Castoe Lab


Department of Biology

University of Texas Arlington

 

Castoe Lab Members

Stuff I do in the lab

PCR and Sanger Sequencing; Next-Generation Library Preparation (RADseq, RNAseq, shotgun genomes); Phylogenomics; Population Genomics; Microsatellite Scans from Raw Reads or Assembled Genomes; Genome Assembly; Analysis of Next-Generation Sequencing Data


Publications

Google Scholar Citation Link: http://scholar.google.com/citations?user=umOwsMAAAAAJ


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.  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 Online Early: DOI 10.1002/ece3.2996. PDF


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


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


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


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


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


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



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





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


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


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.


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. In Press. Squamate reptile genomics and evolution. In: Handbook of Toxinology: Venom Genomics and Proteomics, P. Gopalakrishnakone (Ed.), Springer Reference Press, New York, NY.


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


Coauthor of Introductory Biology Laboratory Manual:


2013 Aguilar, B., D. Card, J. Chaudhuri, S. Domingues, D. Jangam, H. Liu, W. Mann, C. Marquez, M. Parihar, J. Reyes-Velasco, D. Sanchez, M. Steffenson, M. Walsh. 1441: Cell and Molecular Biology Laboratory Manual. Published by the Beta Phi Chapter of Phi Sigma Society.


Research & Educational Funding

Summary: ~$38,000 research; ~$130,000 salary/education; & ~$3,600 travel support


2016 Card, D.C. UTA Graduate Studies Writing Group Award. UTA. $200.


2016 Card, D.C. UTA ACES Conference Sustainability Award. UTA. $300.


2016 Card, D.C. UTA ACES Conference Provost’s Award. UTA. $200.


2015 Card, D.C. College of Science Dean’s Excellence Scholarship, 2015-2016. UTA. $5,000.


2015 Card, D.C. Genomic basis of convergent phenotypic evolution in island populations of Boa constrictor. UTA Phi Sigma Graduate Society Large Research Grant. $5,000.


2015 Card, D.C. Travel support for the Society for Molecular Biology and Evolution meeting. Institute of Population Genetics. Vienna, Austria. $500.


2015 Castoe, T.A. (P.I.) & D.C. Card (Co P.I.). Genomic basis of convergent phenotypic evolution in island populations of boa constrictors. National Science Foundation Doctoral Dissertation Improvement Grant. $19,695.


2015 Card, D.C. Full travel support for the NESCent Hackathon on Population Genetics in R. NESCent. Durham, NC. $1,800.


2014 Card, D.C. Travel support for the Ecological Genomic Symposium. American Genetics Association. Kansas City, MO. $500.


2014 Card, D.C. Population structure and species evolution of Burmese pythons in Southeast Asia. American Philosophical Society Lewis & Clark Fund for Exploration and Field Research. $5,000.


2014 Card, D.C. Investigating the genomic basis of phenotypic convergence in dwarf insular populations of the Boa constrictor. NSF Graduate Research Fellowship Program. Honorable Mention.


2014 Card, D.C. Travel support for the Phylgonomics Symposium & Software School. University of Texas & Society for Systematic Biology. 2014 Joint Evolution Meetings. Raleigh, NC. $250.


2014 Card, D.C. Sample sequencing of amphibian genomes to establish estimates of repetitive content and genome structure. UTA Phi Sigma Graduate Society Large Research Grant. $5,000.


2013 Card, D.C. Population genomics, origins, and adaptation of invasive Burmese pythons in Florida. Society for the Study of Evolution Rosemary Grant Award 2013. $2,250.


2013 Card, D.C. Travel support for the Mechanisms of Protein Evolution II meeting. SMBE. Denver, CO. $500.


Enhanced Graduate Teaching Assistantship. UT-Arlington. $125,000 for 2012-2017.


Texas Public Educational Grants, UT-Arlington. $12,000 total since 2012.


Chautauqua Region Community Foundation Scholarships. $15,000 total since 2006.


Scientific Presentations and Published Abstracts (Since 2015)

2016 Card, D.C.†, D.R. Schield R.H. Adams, A.L. Andrew, B.W. Perry, F. Mazzotti, M.E. Hunter, K. Hart, & T.A. Castoe. Genome-wide evidence of evolution and adaptation in the invasive Florida python population. Joint Evolution Meetings 2016. Austin, TX.


