k crandall

Keith Crandall

Director, Computational Biology Institute
Faculty: Full-Time
Address: Innovation Hall
Phone: 571-553-0107
[email protected]

Areas of Expertise

Computational Biology, Bioinformatics, Phylogenetics, Infectious disease, Crustacean Systematics, Molecular Evolution, HIV, Population Genetics, Bacterial Genomics, Conservation Genetics

  • Steering Committee - US Node Chair, International Barcode of Life, 2010-Present
  • Editorial Board, PLoS Currents: Tree of Life, 2010-Present
  • Editorial Board, Bioinformatics, 2007-2010
  • Scientific Advisory Board, Canadian Barcode of Life Network, 2005-2009
  • Associate Editor, Bioinformatics, 2005-2007
  • Associate Editor, Evolution, 2005-2007
  • Honorary Research Fellow, Bioinformatics Institute, University of Auckland, 2005-2006
  • Editor, Animal Conservation, 2003-2006
  • Council Member, Society of Systematic Biologists, 2003-2006
  • Executive Vice President, Society of Systematic Biologists, 2003-2006
  • Associate Editor, Molecular Biology and Evolution, 1999-2003
  • Associate Editor, Systematic Biology, 1999-2003
  • Editorial Board, Animal Conservation, 2000-2002
  • Postdoctoral Fellow, University of Texas, 1993-1996

Current Research

My research program has three main aspects.  The first and central component is work on the development and testing through computer simulation of methods for the analysis of DNA sequence data.  We have developed methods for estimating gene genealogies, detecting recombination, detecting selection, and measuring genetic diversity and demographic events in the history of a population.  We develop software to implement many of these methods and then develop software to test our methods and many others by comparison through computer simulation.  Through comparison and tests of robustness to assumption violations, we can gain great insights into why particular methods perform well or poorly and then are in a good position to redevelop improved methodology.  In fact, we are currently embarking on the development of a comprehensive simulation software package that allows one, for the first time, to examine the impact of a host of population genetic phenomena at the same time (e.g., migration, mutation, recombination, selection, fluctuating population sizes, tracking geographic locations of alleles in a population, multiple locus populations, etc.).  Through such studies, we gain a better understanding of the methodology we use to infer evolutionary and population demographic histories and associated parameter estimates when we apply them to empirical data.  Furthermore, such studies provide valuable insights into the development of new and improved theory and methodology for inference from DNA sequence data.

The remaining two aspects of my research program deal with applications of the above methodologies in two fairly distinct arenas.  The first is in molecular ecology, conservation biology, and systematics research.  We have applied the methods developed and tested in our lab (and many others) to examine the populations genetics, historical demography, and molecular ecology of various species of freshwater crayfish.  We have also examined the molecular systematics of a variety of organisms, from the origin of dogs to the origin of freshwater crayfishes.  You will see from my CV that the systematic studies are typically collaborative studies.  I firmly believe in collaboration, especially in systematic studies that require both organismal (including morphological and ecological) expertise and molecular (including phylogenetic analysis) expertise.  We the freshwater crayfishes, we typically are the morphological and taxonomic experts as well.  However, with all the other organismal groups, we develop (often international) teams of expertise to tackle outstanding questions in systematic biology.  We then apply our results to a diversity of biogeographic and conservation biology questions.  These typically lead naturally into broader issues relating to conservation biology such as diagnosing species and the relative importance of different sources of information regarding conservation priorities and conservation status such as ecological data versus genetic data.

The second focus of my empirical research is in the area of the evolution of infectious diseases.  Here our main system has been HIV, but we have also now been very active in bacterial genetics, especially Neisseria gonorrhoeae.  Our main goal with these research projects is to explore the population dynamics of infectious disease, particularly relative to the evolution of drug resistance.  We have been heavily involved in evaluating the performance of multi-locus sequence typing (MLST) methods to track population dynamics of bacterial species.  Our results suggest that these MLST are not as selectively neutral as researcher had hoped and that different MLST work differentially well in a diversity of species.  We plan to continue the exploration of MLST and their application in tracking population dynamics of bacterial agents of bioterrorism, as well as tracking dynamics of infectious disease.   Our extension into bacterial genomics coupled with an interested in environmental samples, has naturally led to an exploration of novel computational techniques to identify pathogens from environmental samples using next-generation sequencing approaches to collect relevant data and novel statistical and computational approaches for analyses.  We are involved in all phases of this work from the molecular approaches to the statistical models to the computational implementation.

The research outlined in these three main areas in my lab has enjoyed a diversity of funding from the National Institutes of Health, the National Science Foundation, and private agencies such as the Alfred P. Sloan Foundation and the Pharmaceutical Manufacturers of America.  My research program is moving evermore into the genomics and bioinformatics arena and applying these insights into conservation management, human health, and biomedical applications.


