H B Shaffer

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Multiple nuclear gene sequences identify phylogenetic species boundaries in the rapidly radiating clade of Mexican ambystomatid salamanders
    David W Weisrock
    Department of Biology, University of Kentucky, Lexington, KY 40506, USA
    Mol Ecol 15:2489-503. 2006
  2. pmc Retention of low-fitness genotypes over six decades of admixture between native and introduced tiger salamanders
    Jarrett 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
  3. pmc Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders
    Benjamin M Fitzpatrick
    Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
    BMC Evol Biol 9:176. 2009
  4. pmc Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles
    Phillip Q Spinks
    Department of Evolution and Ecology, Davis, USA
    BMC Evol Biol 9:56. 2009
  5. pmc Rapid progress on the vertebrate tree of life
    Robert C Thomson
    Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA
    BMC Biol 8:19. 2010
  6. ncbi request reprint Tests of turtle phylogeny: molecular, morphological, and paleontological approaches
    H 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
  7. ncbi request reprint 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 data
    H 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
  8. ncbi request reprint Delimiting species in recent radiations
    H 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
  9. ncbi request reprint The molecular phylogenetics of endangerment: cryptic variation and historical phylogeography of the California tiger salamander, Ambystoma californiense
    H 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
  10. ncbi request reprint Species boundaries, phylogeography and conservation genetics of the red-legged frog (Rana aurora/draytonii) complex
    H Bradley Shaffer
    Section of Evolution and Ecology, and Center for Population Biology, University of California, Davis 95616, USA
    Mol Ecol 13:2667-77. 2004

Detail Information

Publications31

  1. ncbi request reprint Multiple nuclear gene sequences identify phylogenetic species boundaries in the rapidly radiating clade of Mexican ambystomatid salamanders
    David 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...
  2. pmc Retention of low-fitness genotypes over six decades of admixture between native and introduced tiger salamanders
    Jarrett 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...
  3. pmc Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders
    Benjamin 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...
  4. pmc Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles
    Phillip Q Spinks
    Department of Evolution and Ecology, Davis, USA
    BMC Evol Biol 9:56. 2009
    ....
  5. pmc Rapid progress on the vertebrate tree of life
    Robert 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...
  6. ncbi request reprint Tests of turtle phylogeny: molecular, morphological, and paleontological approaches
    H 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...
  7. ncbi request reprint 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 data
    H 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...
  8. ncbi request reprint Delimiting species in recent radiations
    H 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
    ....
  9. ncbi request reprint The molecular phylogenetics of endangerment: cryptic variation and historical phylogeography of the California tiger salamander, Ambystoma californiense
    H 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...
  10. ncbi request reprint Species boundaries, phylogeography and conservation genetics of the red-legged frog (Rana aurora/draytonii) complex
    H 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...
  11. ncbi request reprint Range-wide molecular analysis of the western pond turtle (Emys marmorata): cryptic variation, isolation by distance, and their conservation implications
    Phillip Q Spinks
    Section of Evolution and Ecology, University of California, Davis, California 95616, USA
    Mol Ecol 14:2047-64. 2005
    ....
  12. ncbi request reprint Phylogeographic concordance in the southeastern United States: the flatwoods salamander, Ambystoma cingulatum, as a test case
    Gregory 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...
  13. ncbi request reprint 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...
  14. doi request reprint Fourteen nuclear genes provide phylogenetic resolution for difficult nodes in the turtle tree of life
    Anthony 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...
  15. ncbi request reprint 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...
  16. doi request reprint Landscape genetics of alpine Sierra Nevada salamanders reveal extreme population subdivision in space and time
    Wesley 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...
  17. ncbi request reprint 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
    ....
  18. doi request reprint Nuclear gene phylogeography reveals the historical legacy of an ancient inland sea on lineages of the western pond turtle, Emys marmorata in California
    Phillip Q Spinks
    Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
    Mol Ecol 19:542-56. 2010
    ....
  19. ncbi request reprint Environment-dependent admixture dynamics in a tiger salamander hybrid zone
    Benjamin 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...
  20. ncbi request reprint Turtle phylogeny: insights from a novel nuclear intron
    Matthew 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...
  21. ncbi request reprint Molecular systematics, phylogeography, and the effects of Pleistocene glaciation in the painted turtle (Chrysemys picta) complex
    David E Starkey
    Section of Evolution and Ecology, University of California, Davis, California 95616, USA
    Evolution 57:119-28. 2003
    ....
  22. doi request reprint Rapid color evolution in an aposematic species: a phylogenetic analysis of color variation in the strikingly polymorphic strawberry poison-dart frog
    Ian 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...
  23. doi request reprint Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles
    Robert 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...
  24. doi request reprint Calculating biologically accurate mitigation credits: insights from the California tiger salamander
    Christopher 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...
  25. doi request reprint Conflicting mitochondrial and nuclear phylogenies for the widely disjunct Emys (Testudines: Emydidae) species complex, and what they tell us about biogeography and hybridization
    Phillip 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
    ....
  26. doi request reprint Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtles
    Robert 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...
  27. ncbi request reprint Introduction history and habitat variation explain the landscape genetics of hybrid tiger salamanders
    Benjamin 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...
  28. ncbi request reprint Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles
    Thomas 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...
  29. ncbi request reprint Molecular phylogenetics and evolution of turtles
    James 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...
  30. pmc Hybrid vigor between native and introduced salamanders raises new challenges for conservation
    Benjamin 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...
  31. ncbi request reprint Effects of chytrid and carbaryl exposure on survival, growth and skin peptide defenses in foothill yellow-legged frogs
    Carlos 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...