Castoe Lab

Department of Biology

University of Texas Arlington


Publications                           -pdfs for individual use only-

(Castoe lab students underlined)        Google Scholar Link


Perry, B.W, A.L. Andrew, A.H.M. Kamal, D.C. Card, D.R. Schield, G.I.M. Pasquesi, M. Pelligrino, S.P. Mackessy, S. Chowdhury, S.M. Secor, and T.A. Castoe. 2019. Multi-species comparisons of snakes identify coordinated signaling networks underlying post-feeding intestinal regeneration. Proceedings of the Royal Society B. In Press PDF

Schield, D.R*, B.W. Perry*, R.H. Adams, D.C. Card, T. Jezkova, G.I.M. Pasquesi, Z.L. Nikolakis, K. Row, J.M. Meik, C.F. Smith, S.P. Mackessy, and T.A. Castoe. 2019. Allopatric divergence and secondary contact with gene flow – a recurring theme in rattlesnake speciation. Biological Journal of the Linnean Society 128: 149-169. *joint primary authors.  PDF

Adams, R.H, and T.A. Castoe. 2019. Probabilistic species tree distances: implementing the multispecies coalescent to compare species trees within the same model-based framework used to estimate them. Systematic Biology. In Press PDF

Schield, D.R., D.C. Card, N.M. Hales, B.W. Perry, G.I.M. Pasquesi, H. Blackmon, R.H. Adams, A.B. Corbin, C.F. Smith, B. Ramesh, J.P. Demuth, E. Betran, M. Tollis, J.M. Meik, S.P. Mackessy and T.A. Castoe. 2019. The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes. Genome Research 29: 590-601. PDF Genome and annotation files hosted on Figshare

Adams, R.H, D.R. Schield, and T.A. Castoe. 2019. Recent advances in the inference of gene flow from population genomic data. Current Molecular Biology Reports. PDF

Adams, R.H, and Castoe, T.A. 2019. Statistical binning suffers profound model violation due to gene tree error incurred by trying to avoid gene tree error. Molecular Phylogenetics and Evolution 134: 164-171.  PDF

Pinto, B.J., D.C. Card, T.A. Castoe, R. Diaz, S. Nielsen, P. Trainor, and T. Gamble. 2019. The transcriptome of the Veiled Chameleon (Chamaeleo calyptratus): a resource for studying the evolution and development of vertebrates. Developmental Dynamics 2019:1–7; PDF


Perry, B.W, D.R. Schield, and T.A. Castoe. 2018. Evolution: Plasticity versus selection, or plasticity and selection? Current Biology 28:R1104-R1106. PDF

Pasquesi, G.I.M., Adams, R.H., D.C. Card, D.R. Schield, B.W. Perry, A.B. Corbin, J. Reyes-Velasco, R.P. Ruggiero, M.W. Vandewege, J.A. Shortt, and T.A. Castoe. 2018. Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals. Nature Communications 9:2774. PDF

Card, D.C., B. Perry, R.H. Adams, D.R. Schield, A. Young, A.L. Andrew, T. Jezkova, M.R. Walsh, M. Rockford, F. Mazzotti, K. Hart, M. Hunter, and T.A. Castoe. 2018. Novel ecological and climatic conditions drive rapid adaptation in invasive Florida Burmese pythons. Molecular Ecology 27:4744-4757. PDF

Perry, B.W, Card, D.C., Pasquesi, G.I.M., Adams, R.H., Schield, D.R., N.R. Hales, A.B. Corbin, J.P. Demuth, F.G. Hoffmann, M.W. Vandewege, R. Schott, N. Bhattacharyya, B.S.W. Chang, N.R. Casewell, G. Whiteley, J. Reyes-Velasco, S.P. Mackessy, K.B. Storey, T. Gamble, K.K. Biggar, C.N. Passow, C. Kuo, S.E. McGaugh, A.M. Bronikowski, J. de Koning, S.V. Edwards, M.E. Pfrender, P. Minx,  E.D. Brodie III, E.D. Brodie, Jr., W.C. Warren, and T.A. Castoe. 2018. Molecular adaptations for sensing and securing prey, and insight into amniote genome diversity, from the garter snake genome. Genome Biology and Evolution. 10:2110-2129. PDF

Adams, R.H., D.C. Card, D.R. Schield, and T.A. Castoe. 2018. Assessing the impacts of positive selection on coalescent-based species tree estimation and species delimitation. Systematic Biology  67:1076-1090. PDF

Strickland, J.L., Smith, C., Mason A.J., Schield, D.R., Borja, M, Castañeda-Gaytán, G., Spencer, C.L., Smith, L., Trápaga, A., Bouzid, N.M., Campillo-García, G., Flores-Villela, O.A., Antonio-Rangel, D., Rokyta, Castoe, T.A., D.R., Mackessy, S.P., and Parkinson, C.L. 2018. Evidence for divergent patterns of local selection driving venom variation in Mojave Rattlesnakes (Crotalus scutulatus). Scientific Reports 8: 17622. PDF

