Dr Matthew Brandley

A08 - Heydon-Laurence Building
The University of Sydney

Selected grants

2012

  • How does viviparity evolve Genetic perspectives from a unique model system; Brandley M; Australian Research Council (ARC)/Discovery Early Career Researcher Award (DECRA).

2010

  • Gene expression and the evolution of viviparity and the placenta in reptiles; Brandley M, Brandley M, Thompson M; DVC Research/Postdoctoral Research Fellowship Scheme.

Selected publications

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Journals

  • Near, T., Dornburg, A., Tokita, M., Suzuki, D., Brandley, M., Friedman, M. (2014). Boom and bust: Ancient and recent diversification in bichirs (polypteridae: Actinopterygii), a relictual lineage of ray-finned fishes. Evolution, 68(4), 1014-1026. [More Information]
  • Dornburg, A., Brandley, M. (2014). Patterns of molecular evolution in cetaceans and their implications for uncorrelated relaxed-clock models. Molecular Biology and Evolution.
  • Brandley, M., Kuriyama, T., Hasegawa, M. (2014). Snake and Bird Predation Drive the Repeated Convergent Evolution of Correlated Life History Traits and Phenotype in the Izu Island Scincid Lizard (Plestiodon latiscutatus). PLoS One, 9(3), 1-15. [More Information]
  • Van Dyke, J., Brandley, M., Thompson, M. (2014). The evolution of viviparity: molecular and genomic data from squamate reptiles advance understanding of live birth in amniotes. Reproduction, 147(1), R15-R26. [More Information]
  • Andrews, R., Brandley, M., Greene, V. (2013). Developmental sequences of squamate reptiles are taxon specific. Evolution and Development, 15(5), 326-343. [More Information]
  • Burbrink, F., Chen, X., Myers, E., Brandley, M., Pyron, R. (2012). Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation. Proceedings of the Royal Society B: Biological Sciences, 279(1748), 4817-4826. [More Information]
  • Dornburg, A., Moore, J., Webster, R., Warren, D., Brandley, M., Iglesias, T., Wainwright, P., Near, T. (2012). Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei: Beryciformes: Holocentridae): Reconciling more than 100 years of taxonomic confusion. Molecular Phylogenetics and Evolution, 65(2), 727-738. [More Information]
  • Murphy, B., Brandley, M., Murphy, C., Thompson, M. (2012). Morphology and development of the placentae in Eulamprus quoyii group skinks (Squamata: Scincidae). Journal of Anatomy, 220(5), 454-471. [More Information]
  • Dornburg, A., Brandley, M., McGowen, M., Near, T. (2012). Relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (Mammalia: Cetacea). Molecular Biology and Evolution, 29(2), 721-736. [More Information]
  • Brandley, M., Ota, H., Hikida, T., Nieto Montes de Oca, A., Feria-Ortiz, M., Guo, X., Wang, Y. (2012). The phylogenetic systematics of blue-tailed skinks (Plestiodon) and the family Scincidae. Zoological Journal of the Linnean Society, 165(1), 163-189. [More Information]
  • Brandley, M., Young, R., Warren, D., Thompson, M., Wagner, G. (2012). Uterine gene expression in the live-bearing lizard, Chalcides ocellatus, reveals convergence of squamate reptile and mammalian pregnancy mechanisms. Genome Biology and Evolution, 4(3), 394-411. [More Information]
  • Kuriyama, T., Brandley, M., Katayama, A., Mori, A., Honda, M., Hasegawa, M. (2011). A time-calibrated phylogenetic approach to assessing the phylogeography, colonization history and phenotypic evolution of snakes in the Japanese Izu Islands. Journal of Biogeography, 38(2), 259-271. [More Information]
  • Brandley, M., Wang, Y., Guo, X., Nieto Montes de Oca, A., Feria-Ortiz, M., Hikida, T., Ota, H. (2011). Accommodating Heterogenous Rates of Evolution in Molecular Divergence Dating Methods: An Example Using Intercontinental Dispersal of Plestiodon (Eumeces) Lizards. Systematic Biology, 60(1), 3-15. [More Information]
