Publications

2018

Caviedes-Solis, I. W. and A. D. Leaché. 2018. Leap frogging the Mexican highlands: Influence of biogeographical and ecological factors on highland species diversification.
Biological Journal of the Linnean Society, 123: 767-781.

Grummer, J. A., Avila, L., Morando, M., Sites Jr, J. W., and A. D. Leaché. 2018. Phylogenomic evidence for a recent and rapid radiation in lizards of the Patagonian Liolaemus fitzingerii species group.
Molecular Phylogenetics and Evolution, 125: 243-254.

Harris, R. B., Alström, P., Ödeen, A., and A. D. Leaché. 2018. Discordance between genomic divergence and phenotypic variation in a rapidly evolving avian genus (Motacilla).
Molecular Phylogenetics and Evolution, 120: 183-195.

Jongsma, G. F. M., Barej, M. F., Barratt, C. D., Burger, M., Conradie, W., Ernst, R., Greenbaum, E., Hirschfeld, M., Leaché, A. D., Penner, J., Portik, D. M., Rödel, M.-O., and D. C. Blackburn. 2018. Diversity and biogeography of frogs in the genus Amnirana (Anura: Ranidae) across sub-Saharan Africa.
Molecular Phylogenetics and Evolution, 120:274-285.

Ofori-Boateng, C., Leaché, A. D., Obeng-Kankam, B. , Kouamé, N. G., Hillers, , A., and M.-O. Rödel. 2018. A new species of Puddle Frog, genus Phrynobatrachus (Amphibia: Anura: Phrynobatrachidae) from Ghana.
Zootaxa, 4374: 565-578.

Psonis, N., Antoniou, E., Karameta, E., Leaché, A. D., Kotsakiozi, P., Darriba, D., Kozlov, A., Stamatakis, A., Poursanidis, D., Kukushkin, O., Jablonski, D., Crnobrnja-Isailovic, J., Gherghel, I., Lymberakis, P., and N. Poulakakis. 2018. Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system.
Molecular Phylogenetics and Evolution, 125: 100-115.

Wagner, P., Greenbaum, E. , Bauer, A. M., Kusamba C., and A. D. Leaché. 2018. Lifting the blue-headed veil – Integrative taxonomy of the Acanthocercus atricollis species complex (Squamata: Agamidae).
Journal of Natural History, 52: 771-817.

2017

Furbush, R., Caviedes-Solis, I. W., Méndez-de la Cruz, F. R., and A. D. Leaché. 2017. Missing in action for nearly 50 years: rediscovery of the Mexican treefrog Duellmanohyla ignicolor (Anura: Hylidae).
Mesoamerican Herpetology, 4:120-127.

Grummer, J. A. and A. D. Leaché. 2017. Do dams also stop frogs? Assessing population connectivity of coastal tailed frogs (Ascaphus truei) in the North Cascades National Park Service Complex.
Conservation Genetics 18:439-451.

Leaché, A. D., Grummer, J. A., Miller, M., Krishnan, S., Fujita, M. K., Böhme, W., Schmitz, A., LeBreton, M., Ineich, I., Chirio, L., Ofori-Boateng, C., Eniang, E. A., Greenbaum, E., Rödel, M.-O., 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.

Leaché, A. D. and J. R. Oaks. 2017. The utility of single nucleotide polymorphism (SNP) data in phylogenetics.
Annual Review of Ecology, Evolution, and Systematics, 48:69-84.

Leaché, A. D., Grummer, J. A., Harris, R. B., and I. Breckheimer. 2017. Evidence for concerted movement of nuclear and mitochondrial clines in a lizard hybrid zone.
Molecular Ecology, 26:2306-2316.

Nieto-Montes de Oca, A., Barley, A. J., Meza-Lázaro, R. N., García-Vázquez, U. O., Zamora-Abrego, J. G., Thomson, R. C., and A. D. Leaché. 2017. Phylogenomics and species delimitation in the knob-scaled lizards of the genus Xenosaurus (Squamata: Xenosauridae) using ddRADseq data reveal a substantial underestimation of diversity.
Molecular Phylogenetics and Evolution, 106:41-253.

Panzera, A., Leaché, A. D., D’Elia, G., and P. F. Victoriano. 2017. Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data.
PeerJ, 5:e3941.

