Publications
PDFs for individual use only
2023
Farleigh, K., A. Ascanio, M.E. Farleigh, D.R. Schield, D.C. Card, M. Leal, T.A. Castoe, T. Jezkova, and J.A. Rodríguez-Robles. 2023. Signals of differential introgression in the genome of natural hybrids of Caribbean anoles. Molecular Ecology 32: 6000–6017. link PDF
Smith, C.F., 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. link PDF
Smith, C.F., Nikolakis, Z.L., Perry, B.W., Ivey, K., Schield, D.R., Balchan, N.R., Parker, J., Hansen, K.C., Saviola, A.J., Castoe, T.A., Mackessy, S.P. 2023. Snakes on a plain: Biotic and abiotic factors determine venom compositional variation in a wide-ranging generalist rattlesnake. BMC Biology 21: 136. link PDF
Carter, J.K., R.T. Kimball, E.R. Funk, N.C. Kane, D.R. Schield, G.M. Spellman, and R.J. Safran. 2023. Estimating phylogenies from genomes: A beginner’s review of commonly used genomic data in vertebrate phylogenomics. Journal of Heredity. link PDF
2022
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 evo.14612. link PDF
Schield, D.R., B.W. Perry, R.H. Adams, M.L. Holding, Z.L. Nikolakis, S.S. Gopalan, C.F. Smith, J.M. Parker, J.M. Meik, M. DeGiorgio, S.P. Mackessy, and T.A. Castoe. The roles of balancing selection and recombination in the evolution of rattlesnake venom. Nature Ecology and Evolution 6: 1367-1380. link PDF Supplement
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. link PDF
Gopalan, S.S., B.W. Perry, D.R. Schield, C.F. Smith, S.P. Mackessy, and T.A. Castoe. Origins, genomic structure and copy number variation of snake venom myotoxins. Toxicon 216: 92-106. link PDF
Perry, B.W., S.S. Gopalan, G.I.M. Pasquesi, D.R. Schield, A.K. Westfall, C.F. Smith, I. Koludarov, P.T. Chippendale, M.W. Pellegrino, E.B. Chuong, S.P. Mackessy, and T.A. Castoe. Snake venom gene expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways. Genome Research 32: 1058–1073. link PDF
Turbek, S.P., D.R. Schield, E.S.C. Scordato, A. Contina, X. Da, Y. Liu, E. Pagani-núñez, Q. Ren, C.C.R. Smith, C. Stricker, M. Wunder, D. Zonana, and R.J. Safran. 2022. A migratory divide spanning two continents is associated with genomic and ecological divergence. Evolution. link 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: 1-14. link pdf
Westfall, A.K., B.W. Perry, A.H.M. Kamal, N.R. Hales, J.C. Kay, M. Sapkota, D.R. Schield, M.W. Pellegrino, S.M. Secor, S.M. Chowdhury, and T.A. Castoe. 2022. Identification of an integrated stress and growth response signaling switch that directs vertebrate intestinal regeneration. BMC Genomics 23: 6. link PDF
2021
Alaya, M.J.†, J.K. Carter†, A.S. Fachon†, S.M. Flaxman†, M.A. Gil†, H.V. Kenny, Z.M. Laubach†, S.A. Madden†, M.T. McDermott†, A. Medina-García†, R.J. Safran†, E. Scherner†, D.R. Schield†, S. Vasquez-Rey†, and J. Volckens†. Belonging in STEM: an interactive, iterative approach to create and maintain a diverse learning community. Trends in Ecology and Evolution 36: 964–967. (†Co-first authors) link PDF
Farleigh, K., S.A. Vladimirova, C. Blair, J.T. Bracken, N. Koochekian, N. Finger, D.R. Schield, D.C. Card, J. Henault, A.D. Leaché, 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: 2313-2332. link PDF
Schield, D.R., E.S.C. Scordato, C.C.R. Smith, J.K. Carter, S.I. Cherkaoui, S. Gombobaatar, S. Hajib, S. Hanane, A.K. Hund, K. Koyama, W. Liang, Y. Liu, N. Magri, A. Rubtsov, B. Sheta, S.P. Turbek, M.R. Wilkins, L. Yu, and R.J. Safran. 2021. Sex-linked genetic diversity and differentiation in a globally distributed avian species complex. Molecular Ecology 30: 2313-2332. Link 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, Boca Raton FL. PDF
Schortt, 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 highlights critical challenges facing end-game elimination efforts. Scientific Reports 11: 6884. Link 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 122: 221-227. Link PDF
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2020
Schield, D.R., G.I.M. Pasquesi, B.W. Perry, R.H. Adams, Z.L. Nikolakis, A.K. Westfall, 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. Link PDF
- (Recombination maps are available here)
Z.L. Nikolakis, 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. 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.
B.W. Perry, D.R. Schield, R.H. Adams, and T.A. Castoe. Microchromosomes exhibit distinct features of vertebrate chromosome structure and function with underappreciated ramifications for genome evolution. Molecular Biology and Evolution. Link PDF
Perry, B.W., D.R. Schield, A.K. Westfall, S.P. Mackessy, and T.A. Castoe. Physiological demands and signaling mechanisms associated with snake venom production and storage illustrated by transcriptional analyses of venom glands. Scientific Reports 10: 18083. link PDF
Pasquesi, G.I.M., B.W. Perry, R.P. Ruggiero, M.W. Vandewege, 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. Link PDF.