  • Dornburg, A., Warren, D., Iglesias, T., Brandley, M. (2011). Natural History Observations of the Ichthyological and Herpetological Fauna on the Island of Curacao (Netherlands). Peabody Museum of Natural History. Bulletin, 52(1), 181-186. [More Information]
  • He, K., Li, Y., Brandley, M., Lin, L., Wang, Y., Zhang, Y., Jiang, X. (2010). A multi-locus phylogeny of Nectogalini shrews and influences of the paleoclimate on speciation and evolution. Molecular Phylogenetics and Evolution, 56(2), 734-746. [More Information]
  • Brandley, M., Wang, Y., Guo, X., Nieto Montes de Oca, A., Feria-Ortiz, M., Hikida, T., Ota, H. (2010). Bermuda as an Evolutionary Life Raft for an Ancient Lineage of Endangered Lizards. PLoS One, 5(6), e11375-1-e11375-4. [More Information]
  • Suzuki, D., Brandley, M., Tokita, M. (2010). Correction: The mitochondrial phylogeny of an ancient lineage of ray-finned fishes (Polypteridae) with implications for the evolution of body elongation, pelvic fin loss, and craniofacial morphology in Osteichthyes. BMC Evolutionary Biology.
  • Kohlsdorf, T., Lynch, V., Rodrigues, M., Brandley, M., Wagner, G. (2010). Data and Data-Interpretation in the Study of Limb Evolution: A Reply to Galis et al. on the Re-Evolution of Digits in the Lizard Genus Bachia. Evolution, 64(8), 2477-2485. [More Information]
  • Brandley, M., Guiher, T., Pyron, R., Winnie, C., Burbrink, F. (2010). Does dispersal across an aquatic geographic barrier obscure phylogeographic structure in the diamond-backed watersnake (Nerodia rhombifer)? Molecular Phylogenetics and Evolution, 57(2), 552-560. [More Information]
  • Suzuki, D., Brandley, M., Tokita, M. (2010). The mitochondrial phylogeny of an ancient lineage of ray-finned fishes (Polypteridae) with implications for the evolution of body elongation, pelvic fin loss, and craniofacial morphology in Osteichthyes. BMC Evolutionary Biology, 10(1), 1-12. [More Information]
  • Vincent, S., Brandley, M., Herrel, A., Alfaro, M. (2009). Convergence in trophic morphology and feeding performance among piscivorous natricine snakes. Journal of Evolutionary Biology, 22(6), 1203-1211. [More Information]
  • Brandley, M., Warren, D., Leache, A., McGuire, J. (2009). Homoplasy and Clade Support. Systematic Biology, 58(2), 184-198. [More Information]
  • Xiong, Y., Brandley, M., Xu, S., Zhou, K., Yang, G. (2009). Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales. BMC Evolutionary Biology, 9(1), 1-13. [More Information]
  • Brandley, M., Huelsenbeck, J., Wiens, J. (2008). 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. Evolution, 62(8), 2042-2064. [More Information]
  • Brandley, M., Leache, A., Warren, D., McGuire, J. (2006). Are Unequal Clade Priors Problematic for Bayesian Phylogenetics? Systematic Biology.
  • Brandley, M., Wynn, A., de Queiroz, K. (2006). Karyotype and Relationships of Anolis desechensis. Journal of Herpetology.
  • Wiens, J., Brandley, M., Reeder, T. (2006). Why Does a Trait Evolve Multiple Times Within a Clade? Repeated Evolution of Snake-Like Body Form in Squamate Reptiles. Evolution.
  • Schmitz, A., Brandley, M., Mausfield, P., Vences, M., Glaw, F., Nussbaum, R., Reeder, T. (2005). Opening the black box: phylogenetics and morphological evolution of the Malagasy fossorial lizards of the subfamily "Scincinae". Molecular Phylogenetics and Evolution.
  • Brandley, M., Schmitz, A., Reeder, T. (2005). Partitioned Bayesian Analyses, Partition Choice, and the Phylogenetic Relationships of Scincid Lizards. Systematic Biology.
  • Brandley, M., de Queiroz, K. (2004). Phylogeny, ecomorphological evolution, and historical biogeography of the Anolis cristatellus series. Herpetological Monographs.

Conferences

  • Griffith, O., Brandley, M., Belov, K., Thompson, M. (2013). Gene expression and the evolution of placental functions in reptiles. Genetics Society of AustralAsia Inc Annual Conference Sydney - Genetics in the Harbour City, Sydney: Genetics Society of AustralAsia, Inc.

