Publications

Underlined authors: members of the Adams Analytics Group

• TraitTrainR: accelerating large-scale simulation under models of continuous trait evolution. Roa Lozano J, Duncan M, McKenna D, Castoe T, DeGiorgio M, Adams R. 2025. Bioinformatics Advances

• A tale of too many trees: A conundrum for phylogenetic regression.. Adams R, Roa Lozano J, Duncan M,Green J Assis R, DeGiorgio M. Accepted 2025. Molecular Biology and Evolution

• Robust Phylogenetic Regression. Adams R, Cain Z, Assis R, DeGiorgio D. 2024. Systematic Biology

• A chromosome-level reference genome for the common bed bug, Cimex lectularius, with identification of sex chromosomes. Miles L, Adams R, Francioli Y, Card D, Castoe T, Booth W. Journal of Heredity

• Functional and evolutionary insights into chemosensation and specialized herbivory from the genome of the red milkweed beetle, Tetraopes tetrophthalmus (Cerambycidae: Lamiinae). Adams R, Terrence S, Mitchell R, Price M, Shen R, McKenna D 2024. Journal of Heredity

• Investigating a Role for Model-Based Inquiry in an Undergraduate Introductory Biology Lab. Karen K, Snyder B, Adams R. 2024 The American Biology Teacher

• The genome of the invasive and broadly polyphagous Diaprepes root weevil, Diaprepes abbreviatus (Coleoptera), reveals an arsenal of putative polysaccharide-degrading enzymes. Sylvester T,Adams R, Hunter W, Li X, Rivera-Marchand B, Shen R, Shin NR, McKenna D. 2024 Journal of Heredity

• Comparative analyses of the banded alder borer (Rosalia funebris) and Asian longhorned beetle (Anoplophora glabripennis) genomes reveal significant differences in genome architecture and gene content among these and other Cerambycidae. Sylvester T,Adams R, Mitchell R, Ray A, Shen R, Shin N R, McKenna D. 2024 Journal of Heredity

• Diverse gene regulatory mechanisms alter rattlesnake venom gene expression at fine evolutionary scales. Gopalan S, Perry B, Francioli Y, Schield D, Guss H, Bernstein J, Ballard K, Smith C, Saviola A,Adams R, Mackessy S, Castoe T. 2024 Genome Biology and Evolution

• Mitochondrial DNA variation in honey bee (Apis mellifera) colonies from Arkansas. Cleary D,Adams R, Szalanski A. 2024 Journal of Apicultural Research

• Likelihood-based tests of species tree hypotheses. Adams R, DeGiorgio M. 2023. Molecular Biology and Evolution

• Single-cell heterogeneity in snake venom expression is hardwired by co-option of regulators from progressively activated pathways. Westfall A, Gopalan S, Perry B, Adams R, Saviola A, Mackessy S, Castoe T. 2023. Genome Biology and Evolution

• The roles of balancing selection and recombination in the evolution of rattlesnake venom. Schield D, Perry B, Adams R, Holding M, Nikolakis Z, Gopalan S, Smith C, Parker S, DeGiorgio M, Mackessy S, and Castoe T. 2022. Nature Ecology and Evolution.

• Fifty million years of beetle evolution along the Antarctic Polar Front. Baird H, Shin S, Oberprieler R, Hullé M, Vernon P, Moon K, Adams R, McKenna D, Chown S Proceedings of the National Academy of Sciences 2021. PNAS Commentary VIDEO

• Evidence that genomic incompatibilities and other multilocus processes impact fitness in a rattlesnake hybrid zone Nikolakis Z, Schield D, Westfall A, Perry B, Ivey K, Orton R, Hales N, Adams R, Meik J, Parker J, Smith C, Gompert Z, Mackessy S, and Castoe T Evolution. 2022.

• Prospects for genomic surveillance for selection in schistosomiasis Nikolakis Z, Adams R, Wade K, Lund A, Carlton E, Castoe T, Pollock D Frontiers in Epidemiology 2022.

• Of traits and trees: probabilistic distances for dissecting the interplay among phylogeny, model, and data. Adams R, Blackmon H, and DeGiorgio M. Systematic Biology(2021) PDF

• Probabilistic species tree distances: implementing the multispecies coalescent to compare species trees within the same model-based framework used to estimate them. Adams R, and Castoe T. 2020. Systematic Biology PDF

• PhyloWGA: chromosome-aware phylogenetic interrogation of whole genome alignments. Adams R, Castoe T., and DeGiorgio M. 2020. Bioinformatics PDF

• Microchromosomes exhibit distinct features of vertebrate chromosome structure and function with underappreciated ramifications for genome evolution.. Perry B, Schield D, Adams R, and Castoe T. 2020. Molecular Biology and Evolution PDF

• Genome-wide SNPs clarify lineage diversity confused by coloration in coralsnakes of the Micrurus diastema (Serpentes: Elapidae) species complex. *Reyes-Velasco J, *Adams R, S. Boissinot, C.L. Parkinson, J.A. Campbell, Castoe T, and E.N. Smith. 2020. Molecular Phylogenetics and Evolution.*co-first author PDF.

