Publications

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Featured Cover Articles

2024

  • Westfall, A.K, S.S. Gopalan, J.C. Kay, T.S. Tippets, K. Lackey, S.M. Choudhury, M.W. Pellegrino, and T.A. Castoe. 2024 Single-cell resolution of python intestinal regeneration without crypts illuminates conserved vertebrate regenerative mechanisms. Proceedings of the National Academy of Sciences USA, 121:e2405463121. PDF
  • Gopalan, S.S., B.W. Perry, Y.Z. Francioli, D.R. Schield, H.D. Guss, J.M. Bernstein, K. Ballard, C.F. Smith, A.J. Saviola, R.H. Adams, S.P. Mackessy, and T.A. Castoe. 2024. Diverse gene regulatory mechanisms alter rattlesnake venom gene expression at fine evolutionary scales. Genome Biology and Evolution. 16(7), evae110. PDF
  • Smith, C..F., C.M. Modahl, D. Ceja-Galindo, K.Y. Larson, S.P. Maroney, L. Bahrabadi, N.P. Brandehoff, B.W. Perry, M.C. MaCabe, D. Petras, B. Lamonte, J.J. Calvete, T.A. Castoe, S.P. Mackessy, K.C. Hansen, A.J. Saviola. 2024. Assessing target
    specificity of the small molecule inhibitor Marimastat to snake venom toxins: a novel application of thermal proteome profiling. Molecular and Cellular Proteomics, 23: 100779. PDF
  • Lozano, J.R., M. Duncan, D. McKenna, T.A. Castoe, M. DeGiorgio, and R.H. Adams. In Press. TraitTrainR: Accelerating large-scale simulation under models of trait evolution. Bioinformatics Advances.
  • Miles, L.S., R.H. Adams, Y.F. Francioli, D.C. Card, T.A. Castoe, and W. Booth. In Press. A chromosome-level reference genome for the common bed bug, Cimex lectularius, with identification of sex chromosomes. Journal of Heredity.
  • Meik, J.M., J.A. Watson, D.R. Schield, B.W. Perry, Y.Z. Francioli, H.D. Guss, S.P. Mackessy, and T.A. Castoe. 2024. Climatic temperature and precipitation jointly influence body size in species of western rattlesnakes. Royal Society Open Science 11: 240345. PDF
  • Maag, D.W., Y.Z. Francioli, T.A. Castoe, G.W. Schuett, and R.W. Clark. 2024. The spatial ecology of Mojave Rattlesnakes (Crotalus scutulatus), Prairie Rattlesnakes (C. viridis), and their hybrids in southwestern New Mexico, USA. Biological Journal of the Linnean Society.  Preprint-PDF

2023

  • Westfall, A.K.*, S.S. Gopalan*, B.W. Perry, R.H. Adams, A. Saviola, S.P. Mackessy, and T.A. Castoe. 2023. Single-cell heterogeneity in snake venom expression is hardwired by co-option of regulators from progressively activated pathways. Genome Biology and Evolution 15: evad109. *joint primary authors. PDF  Supplementary Data
  • Smith, C., Z.L. Nikolakis, B.W. Perry, D.R. Schield, N. Balchan, J. Parker, K.C. Hansen, A.J. Saviola, T.A. Castoe and S.P. Mackessy. 2023. Snakes on a plain: complex biotic and abiotic factors determine venom variation in North America’s widest-ranging rattlesnake. BMC Biology 21: 136.  PDF
  • Nachman, M.W., E.J. Beckman, …T.A. Castoe…[118 coauthors total], E.A. Wommack, and R.M. Zink. 2023. Specimen collection is essential for modern science. PLoS Biology 21: e3002318. PDF.
  • Smith, C., Z.L. Nikolakis, B.W. Perry, D.R. Schield, J.M. Meik, A.J. Saviola, T.A. Castoe, J. Parker, and S.P. Mackessy. 2023. The best of both worlds: rattlesnake hybrid zones generate complex combinations of divergent venom phenotypes that retain high toxicity. Biochimie 213: 176-189. PDF
  • Maag, D.W., Y.Z. Francioli, N. Shaw, N., A. Soni, T.A. Castoe, G.W. Schuett, and R.W. Clark. 2023. Hunting behavior and feeding ecology of Mojave Rattlesnakes (Crotalus scutulatus), Prairie Rattlesnakes (C. viridis), and their hybrids in southwestern New Mexico. Ecology and Evolution 13: e10683. PDF
  • Farleigh, K., A. Ascanio, M.E. Farleigh, D.R. Schield, D.C. Card, M. Leal, T.A. Castoe, T. Jezkova, J.A. Rodriguez-Robles. 2023. Signals of differential introgression in the genome of natural hybrids of Caribbean anoles. Molecular Ecology. 2023:6000-6017. PDF
  • Smith, C, N.P. Brandehoff, L. Pepin, M.C. McCabe, T.A. Castoe, S.P. Mackessy, T. Nemkov, K.C. Hansen, A.J. Saviola. 2023. Feasibility of detecting snake envenomation biomarkers from dried blood spots. Analytical Science Advances. 4: 26-36. PDF