Schott, R.K., A. Van Nynatten, D.C. Card, T.A.Castoe, and B.S.W. Chang. 2018. Shifts in selective pressures on snake phototransduction genes associated with photoreceptor transmutation and dim-light ancestry. Molecular Biology and Evolution 35: 1376-1389. PDF

Schield, D.R, D.C. Card, R.H Adams, A.B. Corbin, T. Jezkova, N.R. Hales, J.M. Meik, C.L. Spencer, L.L. Smith, G. Campillo Garcia, N.M. Bouzid, J.L. Strickland, R.W. Bryson Jr., C.L. Parkinson, O. Flores-Viella, S.P. Mackessy and T.A. Castoe. 2018. Cryptic genetic diversity, population structure, and gene flow in Mohave rattlesnakes (Crotalus scutulatus). Molecular Phylogenetics and Evolution 127:669-681. PDF

Card, D.C., D.R. Schield, and T.A. Castoe. 2018. Plasticity and local adaptation explain lizard cold tolerance. Molecular Ecology 27: 2173-2175. PDF

Adams, R.H., D.C. Card, D.R. Schield, A.B. Corbin, and T.A. Castoe. 2018. ThetaMater: Bayesian estimation of population size parameter θ from genomic data. Bioinformatics 34: 1072-1073. PDF

Hales, N., D.R. Schield, A.L. Andrew, D.C. Card, Walsh, M., and T.A. Castoe. 2018. Contrasting gene expression programs correspond with predator-induced phenotypic plasticity within and across-generations in Daphnia. Molecular Ecology 26: 5003-5015. PDF


            See also commentary: Bell. A.M., and L.R. Stein. 2018. Transgenerational and developmental plasticity at the molecular level: Lessons from Daphnia. Molecular Ecology 26: 4859-4861. PDF


Gamble, T., T.A. Castoe, S.V. Nielsen, J.L. Banks, D.C. Card, D.R. Schield, G.W. Schuett, and W. Booth. 2017. The discovery of XY sex chromosomes in a Boa and Python. Current Biology 27: 2148-2153.e4. PDF


            See also commentary: Emerson, J.J. 2017. Evolution: a paradigm shift in snake sex chromosome genetics. Current Biology. 27: R800-R803. PDF

Andrew, A.L.*, B. Perry*, D.C. Card, D.R. Schield, R.P. Ruggiero, S.E. McGaugh, A. Chowdhary, S.M. Secor, and T.A. Castoe. 2017. Growth and stress response mechanisms underlying post-feeding regenerative organ growth in the Burmese python. BMC Genomics 18:338. (*co-first authors) PDF

Schield, D.R., R.H. AdamsD.C. Card, B.W. Perry, G.I.M. Pasquesi, T. Jezkova, D.M. Portik, A.L. Andrew, C.L. Spencer, E.E. Sanchez, M.K. Fujita, S.P. Mackessy, and T.A. Castoe. 2017. Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes. Ecology and Evolution 7: 3951-3966. PDF

Adams, R.H., D.R. Schield, D.C. Card, H. Blackmon, and T.A. Castoe. 2017. GppFst: Genomic posterior predictive simulations of Fst and dXY for identifying outlier loci from population genomic data. Bioinformatics 33:1414-1415. PDF   see also Software Page (GppFst)

Schott, R.K., B. Panesr, D.C. Card, T.A. Castoe, and B.S.W. Chang. 2017. Targeted hybrid enrichment of complete coding regions across divergent species. Genome Biology and Evolution 9:398-414. PDF

Shortt, J.A., D.C. Card, D.R. Schield, L. Yang, B. Zhong, T.A. Castoe, E.J. Carlton, and D.D. Pollock. 2017. Whole genome amplification and targeted genome sequencing in Shistosoma japonicum isolates. PLoS Neglected Tropical Diseases 11: e0005292. PDF

Cox, R.M., C.L. Cox, J.W. McGlothlin, D.C. Card, A.L. Andrew, and T.A. Castoe. 2017. Hormonally mediated increases in sex-biased gene expression accompany the breakdown of between-sex genetic correlations in a sexually dimorphic lizard. American Naturalist 189:315-332. PDF


Verity, R., C. Collins, D.C. Card, S.M. Schaal, L. Wang, and K.E. Lotterhos. 2016. MINOTAUR: A platform for the analysis and visualization of multivariate results from genomic scans with R Shiny. Molecular Ecology Resources. doi:10.1111/1755-0998.12579. PDF