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

Richmond, J. Q., Wood, D. A., Westphal, M. F., Vandergast, A., Leaché, A. D., Saslaw,  L. R., Butterfield, H., and R. N. Fisher. 2017. Persistence of historical population structure in an endangered species despite near-complete biome conversion in California’s San Joaquin Desert.
Molecular Ecology, 26:3618-3635.

2016

Edwards, S. V., Xi, Z., Janke, A., Faircloth, B. C., McCormack, J. E., Glenn, T. C., Zhong, B., Wu, S., Lemmon, E. M., Lemmon, A. R., Leaché, A. D., Liu, L., and C. C. Davis. 2016. Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics.
Molecular Phylogenetics and Evolution, 94:447-462.

Fong, J. J., Li, P.-P., Yang, B.-T., Zhou, Z.-Y., Leaché, A. D., Min, M.-S., and B. Waldman. 2016. Influence of geology and human activity on the genetic structure and demography of the Oriental fire-bellied toad (Bombina orientalis).
Molecular Phylogenetics and Evolution 97: 69-75.

Grummer, J. A. and A. D. Leaché. 2016. Survey for Batrachochytrium dendrobatidis in the North Cascades National Park Service Complex, Washington, USA.
Herpetological Review, 47:392-394.

Leaché, A. D., Banbury, B. L., Linkem, C. W., and A. Nieto-Montes de Oca. 2016. Phylogenomics of a rapid radiation: Is chromosomal evolution linked to increased diversification in North American spiny lizards (Genus Sceloporus)?
BMC Evolutionary Biology, 16:63.

Levy, H., Clucas, G. V., Rogers, A. D., Leaché, A. D., Ciborowski, K. L., Polito, M. J., Lynch, H. J., Dunn, M. J., and  T. Hart. 2016. Population structure and phylogeography of the Gentoo Penguin (Pygoscelis papua) across the Scotia Arc.
Ecology and Evolution, 6:1834-1853.

Linkem, C. W., Minin, V. N., and A. D. Leaché. 2016. Detecting the anomaly zone in species trees and evidence for a misleading signal in higher-level skink phylogeny (Squamata: Scincidae).
Systematic Biology, 65:465-477.

2015

Caviedes-Solis, I. W., Bouzid, N. M., Banbury, B. L., and A. D. Leaché. 2015. Uprooting phylogenetic uncertainty in coalescent species delimitation: a meta-analysis of empirical studies.
Current Zoology, 61:866-873. PDF

Genomic Resources Development Consortium, Arthofer, W., Banbury, B., Carneiro, M., Cicconardi, F., Duda, T. F. ,Harris, R., Kang, D. S., Leaché, A. D., et al. 2015. Genomic resources notes accepted 1 August 2014–30 September 2014.
Molecular Ecology Resources, 15: 228-229. PDF

Grummer, J. A., Calderón, M. L., Nieto-Montes de Oca, A., Smith, E. N., Mendez-de la Cruz, F., and A. D. Leaché. 2015. Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands. Molecular Ecology, 24:1523-1542.

Leaché, A. D., and C. W. Linkem. 2015. Phylogenomics of horned lizards (genus: Phrynosoma) using targeted sequence capture data.
Copeia, 103:586-594. PDF

Leaché, A. D., Banbury, B. L., Felsenstein, J., Nieto-Montes de Oca, A., and A. Stamatakis. 2015. Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies.
Systematic Biology, 64:1032-1047. DOI: 10.1093/sysbio/syv053.

Leaché, A. D., Chavez, A. S., Jones, L. N., Grummer,GBEcover J. A., Gottscho, A. D., and C. W. Linkem. 2015. Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing.
Genome Biology and Evolution, 7:706-719. PDF

Rockney, H. J., Ofori-Boateng, C., Porcino, N., and A. D. Leaché. 2015. A comparison of DNA barcoding markers in West African frogs.
African Journal of Herpetology, 64:135-147. PDF

Sheldon, K. S., Leaché, A. D., and F. B. Cruz. 2015. The influence of temperature seasonality on elevational range size across latitude: a test using Liolaemus lizards
Global Ecology and Biogeography, 24:632-641. PDF

2014

Harris, R. B., Birks, S. M., and A. D. Leaché. 2014. Incubator birds: biogeographic origins and evolution of underground nesting in megapodes (Galliformes: Megapodiidae).
Journal of Biogeography, 41:2045-2056. PDF

