Leaché A. D. , H. R. Davis, S. Singhal, M. K. Fujita, M. Lahti, K. R. Zamudio. 2021. Phylogenomic Assessment of Biodiversity Using a Reference-Based Taxonomy: An Example With Horned Lizards (Phrynosoma). Front. Ecol. Evol. 9:678110. doi: 10.3389/fevo.2021.678110 

Shrimpton, S. J., J. W. Streicher, D. J. Gower, R. C. Bell, M. K. Fujita, R. K. Schott, and K. N. Thomas. 2021. Eye-body allometry across biphasic ontogeny in anuran amphibians. Evolutionary Ecology 35: 337–359.

Thomas, K. N., D. J. Gower, R. C. Bell, M. K. Fujita, R. K. Schott, and J. W. Streicher. 2020. Eye size and investment in frogs and toads correlate with adult habitat, activity pattern and breeding ecology. Proceedings of the Royal Society B 287:20201393

Firneno, T. J. Jr., O’Neill, J. R., D. M. Portik, A. H. Emery, J. H. Townsend, and M. K. Fujita. 2020. Finding complexity in complexes: Assessing the causes of mitonuclear discordance in a problematic species complex of Mesoamerican toads. Molecular Ecology 29(18): 3543-3559.

Maldonado, J., T. J. Firneno Jr., C. Roelke, N. Rains, J. Mwgiri, and M. K. Fujita. 2020. Transcriptomes sequencing reveals signatures of positive selection in the spot-tailed earless lizard. PLoS One 15(6): e0234504 .

Fujita, M. K., S. Singhal, T. O. Brunes, and J. A. Maldonado. 2020. Evolutionary Dynamics and Consequences of Parthenogenesis in Vertebrates. Annual Reviews in Ecology, Systematics, and Evolution 51:191-214.

O’ Connell, K., J. Oaks, A. Hamidy, K. Shaney, N. Kurniawan, E. Smith, and M. K. Fujita. 2020. Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs (Rhacophorus). Molecular Ecology 29(16): 2994-3009.

Shaney, K. J., J. Maldonado, U. Smart, P. Thammachoti, M. K. Fujita, A. Hamidy, N. Kurniawan, M. B. Harvey, and E. N. Smith. 2020. Phylogeography of montane dragons could shed light light on the history of forests and diversification processes on Sumatra. Molecular Phylogenetics and Evolution 149: 106840.

Leaché, A.D, J. R. Oaks, C. Ofori-Boateng, and M. K. Fujita. 2020. Comparative phylogeography of West African amphibians and reptiles. Evolution 74(4): 716-724.

Leache, A. D., D. M. Portik , D. Rivera, M-O-Rodel, J. Penner, V. Gvozdik, E. Greenbaum, G. F. M. Jongsma, C. Ofori-Boateng, M. Burger, E. A. Eniang, R. C. Bell, M. K. Fujita. 2019. Exploring rain forest diversification using demographic model testing in the Africa foam-nest treefrog Chiromantis rufescens. Journal of Biogeography 46(12): 2706-2721.

Krishnan, S., C. Ofori-Boateng, M. K. Fujita, A. D. Leaché. 2019. Geographic variation in West African Agama picticauda: insights from genetics, morphology, and ecology. African Journal of Herpetology 68:33-49.

O’Connell, K.A., Di Santo, V., Maldonado, J., Molina, E., Fujita, M.K. 2019. A Tale of Two Skates: Comparative Phylogeography of North American Skate Species with Implications for Conservation. Copeia 107(2): 297-304.

Charles, K., R. Bell, D. Blackburn, M. Burger, M. K. Fujita, V. Gvoždík, G. Jongsma, M. Kouete, A. Leaché, D. Portik. 2018. Sky, sea, and forest islands: diversification in the African lead-folding from Afrixalus paradorsalis (Anura: Hyperoliidae) of Lower Guinea. Journal of Biogeography 45(8): 1781-1794.