Reference Works

  • Wiens, J., Brandley, M. (2009). Evolution of Limblessness. Grzimek's Animal Life. (pp. 1-15). United States: Gale.

2014

  • Near, T., Dornburg, A., Tokita, M., Suzuki, D., Brandley, M., Friedman, M. (2014). Boom and bust: Ancient and recent diversification in bichirs (polypteridae: Actinopterygii), a relictual lineage of ray-finned fishes. Evolution, 68(4), 1014-1026. [More Information]
  • Dornburg, A., Brandley, M. (2014). Patterns of molecular evolution in cetaceans and their implications for uncorrelated relaxed-clock models. Molecular Biology and Evolution.
  • Brandley, M., Kuriyama, T., Hasegawa, M. (2014). Snake and Bird Predation Drive the Repeated Convergent Evolution of Correlated Life History Traits and Phenotype in the Izu Island Scincid Lizard (Plestiodon latiscutatus). PLoS One, 9(3), 1-15. [More Information]
  • Van Dyke, J., Brandley, M., Thompson, M. (2014). The evolution of viviparity: molecular and genomic data from squamate reptiles advance understanding of live birth in amniotes. Reproduction, 147(1), R15-R26. [More Information]

2013

  • Andrews, R., Brandley, M., Greene, V. (2013). Developmental sequences of squamate reptiles are taxon specific. Evolution and Development, 15(5), 326-343. [More Information]
  • Griffith, O., Brandley, M., Belov, K., Thompson, M. (2013). Gene expression and the evolution of placental functions in reptiles. Genetics Society of AustralAsia Inc Annual Conference Sydney - Genetics in the Harbour City, Sydney: Genetics Society of AustralAsia, Inc.

2012

  • Burbrink, F., Chen, X., Myers, E., Brandley, M., Pyron, R. (2012). Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation. Proceedings of the Royal Society B: Biological Sciences, 279(1748), 4817-4826. [More Information]
  • Dornburg, A., Moore, J., Webster, R., Warren, D., Brandley, M., Iglesias, T., Wainwright, P., Near, T. (2012). Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei: Beryciformes: Holocentridae): Reconciling more than 100 years of taxonomic confusion. Molecular Phylogenetics and Evolution, 65(2), 727-738. [More Information]
  • Murphy, B., Brandley, M., Murphy, C., Thompson, M. (2012). Morphology and development of the placentae in Eulamprus quoyii group skinks (Squamata: Scincidae). Journal of Anatomy, 220(5), 454-471. [More Information]
  • Dornburg, A., Brandley, M., McGowen, M., Near, T. (2012). Relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (Mammalia: Cetacea). Molecular Biology and Evolution, 29(2), 721-736. [More Information]
  • Brandley, M., Ota, H., Hikida, T., Nieto Montes de Oca, A., Feria-Ortiz, M., Guo, X., Wang, Y. (2012). The phylogenetic systematics of blue-tailed skinks (Plestiodon) and the family Scincidae. Zoological Journal of the Linnean Society, 165(1), 163-189. [More Information]
  • Brandley, M., Young, R., Warren, D., Thompson, M., Wagner, G. (2012). Uterine gene expression in the live-bearing lizard, Chalcides ocellatus, reveals convergence of squamate reptile and mammalian pregnancy mechanisms. Genome Biology and Evolution, 4(3), 394-411. [More Information]

2011

  • Kuriyama, T., Brandley, M., Katayama, A., Mori, A., Honda, M., Hasegawa, M. (2011). A time-calibrated phylogenetic approach to assessing the phylogeography, colonization history and phenotypic evolution of snakes in the Japanese Izu Islands. Journal of Biogeography, 38(2), 259-271. [More Information]
  • Brandley, M., Wang, Y., Guo, X., Nieto Montes de Oca, A., Feria-Ortiz, M., Hikida, T., Ota, H. (2011). Accommodating Heterogenous Rates of Evolution in Molecular Divergence Dating Methods: An Example Using Intercontinental Dispersal of Plestiodon (Eumeces) Lizards. Systematic Biology, 60(1), 3-15. [More Information]
  • Dornburg, A., Warren, D., Iglesias, T., Brandley, M. (2011). Natural History Observations of the Ichthyological and Herpetological Fauna on the Island of Curacao (Netherlands). Peabody Museum of Natural History. Bulletin, 52(1), 181-186. [More Information]

