Matthew C Brandley

Summary

Publications

  1. pmc Uterine gene expression in the live-bearing lizard, Chalcides ocellatus, reveals convergence of squamate reptile and mammalian pregnancy mechanisms
    Matthew C Brandley
    Department of Ecology and Evolutionary Biology, Yale University, USA
    Genome Biol Evol 4:394-411. 2012
  2. doi request reprint Accommodating heterogenous rates of evolution in molecular divergence dating methods: an example using intercontinental dispersal of Plestiodon (Eumeces) lizards
    Matthew C Brandley
    Museum of Vertebrate Zoology, Department of Integrative Biology, University of California, Berkeley, CA 94720 3160, USA
    Syst Biol 60:3-15. 2011
  3. doi request reprint Does dispersal across an aquatic geographic barrier obscure phylogeographic structure in the diamond-backed watersnake (Nerodia rhombifer)?
    Matthew C Brandley
    University of California, Museum of Vertebrate Zoology, Department of Integrative Biology, Berkeley, CA, USA
    Mol Phylogenet Evol 57:552-60. 2010
  4. doi request reprint Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei: Beryciformes: Holocentridae): reconciling more than 100 years of taxonomic confusion
    Alex Dornburg
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Mol Phylogenet Evol 65:727-38. 2012
  5. doi request reprint Homoplasy and clade support
    Matthew C Brandley
    Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720 3160, USA
    Syst Biol 58:184-98. 2009
  6. pmc Bermuda as an evolutionary life raft for an ancient lineage of endangered lizards
    Matthew C Brandley
    Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California, United States of America
    PLoS ONE 5:e11375. 2010
  7. ncbi request reprint Are unequal clade priors problematic for Bayesian phylogenetics?
    Matthew C Brandley
    Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720 3160, USA
    Syst Biol 55:138-46; author reply 147-51. 2006
  8. ncbi request reprint Rates and patterns in the evolution of snake-like body form in squamate reptiles: evidence for repeated re-evolution of lost digits and long-term persistence of intermediate body forms
    Matthew C Brandley
    Museum of Vertebrate Zoology, University of California, Berkeley, California 94270, USA
    Evolution 62:2042-64. 2008
  9. ncbi request reprint Boom and bust: ancient and recent diversification in bichirs (Polypteridae: Actinopterygii), a relictual lineage of ray-finned fishes
    Thomas J Near
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, 06520 Peabody Museum of Natural History, Yale University, New Haven, Connecticut, 06520
    Evolution 68:1014-26. 2014
  10. pmc Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation
    Frank T Burbrink
    Department of Biology, The College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY 10314, USA
    Proc Biol Sci 279:4817-26. 2012

Detail Information

Publications12

  1. pmc Uterine gene expression in the live-bearing lizard, Chalcides ocellatus, reveals convergence of squamate reptile and mammalian pregnancy mechanisms
    Matthew C Brandley
    Department of Ecology and Evolutionary Biology, Yale University, USA
    Genome Biol Evol 4:394-411. 2012
    ..ocellatus pregnancy are likely a result of regulation of genes continually expressed in the uterus rather than the initiation of expression of unique genes...
  2. doi request reprint Accommodating heterogenous rates of evolution in molecular divergence dating methods: an example using intercontinental dispersal of Plestiodon (Eumeces) lizards
    Matthew C Brandley
    Museum of Vertebrate Zoology, Department of Integrative Biology, University of California, Berkeley, CA 94720 3160, USA
    Syst Biol 60:3-15. 2011
    ..Analyses that best capture the rate of evolution in the combined data set infer that this exchange occurred via Beringia ∼18.0-30 Ma...
  3. doi request reprint Does dispersal across an aquatic geographic barrier obscure phylogeographic structure in the diamond-backed watersnake (Nerodia rhombifer)?
    Matthew C Brandley
    University of California, Museum of Vertebrate Zoology, Department of Integrative Biology, Berkeley, CA, USA
    Mol Phylogenet Evol 57:552-60. 2010
    ..Nonetheless, the coalescent simulations that account for limited migration suggest that the Mississippi River was an important feature that shaped the phylogeographic history of this aquatic snake in the USA despite limited gene flow...
  4. doi request reprint Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei: Beryciformes: Holocentridae): reconciling more than 100 years of taxonomic confusion
    Alex Dornburg
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Mol Phylogenet Evol 65:727-38. 2012
    ..We propose a new classification for Holocentrinae, recognizing four lineages that are treated as genera: Sargocentron Fowler, 1904, Holocentrus Scopoli, 1777, Flameo Jordan and Evermann, 1898, and Neoniphon Castelnau, 1875...
  5. doi request reprint Homoplasy and clade support
    Matthew C Brandley
    Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720 3160, USA
    Syst Biol 58:184-98. 2009
    ..These results may be especially relevant to "deep" phylogenetic problems, such as reconstructing the tree of life, as they represent the largest possible extremes of time and evolutionary rates, 2 factors that cause homoplasy...
  6. pmc Bermuda as an evolutionary life raft for an ancient lineage of endangered lizards
    Matthew C Brandley
    Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California, United States of America
    PLoS ONE 5:e11375. 2010
    ..Threats such as habitat destruction, littering, and non-native species have severely reduced the population size of this highly endangered lizard...
  7. ncbi request reprint Are unequal clade priors problematic for Bayesian phylogenetics?
    Matthew C Brandley
    Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720 3160, USA
    Syst Biol 55:138-46; author reply 147-51. 2006
  8. ncbi request reprint Rates and patterns in the evolution of snake-like body form in squamate reptiles: evidence for repeated re-evolution of lost digits and long-term persistence of intermediate body forms
    Matthew C Brandley
    Museum of Vertebrate Zoology, University of California, Berkeley, California 94270, USA
    Evolution 62:2042-64. 2008
    ..Finally, although loss of digits is common, we find statistically significant support for at least six examples of the re-evolution of lost digits in the forelimb and hind limb...
  9. ncbi request reprint Boom and bust: ancient and recent diversification in bichirs (Polypteridae: Actinopterygii), a relictual lineage of ray-finned fishes
    Thomas J Near
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, 06520 Peabody Museum of Natural History, Yale University, New Haven, Connecticut, 06520
    Evolution 68:1014-26. 2014
    ....
  10. pmc Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation
    Frank T Burbrink
    Department of Biology, The College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY 10314, USA
    Proc Biol Sci 279:4817-26. 2012
    ..It also suggests that processes of phenotypic diversification cannot be predicted solely from the existence of an AR or knowledge of the process of diversification...
  11. doi request reprint Relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (Mammalia: Cetacea)
    Alex Dornburg
    Department of Ecology and Evolutionary Biology, Yale University, USA
    Mol Biol Evol 29:721-36. 2012
    ..We interpret the use of external calibrations in divergence time studies in light of these results, suggesting that rate shifts at deep time scales may mislead inferences of absolute molecular rates and ages...
  12. ncbi request reprint Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards
    Matthew C Brandley
    Department of Biology, San Diego State University, San Diego, CA, 92182 4614, USA
    Syst Biol 54:373-90. 2005
    ..Amphiglossus, Chalcides, the acontines Acontias and Typhlosaurus, and Scincinae are paraphyletic. The globally widespread "Eumeces" is polyphyletic and we make necessary taxonomic changes...