Robert Thomson - Publications

Biology University of Hawaii, Honolulu, HI, United States 
Evolutionary biology, phylogenetics, and conservation biology

41 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Thomson RC, Spinks PQ, Shaffer HB. A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33558231 DOI: 10.1073/pnas.2012215118  1
2020 Harrington SM, Wishingrad V, Thomson RC. Properties of Markov Chain Monte Carlo Performance Across Many Empirical Alignments. Molecular Biology and Evolution. PMID 33185685 DOI: 10.1093/molbev/msaa295  0.48
2020 Hime PM, Lemmon AR, Lemmon ECM, Prendini E, Brown JM, Thomson RC, Kratovil JD, Noonan BP, Pyron RA, Peloso PLV, Kortyna ML, Keogh JS, Donnellan SC, Mueller RL, Raxworthy CJ, et al. Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life. Systematic Biology. PMID 32359157 DOI: 10.1093/Sysbio/Syaa034  0.64
2019 Campillo LC, Barley AJ, Thomson RC. Model-based species delimitation: are coalescent species reproductively isolated? Systematic Biology. PMID 31688934 DOI: 10.1093/Sysbio/Syz072  1
2018 Barley AJ, Nieto-Montes de Oca A, Reeder TW, Manríquez-Morán NL, Arenas Monroy JC, Hernández-Gallegos O, Thomson RC. Complex patterns of hybridization and introgression across evolutionary timescales in Mexican whiptail lizards (Aspidoscelis). Molecular Phylogenetics and Evolution. 132: 284-295. PMID 30562610 DOI: 10.1016/J.Ympev.2018.12.016  1
2018 Gray LN, Barley AJ, Poe S, Thomson RC, Nieto-Montes de Oca A, Wang IJ. Phylogeography of a widespread lizard complex reflects patterns of both geographic and ecological isolation. Molecular Ecology. PMID 30525264 DOI: 10.1111/Mec.14970  1
2018 Richards EJ, Brown JM, Barley AJ, Chong RA, Thomson RC. Variation across mitochondrial gene trees provides evidence for systematic error: How much gene tree variation is biological? Systematic Biology. PMID 29471536 DOI: 10.1093/Sysbio/Syy013  1
2018 Brown JM, Thomson RC. The behavior of Metropolis-coupled Markov chains when sampling rugged phylogenetic distributions. Systematic Biology. PMID 29462409 DOI: 10.1093/Sysbio/Syy008  0.64
2017 Thomson RC, Spinks PQ, Bradley Shaffer H. Molecular phylogeny and divergence of the Map Turtles (Emydidae: Graptemys). Molecular Phylogenetics and Evolution. PMID 29242165 DOI: 10.1016/J.Ympev.2017.11.012  0.92
2017 Höhna S, Coghill LM, Mount GG, Thomson RC, Brown JM. P3: Phylogenetic Posterior Prediction in RevBayes. Molecular Biology and Evolution. PMID 29136211 DOI: 10.1093/Molbev/Msx286  0.64
2017 Barley AJ, Brown JM, Thomson RC. Impact of Model Violations on the Inference of Species Boundaries Under the Multispecies. Systematic Biology. PMID 28945903 DOI: 10.1093/Sysbio/Syx073  1
2016 Brown JM, Thomson RC. Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses. Systematic Biology. PMID 28003531 DOI: 10.1093/Sysbio/Syw101  0.64
2016 de Oca AN, Barley AJ, Meza-Lázaro RN, García-Vázquez UO, Zamora-Abrego JG, Thomson RC, Leaché AD. Corrigendum to "Phylogenomics and species delimitation in the knob-scaled lizards of the genus Xenosaurus (Squamata: Xenosauridae) using ddRADseq data reveal a substantial underestimation of diversity" [Mol. Phylogen. Evol. 106 (2017) 241-253]. Molecular Phylogenetics and Evolution. PMID 27816561 DOI: 10.1016/J.Ympev.2016.11.002  1
2016 de Oca AN, Barley AJ, Meza-Lázaro RN, García-Vázquez UO, Zamora-Abrego JG, Thomson RC, Leaché AD. Phylogenomics and species delimitation in the knob-scaled lizards of the genus Xenosaurus (Squamata: Xenosauridae) using ddRADseq data reveal a substantial underestimation of diversity. Molecular Phylogenetics and Evolution. PMID 27720785 DOI: 10.1016/J.Ympev.2016.09.001  1
2016 Spinks PQ, Thomson RC, McCartney-Melstad E, Bradley Shaffer H. Phylogeny and temporal diversification of the New World pond turtles (Emydidae). Molecular Phylogenetics and Evolution. PMID 27400630 DOI: 10.1016/J.Ympev.2016.07.007  1
2016 Barley AJ, Thomson RC. Assessing the performance of DNA barcoding using posterior predictive simulations. Molecular Ecology. PMID 26915049 DOI: 10.1111/Mec.13590  1
2016 Dong CM, Engstrom TN, Thomson RC. Origins of softshell turtles in Hawaii with implications for conservation Conservation Genetics. 17: 207-220. DOI: 10.1007/S10592-015-0772-7  1
2015 Barley AJ, Monnahan PJ, Thomson RC, Grismer LL, Brown RM. Sun skink landscape genomics: assessing the roles of micro-evolutionary processes in shaping genetic and phenotypic diversity across a heterogeneous and fragmented landscape. Molecular Ecology. 24: 1696-712. PMID 25763872 DOI: 10.1111/Mec.13151  1
2014 Thomson RC, Plachetzki DC, Mahler DL, Moore BR. A critical appraisal of the use of microRNA data in phylogenetics. Proceedings of the National Academy of Sciences of the United States of America. 111: E3659-68. PMID 25071211 DOI: 10.1073/Pnas.1407207111  1
