Mark Holder

Associate Professor, Ecology and Evolutionary Biology
785-864-5789
Haworth Hall, room 6031

Dr. Mark Holder develops statistical and computational approaches for estimating genealogical relationships.

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.

Selected Publications

  • Oaks, J. R., J. A. Sukumaran, J. A. Esselstyn, C. W. Linkem, C. D. Siler, M. T. Holder, and R. M. Brown. 2013. "Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events." Evolution. 67. 991–1010.
  • Liberles, D. A. et al. 2012. "The interface of protein structure, protein biophysics, and molecular evolution" Protein Science. 21(6). 769-785.
  • Liu, K., T. J. Warnow, M. T. Holder, S. Nelesen, J. Yu, A. Stamatakis, and C. R. Linder. 2012. "SATé-II: Very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees" Systematic Biology. 61(1). 90-106.
  • Peterson, A. T. and M. T. Holder. 2012. "Phylogenetic assessment of filoviruses: How many lineages of Marburgvirus?" Ecology and Evolution. 2. 1826-1833.
  • Vos, R. A. et al. 2012. "NeXML: Rich, extensible, and verifiable representation of comparative data and metadata" Systematic Biology. 61(4). 675-689.
 
  • Ayres, D. L. et al. 2012. "BEAGLE: An application programming interface and high-performance computing library for statistical phylogenetics" Systematic Biology. 61(1). 170-173.
  • Koch, J. M. and M. T. Holder. 2012. "An algorithm for calculating the probability of classes of data patterns on a genealogy" PLOS Currents Tree of Life.
  • Heath, T. A., M. T. Holder, and J. P. Huelsenbeck. 2012. "A Dirichlet process prior for estimating lineage-specific substitution rates" Molecular Biology and Evolution. 29(3). 939-955.
  • Lakner, C., M. T. Holder, N. Goldman, and G. J. P. N. Naylor. 2011. "What’s in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood" Systematic Biology. 60(2). 161-174.
  • Edgcomb, V. et al. 2011. "Protistan microbial observatory in the Cariaco Basin, Caribbean. I. species richness and endemicity" ISME Journal. 5(8). 1344-1356.
  • Sukumaran, J. A. and M. T. Holder. 2011. "Ginkgo: spatially-explicit simulator of complex phylogeographic histories" Molecular Ecology Resources. 11(2). 364-369.
  • Holder, M. T. and M. Steel. 2011. "Estimating phylogenetic trees from pairwise likelihoods and posterior probabilities of substitution counts" Journal of Theoretical Biology. 280(1). 159-166.
 
  • Evans, N. M., M. T. Holder, M. S. Barbeitos, B. Okamura, and P. Cartwright. 2010. "The phylogenetic position of Myxozoa: Exploring conflicting signals in phylogenomic and ribosomal data sets" Molecular Biology and Evolution. 27(12). 2733-2746.
  • Peterson, A. T., S. Knapp, R. P. Guralnick, J. M. Soberón, and M. T. Holder. 2010. "The big questions for biodiversity informatics" Systematics and Biodiversity. 8(2). 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, M. T., J. A. Sukumaran, and R. M. Brown. 2010. "Recent developments in Bayesian phylogenetics" Bayesian Modeling in Bioinformatics. edited by Dey, D. K., S. Ghosh, and B. K. Mallick. 193–232.
  • Allman, E. S., M. T. Holder, and J. A. Rhodes. 2010. "Estimating trees from filtered data: Identifiability of models for morphological phylogenetics" Journal of Theoretical Biology. 263(1). 108-119.
  • Sukumaran, J. A. and M. T. Holder. 2010. "DendroPy: A Python library for phylogenetic computing" Bioinformatics. 26(12). 1569-1571.
  • Holder, M. T., J. A. Sukumaran, and R. M. Brown. 2010. "Bayesian Approaches to Phylogenetic Analysis" Bayesian Modeling in Bioinformatics. edited by Dey, D. K., S. Ghosh, and B. K. Mallick. 1-39.
  • Holder, M. T., D. J. Zwickl, and C. Dessimoz. 2008. "Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes" Philosophical Transactions of the Royal Society of London B: Biological Sciences. 363. 4012-4013.
  • Holder, M. T., J. A. Sukumaran, and P. O. Lewis. 2008. "A justification for reporting majority-rule consensus tree in Bayesian phylogenetics" Systematic Biology. 57(5). 814-821.
  • Lapp, H. et al. 2007. "The 2006 NESCent phyloinformatics hackathon: A field report" Evolutionary Bioinformatics. 3. 357-366.
  • Kichler Holder, K. and M. T. Holder. 2007. "Phylogeography and Population Genetics of Ridley Turles" Biology and Conservation of Ridley Turles. edited by Plotkin, P. T.. 107-118.
  • Alfaro, M. E. and M. T. Holder. 2006. "The posterior and the prior in Bayesian phylogenetics" Annual Review of Ecology, Evolution, and Systematics. 37. 19-42.
  • Gelfand, A. E., J. A. Silander, S. Wu, A. M. Latimer, P. O. Lewis, A. G. Rebelo, and M. T. Holder. 2006. "Explaining species distribution patterns through hierarchical modeling" Bayesian Analysis. 1. 41-92.
  • Lewis, P. O., M. T. Holder, and K. E. Holsinger. 2005. "Polytomies and Bayesian phylogenetic inference" Systematic Biology. 54. 241-253.
  • Holder, M. T., P. O. Lewis, D. L. Swofford, and B. Larget. 2005. "Hastings ratio of the local proposal used in Bayesian phylogenetics" Systematic Biology. 54. 961-965.
  • Zwickl, D. J. and M. T. Holder. 2004. "Model parameterization, prior distributions and the general time-reversible model in Bayesian phylogenetics" Systematic Biology. 53. 877-888.
  • Holder, M. T. and P. O. Lewis. 2003. "Phylogeny estimation: Traditional and Bayesian approaches" Nature Reviews Genetics. 43. 275-284.
  • Brauer, M. J., M. T. Holder, L. A. Dries, D. J. Zwickl, P. O. Lewis, and D. M. Hillis. 2002. "Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference" Molecular Biology and Evolution. 19(10). 1717-1726.
  • Holder, M. T., J. A. Anderson, and A. K. Holloway. 2001. "Difficulties in detecting hybridization" Systematic Biology. 50(6). 978-982.
  • Holder, M. T., M. V. Erdmann, T. P. Wilcox, R. L. Caldwell, and D. M. Hillis. 1999. "Two living species of coelacanths?" Proceedings of the National Academy of Sciences. 96(22). 12616–12620.
  • Kichler, K. L., M. T. Holder, S. K. Davis, R. Marquez, and D. Owens. 1999. "Detection of multiple paternity in the Kemp’s ridley sea turtle with limited sampling" Molecular Ecology. 8. 819-830.

    One of 34 U.S. public institutions in the prestigious Association of American Universities
    26 prestigious Rhodes Scholars — more than all other Kansas colleges combined
    Nearly $290 million in financial aid annually
    1 of 9 public universities with outstanding study abroad programs.
    —U.S. News & World Report
    46 nationally ranked graduate programs.
    —U.S. News & World Report
    Top 50 nationwide for size of library collection.
    —ALA
    $275 million in externally funded research expenditures
    23rd nationwide for service to veterans —"Best for Vets," Military Times