Castoe Lab


Department of Biology

University of Texas Arlington

 

Publications                           -pdfs for individual use only-

(Castoe lab students underlined)        Google Scholar Link


2017


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. In Press. Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes. Ecology and Evolution.


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. In Press. Growth and stress response mechanisms underlying post-feeding regenerative organ growth in the Burmese python. BMC Genomics. PDF


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


Schott, R.K., B. Panesr, D.C. Card, T.A. Castoe, and B.S.W. Chang. In Press. Targeted hybrid enrichment of complete coding regions across divergent species. Genome Biology and Evolution. 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: 000-000. 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. 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


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. (in press). 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



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


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. In Press. A role for genomics in rattlesnake research – current knowledge and future potential. In: Rattlesnakes of Arizona, G.W. Schuett, L.W. Porras, and R.S. Reiserer (Eds.), Eco Books.


Mackessy, S.P, and T.A. Castoe. In Press. Deciphering the evolution of venoms in rattlesnakes: venom and the venom apparatus. In: Rattlesnakes of Arizona, G.W. Schuett, L.W. Porras, and R.S. Reiserer (Eds.), Eco Books.


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 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 


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:

http://www.snakegenomics.ToddCastoe/Home.html

 

WHAT WE DO IN  THE LAB
Evolutionary Genomics

Reptiles, esp. Snake Genomics

Genomics of Extreme Adaptations

Systems Biology

Population Genomics

UTA LINKS

   UTA

        Biology Department

            Graduate Admissions

            Genome Biology Group

            Amphibian and Reptile

            Diversity Research Center