HILLIS, DAVID M

David Hillis

Professor
Department of Integrative Biology

Alfred W. Roark Centennial Professor in Natural Sciences

Molecular evolution, phylogenetics, and systematics

dhillis@austin.utexas.edu

Phone: 512-471-5792

Office Location
PAT 132

Postal Address
The University of Texas at Austin
Department of Integrative Biology, College of Natural Sciences
2415 Speedway
Austin, TX 78712

Research Summary:
Evolutionary biology provides a conceptual framework for understanding patterns of molecular diversity. For instance, phylogenetic analyses have permeated most fields of molecular biology in recent years, from studies of the epidemiology of human immunodeficiency viruses to studies of the origin of life. Work in my lab is divided into two main areas: empirical studies of molecular evolution and the development of evolutionary theory and methodology. The empirical studies include experimental manipulation of viruses to study evolution in vitro, phylogenetic analyses of highly conserved genes, and studies of molecular processes that give rise to new genes or maintain the structure of multigene families. The theoretical and methodological work is centered on finding the best ways to estimate phylogenies from molecular sequences and on simulations of molecular evolution using supercomputers.

Recent Publications:

For complete list, see https://scholar.google.com/citations?user=TUgQVOYAAAAJ

To download pdf's of my publications, see http://www.zo.utexas.edu/faculty/antisense/DownloadHillisPubs.html

Some example publications from my lab:

2016 Liebeskind, B. J., H. A. Hofmann, D. M. Hillis, and H. H. Zakon. The complex homology of animal nervous systems. Trends in Ecology and Evolution 31:127-135. doi: 10.1016/j.tree.2015.12.005

2016 Yuan, Z.-Y., W.-W. Zhou, X. Chen, N. A. Poyarkov, H.-M. Chen, N.-H. Jang-Liaw, W.-H. Chou, K. Iizuka, M.-S. Min, S. L. Kuzmin, Y.-P. Zhang, D. C. Cannatella, D. M. Hillis, and J. Che. Spatiotemporal diversification of the true frogs (genus Rana): A historical framework for a widely studied group of model organisms. Systematic Biology 65:824-842. doi: 10.1093/sysbio/syw055

2016 Wright, A. M., G. T. Lloyd, and D. M. Hillis. Modeling character change heterogeneity in phylogenetic analyses of morphology through the use of priors. Systematic Biology 65:602-611. doi: 10.1093/sysbio/syv122

2015 Wright, A. M., K. M. Lyons, M. C. Brandley, and D. M. Hillis. Which came first: The lizard or the egg? Robustness in phylogenetic reconstruction of ancestral states. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 324:504-516. doi: 10.1002/jez.b.22642.

2015 Sun, Y.B., Z.-J. Xiong, X.-Y. Xiang, X.-L. Tu, W.-W. Zhou, S.-P. Liu, L. Zhong, L. Wang, D.-D. Wu, Y. Li, B.-L. Zhang, C.-L. Zhu, M.-M. Yang, H.-M. Chen, F. Li, L. Zhou, S.-H. Feng, C. Huang, G.-J. Zhang, D. M. Irwin, D. M. Hillis, R. W. Murphy, J. Che, J. Wang, and Y.-P. Zhang. 2015. Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of vertebrate genomes. Proceedings of the National Academy of Sciences USA 112:E1257-E1262. doi: 10.1073/pnas.1501764112.

2015 Liebeskind, B.J., D. M. Hillis, and H. H. Zakon. 2015. Convergence of ion channel genome content in early animal evolution. Proceedings of the National Academy of Sciences USA 112:E846-E851. doi: 10.1073/pnas.1501195112

2015 McTavish, E. J., and D. M. Hillis. 2015. How do SNP ascertainment schemes and population demographics affect inferences about population history? BMC Genomics 16:266 (1-13). doi: 10.1186/s12864-015-1469-5.

2014 McTavish, E. J., and D. M. Hillis. 2014. A genomic approach for distinguishing between recent and ancient admixture in cattle. Journal of Heredity 105:445-456. doi:10.1093/jhered/esu001

2014 Li, T., J. Hua, A. M. Wright, Y. Cui, Q. Xie, W. Bu, and D. M. Hillis. Long-branch attraction and the phylogeny of true water bugs (Hemiptera: Nepomorpha) as estimated from mitochondrial genomes. BMC Evolutionary Biology 14:99 (1-12). doi:10.1186/1471-2148-14-99

2014 Wright, A. M., and D. M. Hillis. 2014. Bayesian analysis using a simple likelihood model outperforms parsimony for estimation of phylogeny from discrete morphological data. PLOS ONE 9:e109210 (1­-6). doi: 10.1371/journal.pone.0109210

2013 Liebeskind, B. J., D. M. Hillis, and H. H. Zakon. Independent acquisition of sodium selectivity in bacterial and animal sodium channels. Current Biology 23:R948-R949.