2022

  • Perry, B.W, S.S. Gopalan, G.I.M. Pasquesi, D.R. Schield, A.K. Westfall, C. Smith, I. Koludarov, P.T. Chippindale, M.W. Pellegrino, E.B. Choung, S.P. Mackessy, and T.A. Castoe. 2022. Snake venom expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways. Genome Research. 32: 1058-1073. PDF  Supplementary Material   –PRESS Release
  • Schield, D.R., B.W. Perry, R.H. Adams, M.L. Holding, Z. L. Nikolakis, S.S. Gopalan, C.F. Smith, J.M. Parker, M. DeGiorgio, S.P. Mackessy, and T.A. Castoe. 2022. The roles of balancing selection and recombination in the evolution of rattlesnake venom. Nature Ecology & Evolution 6: 1367-1380. PDF
  • Chamsedine, D., S.A. Mahmud, A.K. Westfall, T.A. Castoe, R.E. Berg and M.W. Pellegrino. 2022. The mitochondrial UPR regulator ATF5 promotes intestinal barrier function via control of the satiety response. Cell Reports 41: 11789. PDF 
  • Nikolakis, Z.L., D.R. Schield, A.K. Westfall, B.W. Perry, K.N. Ivey, R.W. Orton, N.R. Hales, R.H. Adams, J.M. Meik, J. Parker, C.F. Smith, Z. Gompert, S.P. Mackessy, and T.A. Castoe. 2022. Evidence that genomic incompatibilities and other multilocus processes impact hybrid fitness in a rattlesnake hybrid zone. Evolution 76: 2513-2530.  journal cover article (see cover). PDF 
  • Lund, A.J., K.J. Wade, Z.L. Nikolakis, K. Ivey, B.W. Perry, H. Pike, S.H. Paul, T.A. Castoe, D.D. Pollock, and E.J. Carlton. 2022. Integrating genomic and epidemiologic data to accelerate progress towards schistosomiasis elimination. eLife 11: e79320. PDF
  • Nikolakis, Z.L., E.J. Carlton, D.D. Pollock and T.A. Castoe. 2022. A genomic can of worms for schistosome host specificity. Trends in Parasitology 38: 496-497. PDF
  • Nikolakis, Z.L, R.H. Adams, K.J. Wade, A. Lund, E.J. Carlton, T.A. Castoe* and D.D. Pollock*. 2022. Prospects for genomic surveillance for selection in schistosome parasites. Frontiers in Epidemiology 2:932021. (* joint corresponding authors). PDF.
  • Schield, D.R., B.W. Perry, D.C. Card, G.I.M. Pasquesi, A.K. Westfall, S.P. Mackessy, and T.A. Castoe. 2022. The rattlesnake W chromosome: a GC-rich retroelement refugium with retained gene function across ancient evolutionary strata. Genome Biology and Evolution. 14: evac116.  PDF   Supplementary Files and Scripts
  • Westfall, A.K., B.W. Perry, A.H. Kamal, N.R. Hales, J. Kay, M. Sapkota, D.R. Schield, M. Pellegrino, S.M. Secor, S.M. Chowdhury, and T.A. Castoe. 2022. Identification of an integrated stress and growth response switch that directs vertebrate intestinal regeneration. BMC Genomics. 23: 6. PDF
  • Gopalan, S.S., B.W. Perry, D.R. Schield, C. Smith, S.P. Mackessy, and T.A. Castoe. 2022. Origins, genomic structure, and copy number variation of snake venom myotoxins. Toxicon 216: 92-106. PDF

