Publications

2017

Brown, Jeremy M; Thomson, Robert C

Bayes Factors Unmask Highly Variable Information Content, Bias, and Extreme Influence in Phylogenomic Analyses Journal Article

Systematic Biology, 66 (4), pp. 517–530, 2017, ISSN: 1076836X.

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Barley, Anthony J; Brown, Jeremy M; Thomson, Robert C

Impact of Model Violations on the Inference of Species Boundaries Under the Multispecies Coalescent Journal Article

Systematic Biology, 0 (0), pp. syx073, 2017, ISSN: 1063-5157.

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Nieto-Montes de Oca, Adrián ; Barley, Anthony J; Meza-Lázaro, Rubi N; García-Vázquez, Uri O; Zamora-Abrego, Joan G; Thomson, Robert C; Leaché, Adam D

Phylogenomics and species delimitation in the knob-scaled lizards of the genus Xenosaurus (Squamata: Xenosauridae) using ddRADseq data reveal a substantial underestimation of diversity Journal Article

Molecular Phylogenetics and Evolution, 106 , pp. 241–253, 2017, ISSN: 10557903.

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Richards, Emilie J; Brown, Jeremy M; Barley, Anthony J; Chong, Rebecca A; Thomson, Robert C

Unexpected variation across mitochondrial gene trees and evidence for systematic error: How much gene tree variation is biological? Unpublished

2017.

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2016

Spinks, Phillip Q; Thomson, Robert C; McCartney-Melstad, Evan; Shaffer, Bradley H

Phylogeny and temporal diversification of the New World pond turtles (Emydidae) Journal Article

Molecular Phylogenetics and Evolution, 103 , pp. 85–97, 2016, ISSN: 10557903.

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Barley, Anthony J; Thomson, Robert C

Assessing the performance of DNA barcoding using posterior predictive simulations Journal Article

Molecular Ecology, 25 (9), pp. 1944–1957, 2016, ISSN: 09621083.

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Thomson, Robert C

Here be monsters Miscellaneous

2016.

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Thomson, Robert C; Wright, Amber N; Shaffer, Bradley H

California amphibian and reptile species of special concern Book

University of California Press, Oakland, 2016, ISBN: 9780520290907.

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Dong, Caroline M; Engstrom, Tag N; Thomson, Robert C

Origins of softshell turtles in Hawaii with implications for conservation Journal Article

Conservation Genetics, 17 (1), pp. 207–220, 2016, ISSN: 15729737.

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2015

Barley, Anthony J; Monnahan, Patrick J; Thomson, Robert C; Grismer, Lee L; Brown, Rafe M

Sun skink landscape genomics: Assessing the roles of micro-evolutionary processes in shaping genetic and phenotypic diversity across a heterogeneous and fragmented landscape Journal Article

Molecular Ecology, 24 (8), pp. 1696–1712, 2015, ISSN: 1365294X.

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2014

Spinks, Phillip Q; Thomson, Robert C; Gidiş, Müge; Bradley Shaffer, H

Multilocus phylogeny of the New-World mud turtles (Kinosternidae) supports the traditional classification of the group Journal Article

Molecular Phylogenetics and Evolution, 76 (1), pp. 254–260, 2014, ISSN: 10557903.

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Thomson, R; Plachetzki, D; Mahler, L; Moore, B

Estimating Phylogeny from microRNA Data: A Critical Appraisal Journal Article

bioRxiv, (808), pp. 0–31, 2014.

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Spinks, Phillip Q; Thomson, Robert C; Shaffer, Bradley H

The advantages of going large: Genome-wide SNPs clarify the complex population history and systematics of the threatened western pond turtle Journal Article

Molecular Ecology, 23 (9), pp. 2228–2241, 2014, ISSN: 1365294X.

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Thomson, R C; Plachetzki, D C; Mahler, D L; Moore, B R

A critical appraisal of the use of microRNA data in phylogenetics Journal Article

Proceedings of the National Academy of Sciences, 111 (35), pp. E3659–E3668, 2014, ISSN: 0027-8424.