Leaché, A. D., Wagner, P., Linkem, C. W., Böhme, W., Papenfuss, T. J., Chong, R. A., Lavin, B. R., Bauer, A. M., Nielsen, S., Greenbaum, E., Rödel, M-O., Schmitz, A., LeBreton, M., Ineich, I., Chirio, L., Eniang, E. A., Baha El Din, S., Lemmon, A. R., and F. T. Burbrink. 2014. A hybrid phylogenetic-phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification.
Molecular Phylogenetics and Evolution, 79:215-230. PDF

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

Leaché, A. D., Harris, R. B., Rannala, B., and Z. Yang. 2014. The influence of gene flow on species tree estimation: A simulation study.
Systematic Biology, 63:17-30. PDF

Wagner, P., Leaché, A. D., 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. PDF

2013

GBE

Leaché, A. D., Harris, R. B., Maliska, M. E., and C. W. Linkem. 2013. Comparative species divergence across eight triplets of spiny lizards (Sceloporus) using genomic sequence data.
Genome Biology and Evolution, 5:2410-2419. PDF

Leaché, A. D., Palacios, J. A., Minin, V. N., and R. W. Bryson Jr. 2013. Phylogeography of the Trans-Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of southeastern Mexico.
Biological Journal of the Linnean Society, 110:852-865. PDF

Penner, J., Adum, G. B., McElroy, M. T., Doherty-Bone, T., Hirschfeld, M., Sandberger, L., Weldon, C., Cunningham,  A. A., Ohst, T., Wombwell, E., Portik, D. M., Reid, D., Hillers, A., Ofori-Boateng, C., Oduro, W., Plötner, J., Ohler, A., Leaché, A. D.,  and M.-O. Rödel. 2013. West Africa – a safe haven for frogs? A sub-continental assessment of the chytrid fungus (Batrachochytrium dendrobatidis).
PLoS ONE, 8(2):e56236. PDF

Sherman, E. M., and A. D. Leaché. 2013. Molecular identification of a hitchhiking frog.
Northwestern Naturalist, 94:81-84. PDF

Wagner, P., Leaché, A. D., Mazuch, T., and W. Böhme. 2013. Additions to the lizard diversity of the Horn of Africa: two new species in the Agama spinosa group.
Amphibia-Reptilia, 34:363-387. PDF

2012

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

Rödel, M-O., Barej, M. F., Hillers, A., Leaché, A. D., Kouamé, N. G., Ofori-Boateng, C., Assemian, N. E., Tohé, B., Penner, J., Hirschfeld, M., Doumbia, J., Gonwouo, L. N., Nopper, J., Brede, C., Diaz, R., Fujita, M. K., Gil, M., Segniagbeto, G. H., Ernst, R., and L. Sandberger. 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.

2011

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: Biological Sciences, 278:493-495. PDF

Leaché, A. D. 2011. Multi-Locus estimates of population structure and migration in a fence lizard hybrid zone.
PLoS ONE, 6(9):e25827. PDF

Leaché, A. D., and B. Rannala. 2011. The accuracy of species tree estimation under simulation: a comparison of methods.
Systematic Biology, 60:126-137PDF

Prasad, V., Strömberg, C. A. E., Leaché, A. D., Samant, B., Patnaik, R., Tang, L., Mohabey, D. M., Ge, S., and A. Sahni. 2011. Late Cretaceous origin of the rice tribe provides evidence for early diversification in Poaceae.
Nature Communications, DOI: 10.1038/ncomms1482PDF

2010

Blackburn, D. C., Gvoždík, V., and A. D. Leaché. 2010. A new squeaker frog (Arthroleptidae: Arthroleptis) from the mountains of Cameroon and Nigeria.
Herpetologica, 66:335-348. PDF

Leaché, A. D. 2010. Species trees for spiny lizards (genus Sceloporus): identifying points of concordance and conflict between nuclear and mitochondrial data.
Molecular Phylogenetics and Evolution, 54:162-171PDF

Leaché, A. D., Helmer, D., and C. Moritz. 2010. Phenotypic evolution in high elevation populations of western fence lizards (Sceloporus occidentalis) in the Sierra Nevada Mountains.
Biological Journal of the Linnean Society, 100:630-641PDF

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

2009

Brandley, M. C., Warren, D. L., Leaché, A. D., and J. A. McGuire. 2009. Homoplasy and clade support.
Systematic Biology, 58:184-198. PDF

