David Hillis

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:

2024. Dobbins, B. A., R. U. Tovar, B. J. Oddo, T. J. Devitt, D. M. Hillis*, and D. M. Garcia* (*: corresponding authors). 2024. PAX6 protein in neuromasts of the lateral line system of paedomorphic salamanders (Eurycea). PLoS One e0293163. https://doi.org/10.1371/journal.pone.0293163

2023. Smith, C. H., B. J. Pinto, M. Kirkpatrick, D. M. Hillis, J. M. Pfeiffer, J. C. Havird. 2023. A tale of two paths: The evolution of mitochondrial recombination in bivalves with doubly uniparental inheritance. Journal of Heredity 114: 199-206. https://doi.org/10.1093/jhered/esad004

2023. Neemuchwala, S., N. A. Johnson, J. M. Pfeiffer, M. Lopes-Lima, A. Gomes-dos-Santos, E. Froufe, D. M Hillis, and C. H. Smith. 2023. Coevolution with host fishes shapes life histories in a highly specialized group of freshwater mussels (Unionida: Quadrulini). Bulletin of the Society of Systematic Biologists 1: 8998. https://doi.org/10.18061/bssb.v1i6.8998

2023. Chambers, E. A, R. D. Tarvin, J. C. Santos, S. R. Ron, M. Betancourth, A. Amézquita, D. M. Hillis, M. V. Matz, and D. C. Cannatella. 2023. 2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics. Ecology and Evolution 13: e9842. https://doi.org/10.1002/ece3.9842

2023. Chambers, E. A., T. L. Marshall, and D. M. Hillis. 2023. The importance of contact zones for distinguishing interspecific from intraspecific geographic variation. Systematic Biology 72: 357–371, https://doi.org/10.1093/sysbio/syac056.

2022. Fu, T.-T., Y.-B. Sun, W. Gao, C. Long, C-H Yang, X. Yang, Y. Zhang, X.-Q. Lan, S. Huang, J. Jin, R. Murphy, Y. Zhang, R. Lai, D. M. Hillis, Y.-P. Zhang, and J. Che. 2022. The highest-elevation frog provides insights into mechanisms and evolution of defenses against high ultraviolet radiation. Proceedings of the National Academy of Sciences USA, 119:e2212406119, doi.org/10.1073/pnas.2212406119.

2022. Hillis, D. M. Species, clades, and their relationship to paraphyly and monophyly: Examples from the Pantherophis obsoletus complex. Herpetological Review 53:47–53.

2022. Hillis, D. M. Distinguishing intraspecific geographic variation from distinct species boundaries. Sonoran Herpetologist 35: 49–54.

2022. Wu, W., Y.-D. Gao, D.-C. Jiang, J. Lei, J.-L. Ren, W. Liao, C. Deng, Z. Wang, D. M. Hillis, Y.-P. Zhang, and J-T. Li. Genomic adaptations for arboreal locomotion in Asian flying treefrogs. Proceedings of the National Academy of Sciences USA 119: e2116342119, doi.org/10.1073/pnas.2116342119

2021. Hillis, D. M., E. A. Chambers, and T. J. Devitt. Contemporary methods and evidence for species delimitation. Ichthyology & Herpetology 109: 895–903, https://doi.org/10.1643/h2021082.

2021. Marshall, T. L., E. A. Chambers, M. V. Matz, and D. M. Hillis. How mitonuclear discordance and geographic variation have confounded species boundaries in a widely studied snake. Molecular Phylogenetics and Evolution 162: 107194, doi: 10.1016/j.ympev.2021.107194.

2021. Hillis, D. M., and W. Wüster. Taxonomy and nomenclature of the Pantherophis obsoletus complex. Herpetological Review 52:51–52.

2021. Hillis, D. M. New and not-so-new conceptualizations of species and subspecies: A reply to the “It’s species all the way down” view. Herpetological Review 52:49–50.