2010

  • He, K., Li, Y., Brandley, M., Lin, L., Wang, Y., Zhang, Y., Jiang, X. (2010). A multi-locus phylogeny of Nectogalini shrews and influences of the paleoclimate on speciation and evolution. Molecular Phylogenetics and Evolution, 56(2), 734-746. [More Information]
  • Brandley, M., Wang, Y., Guo, X., Nieto Montes de Oca, A., Feria-Ortiz, M., Hikida, T., Ota, H. (2010). Bermuda as an Evolutionary Life Raft for an Ancient Lineage of Endangered Lizards. PLoS One, 5(6), e11375-1-e11375-4. [More Information]
  • Suzuki, D., Brandley, M., Tokita, M. (2010). Correction: The mitochondrial phylogeny of an ancient lineage of ray-finned fishes (Polypteridae) with implications for the evolution of body elongation, pelvic fin loss, and craniofacial morphology in Osteichthyes. BMC Evolutionary Biology.
  • Kohlsdorf, T., Lynch, V., Rodrigues, M., Brandley, M., Wagner, G. (2010). Data and Data-Interpretation in the Study of Limb Evolution: A Reply to Galis et al. on the Re-Evolution of Digits in the Lizard Genus Bachia. Evolution, 64(8), 2477-2485. [More Information]
  • Brandley, M., Guiher, T., Pyron, R., Winnie, C., Burbrink, F. (2010). Does dispersal across an aquatic geographic barrier obscure phylogeographic structure in the diamond-backed watersnake (Nerodia rhombifer)? Molecular Phylogenetics and Evolution, 57(2), 552-560. [More Information]
  • Suzuki, D., Brandley, M., Tokita, M. (2010). The mitochondrial phylogeny of an ancient lineage of ray-finned fishes (Polypteridae) with implications for the evolution of body elongation, pelvic fin loss, and craniofacial morphology in Osteichthyes. BMC Evolutionary Biology, 10(1), 1-12. [More Information]

2009

  • Vincent, S., Brandley, M., Herrel, A., Alfaro, M. (2009). Convergence in trophic morphology and feeding performance among piscivorous natricine snakes. Journal of Evolutionary Biology, 22(6), 1203-1211. [More Information]
  • Wiens, J., Brandley, M. (2009). Evolution of Limblessness. Grzimek's Animal Life. (pp. 1-15). United States: Gale.
  • Brandley, M., Warren, D., Leache, A., McGuire, J. (2009). Homoplasy and Clade Support. Systematic Biology, 58(2), 184-198. [More Information]
  • Xiong, Y., Brandley, M., Xu, S., Zhou, K., Yang, G. (2009). Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales. BMC Evolutionary Biology, 9(1), 1-13. [More Information]

2008

  • Brandley, M., Huelsenbeck, J., Wiens, J. (2008). 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. Evolution, 62(8), 2042-2064. [More Information]

2006

  • Brandley, M., Leache, A., Warren, D., McGuire, J. (2006). Are Unequal Clade Priors Problematic for Bayesian Phylogenetics? Systematic Biology.
  • Brandley, M., Wynn, A., de Queiroz, K. (2006). Karyotype and Relationships of Anolis desechensis. Journal of Herpetology.
  • Wiens, J., Brandley, M., Reeder, T. (2006). Why Does a Trait Evolve Multiple Times Within a Clade? Repeated Evolution of Snake-Like Body Form in Squamate Reptiles. Evolution.

2005

  • Schmitz, A., Brandley, M., Mausfield, P., Vences, M., Glaw, F., Nussbaum, R., Reeder, T. (2005). Opening the black box: phylogenetics and morphological evolution of the Malagasy fossorial lizards of the subfamily "Scincinae". Molecular Phylogenetics and Evolution.
  • Brandley, M., Schmitz, A., Reeder, T. (2005). Partitioned Bayesian Analyses, Partition Choice, and the Phylogenetic Relationships of Scincid Lizards. Systematic Biology.

2004

  • Brandley, M., de Queiroz, K. (2004). Phylogeny, ecomorphological evolution, and historical biogeography of the Anolis cristatellus series. Herpetological Monographs.

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