Leaché, A. D., and J. W. Sites Jr. 2009. Chromosome evolution and diversification in North American spiny lizards (genus Sceloporus).
Cytogenetic and Genome Research, 127:166-181PDF

Leaché, A. D., Chong, R. A., Papenfuss, T. J., Wagner, P., Böhme, W., Schmitz, A., Rödel, M. O., LeBreton, M., Ineich, I., Chirio, L., Bauer, A., Eniang, E. A., and S. Baha El Din. 2009. Phylogeny of the genus Agama based on mitochondrial DNA sequence data.
Bonner zoologische Beiträge, 56:273-278. PDF

Leaché, A. D. 2009. Species tree discordance traces to phylogeographic clade boundaries in North American fence lizards (Sceloporus).
Systematic Biology, 58:547-559. PDF

pnas

Leaché, A. D., Koo, M. S., Spencer, C. L., Papenfuss, T. J., Fisher, R. N., and J. A. McGuire. 2009. Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex (Phrynosoma).
Proceedings of the National Academy of Sciences, USA, 106:12418-12423. PDF

Wagner, P., Ineich, I., Leaché, A. D., Wilms, T., Trape, S., Mane, Y., Böhme, W., and A. Schmitz. 2009. Studies on African Agama VI. Taxonomic status of the West African Agama (Sauria: Agamidae) with prominent tail crests: Agama boulengeri Lataste 1886, Agama insularis Chabanaud, 1918 and Agama cristata Mocquard, 1905.
Bonner zoologische Beiträge, 
56:239-253. PDF

2007

Leaché, A. D., and D. G. Mulcahy. 2007. Phylogeny, divergence times, and species limits of spiny lizards (Sceloporus magister species group) in western North American deserts and Baja California.
Molecular Ecology, 16:5216-5233. PDF

Leaché, A. D., Crews, S. C., and M. J. Hickerson. 2007. Two waves of diversification in mammals and reptiles of Baja California revealed by hierarchical Bayesian analysis.
Biology Letters, 3:646-650. PDF

Leaché, A. D., and C. J. Cole. 2007. Hybridization between multiple fence lizard lineages in an ecotone: Locally discordant variation in mitochondrial DNA, chromosomes, and morphology.
Molecular Ecology, 16:1035-1054. PDF

2006

Angilletta, M. J., Oufiero, C. E., and A. D. Leaché. 2006. Direct and indirect effects of environmental temperature on the evolution of reproductive strategies: An information-theoretic approach.
American Naturalist, 168:E123-E135. PDF

Brandley, M. C., Leaché, A. D., Warren, D. L., and J. A. McGuire. 2006. Are unequal clade priors problematic for Bayesian phylogenetics?
Systematic Biology, 55:138-146. PDF

Leaché, A. D., Rödel, M-O, Linkem, C. W., Diaz, R. E., Hillers, A., and M. K. Fujita. 2006. Biodiversity in a forest island: Reptiles and amphibians of the West African Togo Hills.
Amphibian and Reptile Conservation, 4:22-45. PDF

Leaché, A. D., and J. A. McGuire. 2006. Phylogenetic relationships of horned lizards (Phrynosoma) based on nuclear and mitochondrial data: Evidence for a misleading mitochondrial gene tree.
Molecular Phylogenetics and Evolution, 39:628-644. PDF

2005

Leaché, A. D. 2005. Results of a herpetological survey in Ghana and a new country record.
Herpetological Review, 36(1):16-19. PDF

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

2004

Angilletta, M. J., Niewiarowski, P. H., Dunham, A. E., Leaché, A. D., and W. Porter. 2004. Bergmann’s clines in ectotherms: Illustrating a life-history perspective with sceloporine lizards.
American Naturalist, 164:E168-E183. PDF

Niewiarowski, P. H., Angilletta, M. J., and A. D. Leaché. 2004. Phylogenetic comparative analysis of life history variation among populations of the lizard Sceloporus undulatus: An example and prognosis.
Evolution, 58:619-633. PDF

20022002

Leaché, A. D., and T. W. Reeder. 2002. Molecular systematics of the eastern fence lizard (Sceloporus undulatus): A comparison of parsimony, likelihood, and Bayesian approaches.
Systematic Biology, 51:44-68. PDF