Streicher, J.W., J.P. McEntee, L. Drzich, D.C. Card, D.R. Schield, U. Smart, C.L. Parkinson, T. Jezkova, E.N. Smith, and T.A. Castoe. 2016. Genetic surfing, not
allopatric divergence, explains spatial sorting of mitochondrial haplotypes in highly venomous coralsnakes. Evolution 70:1435-1449. PDF  Supplementary Material   [Cover Article]

Card, D.C., D.R Schield, R.H. Adams, A.B. Corbin, B.W. Perrry, A.L. Andrew, G.I.M. Pasquesi, E.N. Smith, T. Jezkova, S.M. Boback, W. Booth, and T.A. Castoe. 2016. Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism. Molecular Phylogenetics and Evolution 102:104-116. PDF

McGlothlin, J., M. Kobliela, C.R. Feldman, T.A. Castoe, F.J. Vonk, M.K. Richardson, E.D. Brodie Jr., M. E. Pfrender, E.D. Brodie III. 2016. Historical contingency
in a multigene family facilitates adaptive evolution of toxin resistance. Current Biology 26: 1616-1621. [Cover Article] PDF

Shaney, K.J., R.H. Adams, N. Kurniawan, A. Hamidy, E.N. Smith, and T.A. Castoe. In Press. A suite of potentially amplifiable microsatellite loci for reptiles of conservation concern from Africa and Asia. Conservation Genetics Resources 8: 309. PDF

Adams. R.H., H.G. Blackman, J. Reyes-Velasco, D.R. Schield, D.C. Card, A.L. Andrew, N. Waynewood, and T.A. Castoe. 2016. Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution. Genome 59:295-310 PDF

Schield, D.R, D.C. Card, J. Reyes-Velasco, A.L. Andrew, C.A. Modahl, S.M. Mackessy, D.D. Pollock, and T.A. Castoe. 2016. A role for genomics in rattlesnake research – current knowledge and future potential. Pp. 25-48. In: Rattlesnakes of Arizona, G.W. Schuett, L.W. Porras, and R.S. Reiserer (Eds.), Eco Books. PDF (book format: PDF)

Mackessy, S.P, and T.A. Castoe. 2016. Deciphering the evolution of venoms in rattlesnakes: venom and the venom apparatus. Pp. 49-98. In: Rattlesnakes of Arizona, G.W. Schuett, L.W. Porras, and R.S. Reiserer (Eds.), Eco Books. PDF (book format: PDF)

Doan, T.M., A.J. Mason, T.A. Castoe, M.S. Sasa, and C.L. Parkinson. 2016. Diversification of Middle American palm pitvipers and recognition of a cryptic species of highland Bothriechis (Squamata). Zootaxa 4138: 271-290. PDF

Vandewege, M.W., S. Magnum, T. Gabaldon, T.A. Castoe, D.A. Ray, and F.G. Hoffman. 2016. Contrasting patterns of evolutionary diversification in the olfactory repertoires of reptiles and birds. Genome Biology and Evolution 8:470-480. PDF

Walsh, M.R., T.A. Castoe, J. Holmes, M. Packer, K. Biles, M. Walsh, D.M. Post, S.B. Munch. 2016. Local adaptation in transgenerational responses to predators. Proceedings of the Royal Society B: Biological Sciences 283: 20152271. PDF

Schield, D.R., M.F. Walsh, D.C. CardA.L. Andrew, R.H. Adams, and T.A. Castoe. 2016. EpiRadSeq: genome-wide analysis of shifts in DNA methylation using next-generation s
equencing. Methods in Ecology and Evolution 7:60-69.  Cover Article PDF


Saviola, A.J., D. Pla, L. Sanz, T.A. Castoe, J.J. Calvete, and S.P. Mackessy. 2015. Comparative snake venomics of the Prairie rattlesnake (Crotalus viridis viridis) and assessment of the immunoreactivity of the commercial antivenom CroFab. J. Proteomics 121:28-43. PDF

Andrew, A.L., D.C. Card, R.P. Ruggiero, D.R. Schield, R.H. Adams, D.D. Pollock, S.M. Secor, and T.A. Castoe. 2015. Rapid changes in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding. Physiological Genomics 47:147-157. PDF

Schield, D.R., D.C. Card, R.H. Adams, T. Jezkova, J. Reyes-Velasco, F.N. Proctor, C.L. Spencer, H.-W. Herrmann, S.P. Mackessy, and T.A. Castoe. 2015. Incipient speciation with biased gene flow between two lineages of the Western Diamondback Rattlesnake (Crotalus atrox). Molecular Phylogenetics and Evolution 83: 213-223. PDF

Jezkova, T., B.R. Riddle, D.C. Card, D.R. Schield, M.E. Eckstut, and T.A. Castoe. 2015. Genetic consequences of a post-glacial range expansion in two co-distributed rodents (genus Dipodemys) depend on ecology and genetic locus. Molecular Ecology 24: 83-97. PDF