  • Koochekian, N., A. Ascanio, K. Farleigh, D.C. Card, D.R. Schield, T.A. Castoe, and T. Jezkova. 2022. A chromosome-level genome assembly and annotation of the Desert Horned Lizard, Phrynosoma platyrhinos, provides insight into chromosomal rearrangements among reptiles. Gigascience 11: giab098. PDF

2021

  • Farleigh, K., S. Vladimiroa, C. Blair, J.T. Bracken, N. Finger, N. Koochekian, J. Henault, D.R. Schield, D.C. Card, A. Leache, T.A. Castoe, and T. Jezkova. 2021. The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos). Molecular Ecology 30: 4481-4496. PDF

  • Card, D.C., F.J. Vonk, S. Smallbrugge, N.R. Casewell, W. Wüster,  T.A. Castoe, G.W Schuett, W. Booth. 2021. Genome-wide data implicate terminal fusion automixis in King Cobra facultative parthenogenesis. Scientific Reports. 11: 271. PDF
  • Shortt, J.A., L.E. Timm, N.R. Hales, Z.L. Nikolakis, D.R. Schield, B.W. Perry, Y. Liu, B. Zhong, T.A. Castoe, E.J. Carlton, and D.D. Pollock. 2021. Population genomic analyses of schistosome parasites highlight critical challenges facing endgame elimination efforts. Scientific Reports 11: 6884. PDF
  • Schield, D.R., B.W. Perry, Z.L. Nikolakis, S.P. Mackessy, and T.A. Castoe. 2021. Population genomic analyses confirm male-biased mutation rates in snakes. Journal of Heredity 112: 221.227. PDF
  • Nikolakis, Z.L.*, N.R. Hales*, B.W. Perry, D.R. Schield, L.E. Timm, Y., Liu, B. Zhong, K.J. Kechris, D.D. Pollock, E. Carlton, and T.A. Castoe. 2021. Patterns of transmission, relatedness, and genetic diversity inferred from whole genome sequencing of archival blood fluke miracidia (Schistosoma japonicum). PLoS Neglected Tropical Diseases 15: e0009020. (*co-first authors). PDF
  • Schield, D.R., B.W. Perry, G.I.M. Pasquesi, R.W. Orton, Z.L. Nikolakis, A.K. Westfall, and T.A. Castoe. 2021. Applications of genomics and related technologies for studying reptile venoms. Pp. 29-42. In: Handbook of Venoms and Toxins of Reptiles, Second Edition, S.P. Mackessy (Ed.), CRC Press. PDF
  • Adams, R.H., T.A. Castoe, and M. DeGiorgio. 2021. PhyloWGA: chromosome-aware phylogenetic interrogation of whole genome alignments. Bioinformatics 37:1923-1925. PDF – Supplementary Material – Code.

