Publications
Peer-reviewed research from the Lemmon Lab
Links go to the publisher page via the paper's DOI. Use the preprint link when a free version is posted. Publisher PDFs are not hosted here.
2026
Mukhopadhyay, A., V. G. Kamath, J. M. McDowell, A. S. Acord, R. K. Alluri, G. J. Rose, E. Moriarty Lemmon. Submitted. Standing neuronal variation enables diversification of mate recognition circuits during speciation by reinforcement. Journal of Comparative Physiology A.
Read, W., I. Brennan, S. Tiatragul, P. M. Oliver, R. A. Pyron, T. Jackman, A. R. Lemmon, E. Moriarty Lemmon, C. Austin, C. Moritz, J. Scott Keogh, S. M. Zozaya, A. Bauer. Submitted. Swept ashore: Transoceanic dispersals and the biogeographic origins of Australian gekkonid lizards. EcoEvoRxiv: https://ecoevorxiv.org/repository/view/14023/. DOI · preprint
Mohan, Ashwini V; Kaliontzopoulou, Antigoni; Rancilhac, Loïs; Scherz, Mark D.; Irisarri, Iker; Gippner, Sven; Lemmon, E. Moriarty; Lemmon, Alan R; Glaw, Frank; Bauer, Aaron M; Vences, Miguel; García-Porta, Joan. Submitted. Geographic isolation and macroclimate shape phenotypic and phylogenetic diversity in the day gecko radiation. Systematic Biology.
Stukel, M., N. J. Matzke, J. Douglas, T. P. Ruschel, S. Puissant, B. W. Price, M. Villet, A. R. Lemmon, E. Moriarty Lemmon, C. Simon. Submitted. Phylogenomics and fossilized birth-death dating reveals Gondwanan origin and extensive post-Cretaceous diversification of worldwide Cicadidae. Systematic Biology. preprint
Granados Mendoza, C., K. J. Romero-Soler, R. N. Meza-Lázaro, A. Benítez-Villaseñor, M. Á. Alcalá-Gaxiola, D. Cruz Plancarte; G. A. Salazar, S. Magallón, E. J. Gouda, I. M. Ramírez-Morillo, A. J. Rossado; I. Larridon, C. J. Ramírez-Díaz, S. I. Vera-Paz, D. D. Díaz Contreras Díaz, E. Moriarty Lemmon, A. R. Lemmon; S. Wanke. Submitted. Integrating universal enrichment kits and shallow sequencing to assess Bromeliaceae (Poales) subfamilial phylogenomic relationships and divergence times. Molecular Phylogenetics and Evolution.
Haji, D., J. Vailionis, M. Stukel, E. Gordon, E. Moriarty Lemmon, A. Lemmon, D. Marshall, J. P. McCutcheon, C. Simon. Submitted. Host-associated microbial diversity in New Zealand cicadas uncovers elevational structure and replacement of obligate bacterial endosymbionts by Ophiocordyceps fungal pathogens. bioRxiv. preprint
Ochoa, C. A., G. Rose, E. Moriarty Lemmon. Submitted. Behavioural evidence of neuronal repurposing during speciation by reinforcement in chorus frogs. Behavioral Ecology and Sociobiology.
McDaniels, C. X., N. Povelikin, M. Dye, M. L. Kortyna, R. C. Jadin, S. A. Orlofske, E. Moriarty Lemmon, et al. Submitted. The Tangled History and Taxonomy of an Iconic Chorus Frog Complex Clarified using Genomic Analyses. bioRxiv 2026.03.09.710633. preprint
Ziegler, K., E. Moriarty Lemmon, and A. R. Lemmon. In revision. De novo genome assembly for the Upland chorus frog (Pseudacris feriarum). G3: Genes, Genomes, Genetics.
Burke, H., L. Serrano, E. Moriarty Lemmon, and C. Whitcher. In revision. Finding Fluorescence: Utilizing community science to document novel biofluorescence occurrences and encourage community engagement in science. bioRxiv 2024.04.24.590905. preprint
Dye, M., A.R. Lemmon, E. Moriarty Lemmon. In press. Reinforcement drives the evolution of increased variation in temperature-driven acoustic plasticity. Animal Behaviour.