BA Kalamazoo College, 1987 (Mathematics and Biology)
MA Washington University in St. Louis, 1993 (Statistics)
PhD Washington University in St. Louis, 1993 (Biology & Biomedical Sciences)


For a complete publication list, please visit Dr. Crandall's GoogleScholar page.

Richman, N.I., Böhm, M., Adams, S.B., Alvarez, F., Bergey, E.A., Bunn, J.J., Burnham, Q., Cordeiro, J., Coughran, J., Crandall, K.A. and Dawkins, K.L., 2015. Multiple drivers of decline in the global status of freshwater crayfish (Decapoda: Astacidea). Philosophical Transactions of the Royal Society of London B: Biological Sciences, 370(1662), p.20140060.

Hinchliff, C.E., Smith, S.A., Allman, J.F., Burleigh, J.G., Chaudhary, R., Coghill, L.M., Crandall, K.A., Deng, J., Drew, B.T., Gazis, R. and Gude, K., 2015. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proceedings of the National Academy of Sciences, 112(41), pp.12764-12769.

Owen, C.L., Bracken-Grissom, H., Stern, D. and Crandall, K.A., 2015. A synthetic phylogeny of freshwater crayfish: insights for conservation. Philosophical Transactions of the Royal Society of London B: Biological Sciences, 370(1662), p.20140009.

Bracken-Grissom, H.D., Ahyong, S.T., Wilkinson, R.D., Feldmann, R.M., Schweitzer, C.E., Breinholt, J.W., Bendall, M., Palero, F., Chan, T.Y., Felder, D.L. and Robles, R., 2014. The emergence of lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (Decapoda: Achelata, Astacidea, Glypheidea, Polychelida). Systematic Biology, 63(4), pp.457-479.

Hong, C., Manimaran, S., Shen, Y., Perez-Rogers, J.F., Byrd, A.L., Castro-Nallar, E., Crandall, K.A. and Johnson, W.E., 2014. PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples. Microbiome, 2(1), p.1.

Byrd, A.L., Perez-Rogers, J.F., Manimaran, S., Castro-Nallar, E., Toma, I., McCaffrey, T., Siegel, M., Benson, G., Crandall, K.A. and Johnson, W.E., 2014. Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data. BMC bioinformatics, 15(1), p.1.

Pérez-Losada, M., Cabezas, P., Castro-Nallar, E. and Crandall, K.A., 2013. Pathogen typing in the genomics era: MLST and the future of molecular epidemiology. Infection, Genetics and Evolution, 16, pp.38-53.

Francis, O.E., Bendall, M., Manimaran, S., Hong, C., Clement, N.L., Castro-Nallar, E., Snell, Q., Schaalje, G.B., Clement, M.J., Crandall, K.A. and Johnson, W.E., 2013. Pathoscope: species identification and strain attribution with unassembled sequencing data. Genome research, 23(10), pp.1721-1729.

Drew, B.T., Gazis, R., Cabezas, P., Swithers, K.S., Deng, J., Rodriguez, R., Katz, L.A., Crandall, K.A., Hibbett, D.S. and Soltis, D.E., 2013. Lost branches on the tree of life. PLoS biology, 11(9).

Peters, J.L., Roberts, T.E., Winker, K. and McCracken, K.G., 2012. Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history. PLoS One, 7(2), p.e31972.

Castro-Nallar, E., Pérez-Losada, M., Burton, G.F. and Crandall, K.A., 2012. The evolution of HIV: inferences using phylogenetics. Molecular phylogenetics and evolution, 62(2), pp.777-792.

Castro-Nallar, E., H. Chen, S. Gladman, S.C. Moore, T. Seemann, I.B. Powell, A. Hillier, K.A. Crandall, and P.S. Chandry. 2012. Population genomics and phylogeography of an Australian dairy factory derived lytic bacteriophage. Genome Biology and Evolution 4(2):1-12.

Barber, B.R., P. J. Unmack, M. Pérez-Losada, J. B. Johnson, and K. A. Crandall. 2011. Different processes lead to similar patterns: a test of codivergence and the role of sea level and climate changes in shaping a southern temperate freshwater assemblage. BMC Evolutionary Biology 11:343 doi:10.1186/1471-2148-11-343

Bybee, S.M., H. Bracken-Grissom, B.D. Haynes, R.A. Hermansen, R. L. Byers, M.J. Clement, J.A. Udall, E.R. Wilcox, K. A. Crandall. 2011. Targeted amplicon sequencing (TAS): A scalable next-gen approach to multi-locus, multi-taxa phylogenetics. Genome Biology and Evolution 3:1312-1323. doi:10.1093/gbe/evr106.