2013 Abrams, J., D. C. Cannatella, D. M. Hillis, and S. L. Sawyer. Recent host-shifts in ranaviruses: Signatures of positive selection in the viral genome. Journal of General Virology 94: 2082-2093. doi: 10.1099/vir.0.052837-0.

2013 Zhang, P., D. Liang, R.-L. Mao, D. M. Hillis, D. B. Wake and D. C. Cannatella. Efficient sequencing of anuran mtDNAs and a mitogenomic exploration of the phylogeny and evolution of modern frogs. Molecular Biology and Evolution 30:1899-1915. doi: 10.1093/molbev/mst091.

2013 Hedtke, S. M., M. J. Morgan, D. C. Cannatella, and D. M. Hillis. 2013. Targeted enrichment: Maximizing orthologous gene comparisons across deep evolutionary time. PLoS ONE 8(7): e67908. doi:10.1371/journal.pone.0067908.

2013 McTavish,, E. J., J. E. Decker, R. D. Schnabel, J. F. Taylor, and D. M. Hillis. New World cattle show ancestry from multiple independent domestication events. Proceedings of the National Academy of Sciences USA 110:E1398-E1406. doi: 10.1073/pnas.1303367110.

2013 Li, J.-T., Y. Li, S. Klaus, D.-Q. Rao, D. M. Hillis, and Y.-P. Zhang. Diversification of rhacophorid frogs provides evidence for accelerated faunal exchange between India and Eurasia during the Oligocene. Proceedings of the National Academy of Sciences USA 110:3441-3446. doi: 10.1073/pnas.1300881110.

2012 Liebeskind, B. J., D. M. Hillis, and H. H. Zakon. Phylogeny unites animal sodium channels with fungal calcium channels in an ancient, voltage-insensitive clade. Molecular Biology and Evolution 29:3613-3616. doi: 10.1093/molbev/mss182.

2012 Losos, J. B., D. M. Hillis, and H. W. Greene. Who speaks with a forked tongue? Science 338:1428-1429. doi: 10.1126/science.1232455.

2012 Schonhuth, S., D. M. Hillis, D. A. Neely, L. Lozano-Vilano, A. Perdices, and R. L. Mayden, Phylogeny, diversity, and species delimitation in the North American Round-Nosed Minnows (Teleostei: Dionda), as inferred from mitochondrial and nuclear DNA sequences, Molecular Phylogenetics and Evolution 62: 427-446 

2011 Hedtke, S. M., M. Glaubrecht, and D. M. Hillis, Rare gene capture in a predominantly androgenetic species, Proceedings of the National Academy of Sciences USA 108: 9520-9524 

2011 Liebeskind, B. J., D. M. Hillis, and H. H. Zakon, Evolution of sodium channels predates the origin of nervous systems in animals, Proceedings of the National Academy of Sciences USA 108: 9154-9159 

2011 Hedtke, S. M., and D. M. Hillis, The potential role of androgenesis in cytoplasmic-nuclear phylogenetic discordance, Systematic Biology 60: 87-109 

2010 Scaduto, D. I., J. M. Brown, W. C. Haaland, D. J. Zwickl, D. M. Hillis, and M. L. Metzker, Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences, Proceedings of the National Academy of Sciences USA 107: 21242-21247

2010 Lellis, A. D., M. L. Allen, A. W. Aertker, J. K. Tran, D. M. Hillis, C. R. Harbin, C. Caldwell, D. R. Gaillie, and K. S. Browning. 2010. Deletion of the eIFiso4G subunit of the Arabidopsis eIFiso4F translation initiation complex impairs health and viability. Plant Molecular Biology 74:249-263. doi: 10.1007/s11103-010-9670-z.

2010 Hillis, D. M. 2010. Phylogenetic progress and applications of the tree of life. Pages 421-449 in Evolution Since Darwin: The First 150 Years (M. A. Bell, W. F. Eanes, and D. J. Futuyma, eds.), Sinauer Associates, Sunderland, MA.

2010 Honeycutt, R. L., D. M. Hillis, and J. W. Bickham. 2010. Biodiversity discovery and its importance to conservation. Pages 1-34 in Molecular Approaches in Natural Resource Conservation (A. DeWoody, J. Bickham, C. Michler, K. Nichols, G, Rhodes, and K. Woeste, eds.), Cambridge University Press.

 

Member of National Academy of Sciences

Member of American Academy of Arts and Sciences

MacArthur Fellow