Publications

Brown, JM, RC Thomson. in press. Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses. Systematic Biology
Nieto-Montes de Oca, A, AJ Barley, RN Meza-Lazaro, UO Garcia-Vazquez, JG Zamora-Abrego, RC Thomson, AD Leache. in press. Phylogenomics and species delimitation in the knob-scaled lizards of the genus Xenosaurus (Squamata: Xenosauridae) using ddRADseq data reveal a substantial under-estimation of diversity. Molecular Phylogenetics and Evolution. doi: 10.1016/j.ympev.2016.09.001
Thomson, RC, AN Wright, HB Shaffer. 2016. California amphibian and reptile species of special concern. University of California Press. University of California Press. Oakland, CA. 390 p. ISBN: 9780520290907
Assessing the performance of DNA barcoding using posterior predictive simulations. Molecular Ecology. 25:1930- 1943 doi: 10.1111/mec.13590
Spinks, PQ, RC Thomson, E McCartney-Melstad, HB Shaffer. 2016. Phylogeny and temporal diversification of the New World pond turtles (Emydidae). Molecular Phylogenetics and Evolution. 103:85-97 doi: 10.1016/j.ympev.2016.07.007
Dong, CM, TN Engstrom, RC Thomson. 2016. Origins of softshell turtles in Hawaii with considerations for conservation. Conservation Genetics. 17:207-220 doi: 10.1007/s10592-015-0772-7
Barley, AJ, PJ Monnahan, RC Thomson, LL Grismer, RM Brown. 2015. Sun skink landscape genomics: assessing how microevolutionary processes shape genetic and morphological diversity across a heterogeneous and fragmented landscape. Molecular Ecology. 24:1696-1712 doi: 10.1111/mec.13151
Thomson, RC, DC Plachetzki, DL Mahler, BR Moore. 2014. Estimating Phylogeny from microRNA Data: A Critical Appraisal. Proceedings of the National Academy of Sciences, USA. 111:E3659-E3668 doi: 10.1073/pnas.1407207111
Spinks, PQ, RC Thomson, HB Shaffer. 2014. The advantages of going large: genome-wide SNPs clarify the complex population history and systematics of the threatened western pond turtle. Molecular Ecology. 23: 2228-2241 doi: 10.1111/mec.12736
Long, EC, RC Thomson, AM Shapiro. 2014. A time-calibrated phylogeny of the butterfly tribe Melitaeini. Molecular Phylogenetics and Evolution. 79: 69-81 doi: 10.1016/j.ympev.2014.06.010
Spinks, PQ, RC Thomson, M Gidis, HB Shaffer. 2014. Multilocus phylogeny of the New-World mud turtles (Kinosternidae) supports the traditional classification of the group. Molecular Phylogenetics and Evolution. 76: 254-260 doi:10.1016/j.ympev.2014.03.025
Shaffer, HB, P Minx, DE Warren, AM Shedlock, RC Thomson, N Valenzuela, J Abramyan, D Badenhorst, KK Biggar, GM Borchert, CW Botka, RM Bowden, EL Braun, AM Bronikowski, BG Bruneau, LT Buck, B Capel, TA Castoe, M Czerwinski, KD Delehaunty, SV Edwards, CC Fronick, MK Fujita, L Fulton, TA Graves, RE Green, W Haerty, R Hariharan, LW Hillier, AK Holloway, D Janes, FJ Janzen, C Kandoth, L Kong, APJ de Koning, Y Li, R Literman, SE McGaugh, L Mork, M O’Laughlin, RT Paitz, DD Pollock, CP Ponting, S Radhakrishnan, BJ Raney, JM Richman, J St. John, T Schwartz, A Sethuraman, PQ Spinks, KB Storey, N Thane, T Vinar, LM Zimmerman, WC Warren, ER Mardis, and RK 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 doi:10.1186/gb-2013-14-3-r28 go to paper
Lambert MR, SN Nielsen, AN Wright, RC Thomson, HB Shaffer. 2013. Microhabitat characteristics favor introduced red-eared sliders over threatened western pond turtles in a human-dominated landscape. Chelonian Conservation and Biology. 12:192-199download paper
Spinks PQ, RC Thomson, GB Pauly, CE Newman, G. Mount, HB Shaffer. 2013. Misleading phylogenetic inferences based on single-exemplar sampling in the turtle genus Pseudemys. Molecular Phylogenetics and Evolution. 68:269-281download paper