2016 Schield, D.R.†, R.H. Adams, D.C. Card, B.W. Perry, T. Jezkova, A.L. Andrew, G.I. Pasquesi, S. Mackessy, & T.A. Castoe. Patterns of speciation and delimitations of populations, species, and genomic adaptations across widely-distributed North American rattlesnake lineages. Joint Evolution Meetings 2016. Austin, TX.


2016 Streicher, J.W.†, J. McEntee, L. Drzich, D.C. Card, D.R. Schield, U. Smart, C. Parkinson, T. Jezkova, E.N. Snith, & T.A. Castoe. Genetic surfing, not allopatric divergence, explains spatial sorting of mitochondrial haplotypes in venomous coralsnakes. Joint Evolution Meetings 2016. Austin, TX.


2016 Lotterhos, K.E.†, D.C. Card, C. Collins, S.M. Schaal, L. Wang, & R. Verity. Multivariate outliers improve the signal-to-noise ratio in genome scans. Joint Evolution Meetings 2016. Austin, TX.


2016 Adams, R.H.†, D.R. Schield, D.C. Card, & T.A. Castoe. Friend or Foe: Investigating the impacts of positive selection on multispecies coalescent inferences. Joint Evolution Meetings 2016. Austin, TX.


2016 Jezkova, T.†, T.A. Castoe, M. Leal, D.C Card, D.R. Schield, D. Elzinga, & J. Rodriguez-Robles. A peculiar case of hybridization with advantageous mtDNA introgression and lack of nuclear introgression in Caribbean anoles. Joint Evolution Meetings 2016. Austin, TX.


2016 Perry, B.W.†, A.L. Andrew, D.C. Card, S. Secor, & T.A. Castoe. Intestinal regeneration in the garden of eatin’: Comparative genomic analysis of extreme intestinal regenertion growth in snakes paves the path for translational research in human systems. Joint Evolution Meetings 2016. Austin, TX.


2016 Cox, C.†, N.B. Pollock, H. John-Alder, A.L. Andrew, D.C. Card, T.A. Castoe, & R. Cox. Evolutionary lability in the modulation of sex-biased gene expression by testosterone. Joint Evolution Meetings 2016. Austin, TX.


2016 Pasquesi, G.I.†, D.C. Card, R.H. Adams, A.B. Corbin, D.R. Schield, & T.A. Castoe. Evolutionary dynamics of genomic repeat element landscapes across 200 million years of squamate evolution. Joint Evolution Meetings 2016. Austin, TX.


2016 Verity, R., C. Collins, D.C. Card†, S.M. Schaal, L. Wang, & K.E. Lotterhos. MINOTAUR. IEvoBio Meeting at Evolution 2016. Austin, TX.


2016 Castoe, T.A.†, G.I. Pasquesi, R.H. Adams, D.C. Card, & D.R. Schield. Sample sequencing 68 squamate genomes reveals extensive genomic repeat landscape dynamics. International Congress on Transposable Elements. Saint Malo, France.


2016 Card, D.C.†, D.R. Schield, R.H. Adams, M. Hunter, K. Hart, & T.A. Castoe. Genome-wide evidence of evolution and adaptation in the invasive Florida python population. Annual Celebration of Excellence by Students (UTA-ACES). Arlington, TX.


2016 Adams, R.H.†, D.R. Schield, D.C. Card, & T.A. Castoe. Natural selection and multispecies coalescent models: Investigating the impacts of directional selection on phylogenetic inferences of recently-diverged species complexes. Annual Celebration of Excellence by Students (UTA-ACES). Arlington, TX.


2016 Andrew, A.L.†, D.C Card, D.R. Schield, B.W. Perry, R.H. Adams, R.P. Ruggiero, D.D. Pollock, S.M. Secor, & T.A Castoe. Dynamics of gene expression and mechanisms of growth throughout post-prandial organ regeneration in the Burmese python. Annual Celebration of Excellence by Students (UTA-ACES). Arlington, TX.