2020

  • Perry, B.W., D.R. Schield, R.H. Adams, and T.A. Castoe. 2020. Microchromosomes exhibit distinct features of vertebrate chromosome structure and function with underappreciated ramifications for genome evolution. Molecular Biology and Evolution. 38(3):904–910. PDF.
  • Perry, B.W, D.R. Schield, A.K. Westfall, S.P. Mackessy and T.A. Castoe. 2020. Physiological demands and signaling associated with snake venom production and storage illustrated by transcriptional analyses of venom glands. Scientific Reports 10: 18083. PDF – Supplementary Material
  • Pollock, D.D.*/T.A.Castoe*, B.W. Perry, S. Lytras, K. Wade, D.L. Robertson, E.C. Holmes, M.F. Boni, S.L. Kosakovsky Pond, R. Parry, E.J. Carlton, J. Wood, P.S. Pennings, and R. Goldstein. 2020. Viral CpG deficiency provides no evidence that dogs were intermediate hosts of SARS-CoV-2. Molecular Biology and Evolution 37:2706-2710. [*co-first authors]. PDF
  • Boni, M.F., P. Lemey, X. Jiang, T. Tsan-Yuk Lam, B.W. Perry, T.A. Castoe, A. Rambout, and D.L. Robinson. 2020. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nature Microbiology  5:1408-1417. PDF – Supplementary Material
  • Schield, D.R, G.I.M. Pasquesi, B.W. Perry, R.H. Adams, Z. L. Nikolakis, R.W. Orton, J.M. Meik, S.P. Mackessy, and T.A. Castoe. 2020. Snake recombination landscapes are concentrated in functional regions despite PRDM9. Molecular Biology and Evolution  37:1272-1294. PDF
  • Adams, R.H., and T.A. Castoe. 2020 Probabilistic species tree distances: implementing the multispecies coalescent to compare species trees within the same model-based framework used to estimate them. Systematic Biology.  69:194-207. PDF
  • Pasquesi, G.I.M., R.P. Ruggiero, B.W. Perry, M.W. Vandewedge, D.R. Schield, and T.A. Castoe. 2020. Vertebrate lineages exhibit diverse patterns of transposable element regulation and expression across tissues. Genome Biology and Evolution 12:506-521. PDF
  • Kazi, M.I., B.W. Perry, D.C. Card, R.D. Schargel, H.B. Ali, V.C. Obuekwe, M. Sapkota, K.N. Kang, M.W. Pelligrino, D.E. Greenberg, T.A. Castoe, and J.M. Boll. 2020. Discovery and characterization of New Delhi metallo-β-lactamase-1 inhibitor peptides that potentiate meropenem-dependent killing of carbapenem-resistant Enterobacteriaceae. Journal of Antimicrobial Chemotherapeutics 75:2843-2851. PDF
  • Reyes-Velasco, J.*, R.H. Adams*, S. Boissinot, C.L. Parkinson, J.A. Campbell, T.A. Castoe, and E.N. Smith. 2020. Genome-wide SNPs clarify lineage diversity confused by coloration in coralsnakes of the Micrurus diastema (Serpentes: Elapidae) species complex. Molecular Phylogenetics and Evolution 147: 106770. (*co-first authors). PDF
  • Campbell, J.A., D.R. Frost, and T.A Castoe. 2020. A new generic name for jumping pitvipers (Serpentes: Viperidae). Revista Latinoamericana de Herpetologia 2:52-53. PDF

2019

  • Schield, D.R., C. Card, N.R. 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   see Data page for genome and annotation files
  • Casewell N.R., D. Petras, D.C. Card, V. Suranse, A.M. Mychajliw, D. Richards, I. Koludarov, L.-O. Albulescu, J. Slagboom, B.-F. Hempel, N.M. Ngum, R.J. Kennerley, J.L. Brocca, G. Whiteley, R.A. Harrison, F.M. Bolton, J. Debono, F.J. Vonk, J. Alföldi, J. Johnson, E. Karlsson, K. Lindblad-Toh, I. Mellor, R.D.  Süssmuth, B.G. Fry BG, S. Kuruppu, W.C. Hodgson, J. Kool, T.A. Castoe, I. Barnes, K. Sunagar,  E.A.B. Undheim and S.T. Turvey. 2019. Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals. Proceedings of the National Academy of Sciences USA 116: 25745-25755. PDF
  • Card, D.C., R.H. Adams, D.R. Schield, B.W. Perry, A.B. Corbin, G.I.M. Pasquesi, K. Row, J.M. Daza, W. Booth, C.E. Montgomery, S.M. Boback, and T.A. Castoe. 2019. Genomic basis of convergent island dwarf phenotypes in boa constrictors. Genome Biology and Evolution 11:3123-3143.  PDF
  • Perry, B.W., L. Andrew, A.H.M. Kamal, D.C. Card, D.R. Schield, G.I.M. Pasquesi, M. Pellegrino, 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  286: 20190910. 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 Castoe, T.A. 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
  • Watson, J.A, C.L. Specer, D.R. Schield, B.O. Butler, L.L. Smith, O. Flores-Viella, J.A. Campbell, S.P. Mackessy, T.A. Castoe, and J.M. Meik. 2019. Geographic variation in morphology in the Mohave Rattlesnake (Crotalus scutulatus Kennicott 1861) (Serpentes: Viperidae): implications for species boundaries. Zootaxa 4683: 129-143. PDF
  • Adams, R.H., 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. Supergene validation: a model-based protocol for assessing the accuracy of non-model-based supergene methods. MethodsX 6: 2181-2188. PDF
  • Pinto, B.J., 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