Spinks PQ, RC Thomson, Y Zhang, J Che, Y Wu, HB Shaffer. 2012. Species boundaries and phylogenetic relationships in the critically endangered Asian box turtle genus Cuora. Molecular Phylogenetics and Evolution. 63:656-667 download paper
Spinks PQ, RC Thomson, B Hughes, B Moxley, RM Brown, A Deismos, HB Shaffer. 2012. Cryptic variation and the tragedy of unrecognized taxa: the case of international trade in the spiny turtle Heosemys spinosa (Testudines: Geoemydidae). Zoological journal of the Linnean Society. 164: 811-824. download paper
Holzman R, DC Collar, SA Price, CD Hulsey, RC Thomson, PC Wainwright. 2012. Biomechanical trade-offs bias rates of evolution in the feeding apparatus of fishes. Proceedings of the Royal Society – Series B. 279: 1287-1292. download paper
Johnson, JR, RC Thomson, SJ Micheletti, HB Shaffer. 2011. The origin of tiger salamander populations in California: Introductions or relicts? Conservation Genetics. 12: 355-370 go to paper
Thomson, RC, HB Shaffer. 2010. Rapid progress on the vertebrate tree of life. BMC Biology. 8: 19 go to paper
Thomson, RC, IJ Wang, JR Johnson. 2010. Invited Review: Genome-enabled development of molecular markers for ecology, evolution, and conservation. Molecular Ecology. 19: 2184-2195 download paper
Thomson, RC, PQ Spinks HB Shaffer. 2010. Distribution and abundance of exotic red-eared sliders (Trachemys scripta elegans) in California’s Sacramento River basin and possible impacts on native western pond turtles (Emys marmorata). Chelonian Conservation and Biology. 9: 297-302 download paper
Spinks PQ, RC Thomson, AJ Barley, HB Shaffer. 2010. Testing avian, squamate, and mammalian nuclear markers for cross amplification in turtles. Conservation Genetics Resources. 2: 127–129 go to paper
Barley AJ, PQ Spinks, RC Thomson, HB Shaffer. 2010. Fourteen nuclear genes provide phylogenetic resolution for difficult nodes in the turtle tree of life. Molecular Phylogenetics and Evolution. 55: 1189-1194 download paper
Thomson, RC, HB Shaffer. 2010. Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles. Systematic Biology. 59: 42-58 download paper
Spinks PQ, RC Thomson, HB Shaffer. 2010. Nuclear gene phylogeography reveals the historical legacy of an ancient inland sea on lineages of the western pond turtle, Emys marmorata in California. Molecular Ecology. 19: 542-556 download paper
Thomson, RC. 2009. PhyLIS: a simple Gnu/Linux distribution for phylogenetics and phyloinformatics. Evolutionary Bioinformatics. 5: 91-95 go to paper
Spinks PQ, RC Thomson, GA Lovely and HB Shaffer. 2009. Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from Emydid turtles. BMC Evolutionary Biology. 9: 56 go to paper
Spinks PQ, RC Thomson, HB Shaffer. 2009. A reassessment of Cuora cyclornata Blanck, McCord and Le, 2006 (Testudines, Geoemydidae) and a plea for taxonomic stability. Zootaxa. 2018: 58-68 go to paper
Thomson, RC, AM Shedlock, SV Edwards, HB Shaffer. 2008. Developing markers for multilocus phylogenetics in non-model organisms: a test case with turtles. Molecular Phylogenetics and Evolution. 49: 514-525 download paper
Iverson, JB, RM Brown, TS Akre, TJ Near, M Le, RC Thomson, DE Starkey. 2007. In search of the tree of life for turtles. in Defining Turtle Diversity: Proceedings of a workshop on genetics, ethics, and taxonomy of tortoises and Freshwater turtles. HB Shaffer, NN Fitzsimmons, A Georges, AGJ Rhodin , Eds. Chelonian Research Monographs 4: 85-106 download paper
Shaffer, HB and RC Thomson. 2007. Delimiting species in recent radiations. Systematic Biology 56(6): 896-906 download paper