Koepfli, K.-P., B. Paten, A. Antunes, K. Belov, C. Bustamante, T.A. Castoe, H. Clawson, A. Crawford, D. Distel, R. Durbin, D. Earl, M.K. Fujita, T. Gamble, A. Georges, N. Gemmell, J.M. Graves, R.E. Green, G. Hickey, E. Jarvis, W. Johnson, I. Korf, R. Kuhn, D. Larkin, H. Lewin, J.V. Lopez, J. Ma, T.M. Bonet, W. Miller, R. Murphy, P. Pevzner, B. Shapiro, C. Steiner, G. Tamazian, B. Vanketesh, J. Wang, E. Wiley, H. Yang, G. Zhang, D. Haussler, O. Ryder, S.J. O’Brien. 2015. The Genome 10K Project and the state of vertebrate genomics: a way forward. Annual Review of Animal Biosciences 3: 57-111. PDF


Reyes-Velasco J., D.C. Card, A.L. Andrew, K.J. Shaney, R.H. Adams, D.R. Schield, N.R. Casewell, S.P. Mackessy, and T.A. Castoe. 2014. Expression of venom gene homologs in diverse python tissues suggests a new model for the evolution of snake venom. Molecular Biology and Evolution 32:173-183. PDF  Supplementary Material

Greene, R.E., E.L. Braun, J. Armstrong, D. Earl, N. Nguyen, M.W. Vandewedge, J.A. St John, S. Capelia-Gutierrez, T.A. Cas
toe, C. Kern, M.K. Fujita, J.C. Opazo, J. Jerka, K. Kojima, J. Caballero, R.M. Hubley, A.A.F. Smit, R.N. Platt, C.A. Lavoie, M. Ramakodi, J.W. Finger, A. Suh, S. Isberg, L. Miles, A. Chong, W. Jaratierdsiri, J. Gongora, C. Moran, A. Iriarte, B.C. Faircloth, J. McCormack, S. Burgess, S.V. Edwards, E. Lyons, C. Williams, M. Breen, C.R. Gresham, D.G. Peterson, J. Schmitz, D.D. Pollock, D. Houssler, E.W. Triplett, G. Zhang, N. Irie, E.D. Jarvis, C.A. Brochu, C. Schmidt, F. McCarthy, F.G. Hoffman, T.C. Glenn, T. Gabladon, B. Paten, and D.A. Ray. 2014. The genomes of three crocodilians provide insight into Archosaur evolution. Science 346: 1254449. PDF

Greene, R.E., ..., T.A. Castoe, (53 total authors)..., and D.A. Ray. 2014. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. [Author’s summary]. Science 346: 1335. PDF

Li, C., Y. Zhang, J. Li, L. Kong, H. Hu, H. Pan, L. Xu, Y. Deng, Q. Li, L. Jin, H. Yu, Y. Chen, B. Liu, L. Yang, S. Liu, Y. Zhang, Y. Lang, J. Xia, W. He, Q. Shi, S. Sabramanian, C.D. Miller, S. Meader, C.M. Rands, M.K. Fujita, M.J. Greenwold, T.A. Castoe, D.D. Pollock, W. Gu, K. Nam, H. Ellegren, S.Y.W. Ho, D.W. Burt, C.P. Ponting, E.D. Jarvis, M.T.P. Gilbert, H. Yang, J. Wang, D.M. Lambert, J. Wang, G. Zhang. In Press. Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment. Gigascience 3: 27. PDF

Fike, J.A., S.J. Oyler-McCance, S.J. Zimmerman, T.A. Castoe. 2014. Development of 13 microsatellites for Gunnison Sage-grouse (Centrocercus minimus) using next-generation shotgun sequencing and their utility in Greater Sage-grouse (Centrocercus urophasianus). Conservation Genetics Resources 7:211-214. PDF

Gilbert, C., J.M. Meik, D. Dashevsky, D.C. Card, T.A. Castoe, and S. Schaack. Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes. 2014. Proceedings of the Royal Society B: Biological Sciences 22:1471-2954. PDF

Card, D.C., D.R. Schield, J. Reyes-Velasco, A.L. Andrew, R.P. Ruggiero, D.D. Pollock, D.F. Tomback, S.J. Oyler-McCance, M.K. Fujita, and T.A. Castoe. 2014. Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies. PLoSOne 9: e106649. PDF

Shaney, K.J., D.R. Schield, D.C. Card, R.P. Ruggiero, D.D. Pollock. S.P. Mackessy, T.A. Castoe. 2014. Squamate reptile genomics and evolution. In: Handbook of Toxinology: Venom Genomics and Proteomics, P. Gopalakrishnakone (Ed.), Springer Reference Press, New York, NY. PDF