2014 Long EC, Thomson RC, Shapiro AM. A time-calibrated phylogeny of the butterfly tribe Melitaeini. Molecular Phylogenetics and Evolution. 79: 69-81. PMID 24952320 DOI: 10.1016/J.Ympev.2014.06.010  1
2014 Spinks PQ, Thomson RC, Gidi? M, Bradley Shaffer H. Multilocus phylogeny of the New-World mud turtles (Kinosternidae) supports the traditional classification of the group. Molecular Phylogenetics and Evolution. 76: 254-60. PMID 24704303 DOI: 10.1016/J.Ympev.2014.03.025  1
2014 Spinks PQ, Thomson RC, Shaffer HB. The advantages of going large: genome-wide SNPs clarify the complex population history and systematics of the threatened western pond turtle. Molecular Ecology. 23: 2228-41. PMID 24673803 DOI: 10.1111/Mec.12736  1
2013 Spinks PQ, Thomson RC, Pauly GB, Newman CE, Mount G, Shaffer HB. Misleading phylogenetic inferences based on single-exemplar sampling in the turtle genus Pseudemys. Molecular Phylogenetics and Evolution. 68: 269-81. PMID 23583419 DOI: 10.1016/J.Ympev.2013.03.031  1
2013 Shaffer HB, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, et al. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology. 14: R28. PMID 23537068 DOI: 10.1186/Gb-2013-14-3-R28  1
2013 Lambert MR, Nielsen SN, Wright AN, Thomson RC, Shaffer HB. Habitat features determine the basking distribution of introduced red-eared sliders and native western pond turtles Chelonian Conservation and Biology. 12: 192-199. DOI: 10.2744/Ccb-1010.1  1
2012 Spinks PQ, Thomson RC, Zhang Y, Che J, Wu Y, Shaffer HB. Species boundaries and phylogenetic relationships in the critically endangered Asian box turtle genus Cuora. Molecular Phylogenetics and Evolution. 63: 656-67. PMID 22649793 DOI: 10.1016/J.Ympev.2012.02.014  1
2012 Holzman R, Collar DC, Price SA, Hulsey CD, Thomson RC, Wainwright PC. Biomechanical trade-offs bias rates of evolution in the feeding apparatus of fishes. Proceedings. Biological Sciences / the Royal Society. 279: 1287-92. PMID 21993506 DOI: 10.1098/Rspb.2011.1838  1
2012 Spinks PQ, Thomson RC, Hughes B, Moxley B, Brown R, Diesmos A, Shaffer HB. 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. DOI: 10.1111/J.1096-3642.2011.00788.X  1
2011 Johnson JR, Thomson RC, Micheletti SJ, Shaffer HB. The origin of tiger salamander (Ambystoma tigrinum) populations in California, Oregon, and Nevada: Introductions or relicts? Conservation Genetics. 12: 355-370. DOI: 10.1007/S10592-010-0144-2  1
2010 Thomson RC, Shaffer HB. Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtles. Systematic Biology. 59: 42-58. PMID 20525619 DOI: 10.1093/Sysbio/Syp075  1
2010 Thomson RC, Wang IJ, Johnson JR. Genome-enabled development of DNA markers for ecology, evolution and conservation. Molecular Ecology. 19: 2184-95. PMID 20465588 DOI: 10.1111/J.1365-294X.2010.04650.X  1
2010 Thomson RC, Shaffer HB. Rapid progress on the vertebrate tree of life. Bmc Biology. 8: 19. PMID 20211001 DOI: 10.1186/1741-7007-8-19  1
2010 Spinks PQ, Thomson RC, Shaffer HB. 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: 542-56. PMID 20051011 DOI: 10.1111/J.1365-294X.2009.04451.X  1
2010 Barley AJ, Spinks PQ, Thomson RC, Shaffer HB. Fourteen nuclear genes provide phylogenetic resolution for difficult nodes in the turtle tree of life. Molecular Phylogenetics and Evolution. 55: 1189-94. PMID 19913628 DOI: 10.1016/J.Ympev.2009.11.005  1
2010 Thomson RC, Spinks PQ, Shaffer HB. Distribution and abundance of invasive 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. DOI: 10.2744/Ccb-0820.1  1
2010 Spinks PQ, Thomson RC, Barley AJ, Newman CE, Bradley Shaffer H. Testing avian, squamate, and mammalian nuclear markers for cross amplification in turtles Conservation Genetics Resources. 2: 127-129. DOI: 10.1007/S12686-010-9184-7  1
2009 Spinks PQ, Thomson RC, Lovely GA, Shaffer HB. Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles. Bmc Evolutionary Biology. 9: 56. PMID 19284630 DOI: 10.1186/1471-2148-9-56  1
2009 Thomson RC. PhyLIS: A simple GNU/Linux distribution for phlogenetics and phyloinformatics Evolutionary Bioinformatics. 2009: 91-95.  1
2009 Spinks PQ, Thomson RC, Shaffer HB. A reassessment of Cuora cyclornata Blanck, McCord and Le, 2006 (testudines, geoemydidae) and a plea for taxonomic stability Zootaxa. 58-68.  1
2008 Thomson RC, Shedlock AM, Edwards SV, Shaffer HB. Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles. Molecular Phylogenetics and Evolution. 49: 514-25. PMID 18761096 DOI: 10.1016/J.Ympev.2008.08.006  1
2007 Shaffer HB, Thomson RC. Delimiting species in recent radiations. Systematic Biology. 56: 896-906. PMID 18066926 DOI: 10.1080/10635150701772563  1
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