Roelke, C., J. Maldonado, B. Pope, Firneno, T. Jr., T. LaDuc, T. Hibbits, N. Rains, M. K. Fujita. 2018. Mitochondrial genetic variation within and among Holbrookia lacerata lacerata and Holbrookia lacerata subcaudalis, the Spot-Tailed Earless Lizards of Texas. Journal of Natural History 52:1017-1027.

O’Connell, K. A., A. Hamidy, N. Kurniawan, E. Smith, M. K. Fujita. 2018. Synchronous diversification of parachuting frogs (Genus Rhacophorus) on Sumatra and Java. Molecular Phylogenetics and Evolution 123:101-112.

O’Connell, K. A., E. N. Smith, K. Shaney, U. Arifin, N. Kurniawan, I. Sidik, and M. K. Fujita. 2018. Coalescent species delimitation of a Sumatran parachuting frog. Zoologica Scripta 47(1):33-43.

O’Connell, K. A., U. Smart, E. N. Smith, A. Hamidy, N. Kurniawan, M. K. Fujita. Accepted. Within-island diversification underlies parachuting frog (Rhacophorus) species accumulation on the Sunda Shelf. Journal of Biogeography.

Portik, D.M., Leaché, A.D., Rivera, D., Blackburn, D.C., Rödel, M.-O., Barej, M.F., Hirschfeld, M., Burger, M., and M.K. Fujita. 2017. Evaluating mechanisms of diversification in a Guineo-Congolian tropical forest frog using demographic model selection. Molecular Ecology 26: 5245–5263.

O’Connell, K. A., J. W. Streicher, E. N. Smith and M. K. Fujita. Accepted. Geographical features are the predominant driver of molecular diversification in widely distributed North American Whipsnakes. Molecular Ecology.

Schargel, W. E., G. A. Rivas, J. E. García-Pérez, C. Rivero-Blanco, P. T. Chippindale, and M. K. Fujita. 2017. A new species of Gonatodes (Squamata: Sphaerodactylidae) from the western versant of the Cordillera de Mérida, Venezuela. Zootaxa 4291(3):549-562

Leaché, A.D., J. A Grummer, M.Miller, S. Krishnan, M. K. Fujita, W. Böhme, A. Schmitz, M. LeBreton, I. Ineich, L. Chirio, C. Ofori-Boateng, E. A. Eniang, E. Greenbaum, M-O Rödel, and P. Wagner. 2017. Bayesian inference of species diffusion in the West African Agama agama species group (Reptilia, Agamidae). Systematics and Biodiversity 15:192-203.

Moritz, C., M. K. Fujita, D. Rosauer, R. Agudo, G. Bourke, P. Doughty, R. Palmer, M. Pepper, S. Potter, R. Pratt, M. Scott, M. Tonione, and S. Donnellan. 2016. Multilocus phylogeography reveals nested endemism in a gecko across the monsoonal tropics of Australia. Molecular Ecology 25:1354-1366.

Georges, A., Q. Li, J. Lian, D. O’Meally, J. Deakin, Z. Wang, M. K. Fujita, H. R. Patel, C. E. Holleley, Y. Zhou, X. Zhang, K. Matsubara, P. Water, J.A.M. Graves, S. D. Sarre, and G. Zhang. 2015. High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps. GigaScience, 4(1), 45.

Rodríguez-Robles, J. A., T. Jezkova, M. K. Fujita, P. J. Tolson, and M. A. García. 2015. Genetic divergence and diversity in the Mona and Virgin Islands Boas, Chilabothrus monensis (Epicrates monensis) (Serpentes: Boidae), West Indian snakes of special conservation concern. Molecular Phylogenetics and Evolution 88:144-153.

Meik, J.M., J. W. Streicher, A. M. Lawing, O. Flores-Villela, and M. K. Fujita. 2015. Limitations of climate data for inferring species boundaries: insights from speckled rattlesnakes. PLoS ONE 10(6): e0131435.

