Mark T. Holder
Ph.D., University of Texas, 2001
Phone: (785) 864 5789
Fax: (785) 864-5860
Holder Lab Webpage
Area of Interest and Research
My research revolves around statistical phylogenetics and its applications to evolutionary biology. In particular, I focus on Bayesian techniques for inferring phylogenies. I have contributed to development of Markov chain Monte Carlo methods used to implement Bayesian tree inference, but my primary interest is in the evolutionary models and prior assumptions that underlie these methods. Improvements to models allow us to estimate trees more accurately and assess the error in our estimates. More importantly, the development of richer models lets us use the comparative approach to a wide range of biological problems.
Current Activities/Research Program
Currently, I am working on a collaborative effort to improve the techniques available for multiple sequence alignment. My research group, along with collaborators at the University of Texas, University of Nebraska, University of Georgia, and Penn State University, will focus aligning sequences for the purposes of phylogenetic analysis. In particular, we will try to extend the realm of data set sizes for which it is feasible to use methods that simultaneously align sequences while searching for trees that best explain the data. The focus of the work here at KU will be on fast ways to approximate the maximum likelihood estimate of a phylogeny and history of insertions and deletions.
In the next phase of my research program, I will be building on the emerging field of context-dependent evolutionary models. Most phylogenetic models of sequence evolution make the unrealistic assumption that different sites evolve completely independently of each other. Building on recent Markov chain Monte Carlo techniques (Jensen and Pedersen, Advances in Applied Probability, 32, 2000), researchers have begun to explore models that consider constraints on the entire sequence. For example, the requirement that a protein must fold into a particular three-dimensional structure in order to function, constraints the amino acids that are allowed in a sequence. A mutation in one site may change the state-space of residues allowed at its neighbor (or an interacting site in the folded configuration). Initial efforts to construct phylogenetic models to explicitly accommodate the influence of protein tertiary structure (for examples see Robinson et al., Molecular Biology and Evolution, 20, 2003; Rodrigue et al., Gene, 347,2005; but also see Thorne et al., Molecular Biology and Evolution, 24, 2007). My work will focus on modeling the constraints on protein evolution more accurately. I am also interested in applying this class of context-dependent model to the analysis of morphological character evolution.
Lakner, C, Holder MT, Goldman N, Naylor GJP. 2011. “What's in a Likelihood? Simple Models of Protein Evolution and the Contribution of Structurally Viable Reconstructions to the Likelihood” Systematic Biology.
Kevin Liu, Tandy J. Warnow, Mark T. Holder, Serita Nelesen, Jiaye Yu, Alexandros Stamatakis, and C. Randal Linder 2011. “SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees” Systematic Biology.
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.
SUKUMARAN, J. and M. T. HOLDER. 2010 Ginkgo: spatially-explicit simulator of complex phylogeographic histories. Molecular Ecology Resources, no. doi:10.1111/j.1755-0998.2010.02926.x
Sukumaran, J, Holder MT. 2010. DendroPy: A Python library for phylogenetic computing. Bioinformatics. 26:1569-1571.
Peterson, TA, Knapp S, Guralnick R, Soberón J, Holder MT. 2010. The big questions for biodiversity informatics. Systematics and Biodiversity. 8:159–168
Holder, M. T., P. O. Lewis, and D. L. Swofford.. 2010. The Akaike Information Criterion Will Not Choose the No Common Mechanism Model. Systematic Biology. 59(4):477-485.
Holder, Sukumaran, and Brown. 2009. "Bayesian Approaches to Phylogenetic Analysis"inBayesian Modeling in Bioinformatics. EditorsDipak K. Dey,Samiran Ghosh, andBani K. Mallick. Chapman & Hall/CRC.
Allman, E.S., M. T. Holder, J. A. Rhodes. 2009. Estimating trees from filtered data: Identifiability of models for morphological phylogenetics, Journal of Theoretical Biology. DOI: 10.1016/j.jtbi.2009.12.00
Holder, M. T., J. Sukumaran, and P. O. Lewis. 2008. A justification for reporting majority-rule consensus tree in Bayesian phylogenetics. Systematic Biology 57, 5:814-821.
Holder, M. T., D. J. Zwickl, and C. Desimoz. 2008. Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes. Philosophical transactions of the Royal Society B: Biological sciences. 363: 4012-4013.
Gelfand, A. E., J. A. Silander, Jr., S.-S. Wu, A. M. Latimer, P. O. Lewis, A. G. Regbelo, and M. T. Holder. 2006. Explaining species distribution patterns through hierarchical modeling. Bayesian Analysis, 41: 92.
Michael E. Alfaro and Mark T. Holder. 2006. The Posterior and the Prior in Bayesian Phylogenetics. Annual Review of Ecology, Evolution, and Systematics 37:19-42.
Mark T. Holder, Paul O. Lewis, David L. Swofford and Bret Larget. 2005. Hastings Ratio of the Proposal Used in Bayesian Phylogenetics. Systematic Biology 54:961-965.
Paul O. Lewis, Mark T. Holder and Kent E. Holsinger. 2005. Polytomies and Bayesian phylogenetic inference. Systematic Biology 54:241-253.
Derrick J. Zwickl and Mark T. Holder. 2004. Model Parameterization, Prior Distributions and the General Time-Reversible Model in Bayesian Phylogenetics. Systematic Biology 53:877-888.
Alan E Gelfand, John A.Silander, Jr., Shan-shan Wu, Andrew M. Latimer, Paul O. Lewis, Anthony G. Rebelo and Mark Holder. 2006. Explaining Species Distribution Patterns through Hierarchical Modeling. Bayesian Analysis 1:41-92.
Mark T. Holder and Paul O. Lewis. 2003. Phylogeny Estimation: Traditional and Bayesian Approaches. Nature Reviews Genetics 43:275-284.
Matthew J. Brauer, Mark T. Holder, Laurie A. Dries, Derrick J. Zwickl, Paul O. Lewis and David M. Hillis. 2002. Genetic Algorithms and Parallel Processing in Maximum-Likelihood Phylogeny Inference. Molecular Biology and Evolution 19:1717-1726.
Mark T. Holder, Jennifer A. Anderson and Alisha K. Holloway. 2001. Difficulties in Detecting Hybridization. Systematic Biology 50:978-982.