2016 Pasquesi, G.I.†, D.C. Card, R.H. Adams, D.R. Schield, A.B. Corbin, B.W. Perry, A.L. Andrew, & T.A. Castoe. Sample sequencing 68 squamate genome reveals extensive evolutionary dynamics of genomics repeat element landscapes. Annual Celebration of Excellence by Students (UTA-ACES). Arlington, TX.


2016 Cox, C.L.†, N.B. Pollock, H. John-Alder, A.L Andrew, D.C. Card, T.A. Castoe, & R.M Cox. Sex hormones and the evolution of sexual size dimorphism: the impact of testosterone on sex-biased gene expression and growth-regulatory networks. Society for Integrative and Comparative Biology Meeting. Portland, OR.


2015 Reyes-Velasco, J.†, D.C. Card, A.L. Andrew, K.J. Shaney, R.H. Adams, D.R. Schield, N.R. Casewell, S.P. Mackessy, & T.A. Castoe. Expression of venom gene homologs in diverse python tissues: a new model for the evolution of snake venom and a re-assignment of transcriptome-based definitions of venoms. International Society on Toxinology, 18th World Contress. Oxford, England.


2015 Row, K.W.†*, D.C Card, & T.A. Castoe. Identifying the geneic architecture of insular dwarfism in Boa constrictor through examination of protein coding regions of the NEK4 gene. UT System LSAMP Student Research Conference. El Paso, TX.


2015 Lapp, H.† & Participants of the Population Genetics in R Hackathon. Towards and interoperating ecosystem of tools and resources for population genetics in R International Confereence on Intelligent Systems for Molecular Biology/European Conference on Computational Biology Meeting. Dublin, Ireland.


2015 Card, D.C.†, D.R. Schield, R.H. Adams, W. Booth, S. Boback, & T.A. Castoe. Mitochondrial and nuclear SNP evidence for population genetic structure, independent islands dwarfism, and genes putatively underlying dwarfism traits in Boa constrictor. Society for the Study of Amphibians and Reptiles Meeting. Lawrence, KS.


2015 Castoe, T.A.†, D.C. Card, D.R. Schield, J. Reyes-Velasco, A.L. Andrew, R.H. Adams, & G.I. Pasquesi. Ancient, recent, and ongoing patterns of genome evlution underlying adaptation and innovation in snakes. Society for the Study of Amphibians and Reptiles Meeting. Lawrence, KS.


2015 Andrew, A.L.†, D.C. Card, R.P. Ruggiero, D.R. Schield, R.H. Adams, D.D. Pollock, S.M. Secor, E. La, & T.A. Castoe. Patterns of gene expression underlying extreme physiological remodeling in snakes. Society for the Study of Amphibians and Reptiles Meeting. Lawrence, KS.


2015 Schield, D.R.†, G.I. Pasquesi, R.H. Adams, D.C. Card, & T.A. Castoe. Patterns of selection and introgression following isolation and secondary contact in a widely-distributed rattlesnake species (Crotalus atrox). Society for the Study of Amphibians and Reptiles Meeting. Lawrence, KS.


2015 Adams, R.H.†, D.R. Schield, D.C. Card, S.P. Mackessy, & T.A. Castoe. How does natural selection influence species trees and species delimintation using genome-scale datasets - a case study in rattlesnakes. Society for the Study of Amphibians and Reptiles Meeting. Lawrence, KS.


2015 Card, D.C.†, D.R. Schield, K. Hart, M.E. Hunter, & T.A. Castoe. Evolution and putative adaptation in the invasive Florida Burmese python population inferred using genome-wide RADseq data. Society for Molecular Biology and Evolution Meeting 2015. Vienna, Austria.


2015 Card, D.C.†, D.R. Schield, R.H. Adams, W. Booth, S.M. Boback, & T.A. Castoe. Genomic basis of adaptive island dwarfism in Boa constrictor. Annual Celebration of Excellence by Students (UTA-ACES). Arlington, TX.


2015 Schield, D.R.†, M.R. Walsh, D.C. Card, A.L. Andrew, R.H. Adams, & T.A. Castoe. EpiRADseq: a novel technique for the examination of genome-wide epigenetic patterns. Annual Celebration of Excellence by Students (UTA-ACES). Arlington, TX.