• Snake Recombination Landscapes Are Concentrated in Functional Regions despite PRDM9. Schield D, Pasquesi G, Perry B, Adams R, Nikolakis Z, Orton R, Meik J, Mackessy S, and Castoe T 2020. Molecular Biology and Evolution. PDF

• Recent advances in the inference of gene flow from population genomic data. Adams R, Schield D, and Castoe T. 2019. Current Molecular Biology Reports. PDF

• Statistical binning suffers profound model violation due to gene tree error incurred by trying to avoid gene tree error. Adams R, and Castoe T. 2019. Molecular Phylogenetics and Evolution. PDF

• Supergene validation: a model-based protocol for assessing the accuracy of non-model-based supergene methods. Adams R, and Castoe T. MethodsX 2019. PDF

• Genomic basis of convergent island phenotypes in boa constrictors. Card D, Adams R, Corbin A, Perry B, Andrew A, Pasquesi G, Boback S, and Castoe T. Genome Biology and Evolution. 2019. PDF

• Allopatric divergence and secondary contact with gene flow – a recurring theme in rattlesnake speciation. Schield D,* Perry B*, Adams R, Card D, T. Jezkova, Pasquesi G, Z.L. Nikolakis, K. Row, Meik J, Smith C, Mackessy S, and Castoe T. 2019. Biological Journal of the Linnean Society. *joint primary authors. PDF

• The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes. Schield D, Card D, Hales N, Perry B, Pasquesi G, Blackmon H, Adams R, Corbin A, Smith C, B. Ramesh, Demuth J, Betran E, Tollis M, Meik J, Mackessy S and Castoe T. 2019. Genome Research. PDF

• A database of amphibian karyotypes. Perkins R, Gamboa J, Jonika M, Lo J, Shum A, Adams R, & Blackmon H 2019. Chromosome Research

• Assessing the impacts of positive selection on coalescent-based species tree estimation and species delimitation. Adams R, Card D, Schield D, and Castoe T. 2018. Systematic Biology . PDF

• ThetaMater: Bayesian estimation of population size parameter θ from genomic data. Adams R, Card D, Schield D, Corbin A, and Castoe T. 2018. Bioinformatics. PDF

• Novel ecological and climatic conditions drive rapid adaptation in invasive Florida Burmese pythons. Card D, B. Perry, Adams R, Schield D, Young A, Andrew A, Jezkova T, Walsh M, Rockford M, Mazzotti F, Hart K, Hunter M, and Castoe T. 2018. Molecular Ecology. PDF

• Molecular adaptations for sensing and securing prey, and insight into amniote genome diversity, from the garter snake genome. Perry, B.W, Card D, Pasquesi, G.I.M., Adams R, Schield D, N.R. Hales, Corbin A, Demuth J, F.G. Hoffmann, M.W. Vandewege, R. Schott, N. Bhattacharyya, B.S.W. Chang, N.R. Casewell, G. Whiteley, J. Reyes-Velasco, Mackessy S, K.B. Storey, Gamble, T., 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 Castoe T. 2018. Genome Biology and Evolution. PDF

• Cryptic genetic diversity, population structure, and gene flow in Mohave rattlesnakes Crotalus scutulatus. Schield D, Card D, Adams R, Corbin A, T. Jezkova, N.R. Hales, Meik J, 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, Mackessy S and Castoe T. 2018. Molecular Phylogenetics and Evolution. PDF

• Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals. Pasquesi, G.I.M., Adams R, Card D, Schield D, Perry B, Corbin A, J. Reyes-Velasco, R.P. Ruggiero, M.W. Vandewege, J.A. Shortt, and Castoe T. 2018. Nature Communications. PDF

• Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes. Schield D, Adams R, Card D, Perry B, Pasquesi G, T. Jezkova, D.M. Portik, Andrew A, C.L. Spencer, E.E. Sanchez, M.K. Fujita, Mackessy S, and Castoe T. 2017. Ecology and Evolution. PDF

• GppFst: Genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data. Adams R, Schield D, Card D, Blackmon H, and Castoe T. 2017. Bioinformatics. PDF

• Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution. Adams R, H.G. Blackman, J. Reyes-Velasco, Schield D, Card D, Andrew A, N. Waynewood, and Castoe T. 2016. Genome. Received the Editor’s Choice Award for the journal Genome. PDF

• A suite of potentially amplifiable microsatellite loci for reptiles of conservation concern from Africa and Asia. Shaney, K.J., Adams R, N. Kurniawan, A. Hamidy, E.N. Smith, and Castoe T. 2016. Conservation Genetics Resources. PDF

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

• EpiRadSeq: genome-wide analysis of shifts in DNA methylation using next-generation sequencing. Schield D, M.F. Walsh, Card D, Andrew A, Adams R, and Castoe T. 2016. Methods in Ecology and Evolution. Cover Article. PDF

• Rapid changes in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding. Andrew, A.L., Card D, R.P. Ruggiero, Schield D, Adams R, D.D. Pollock, S.M. Secor, and Castoe T. 2015. Physiological Genomics. PDF

• Incipient speciation with biased gene flow between two lineages of the Western Diamondback Rattlesnake Crotalus atrox. Schield D, Card D, Adams R, T. Jezkova, J. Reyes-Velasco, F.N. Proctor, C.L. Spencer, H-W. Herrmann, Mackessy S, and Castoe T. 2015. Molecular Phylogenetics and Evolution. PDF

• Expression of venom gene homologs in diverse python tissues suggests a new model for the evolution of snake venom. Reyes-Velasco J., Card D, Andrew A, K.J. Shaney, Adams R, Schield D, N.R. Casewell, Mackessy S, and Castoe T. 2015. Molecular Biology and Evolution. PDF