2019
Card, D.C., R.H. Adams, D.R. Schield, B.W. Perry, A.B. Corbin, G.I.M. Pasquesi, K. Row, J. Daza, W. Booth, C. Montgomery, S. Boback, and T.A. Castoe. 2019. Genomic basis of convergent island phenotypes in boa constrictors. Genome Biology and Evolution 11: 3123-3143. Link PDF
Watson, J.A., C.L. Spencer, D.R. Schield, B.O. Butler, L.L. Smith, O. Flores-Villela, J.A. Campbell, S.P. Mackessy, T.A. Castoe, and J.M. Meik. Geographic variation in morphology in the Mohave Rattlesnake (Crotalus scutulatus Kennicott 1861) (Serpentes: Viperidae): implications for species boundaries. Zootaxa 4683: 129-143. Link PDF
Perry, B.W., A.L. Andrew, A.H.M. Kamal, D.C. Card, D.R. Schield, G.I.M. Pasquesi, M.W Pellegrino, S.P. Mackessy, S.M. Chowdhury, S.M. Secor, and T.A. Castoe. Multi-species comparisons of snakes identify coordinated signaling networks underlying post-feeding intestinal regeneration. Proceedings of the Royal Society of London B 286: 20190910. Link 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. Allopatric divergence and secondary contact with gene flow – a recurring theme in rattlesnake speciation. 2019. Biological Journal of the Linnean Society 128: 149-169.
(†Co-first authors) Link 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. Link PDF
- (Genome data are available here)
Adams, R.H., D.R. Schield, and T.A. Castoe. Recent advances in the inference of gene flow from population genomic data. Current Molecular Biology Reports 5: 107-115. (Invited Article). PDF
2018
Strickland, J.L., C.F. Smith, A.J. Mason, D.R. Schield, M. Borja, G. Casteñeda-Gaytán, C.L. Spencer, L.L. Smith, A. Trápaga, N.M. Bouzid, G. Campillo-García, O.A. Flores-Villela, D. Antonio-Rangel, S.P. Mackessy, T.A. Castoe, D.R. Rokyta, and C.L. Parkinson. 2018. Evidence for divergent patterns of local selection driving venom variation in Mojave Rattlesnakes (Crotalus scutulatus). Scientific Reports 8: 17622. Link PDF
Card, D.C., B.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. Link PDF
Perry, B.W., D.R. Schield, and T.A. Castoe. 2018. Evolution: Plasticity versus selection, or plasticity and selection? Current Biology 28:R1104-R1106. Link PDF
Perry, B.W., D.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. Link PDF
Pasquesi, G.I.M., R.H. Adams, 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. Link PDF
Schield, D.R., D.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 10.1016/j.ympev.2018.06.013. Link PDF
Adams, R.H., D.R. Schield, D.C. Card, and Castoe, T.A. 2018. Assessing the impacts of positive selection on coalescent-based species tree estimation and species delimitation. Systematic Biology 67:1076-1090. Link PDF
Card, D.C, D.R. Schield, and T.A. Castoe. Plasticity and local adaptation explain lizard cold tolerance. Molecular Ecology 27: 2173-2175. Link PDF
Adams, R.H., D.R. Schield, D.C. Card, A.B. Corbin, and T.A. Castoe. 2017. ThetaMater: Bayesian estimation of population parameter θ from genomic data. Bioinformatics 34: 1072-1073. Link 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. Link PDF
Andrew, A.L.†, B.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. (†co-first authors) Link 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. Link PDF
Hales, N.R., D.R. Schield, A.L. Andrew, D.C. Card, M.R. Walsh, and T.A. Castoe. 2017. Contrasting gene expression programs underlie predator-induced phenotypic plasticity within and across-generations in Daphnia. Molecular Ecology 26: 5003-5015. Link 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. Link PDF
2016
Adams, R.H., D.R. Schield, D.C. Card, H. Blackmon, and T.A. Castoe. 2016. GppFst: Genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data. Bioinformatics 33:1414-1415. Link 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. In: Rattlesnakes of Arizona, G.W. Schuett, L.W. Porras, and R.S. Reiserer (Eds.), Eco Books. PDF
Card, D.C., D.R Schield, R.H. Adams, A.B. Corbin, B.W. Perry, 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. Link 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 venomous coralsnakes. Evolution 70: 1435-1449. Cover Article. Link PDF
Adams, R.H., H.G. Blackmon, 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. Link 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 sequencing. Methods in Ecology and Evolution 7: 60-69. Cover Article. Link PDF
2015
Andrew, A.L., D.C. Card, R.R. 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 (5): 147-157. Link PDF
Schield, D.R., D.C. Card, J. Reyes-Velasco, T. Jezkova, F.N. Proctor, C.L. Spencer, H.W. Herrmann, S.P. Mackessy, T.A. Castoe. 2014. Incipient speciation and biased gene flow between two lineages of the Western Diamondback Rattlesnake (Crotalus atrox). Molecular Phylogenetics and Evolution 83: 213-223. Link PDF
2014
Jezkova, T., B.R. Riddle, D.C. Card, D.R. Schield, M.E. Eckstut, T.A. Castoe. 2014. Genetic consequences of post-glacial range expansion in two co-distributed rodents (genus Dipodomys) depend on ecology and genetic marker choice. Molecular Ecology 24: 83-97. Link PDF
Reyes-Velasco, J., D.C. Card, A.L. Andrew, K.J. Shaney, R.H. Adams, D.R. Schield, N. 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. Link 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. Link PDF
Shaney, K.J., D.C. Card, D.R. Schield, 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. Link 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. Link PDF
2012
Schield, D.R. and H.L Waye. 2012. Thamnophis radix: tonic immobility. Natural History. Herpetological Review 43(2): 352. PDF