Research Topics
Genomes and GenesSpecies | H B ShafferSummaryAffiliation: University of California Country: USA Publications
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Detail Information
Publications
Multiple nuclear gene sequences identify phylogenetic species boundaries in the rapidly radiating clade of Mexican ambystomatid salamandersDavid W Weisrock
Department of Biology, University of Kentucky, Lexington, KY 40506, USA
Mol Ecol 15:2489-503. 2006..They also demonstrate how EST-based nuclear resources can be used to more fully resolve the phylogenetic history of species radiations...
Retention of low-fitness genotypes over six decades of admixture between native and introduced tiger salamandersJarrett R Johnson
Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA
BMC Evol Biol 10:147. 2010..Additionally, we examined the inheritance of quantitative phenotypic variation to better understand how evolution has progressed since secondary contact...- Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamandersBenjamin M Fitzpatrick
Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
BMC Evol Biol 9:176. 2009..To assess variation of admixture dynamics, we scored a large panel of markers in five wild hybrid populations formed when Barred Tiger Salamanders were introduced into the range of California Tiger Salamanders... - Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtlesPhillip Q Spinks
Department of Evolution and Ecology, Davis, USA
BMC Evol Biol 9:56. 2009.... - Rapid progress on the vertebrate tree of lifeRobert C Thomson
Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA
BMC Biol 8:19. 2010..Here we measure the rate of progress on the tree of life for one clade of particular research interest, the vertebrates... - Tests of turtle phylogeny: molecular, morphological, and paleontological approachesH B Shaffer
Section of Evolution and Ecology and Center for Populatiion Biology, University of California, Davis, California 95616, USA
Syst Biol 46:235-68. 1997..Branch-length analysis and independent dates from the fossil record suggest that these unresolved nodes may represent a rapid radiation of the major cryptodiran lineages 90-120 million years ago... - The genetics of amphibian declines: population substructure and molecular differentiation in the yosemite toad, Bufo canorus (Anura, bufonidae) based on single-strand conformation polymorphism analysis (SSCP) and mitochondrial DNA sequence dataH B Shaffer
Section of Evolution and Ecology, and Center for Population Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
Mol Ecol 9:245-57. 2000..A brief review of other pond-breeding anurans suggests that highly structured populations are often the case, and thus that our results for B. canorus may be general for other species of frogs and toads... - Delimiting species in recent radiationsH Bradley Shaffer
Section of Evolution and Ecology, and Center for Population Biology, University of California, Davis, CA 95616, USA
Syst Biol 56:896-906. 2007.... - The molecular phylogenetics of endangerment: cryptic variation and historical phylogeography of the California tiger salamander, Ambystoma californienseH Bradley Shaffer
Section of Evolution and Ecology, and Center for Population Biology, University of California, Davis, CA 95616, USA
Mol Ecol 13:3033-49. 2004..Our work places patterns of genetic differentiation into both temporal- and landscape-level contexts, providing important insights into the conservation genetics of the California tiger salamander... - Species boundaries, phylogeography and conservation genetics of the red-legged frog (Rana aurora/draytonii) complexH Bradley Shaffer
Section of Evolution and Ecology, and Center for Population Biology, University of California, Davis 95616, USA
Mol Ecol 13:2667-77. 2004..The currently available evidence favours recognition of aurora and draytonii as separate species with a narrow zone of overlap in northern California... - Range-wide molecular analysis of the western pond turtle (Emys marmorata): cryptic variation, isolation by distance, and their conservation implicationsPhillip Q Spinks
Section of Evolution and Ecology, University of California, Davis, California 95616, USA
Mol Ecol 14:2047-64. 2005.... - Phylogeographic concordance in the southeastern United States: the flatwoods salamander, Ambystoma cingulatum, as a test caseGregory B Pauly
Section of Evolution and Ecology, and Center for Population Biology, University of California, Davis, CA 95616, USA
Mol Ecol 16:415-29. 2007..More generally, these results emphasize that in the absence of taxon-specific data, established comparative patterns can provide strong expectations for designing management units for unstudied species of conservation concern... - Large, rapidly evolving intergenic spacers in the mitochondrial DNA of the salamander family Ambystomatidae (Amphibia: Caudata)M L McKnight
Section of Evolution and Ecology, University of California, Davis 95616, USA
Mol Biol Evol 14:1167-76. 1997..As such, it represents one of the few examples of a large and persistent intergenic spacer in the mtDNA of any vertebrate clade... 