  • Pasquesi, G.I.M., Adams, R.H., 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
  • Perry, B.W., R. Schield, and T.A. Castoe. 2018. Evolution: Plasticity versus selection, or plasticity and selection? Current Biology 28:R1104-R1106. PDF 
  • Card, D.C., W. 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., C. Card, J.W. McGlothlin, G.I.M. Pasquesi, R.H. Adams, D.R. Schield, 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, T. Gamble, K.B. Storey, 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., 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
  • Schott, R.K., A. Van Nynatten, 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
  • 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, T.A. Castoe, 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
  • Schield, D.R, C. Card, R.H Adams, A.B. Corbin, T. Jezkova, N.R. Hales, J.M. Meik, B.W. Perry, 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., R. Schield, and T.A. Castoe. 2018. Plasticity and local adaptation explain lizard cold tolerance. Molecular Ecology 27: 2173-2175. PDF
  • Adams, R.H., 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  see also Software Page
  • Hales, N., 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.*, W. 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. (*joint primary authors) PDF
  • Schield, D.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., R. Schield, D.C. Card, H. Blackmon, and T.A. Castoe. 2017. GppFst: Genomic posterior predictive simulations of Fstand dXY for identifying outlier loci from population genomic data. Bioinformatics 33:1414-1415. PDF  see also Software Page (GPPFst)
  • Schott, R.K., B. Panesr, 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., 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, 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

  • 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
  • Streicher, J.W., J.P. McEntee, L. Drzich, 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. [Cover Article]  PDF
  • Adams, R.H., H.G. Blackman,  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
  • Card, D.C., D.R Schield, 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
  • 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
  • Schield, D.R., M.F. Walsh, 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 sequencing. Methods in Ecology and Evolution 7:60-69. [Cover Article] PDF
  • Shaney, K.J., H. Adams, N. Kurniawan, A. Hamidy, E.N. Smith, and T.A. Castoe. 2016. A suite of potentially amplifiable microsatellite loci for reptiles of conservation concern from Africa and Asia. Conservation Genetics Resources 8: 309. PDF
  • Verity, R., C. Collins, 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
  • Schield, D.R, 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
  • 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
  • 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
  • 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

2015

  • Andrew, A.L., 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., 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, 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
  • 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
  • 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

  • Greene, R.E., E.L. Braun, J. Armstrong, D. Earl, N. Nguyen, M.W. Vandewedge, J.A. St John, S. Capelia-Gutierrez, T.A. Castoe, 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
  • Reyes-Velasco J., 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
  • 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
  • Card, D.C., 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
  • Gilbert, C., J.M. Meik, D. Dashevsky, 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
  • Shaney, K.J., 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
  • 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
  • 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, USA110: 20645-20650. PDF

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

  • 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 -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

  • 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
  • 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, andC. stejnegeri). Molecular Phylogenetics and Evolution 69:524-534. 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 illustrate 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

  • 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]
  • 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
  • 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
  • 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
  • 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
  • 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

2011

  • 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
  • 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
  • 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
  • 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
  • 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

  • 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
  • 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. [*Joint primary authors] PDF

2009

  • 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. [Cover Article] [Highly Accessed]  PDF

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

  • 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. , 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
  • 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

2008

  • 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
  • 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

2007

  • 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., 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
  • See quotes from Todd in: “Training postdocs: communication is key”, 2007, by Laura Bonetta in Science 317:1239. 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., 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 Neusticurusand 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 Atractuswith 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. 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. Microhabitat selection in Porthidium nasutum (Serpentes: Viperidae) in Costa Rica, with comments on ontogenetic variation. Herpetological Review 33: 174-175.  PDF