2021. Xu, W., W-J. Dong, T.-T. Fu, W. Gao, F. Yan,, Y.-H. Wu, K. Jiang, J.-Q. Jin, H.-M. Chen, Y.-P. Zhang, D. M. Hillis, and J. Che. Phylogeographic analyses support a Miocene focal point of Himalayan uplift and biological diversification. National Science Review 8:nwaa263, doi: 10.1093/nsr/nwaa263

2020. Gray, L. N., A. J. Barley, D. M. Hillis, C. J. Pavón-Vázquez, S. Poe, and B. A. White. Does breeding season variation affect evolution of a sexual signaling trait in a tropical lizard clade? Ecology and Evolution 10: 3738-3746, doi.org/10.1002/ece3.6167. 2020. Hillis, D. M. 2020. The description and naming of geographic variation within species. Herpetological Review 51:52-56.

2020. Chambers, E. A., and D. M. Hillis. The multispecies coalescent over-splits species in the case of geographically widespread taxa. Systematic Biology 69: 184–193, doi.org/10.1093/sysbio/syz042. 

2019. Jiang, D., K. S. Klaus, Y.-P. Zhang, D. M. Hillis, and J.-T. Li. 2019. Asymmetric biotic interchange across the Bering Land Bridge between Eurasia and North America. National Science Review 6: 739–745, doi.org/10.1093/nsr/nwz035.

2019. Hillis, D. M. Species delimitation in herpetology. Journal of Herpetology 53:3-12, doi.org/10.1670/18-123. 

2019. Gao, W., Y.-B. Sun, W.-W. Zhou, Z.-J. Xiong, L.-N. Chen, H. Li., T.-T. Fu, K. Xu, W. Xu, L. Ma, Y.-J. Chen, X.-Y. Xiang, T. Zeng, S. Zhang, J.-Q. Jin, H.-M. Chen, G.-J. Zhang, D. M. Hillis, X. Ji, Y.-P. Zhang, and J. Che. 2019. Evolution of viviparity: Genomic and transcriptomic investigations of the transition from oviparity to viviparity. Proceedings of the National Academy of Sciences USA 116: 3646-3655. doi.org/10.1073/pnas.1816086116. 

2019. Devitt, T. J., A. M. Wright, D. C. Cannatella, and D. M. Hillis. 2019. Species delimitation in endangered groundwater salamanders: Implications for aquifer management and biodiversity conservation. Proceedings of the National Academy of Sciences USA 116: 2624–2633. doi/10.1073/pnas.1815014116

2018. Sun, Y.-B., T.-T. Fu, J.-Q. Jina, R. W. Murphy, D. M. Hillis, Y.-P. Zhang, and J. Che. Species groups distributed across elevational gradients reveal convergent and continuous genetic adaptation to high elevations. Proceedings of the National Academy of Sciences USA 115 E10634-E10641, doi: 10.1073/pnas.1813593115.

2018. Li, J.-T., Gao, Y.-D., Xie, L., Deng, C., Shi, P., Guan, M.-L., Huang, S., Ren, J.-L., Wu, D.-D., Ding, L., Huang, Z.-Y., Nie, H., Humphreys, D. P., Hillis, D. M., Wang, W.-Z., and Zhang, Y.-P. 2018. Comparative genomic investigation of high-elevation adaptation in ectothermic snakes. Proceedings of the National Academy of Sciences USA 115: 8406-8411, doi: 10.1073/pnas.1805348115. 

2017. Liebeskind, B. J., H. A. Hofmann, D. M. Hillis, and H. H. Zakon. Evolution of animal neural systems. Annual Review of Ecology, Evolution, and Systematics 48:377-398.

2017. Feng,Y.-J., D. C. Blackburn, D. Liang, D. M. Hillis, D. B. Wake, D. C. Cannatella, and P. Zhang. 2017. Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary. Proceedings of the National Academy of Sciences USA 114: E5864–E5870, doi: 10.1073/pnas.1704632114.

2016. Li, T., J. Yang, Y. Li, Y. Cui, Q. Xie, W. Bu, and D. M. Hillis. 2016. A mitochondrial genome of Rhyparochromidae (Hemiptera: Heteroptera) and a comparative analysis of related mitochondrial genomes. Scientific Reports 6:35175 (1-12). doi:10.1038/srep35175

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.