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Long, Elizabeth C; Thomson, Robert C; Shapiro, Arthur M

A time-calibrated phylogeny of the butterfly tribe Melitaeini Journal Article

Molecular Phylogenetics and Evolution, 79 (1), pp. 69–81, 2014, ISSN: 10959513.

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2013

Lambert, Max R; Nielsen, Sharell N; Wright, Amber N; Thomson, Robert C; Shaffer, Bradley H

Habitat Features Determine the Basking Distribution of Introduced Red-Eared Sliders and Native Western Pond Turtles Journal Article

Chelonian Conservation and Biology, 12 (1), pp. 192–199, 2013, ISSN: 1071-8443.

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Spinks, Phillip Q; Thomson, Robert C; Pauly, Gregory B; Newman, Catherine E; Mount, Genevieve; Shaffer, Bradley H

Misleading phylogenetic inferences based on single-exemplar sampling in the turtle genus textlessitextgreaterPseudemystextless/itextgreater Journal Article

Molecular Phylogenetics and Evolution, 68 (2), pp. 269–281, 2013, ISSN: 10557903.

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Bradley Shaffer, H; Minx, Patrick; Warren, Daniel E; Shedlock, Andrew M; Thomson, Robert C; Valenzuela, Nicole; Abramyan, John; Amemiya, Chris T; Badenhorst, Daleen; Biggar, Kyle K; Borchert, Glen M; Botka, Christopher W; Bowden, Rachel M; Braun, Edward L; Bronikowski, Anne M; Bruneau, Benoit G; Buck, Leslie T; Capel, Blanche; Castoe, Todd A; Czerwinski, Mike; Delehaunty, Kim D; Edwards, Scott V; Fronick, Catrina C; Fujita, Matthew K; Fulton, Lucinda; Graves, Tina A; Green, Richard E; Haerty, Wilfried; Hariharan, Ramkumar; Hernandez, Omar; Hillier, LaDeana W; Holloway, Alisha K; Janes, Daniel; Janzen, Fredric J; Kandoth, Cyriac; Kong, Lesheng; de Koning, AP; Li, Yang; Literman, Robert; McGaugh, Suzanne E; Mork, Lindsey; O'Laughlin, Michelle; Paitz, Ryan T; Pollock, David D; Ponting, Chris P; Radhakrishnan, Srihari; Raney, Brian J; Richman, Joy M; St John, John ; Schwartz, Tonia; Sethuraman, Arun; Spinks, Phillip Q; Storey, Kenneth B; Thane, Nay; Vinar, Tomas; Zimmerman, Laura M; Warren, Wesley C; Mardis, Elaine R; Wilson, Richard K

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage Journal Article

Genome Biology, 14 (3), pp. R28, 2013, ISSN: 1465-6906.

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2012

Holzman, R; Collar, D C; a. Price, S; Hulsey, C D; Thomson, R C; Wainwright, P C

Biomechanical trade-offs bias rates of evolution in the feeding apparatus of fishes Journal Article

Proceedings of the Royal Society B: Biological Sciences, 279 (1732), pp. 1287–1292, 2012, ISSN: 0962-8452.

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Spinks, Phillip Q; Thomson, Robert C; Hughes, Bill; Moxley, Brad; Brown, Rafe; Diesmos, Arvin; Shaffer, Bradley H

Cryptic variation and the tragedy of unrecognized taxa: The case of international trade in the spiny turtle Heosemys spinosa (Testudines: Geoemydidae) Journal Article

Zoological Journal of the Linnean Society, 164 (4), pp. 811–824, 2012, ISSN: 00244082.

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Spinks, Phillip Q; Thomson, Robert C; Zhang, Ya Ping; Che, Jing; Wu, Yonghua; Bradley Shaffer, H

Species boundaries and phylogenetic relationships in the critically endangered Asian box turtle genus Cuora Journal Article

Molecular Phylogenetics and Evolution, 63 (3), pp. 656–667, 2012, ISSN: 10557903.