Booth, W., G.W. Schuett, A. Ridgway, D.W. Buxton, T.A. Castoe, G. Bastone, C. Bennett, and W. McMahan. 2014. Facultative parthenogenesis in pythons: new results challenging earlier conclusions. Biological Journal of the Linnean Society 112: 461-468. PDF


Castoe. T.A., A.P.J. de Koning, K.T. Hall, D.C. Card, D.R. Schield, M.K. Fujita, R.P. Ruggiero, J.F. Degner, J.M. Daza, W. Gu, J. Reyes-Velasco, K.J. Shaney, J.M. Castoe, S.E. Fox, A.W. Poole, D. Polanco, J. Dobry, M.W.
Vandewege, Q. Li, R. Schott, A. Kapusta, P. Minx, C. Feschotte, P. Uetz, D.A. Ray, F.G. Hoffmann, R. Bogden, E.N. Smith, B.S.W. Chang, F. Vonk, N.R. Casewell, C.V. Henkel, M.K. Richardson, S.P. Mackessy, A.M. Bronikowski, M. Yandell, W.C. Warren, S.M. Secor, and D.D. Pollock. 2013. The Burmese Python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the National Academy of Sciences, USA 110:20645-20650. PDF  Appendix  DataFile1  Datafile2  Datafile3


Featured in (including quotes from Todd and others):

            Secrets of Snakes. 2013 Science:342:1159. PDF

            Genes For Extremes. 2013. Science 342: 1160-1161. PDF

                -See the Castoe Lab Blog for additional press coverage

Vonk, F.J., N.R. Casewell, C.V. Henkel, A. Heimberg, H.J. Jansen, R.J. R. McCleary, H.M.E. Kerkkamp, R. Vos, I. Guerreiro, J.J. Calvete, W. Wüster, A.E. Woods, J.M. Logan, R.A. Harrison, T.A. Castoe,
A.P.J. de Koning, D.D. Pollock, C. Renjifo, R.B. Currier, D. Salgado, D. Pla, L. Sanz, A.S. Hyder, J.M.C. Ribeiro, J.W. Arntzen, G.E.E.J.M. van den Thillart, M. Boetzer, W. Pirovano, R.P. Dirks, H.P. Spaink, D. Duboule, E. McGlinn, R.M. Kini, M.K. Richardson. 2013. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proceedings of the National Academy of Sciences, USA 10:20651-20656. PDF  Appendix  Datafile1  Datafile2  Datafile3  -Cover Article-

    Featured in (including quotes from Todd and others):

            Genes For Extremes. 2013. Science 342: 1160-1161. PDF

            The Freek Show. 2013 Science:342:1164-1165. PDF

Castoe, T.A., and D.D. Pollock. 2013. Chinese Alligator genome illustrates molecular adaptations underlying extreme Crocodilian traits. Cell Research 2013:1-2. PDF

See quotes from Todd in: Bats and dolphins evolved echolocation in same way”, 2013, by Elizabeth Pennisi in Science 9/04/2013. PDF 

Reyes-Velasco, J., J.M. Meik, E.N. Smith, and T.A. Castoe. 2013. Phylogenetic relationships of the enigmatic longtailed rattlesnakes (Crotalus ericsmithi, C. lannomi, and C. stejnegeri). Molecular Phylogenetics and Evolution 69:524-534. PDF

Schaffer, H.B., ..., T.A. Castoe, (59 total authors)..., R.K. Wilson. 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology. 14:R28. PDF

Ornelas, J.F., V. Sosa, D.E. Soltis, J.M. Daza, C. Gonzalez, P.S. Soltis, C. Gutierrez-Rodriguez, A.E., de los Monteros, T.A. Castoe, C. Bell, and E. Ruiz-Sanchez. 2013. Comparative phylogeographic analyses illistrate the complex evolutionary history of threatened cloud forests of Northern Mesoamerica. PLoS One 8:e56283. PDF

Oyler-McCance, S.J., J.A. Fike, T.A. Castoe, D.F. Tomback, M.B. Wunder, T. Schaming. 2013. Development and characterization of thirteen microsatellite loci in Clark’s nutcracker (Nucifraga columbiana). Conservation Genetics Resources. 5:303-305. PDF


de Koning, A.P.J., W. Gu, T.A. Castoe, and D.D. Pollock. 2012. Phylogenetics, Likelihood, Evolution, and Complexity (PLEX). Bioinformatics 28:2989-2990. PDF

Castoe, T.A., E.L. Braun, A.M. Bronikowski, C.L. Cox, A.R. Davis, A.P.J. de Koning, J. Dobry, M. Fujita, M. Giorgianni, A. Hargreaves, C. Henkel, S.P. Mackessy, D. O’Meally, D. Rokyta, S.M. Secor, J. Streicher, K. Wray, K.D. Yokoyama, and D.D. Pollock. 2012. Report from the first snake genomics and integrative biology meeting. Standards in Genomic Sciences 7:1. PDF