2015 Adams, R.H.†, D.C. Card, J. Reyes-Velasco, D.R. Schield, A.L. Andrew, & T.A. Castoe. Sample sequencing 46 squamate reptiles reveals extensive evolutionary dynamics of genomic repeat landscapes. Annual Celebration of Excellence by Students (UTA-ACES). Arlington, TX.


2015 Andrew, A.L.†, D.C. Card, R.P. Ruggiero, D.R. Schield, R.H. Adams, D.D. Pollock, S.M. Secor, E. La*, & T.A. Castoe. Patterns of gene expression underlying extreme physiological remodeling in snakes. Annual Celebration of Excellence by Students (UTA-ACES). Arlington, TX.


2015 Cox, C.L.†, D.C. Card, A.L. Andrew, T.A. Castoe, & R.M. Cox. Sexual concordance in phenotypic and transcriptomic responses to testosterone in brown anoles. Society for Integrative and Comparative Biology Meeting. West Pal Beach, FL.


† Presenting author

* Undergraduate author


Invited Lectures

2013 Card, D.C. A crash course in genomics for environmental biology. Science Speaker Series. Jamestown Community College. Jamestown, NY.


Service

Ad hoc reviewer

Molecular Ecology Resources, PLOS ONE, Biological Journal of the Linnean Society, Genetica, Reinvention: an International Journal of Undergraduate Research


Undergraduate Mentoring

Acacia Young              LSAMP Scholar        Florida python population genetics & adaptation

Kristopher Rowe        LSAMP Scholar        Boa constrictor candidate gene screening

Laura Drzich               McNair Scholar        Squamate genomics

Elizabeth Nguyen      Honors Research     Transcriptomics of snake physiological remodeling

Frances N. Proctor    Research                   Boa constrictor phylogenetics

Zachary Rodriguez    McNair Scholar        Ahaetulla phylogeography

Jessica Stephens       Research                   Daphnia evolution

Nicole Hales               Research                   Crotalus rattlesnake population genetics

Timothy Witter         Teaching                    Human Anatomy laboratory


Workshop, Meeting, or Symposia Organization

2015. Organizer of Software Carpentry workshop at UT-Arlington. Sponsored by Phi Sigma Biology Graduate Honor Society, Department of Biology, College of Science, & Office of Graduate Studies. Organized a two-day Software Carpentry workshop for 80 graduate level participates from UTA and other Dallas-Fort Worth universities. This workshop provided introductory, hands-on instruction in valuable data analysis software, including manipulating data with the Unix shell, version control with Git/GitHub, and statistic analysis and figure generation using R.


Working Group Participation

2015. Population genetics in R Hackathon. Sponsored and hosted by the National Evolutionary Synthesis Center (NESCent)


Extracurricular

Biology Graduate Student Phi Sigma Society, UTA

    Present: Member                Past: President, Secretary, Manual Sales Coordinator


Graduate Student Advisory Council, Society for the Study of Evolution

    Present: 2-year term


Professional Societies

Society for the Study of Evolution Society for Molecular Biology and Evolution, American Genetics Association, American Association for the Advancement of Science, Consortium for Snake Genomics


Teaching Experience

Graduate Teaching Assistant – UT-Arlington

        2012-Present: Zoology Laboratory (Fall 2012, 2014, 2015, 2016; Spring 2013, 2014,

        2015, 2016; Summer 2013, 2014, 2015, 2016) and Human Anatomy (Fall 2013)


Undergraduate Teaching Assistant – SUNY-ESF

2010-2011: General Biology Laboratory I/II and Introduction to Conservation Biology


Contact information

Email – dcard@uta.edu

Twitter – @darencard

Online – www.darencard.net

Office – ERB 444


 

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

Daren C. Card

Quantitative Biology, Ph.D. Student


Origins

Jamestown, Western New York, NY, USA


Degrees

B.S. Conservation Biology – SUNY College of Environmental Science and Forestry (ESF), Syracuse, NY


Research

My research focuses on population genetics and putative adaptation in recently established snake (Python and Boa) populations. It also encompasses comparative genomics and genome evolution across the vertebrates, mostly focusing on the amphibian and reptilian (specifically squamate) lineages.


See Daren’s personal website at www.darencard.net for more detailed and up-to-date information.