Fourteen nuclear genes provide phylogenetic resolution for difficult nodes in the turtle tree of lifeAnthony J Barley
Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
Mol Phylogenet Evol 55:1189-94. 2010..Within this clade, snapping turtles (Chelydridae) and mud/musk turtles (Kinosternidae) are sister taxa, again with strong support. Our results emphasize the utility of multi-locus datasets in phylogenetic analyses of difficult problems...- Multiple data sets, high homoplasy, and the phylogeny of softshell turtles (Testudines: Trionychidae)Tag N Engstrom
Center for Population Biology and Section of Evolution and Ecology, University of California, Davis, CA 95616, USA
Syst Biol 53:693-710. 2004..Many deep nodes in the softshell turtle phylogeny were confidently recovered only after the addition of largely nonhomoplasious data from the nuclear intron... - Landscape genetics of alpine Sierra Nevada salamanders reveal extreme population subdivision in space and timeWesley K Savage
Department of Evolution and Ecology, and Center for Population Biology, University of California, Davis, CA 95616 8755, USA
Mol Ecol 19:3301-14. 2010..Our study emphasizes the population-level insights that can be gained from high-density sampling in space and time, and the highly substructured population biology that may characterize amphibians in extreme montane habitats... - What insights into the developmental traits of urodeles does the study of interspecific hybrids provide?S R Voss
Center for Population Biology, University of California, Davis 95616, USA
Int J Dev Biol 40:885-93. 1996.... - Nuclear gene phylogeography reveals the historical legacy of an ancient inland sea on lineages of the western pond turtle, Emys marmorata in CaliforniaPhillip Q Spinks
Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
Mol Ecol 19:542-56. 2010.... - Environment-dependent admixture dynamics in a tiger salamander hybrid zoneBenjamin M Fitzpatrick
Center for Population Biology and Section of Evolution and Ecology, University of California, Davis, California 95616, USA
Evolution 58:1282-93. 2004..A third was more likely to have heterozygote excess in ephemeral cattle ponds. These patterns indicate that admixture is influenced by complex genotype-by-environment interactions... - Turtle phylogeny: insights from a novel nuclear intronMatthew K Fujita
Section of Evolution and Ecology, University of California, 1 Shields Avenue, Davis, CA 95616, USA
Mol Phylogenet Evol 31:1031-40. 2004..This is the first study to resolve such relationships with strong statistical support, and we suggest that R35 holds great promise for resolving additional persistent problems in the phylogeny of living turtles... - Molecular systematics, phylogeography, and the effects of Pleistocene glaciation in the painted turtle (Chrysemys picta) complexDavid E Starkey
Section of Evolution and Ecology, University of California, Davis, California 95616, USA
Evolution 57:119-28. 2003.... - Rapid color evolution in an aposematic species: a phylogenetic analysis of color variation in the strikingly polymorphic strawberry poison-dart frogIan J Wang
Department of Evolution and Ecology, University of California, Davis, California 95616, USA
Evolution 62:2742-59. 2008..Our results indicate that shifts in coloration in aposematic species may occur more regularly than predicted and that convergence in coloration may indicate that similar forces are repeatedly driving these shifts... - Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtlesRobert C Thomson
Department of Evolution and Ecology, University of California, 2320 Storer Hall, Davis, CA 95616, USA
Mol Phylogenet Evol 49:514-25. 2008..We presume that our strategy should work well across any similarly divergent clade, suggesting that many-marker datasets can be developed quickly and efficiently for phylogenetic analysis... - Calculating biologically accurate mitigation credits: insights from the California tiger salamanderChristopher A Searcy
Department of Evolution and Ecology and Center for Population Biology, 2320 Storer Hall, 1 Shields Avenue, University of California, Davis, CA 95616 5270, USA
Conserv Biol 22:997-1005. 2008..Use of the density distribution of reproductive value as a basis for mitigation plans is a procedure that can be applied to all endangered species, and it should improve the quality of mitigation decisions... - Conflicting mitochondrial and nuclear phylogenies for the widely disjunct Emys (Testudines: Emydidae) species complex, and what they tell us about biogeography and hybridizationPhillip Q Spinks
Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA
Syst Biol 58:1-20. 2009.... - Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtlesRobert C Thomson
Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA
Syst Biol 59:42-58. 2010..Finally, we discuss some of the remaining pitfalls and concerns associated with supermatrix analyses, provide comparisons to supertree approaches, and suggest areas for future research... - Introduction history and habitat variation explain the landscape genetics of hybrid tiger salamandersBenjamin M Fitzpatrick
Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville 37996, USA
Ecol Appl 17:598-608. 2007..Management favoring natural habitat characteristics may substantially decrease the rate of spread of introduced alleles... - Assessing concordance of fossil calibration points in molecular clock studies: an example using turtlesThomas J Near
Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996 1610, USA
Am Nat 165:137-46. 2005..Many of the truly ancient lineages of turtles are currently represented by a few, often endangered species that deserve high priority as conservation targets... - Molecular phylogenetics and evolution of turtlesJames G Krenz
Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, 50011-3223, USA
Mol Phylogenet Evol 37:178-91. 2005..Our research highlights the utility of molecular data in identifying issues of character homology in morphological datasets, while shedding valuable light on the biodiversity of a globally imperiled taxon... - Hybrid vigor between native and introduced salamanders raises new challenges for conservationBenjamin M Fitzpatrick
Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
Proc Natl Acad Sci U S A 104:15793-8. 2007..The ecological consequences for other native species are unknown... - Effects of chytrid and carbaryl exposure on survival, growth and skin peptide defenses in foothill yellow-legged frogsCarlos Davidson
Environmental Studies Program, San Francisco State University, 1600 Holloway Avenue, San Francisco CA 94132, USA
Environ Sci Technol 41:1771-6. 2007..Skin peptide defenses were significantly reduced after exposure to carbaryl suggesting that pesticides may inhibit this innate immune defense and increase susceptibility to disease...