Lamers, R.P., G. Muthukrishnan, T.A. Castoe, S. Tafur, A.M. Cole, and C.L. Parkinson. 2012. Phylogenetic relationships among Staphylococcus species inferred from multilocus data. BMC Evolutionary Biology 12:171. PDF

Castoe, T.A., J.W. Streicher, J.M. Meik, M.J. Ingrasci, A.W. Poole, A.P.J. de Koning, J.A. Campbell, C.L. Parkinson, E.N. Smith, and D.D. Pollock. 2012. Thousands of microsatellite loci from the venomous coralsnake (Micrurus fulvius) and variability of select loci across populations and related species. Molecular Ecology Resources 12:1105-1113. PDF

Castoe, T.A., A.W. Poole, A.P.J. de Koning, K.L. Jones, D.F. Tomback, S.J. Oyler-McCance, J. Fike, S.L. Lance, J.W. Streicher, E.N. Smith, D.D. Pollock. 2012. Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake. PLoS ONE 7:e30953. PDF  -See also software page-

St. John, J., ..., T.A. Castoe, [47 total authors]..., D.A. Ray. 2012. Sequencing three crocodilian genomes to illumine the evolution of archosaurs and amniotes. Genome Biology 13: 413. PDF [Editor’s Pick]

Jadin, R.C., J.H. Townsend, T.A. Castoe, and J.A. Campbell. 2012. Cryptic diversity in disjunct populations of Middle American Montane Pitvipers: a systematic reassessment of Cerrophidion godmani. Zoologica Scripta 41:455-470. PDF

Wang, B., R. Ekblom, T.A. Castoe, E.P. Jones, R.Kozma, E. Bongcam-Rudloff, D.D. Pollock, and J. Hoglund. 2012. Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development. Open Biology 2:120054. PDF

Sun, C., D.B. Shepard, R.A. Chong, J. Lopez-Arriaza, K.T. Hall, T.A. Castoe, C. Feschotte, D.D. Pollock, and R.L. Mueller. 2012. LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Genome Biology and Evolution 4:168-183. PDF

Nakayama, M., T.A. Castoe, T. Sosinowski, X.L. He, K. Johnson, K. Haskins, D.A. Vignali, L. Gapin, D.D. Pollock, and G.S. Eisenbarth. 2012. Germline TRAV5D-4 T cell receptor sequence targets a primary insulin peptide of NOD mice. Diabetes 61:857-865. PDF


de Koning, A.P.J., W. Gu, T.A. Castoe, and D.D. Pollock. 2011. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genetics 7:e1002384.  PDF  Featured as Research Highlight in Nature Reviews Genetics

Castoe, T.A., A.P.J. de Koning, K.T. Hall, K.D. Yokoyama, W. Gu, E.N. Smith, C. Feschotte, P. Uetz, D.A. Ray, J. Dobry, R. Bogden, S.P. Mackessy, A.M. Bronikowski, W.C. Warren, S.M. Secor, and D.D. Pollock. 2011. Sequencing the genome of the Burmese python (Python molurus bivittatus) - a model for studying extreme adaptations in snakes. Genome Biology 12:406. PDF

Pollock, D.D., A.P.J. de Koning, H. Kim, T.A. Castoe, M. Churchill, and K.J. Kechris. 2011. Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions. PLoS ONE 6:11 e26105. PDF

Castoe, T.A., S.E. Fox, A.P.J. de Koning, A.W. Poole, J.M. Daza, E.N. Smith, T. Mockler, S. Secor, and D.D. Pollock. 2011. A multi-organ transcriptome resource for the Burmese python (Python molurus bivittatus). BMC Research Notes 4:310. PDF

Alföldi J., F. Di Palma, M. Grabherr, C. Williams, L. Kong, E. Mauceli, P. Russell, C.B. Lowe, R. Glor, J.D. Jaffe, D.A. Ray, S. Boissinot, A.M. Shedlock, C. Botka, T.A.
Castoe, J.K. Colbourne, M.K. Fujita, R. Godinez Moreno, B.F. ten Hallers, D. Haussler, A. Heger, D. Heiman, D.E. Janes, J. Johnson, P.J. de Jong, M.Y. Koriabine, P. Novick, C.L. Organ, S.E. Peach, S. Poe, D.D. Pollock, K. de Queiroz, T. Sanger, S. Searle, J.D. Smith, Z. Smith, R. Swofford, J. Turner-Maier, J. Wade, S. Young, A. Zadissa, Genome Sequencing Platform and Whole Genome Assembly Team, S.V. Edwards, T.C. Glenn, C.L. Schneider, J.B. Losos, E.S. Lander, M. Breen, C.P. Ponting, K. Lindblad-Toh. 2011. The genome of Anolis carolinensis, the green anole lizard, and a comparative analysis with birds and mammals. Nature. 477: 587-591. PDF

