Castoe Lab
Department of Biology
University of Texas Arlington
Publications -pdfs for individual use only-
(Castoe lab students underlined) Google Scholar Link
2019
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. https://doi.org/10.1007/s40610-019-00120-0. 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; https://doi.org/10.1002/dvdy.20. PDF
2018
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
2017
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. Adams, D.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
2016
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. Card, A.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
2015
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
2014
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
2013
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
2012
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
2011
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
2010
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)
2009
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
2008
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
2007
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 authors] PDF
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
2006
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
2005
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
2004
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
2003
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
2002
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:
WHAT WE DO IN THE LAB
Evolutionary Genomics
Reptiles, esp. Snake Genomics
Genomics of Extreme Adaptations
Systems Biology
Population Genomics
LAB LINKS
Lab Research
Joining the Lab