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2011

Johnson, Jarrett R; Thomson, Robert C; Micheletti, Steven J; Shaffer, Bradley H

The origin of tiger salamander (Ambystoma tigrinum) populations in California, Oregon, and Nevada: introductions or relicts? Journal Article

Conservation Genetics, 12 (2), pp. 355–370, 2011, ISSN: 1566-0621.

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2010

Thomson, Robert C; Spinks, Phillip Q; Shaffer, Bradley H

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) Journal Article

Chelonian Conservation and Biology, 9 (2), pp. 297–302, 2010, ISSN: 1071-8443.

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Thomson, Robert C; Wang, Ian J; Johnson, Jarrett R

Genome-enabled development of DNA markers for ecology, evolution and conservation. Journal Article

Molecular ecology, 19 (11), pp. 2184–95, 2010, ISSN: 1365-294X.

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Barley, Anthony J; Spinks, Phillip Q; Thomson, Robert C; Shaffer, Bradley H

Fourteen nuclear genes provide phylogenetic resolution for difficult nodes in the turtle tree of life. Journal Article

Molecular phylogenetics and evolution, 55 (3), pp. 1189–94, 2010, ISSN: 1095-9513.

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Spinks, Phillip Q; Thomson, Robert C; Shaffer, Bradley H

Nuclear gene phylogeography reveals the historical legacy of an ancient inland sea on lineages of the western pond turtle, Emys marmorata in California. Journal Article

Molecular ecology, 19 (3), pp. 542–56, 2010, ISSN: 1365-294X.

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Spinks, Phillip Q; Thomson, Robert C; Barley, Anthony J; Newman, Catherine E; Bradley Shaffer, H

Testing avian, squamate, and mammalian nuclear markers for cross amplification in turtles Journal Article

Conservation Genetics Resources, 2 (1), pp. 127–129, 2010, ISSN: 1877-7252.

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Thomson, Robert C; Shaffer, Bradley H

Rapid progress on the vertebrate tree of life. Journal Article

BMC Biology, 8 , pp. 19, 2010, ISSN: 1741-7007.

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Thomson, Robert C; Shaffer, Bradley H

Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtles. Journal Article

Systematic biology, 59 (1), pp. 42–58, 2010, ISSN: 1076-836X.

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2009

Spinks, Phillip Q; Thomson, Robert C; Shaffer, Bradley H

A reassessment of Cuora cyclornata Blanck, McCord and Le, 2006 (Testudines, Geoemydidae) and a plea for taxonomic stability Journal Article

Zootaxa, 2018 , pp. 58–68, 2009, ISSN: 0960-3107.

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Spinks, Phillip Q; Thomson, Robert C; a Lovely, Geoff; Shaffer, Bradley H

Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles. Journal Article

BMC evolutionary biology, 9 , pp. 56, 2009, ISSN: 1471-2148.

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Thomson, Robert C

PhyLIS: A simple GNU / Linux Distribution for phylogenetics and phyloinformatics Journal Article

Evolutionary Bioinformatics, 5 , pp. 91–95, 2009.

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2008

Thomson, Robert C; Shedlock, Andrew M; Edwards, Scott V; Shaffer, Bradley H

Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles. Journal Article

Molecular phylogenetics and evolution, 49 (2), pp. 514–25, 2008, ISSN: 1095-9513.

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2007

Shaffer, Bradley H; Thomson, Robert C

Delimiting species in recent radiations. Journal Article

Systematic biology, 56 (6), pp. 896–906, 2007, ISSN: 1063-5157.

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Iverson, John B; Brown, Rafe M; Akre, Thomas S; Near, Thomas J; Le, Minh; Thomson, Robert C; Starkey, David E

In Search of the Tree of Life for Turtles Inproceedings

Shaffer, Bradley H; FitzSimmons, Nancy N; Georges, Arthur; Rhodin, Anders G J (Ed.): Defining Turtle Diversity: Proceedings of a Workshop on Genetics, Ethics, and Taxonomy of Freshwater Turtles and Tortoises, pp. 85–106, Chelonian Research Foundation, 2007.

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