Castoe, T.A., K. Hall, M.L. Guibotsy Mboulas, W. Gu, A.P.J. de Koning, A.W. Poole, V. Vemulapalli, J.M. Daza, C. Feschotte, and D.D. Pollock. 2011. Discovery of highly divergent repeat landscapes in snake genomes using high throughput sequencing. Genome Biology and Evolution 3:641-653. PDF

Castoe, T.A., A. Bronikowski, E. Brodie III, S.V. Edwards, M. Pfrender, M. Shipiro, D.D. Pollock, W Warren. 2011. A proposal to sequence the genome of a garter snake. Standards in Genomic Sciences 4:257-270. PDF


Harris, J.K., J.W. Sahl, T.A. Castoe, D.D. Pollock, and J.R. Spear. 2010. Comparison of normalization methods for construction of large multiplex amplicon pools for next-generation sequencing. Applied and Environmental Microbiology 76:3863-3868.  PDF

Castoe, T.A., A.P.J. de Koning, D.D. Pollock. 2010. Molecular structure and evolution of genomes. In: Evolutionary Genomics and Systems Biology, G. Caetano-Anolles (Ed.), John Wiley & Sons, New York, NY, pp. 183-202.  PDF 

Daza, J.M.*, Castoe, T.A.*, J.M., and C.L. Parkinson. 2010. Using regional comparative phylogeographic data from snake lineages to infer historical processes in Middle America. Ecography 33: 343-354. [*Contributed equally] PDF

Castoe, T.A., A.P.J. de Koning, and D.D. Pollock. 2010. Adaptive molecular convergence - molecular evolution versus molecular phylogenetics. Communicative and Integrative Biology 3: 67-69. PDF

Castoe, T.A., A.W. Poole, W. Gu, A.P.J. de Koning, J.M Daza, E.N. Smith, and D.D. Pollock. 2010. Rapid identification of thousands of microsatellite loci for the copperhead snake (Agkistrodon contortrix) from modest amounts of 454 shotgun genome sequence. Molecular Ecology Resources 10: 341-347.   PDF  Supplemtary Files (.zip)


Castoe, T.A., A.P.J. de Koning, W. Gu, J.M. Daza, Z.J. Jiang, C.L. Parkinson, and D.D. Pollock. 2009. Dynamic nucleotide mutation gradients and control region usage in squamate reptile mitochondrial genomes. Cytogenetic and Genome Research 127: 112-127. PDF

Castoe, T.A.*, A.P.J. de Koning*, H.M. Kim, W. Gu, B.P. Noonan, G. Naylor, Z.J. Jiang, C.L. Parkinson, and D.D. Pollock. 2009. Evidence for an ancient adaptive
episode of convergent molecular evolution. Proceedings of the National Academy of Sciences USA 106: 8986-8991. [*Contributed equally] [Cover Article] [Highly Accessed]  PDF        Software: CodeML.Ancestral

    See related: Castoe, T.A., A.P.J. de Koning, H.M. Kim, W. Gu, B.P. Noonan, Z.J. Jiang, C.L. Parkinson, and D.D. Pollock. 2008. An ancient adaptive episode of convergent molecular evolution misleads phylogenetic inference. Nature Precedings, npre.2008.2123.1.  PDF  


    PNAS Commentary: Edwards, S. 2009. Natural selection and phylogenetic analysis. Proceedings of the National Academy of Sciences USA 106: 8799-8800.  PDF 

Tonnsman, G., D.D. Pollock, W. Gu, and T.A. Castoe. 2009. Identifying DNA strands using a kernel of classified sequences. 2009 WRI World Congress on Computer Science and Information Engineering 3: 703-707.   PDF

Burbrink, F.T., and T.A. Castoe. Molecular phylogeography of snakes. 2009. In: Snakes: Ecology and Conservation, R. Seigel and S. Mullin (Eds.), Cornell Univ. Press, Ithaca, NY, pp. 38-77.   PDF

Castoe, T.A., J.M. Daza, E.N. Smith, M. Sasa, U. Kuch, P.T. Chippindale, J.A. Campbell, and C.L. Parkinson. 2009. Comparative phylogeography of pitvipers
suggests a consensus of ancient Middle American highland biogeography. Journal of Biogeography 36: 83-103. [Cover Article]   PDF 


Gu, W., T.A. Castoe, D.L. Hedges, M.A. Batzer, and D.D. Pollock. 2008. Analysis of the repeat structure in large genomes using repeat probability clouds. Analytical Biochemistry 380:77-83.  PDF  

Castoe, T.A., Z.J. Jiang, W. Gu, Z. Wang, and D.D. Pollock. 2008. Adaptive evolution and functional redesign of core metabolic proteins in snakes. PLoS ONE 3:e2201.  [Faculty of 1000]   PDF