Toon, A., M. Pérez-Losada, C. Schweitzer, R. Feldmann, M. Carlson, and K. A. Crandall.  2010. Gondwanan radiation of the southern hemisphere crayfish (Decapoda: Parastacidae): Evidence from fossils and molecules.  Journal of Biogeography  37(12):2275-2290.

Hendry, A. P., L. G. Lohmann, J. Cracraft, S. Tillier, C. Haeuser, D. P. Faith, S. Magallon, E. Conti, R. Zardoya, K. Kogure, A. Prieur-Richard, K. A. Crandall, C. A. Joly, C. Moritz, T. Yahara, and M. J. Donoghue.  2010.  Evolutionary biology in biodiversity science, conservation, and policy: A call to action.  Evolution 64(5):1517-1528.

Pérez-Losada, M., D.V. Jobes, F. Sinangil, K.A. Crandall, D. Posada, and P.W. Berman. 2010. Phylodynamics of HIV-1 from a phase III AIDS vaccine trial in North America.  Molecular Biology and Evolution 27:417-425.  doi:10.1093/molbev/msp254

Hickerson, M.J., B.C. Carstens, J. Cavender-Bares, K.A. Crandall, C.H. Graham, J.B. Johnson, L. Rissler, P.F. Victoriano, and A.D. Yoder.  2010.  Phylogeography’s past, present, and future: 10 years after Avise 2000.  Molecular Phylogenetics and Evolution  54(1):291-301.

Pérez-Losada, M., J.T. Høeg, K.A. Crandall. 2009. Remarkable convergent evolution in specialized parasitic Thecostraca (Crustacea).  BMC Biology 7:15.

Lewis-Rogers, N., M. L. Bendall, and K.A. Crandall. 2009. Phylogenetic relationships and molecular adaptation dynamics of human rhinoviruses.  Molecular Biology and Evolution 26:969-981.

Xu, J., M. Pérez-Losada, C.G. Jara, and K.A. Crandall. 2009. Pleistocene glaciation leaves deep signature on the freshwater crab Aegla alacalufi in Chilean Patagonia.  Molecular Ecology 18:904-918.

Crandall, K. A., H. W. Robison, and J. E. Buhay. 2009. Avoidance of extinction through nonexistence: The use of museum specimens and molecular genetics to determine the taxonomic status of an endangered freshwater crayfish.  Conservation Genetics 10:177-189. DOI 10.1007/s10592-008-9546-9

Egan, A.N. and K.A. Crandall. 2008. Divergence and diversification in North American Psoraleeae (Fabaceaae) due to climate change. BMC Biology 6:55.

Song, H., J. E. Buhay, M. F. Whiting, and K. A. Crandall. 2008. Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified.  Proceedings of the National Academy of Sciences, USA 105(36):13486-13491.

Keele, B. F., L. Tazi, S. Gartner, Y. Liu, T. B. Burgon, J. D. Estes, T. C. Thacker, K. A. Crandall, J. C. McArthur, and G. F. Burton.  2008.  Characterization of the follicular dendritic cell reservoir of HIV-1. Journal of Virology 82(11):5548-5561.

Porter, M. L., T. W. Cronin, D. A. McClellan, K. A. Crandall. 2007. Molecular characterization of crustacean visual pigments and the evolution of Pancrustacean opsins. Molecular Biology and Evolution 24(1):253-268.

Pérez-Losada, M., R. G. Christensen, D. A. McClellan, B. J. Adams, R. P. Viscidi, J. C. Demma, and K. A. Crandall. 2006. Comparing phylogenetic codivergence between polyomaviruses and their hosts. Journal of Virology 80(12):5663-5669.

Buhay, J.E., and K. A. Crandall. 2005. Subterranean phylogeography of freshwater crayfishes shows extensive gene flow and surprisingly large population sizes. Molecular Ecology

Agapow, P.-M., O. R. P. Bininda-Emonds, K. A. Crandall, J. L. Gittleman, G. M. Mace, J. C. Marshall, and A. Purvis. 2004. The impact of species concept on biodiversity studies. Quarterly Review of Biology 79(2):161-179.

Porter, M. L., and K. A. Crandall. 2003. Lost along the way: The significance of evolution in reverse. Trends in Ecology and Evolution 18(10):541-547.

Posada, D. and K. A. Crandall. 2001. Evaluation of methods for detecting recombination from DNA sequences using computer simulations. Proceedings of the National Academy of Sciences, U.S.A. 98(24):13757-13762.

Crandall, K.A. and D.M. Hillis. 1997. “Rhodopsin evolution in the dark.” Nature 387:667-668.

Vilá, C., P. Savolainen, J. E. Maldonado, I. R. Amorim, J. E. Rice, R. L. Honeycutt, K. A. Crandall, J. Lundeberg, and R. K. Wayne. 1997. “Multiple and ancient origins of the domestic dog.”  Science 276:1687-1689.