO, Swofford DL, Larget B.  2005.  Hastings Ratio of the LOCAL Proposal Used in Bayesian Phylogenetics. Systematic Biology. 54:961-965.
Holder MT, Steel M.  2011.  Estimating phylogenetic trees from pairwise likelihoods and posterior probabilities of substitution counts. Journal of Theoretical Biology. 280(1):159-166.
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.
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.
Holder MT, Sukumaran J, Lewis PO.  2008.  A justification for reporting majority-rule consensus tree in Bayesian phylogenetics. Systematic Biology. 57:814-821.
Holder MT, Anderson JA, Holloway AK.  2001.  Difficulties in Detecting Hybridization. Systematic Biology. 50:978-982.
Hillis DM, Heath TA, StJohn K.  2005.  Analysis and Visualization of Tree Space. Systematic Biology. 54:471-482.
Hillis DM, Pollock DD, McGuire JA, Zwickl DJ.  2003.  Is sparse taxon sampling a problem for phylogenetic inference? SYSTEMATIC BIOLOGY. 52:124-126.
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.
Heath TA, Holder MT, Huelsenbeck JP.  2012.  A Dirichlet Process Prior for Estimating Lineage-Specific Substitution Rates. Molecular Biology and Evolution. 29(3):939-955.
Heath TA, Zwickl DJ, Kim J, Hillis DM.  2008.  Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Systematic Biology. 57:160-166.