See quotes from Todd in: Training postdocs: communication is key”, 2007, by Laura Bonetta in Science 317:1239. PDF

Jiang, Z.J./T.A. Castoe*, C.C. Austin, F.T. Burbrink, M.D. Herron, J.A. McGuire, C.L. Parkinson, and D.D. Pollock. 2007. Comparative mitochondrial genomics of snakes: substitution rate dynamics and functionality of the duplicate control region. BMC-Evolutionary Biology 7:123. [*Joint primary authorsPDF  

Castoe, T.A., T.S. Stephens, B.P. Noonan, C.L. Calestani. 2007. A novel group of type I polyketide synthases (PKS) in animals and the complex phylogenomics of PKSs. Gene 392:47-58.  PDF  

Castoe, T.A., C.L. Spencer, and C.L. Parkinson. 2007. Phylogeographic structure and historical demography of the western diamondback rattlesnake (Crotalus atrox): a perspective on North American desert biogeography. Molecular Phylogenetics and Evolution 42:193-212.    PDF

Castoe, T.A., E.N. Smith, R.M. Brown, and C.L. Parkinson. 2007. Higher-level phylogeny of Asian and American coralsnakes, their placement within the Elapidae (Squamata), and the systematic affinities of the enigmatic Asian coralsnake Hemibungarus calligaster. Zoological Journal of the Linnean Society 151:809-831.   PDF 


Castoe, T.A., and C.L. Parkinson. 2006. Bayesian mixed models and the phylogeny of pitvipers (Serpentes: Viperidae). Molecular Phylogenetics and Evolution 39:91-110.   PDF


Castoe, T.A., M. Sasa, and C. L. Parkinson. 2005. Modeling nucleotide evolution at the mesoscale: The phylogeny of the Neotropical pitvipers of the Porthidium Group (Viperidae: Crotalinae). Molecular Phylogenetics and Evolution 37:881-898. PDF

Doan, T.M., T.A. Castoe, and W. Arizábal Arriaga. 2005. Phylogenetic relationships of the genus Proctoporus sensu stricto (Squamata: Gymnophthalmidae), with a new species from Puno, southeastern Peru. Herpetologica 61:325-336.  PDF

Reece, J.S., T.A. Castoe, and C.L. Parkinson. 2005. Historical perspectives on population genetics and conservation of three sea turtle species. Conservation Genetics 6:235-251.   PDF

Doan, T.M., and T.A. Castoe. 2005. Phylogenetic taxonomy of the Cercosaurini (Squamata: Gymnophthalmidae), with new genera for species of Neusticurus and Proctoporus. Zoological Journal of the Linnean Society 143:405-416.   PDF

Mulvaney, A., T.A. Castoe, K.G. Ashton, K.L. Krysko, and C.L. Parkinson. 2005. Evidence of population genetic structure within the Florida worm lizard, Rhineura floridana (Amphisbaenia: Rhineuridae). Journal of Herpetology 39:118-124.   PDF 


Castoe, T.A., T.M. Doan, and C.L. Parkinson. 2004. Data partitions and complex models in Bayesian analysis: the phylogeny of gymnophthalmid lizards. Systematic Biology 53:448-469.   PDF 

Herron, M.D., T.A. Castoe, and C.L. Parkinson. 2004. Sciurid phylogeny and the paraphyly of Holarctic ground squirrels (Spermophilus). Molecular Phylogenetics and Evolution 31:1015-1030.   PDF  


Schargel, W.E. and T.A. Castoe. 2003. The hemipenes of some snakes of the semifossorial genus Atractus with comments on variation within the genus. Journal of Herpetology 37: 718-721.  PDF  

Castoe, T.A., P.T. Chippindale, J.A. Campbell, L.A. Ammerman, and C.L. Parkinson. 2003. Molecular systematics of the Middle American jumping pitvipers (genus Atropoides) and phylogeography of the Atropoides nummifer comple. Herpetologica 59: 421-432.  PDF  

Doan, T.M. and T.A. Castoe. 2003. Using morphological and molecular evidence to infer species boundaries within Proctoporus bolivianus Werner (Gymnophthalmidae). Herpetologica 59: 433-450.   PDF  


Castoe, T.A. 2002. Microhabitat selection in Porthidium nasutum (Serpentes: Viperidae) in Costa Rica, with comments on ontogenetic variation. Herpetological Review 33: 174-175.   PDF 

Todd Castoe’s Home Page:



Evolutionary Genomics

Reptiles, esp. Snake Genomics

Genomics of Extreme Adaptations

Systems Biology

Population Genomics



        Biology Department

            Graduate Admissions

            Genome Biology Group

            Amphibian and Reptile

            Diversity Research Center