Li, C., Y. Zhang, J. Li, L. Kong, H. Hu, H. Pan, L. Xu, Y. Deng, Q. Li, L. Jin, H. Yu, Y. Chen, B. Liu, L. Yang, S. Liu, Y. Zhang, Y. Lang, J. Xia, W. He, Q. Shi, S. Sabramanian, C.D. Miller, S. Meader, C.M. Rands, M.K. Fujita, M.J. Greenwold, T.A. Castoe, D.D. Pollock, W. Gu, K. Nam, H. Ellegren, S.Y.W. Ho, D.W. Burt, C.P. Ponting, E.D. Jarvis, M.T.P. Gilbert, H. Yang, J. Wang, D.M. Lambert, J. Wang, G. Zhang. 2014. Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment. Gigascience 3: 27

2014-12-12-Cover-AvianGreene, R.E., E.L. Braun, J. Armstrong, D. Earl, N. Nguyen, M.W. Vandewedge, J.A. St John, S. Capelia-Gutierrez, T.A. Castoe, C. Kern, M.K. Fujita, J.C. Opazo, J. Jerka, K. Kojima, J. Caballero, R.M. Hubley, A.A.F. Smit, R.N. Platt, C.A. Lavoie, M. Ramakodi, J.W. Finger, A. Suh, S. Isberg, L. Miles, A. Chong, W. Jaratierdsiri, J. Gongora, C. Moran, A. Iriarte, B.C. Faircloth, J. McCormack, S. Burgess, S.V. Edwards, E. Lyons, C. Williams, M. Breen, C.R. Gresham, D.G. Peterson, J. Schmitz, D.D. Pollock, D. Houssler, E.W. Triplett, G. Zhang, N. Irie, E.D. Jarvis, C.A. Brochu, C. Schmidt, F. McCarthy, F.G. Hoffman, T.C. Glenn, T. Gabladon, B. Paten, and D.A. Ray. 2014. The genomes of three crocodilians provide insight into Archosaur evolution. Science 346: 1254449

Card, D.C., D.R. Schield, J. Reyes-Velasco, A.L. Andrew, R.P. Ruggiero, D.D. Pollock, D.F. Tomback, S.J. Oyler-McCance, M.K. Fujita, and T.A. Castoe. 2014. Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies. PLoS ONE 9: e106649.

Wagner, P., A. D. Leaché, and M. K. Fujita. 2014. Description of four new West African forest geckos of the Hemidactylus fasciatus Gray, 1842 complex, revealed by coalescent species delimitation. Bonn Zoological Bulletin 63:1-14.

Fujita, M. K. 2014. Book review: Geckos: The Animal Answer Guide. Quarterly Review of Biology 89:191-192.

Streicher, J. W., T. J. Devitt, C. S. Goldberg, J. H. Malone, H. Blackmon, and M. K. Fujita. 2014. Diversifications and asymmetrical gene flow across a heterogeneous landscape: lineage sorting dynamics in polytypic barking frogs (Anura: Craugastoridae). Molecular Ecology 23:3273-3291.

Syst Biol-2014-Cover _ standing material-i1

Leaché, A. D., M. K. Fujita, V. N. Minin, and R. R. Bouckaert. 2014. Species delimitation using genome-wide SNP data. Systematic Biology 63(4):534-542.

Rheindt, F. E., M. K. Fujita, P. R. Wilton, and S. V. Edwards. 2014. Introgression and phenotypic assimilation in Zimmerius Flycatchers (Tyrannidae): Population genetic and phylogenetic inferences from genome-wide SNPs. Systematic Biology 63(2):134-152.

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.

Castoe, T. A., et al. (including M. K. Fujita). 2013. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the National Academy of Sciences USA 110(51):20645-20650.

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 14:R28.

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 to illuminate the evolution of archosaurs and amniotes. Genome Biology 13:415.

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


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 25:252-263.

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.


Pepper, M., M. K. Fujita, C. Moritz, and J. S. Keogh. 2011. Paleoclimate change drove diversification 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. Genome evolution 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.