Matt Fujita's Publications

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Leaché, A. D., M. K. Fujita, V. N. Minin, and R. R. Bouckaert. Accepted. Species delimitation using genome-wide SNP data. Systematic Biology.

Castoe, T. A., et al. (including M. K. Fujita). Accepted. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the National Academy of Sciences USA.

Rheindt, F. E., M. K. Fujita, P. R. Wilton, and S. V. Edwards. Accepted. Introgression and phenotypic assimilation in Zimmerius Flycatchers (Tyrannidae): Population genetic and phylogenetic inferences from genome-wide SNPs. Systematic Biology.

Streicher, J. W., and M. K. Fujita. 2014. Observations on the captive maintenance and reproduction of the Balcones Barking Frog, Craugastor augusti latrans. Herpetological Review 45(1):49-51.

Pepper, M., P. Doughty, M. K. Fujita, C. Moritz, and S. Keogh. 2013. Speciation on the Rocks: Integrated Systematics of the Heteronotia spelea Species Complex (Gekkota; Reptilia) from Western and Central Australia. PLoS ONE 8(11):e78110. 

Shaffer, H. B. et al. (including M. K. Fujita). 2013. The Painted turtle genome: extreme physiological adaptations in a slowly evolving lineage. Genome Biology.

Rands, C. M. D., A. Darling, M. K. Fujita, L. Kong, M. T. Webster, C. Clabaut, R. D. Emes, A. Heger, S. Meader, M. B. Hawkins, M. Eisen, C. Teiling, J. Affourtit, B. Boese, P. R. Grant, B. R. Grant, J. A. Eisen, A. Abzhanov, and C. P. Ponting. 2013. Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence. BMC Genomics 14:95. 

Castoe, T. A. et al. (including M. K. Fujita). 2012. Meeting report from the first snake genomics and integrative biology meeting. Standards in Genomic Sciences 7:1.  

Fong, J. J., J. M. Brown, M. K. Fujita, and B. Boussau. 2012. A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a paraphyletic Lissamphibia. PLoS One 7(11):e48990. 

Rodel, M-O. et al. (including M. K. Fujita). 2012. The genus Astylosternus in the Upper Guinea rainforests, West Africa, with the description of a new species (Amphibia: Anura: Arthroleptidae). Zootaxa 3245:1-29.

Fujita, M. K., A. D. Leaché, F. T. Burbrink, J. A. McGuire, and C. Moritz. 2012. Coalescent-based species delimitation in an integrative taxonomy. Trends in Ecology and Evolution 27(9):480-488.

St. John et al. (including M. K. Fujita).  2012. Sequencing three crocodilian genomes toilluminate the evolution of archosaurs and amniotes. Genome Biology.

Edwards, S. V., S. E. Cameron Devitt, and M. K. Fujita. 2012.  Phylogeography. In: Encyclopedia of Theoretical Ecology.

cover JEB 2012

Robert, J., M. Kearney, H. Diem-Vo, M. K. Fujita, and C. Moritz. 2012. Cyto-nuclear interactions, genome dosage effects and metabolic scaling in parthenogenetic lizards of reciprocal hybrid origin. Journal of Evolutionary Biology.

Pepper, M. R., S. Y. W. Ho, M. K. Fujita, and J. S. Keogh. 2011. Diversification in the face of desertification: mesic refugia and the origins of arid-zone biota. Molecular Phylogenetics and Evolution 61:750-759.

Alfoldi et al. (including M. K. Fujita). 2011. The genome of Anolis carolinensis, the green anole lizard, and a comparative analysis with birds and mammals.  Nature 477:587-591.

Fujita, M. K., S. V. Edwards, and C. P. Ponting. 2011. The Anolis lizard genome: an amniote genome without isochores. Genome Biology and Evolution 3:974-984.

Fong, J. J., and M. K. Fujita. 2011. Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata. Molecular Phylogenetics and Evolution 61:300-307.

Boussau, B., J. M. Brown, and M. K. Fujita.  2011.  Nonadaptive evolution of mitochondrial genome structure.  Evolution 65:2706-2711.

ME Cover April 2011

Pepper, M., M. K. Fujita, C. Moritz, and J. S. Keogh. 2011. Paleoclimate change drovediversification among isolated mountain refugia in the Australia arid zone. Molecular Ecology 20:1529-1545.


Janes, D. E., C. Chapus, Y. Gondo, D. Clayton, S. Sinha, C. Blatti, C. Organ, M. K. Fujita, C.  Balakrishnan, and S. V. Edwards.  2011.  Reptiles and mammals have differentially retained long non-coding sequences from the amniote ancestor. Genome Biology and Evolution 3:102-113.

Fujita, M. K., and A. D. Leaché.  2011.  A coalescent perspective on delimiting and naming species: a reply to Bauer et al. Proceedings of the Royal Society B 278:493-495.

Fujita, M. K., and T. J. Papenfuss.  2011.  Molecular  systematics of Stenodactylus (Gekkonidae), an Afro-Arabian gecko species complex. Molecular Phylogenetics and Evolution 58:71-75.

Leaché, A. D., and M. K. Fujita. 2010. Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). Proceedings of the Royal Society B 277:3071-3077.

Janes, D. E., C. L. Organ, M. K Fujita, A. M. Shedlock, and S. V. Edwards. 2010. Genomeevolution in Reptilia, the sister group of mammals.  Annual Review of Genomics and Human Genetics 11:239-264.

Fujita, M.K., J. A. McGuire, S. Donnellan, and C. Moritz. 2010. Diversification and persistence at the arid-monsoonal interface: Australia-wide biogeography of the Bynoe’s gecko (Heteronotia binoei; Gekkonidae). Evolution 64(8): 2293-2314.

Fujita, M.K., and C. Moritz. 2009. Origin and evolution of parthenogenetic genomes in lizards: current state and future directions. Cytogenetic and Genome Research 127:261-272.

Kearney, M., M.K. Fujita, and J. Ridenour. 2009. Lost sex in the reptiles: constraints and correlations. In: I. Schön, K. Martens, P. van Dijk, editors.  Lost Sex. Springer Netherlands.

Shaffer, H.B., D.E. Starkey, and M.K. Fujita.  2008.  Molecular insights into the systematics of the snapping turtles (Chelydridae).   R.J. Brooks, A.C. Steyermark, and M. S. Finkler, eds., Biology of the Snapping Turtle (Chelydra serpentina).  John Hopkins University Press, Baltimore. 

Fujita, M.K., J.L. Boore, C. Moritz. 2007. Multiple origins and rapid evolution of duplicated mitochondrial genes in parthenogenetic geckos (Heteronotia binoei; Squamata, Gekkonidae).  Molecular Biology and Evolution 24:2775-2786.

Leaché, A.D., M.-O. Rodel, C.W. Linkem, R.E. Diaz, A. Hillers, and M.K. Fujita.  2006.  Biodiversity in a forest island: reptiles and amphibians of the Togo Hills, Kyabobo National Park, Ghana.  Amphibian and Reptile Conservation 4(1): 22-45.

Rödel, M-O., M. Gil, A..C. Agyei, A.D. Leaché, R.E. Diaz, M.K. Fujita, and R. Ernst.  2005.  The amphibians of the forested parts of south-western Ghana.  Salamandra: 41: 107-127.

Fujita, M.K., T.N. Engstrom, D.E. Starkey, and H.B. Shaffer.  2004.  Turtle phylogeny revisited: insights from a novel nuclear intron.  Molecular Phylogenetics and Evolution 31: 1031-1040.

© Matthew Fujita 2012