Ochoa, Carlie Anderson, G. Rose, E. Moriarty Lemmon. In press. Effect of sympatry on discrimination of advertisement and aggressive signals by female chorus frogs. Behavioral Ecology and Sociobiology. DOI
Graboski, R., A. R. Lemmon, E. Moriarty Lemmon, F. G. Grazziotin, and H. Zaher. 2026. The present is (not necessarily) the key to the past: exploring the systematics, biogeography and diversification of the amphisbaenians (Reptilia: Squamata). Zoological Journal of the Linnean Society. DOI
Zaborsky, J. G., J. P. Rose, R. Kriebel, B. Drew, E. Moriarty Lemmon, A. Lemmon, and K. J. Sytsma. 2026. Evaluating the "African Arid Corridor" Hypothesis: a meta-analysis including the phylogenetic and biogeographic history of Sesamothamnus (Pedaliaceae). American Journal of Botany. DOI
Brennan, I. G., C. J. Hoskin, S. J. Richards, A. R. Lemmon, E. Moriarty Lemmon, S. C. Donnellan, J. S. Keogh. 2026. Phylogenomic assessment of microhylid frogs reveals widespread taxonomic confusion in the Asterophryinae and establishes the timing of diversification in Australia. Molecular Phylogenetics and Evolution 224:108676. DOI
Ochoa, C.B., A. Loeven, D.A. Fadool, and E. Moriarty Lemmon. 2026. Evoked patterns of neural activity in chorus frogs reveal candidate mechanisms of enhanced species recognition. Journal of Experimental Biology 229: jeb251686. DOI
Mukhopadhyay, A., V. G. Kamath, J. M. McDowell, A. S. Acord, R. K. Alluri, G. J. Rose, E. Moriarty Lemmon. 2026. Long-interval neurons are selective for slower pulse rates in chorus frogs that are sympatric versus allopatric with congeneric heterospecifics. Journal of Comparative Physiology A. DOI
Waldron, B. P., M. M. Hantak, E. F. Watts, J. C. Uyeda, A. R. Lemmon, E. Moriarty Lemmon, S. R. Kuchta. 2026. Phylogenomics of the woodland salamanders (Plethodon): Reticulate evolution and indistinct species boundaries. Molecular Phylogenetics and Evolution. DOI
2025
Rose, J. P., B. Li, M. J. Sporck-Koehler, E. A. Stacy, K. R. Wood, E. Moriarty Lemmon, A. R. Lemmon, C. Ané, K. J. Sytsma, and T. J. Givnish. 2025. Phylogenomics of the tetraploid Hawaiian lobeliads: implications for their origin, dispersal history, and adaptive radiation. Proceedings of the National Academy of Sciences 122:e2421004122. DOI
Everson, K. M., L. Pozzi, M. A. Barrett, M. E. Blair, M. E. Donohue, P. M. Kappeler, A. C. Kitchener, A. R. Lemmon, E. Moriarty Lemmon, C. J. Pavón-Vázquez, U. Radespiel, B. Randrianambinina, R. M. Rasoloarison, S. Rasoloharijaona, C. Roos, J. Salmona, A. D. Yoder, R. Zenil-Ferguson, D. Zinner, D. W. Weisrock. 2025. Multiple bursts of speciation in Madagascar's endangered lemurs. Nature Communications 16:7070. DOI
Singhal, S., I. Prates, H. Huang, M. R. Grundler, A. R. Lemmon, E. Moriarty Lemmon, P. O. Title, S. C. Donnellan, C. Moritz, D. L. Rabosky. 2025. Adaptive radiation, "taxon murk", and the reality of early burst speciation: an example from Australia's scincid lizards. Evolutionary Journal of the Linnean Society 4, kzaf006. DOI
Skeels, A., H. Sauquet, A. Mast, P. H. Weston, P. M. Olde, G. J. Jordan, R. J. Carpenter, J. Fenker, Z. K. M. Reynolds, A. R. Lemmon, E. Moriarty Lemmon, F. Pichardo Marcano, M. Cardillo. 2025. Paleobiome dynamics shaped a large Gondwanan plant radiation. Proceedings of the National Academy of Sciences of the USA 122: e2502129122. DOI
Waldron, B. P., M. M. Hantak, E. F. Watts, J. C. Uyeda, A. R. Lemmon, E. Moriarty Lemmon, R. P. Guralnick, D. C. Blackburn, S. R. Kuchta. 2025. Loss of a morph is associated with asymmetric character release in a radiation of woodland salamanders. Evolution 79:2369–2382. DOI
Donnellan, S. C., M. J. Mahoney, D. Esquerre, I. Brennan, L. C. Price, A. R. Lemmon, E. Moriarty Lemmon, R. Gunther, P. Monis, T. Bertozzi, J. Scott Keogh, Glenn M. Shea & S. J. Richards. 2025. Phylogenomics informs a generic revision of the Australo-Papuan treefrogs (Anura: Pelodryadidae). Zoological Journal of the Linnean Society 204: zlaf015. DOI
Whitcher, C., V. G. D. Orrico, S. Ron, M. L. Lyra, C. Santana Cassini, R. B. Ferreira, D. Y. M. Nakamura, P. Peloso, M. Rada, M. Rivera-Correa, M. José Sturaro, P. H. Valdujo, C. F. B. Haddad, T. Grant, J. Faivovich, A. R. Lemmon, E. Moriarty Lemmon. 2025. Phylogenetics, biogeography, and life history evolution in the broadly distributed treefrog genus Dendropsophus. Molecular Phylogenetics and Evolution 204:108275. DOI
Waldron, B., E. Watts, D. Morgan, M. Hantak, A.R. Lemmon, E. Moriarty Lemmon, S. Kuchta. 2025. The limits of the metapopulation: Lineage fragmentation in a widespread terrestrial salamander (Plethodon cinereus). Systematic Biology 74:1-15. DOI
2024
Pozzi, L., Everson, K. M., M. A. Barrett, M. E. Blair, M. E. Donohue, P. M. Kappeler, A. C. Kitchener, A. R. Lemmon, E. Moriarty Lemmon, C. J. Pavón-Vázquez, U. Radespiel, B. Randrianambinina, R. M. Rasoloarison, S. Rasoloharijaona, C. Roos, J. Salmona, A. D. Yoder, R. Zenil-Ferguson, D. Zinner, D. W. Weisrock. 2024. Not one, but multiple radiations underlie the biodiversity of Madagascar's endangered lemurs. American Journal of Biological Anthropology 183:139. preprint
Whitcher, C., S. R Ron, F. Ayala-Varela, A. J. Crawford, V. Herrera-Alva, E. Fernando Castillo-Urbina, F. Grazziotin, R. M. Bowman, A. R. Lemmon, E. Moriarty Lemmon. 2024. Evidence for ecological tuning of anuran biofluorescent signals. Nature Communications 15:8884. DOI
Whitcher, C., L. Beaver, E. Moriarty Lemmon. 2024. The effect of biofluorescence on predation upon Cope's gray treefrog: A clay model experiment. Behavioural Processes 215:104996. DOI
Dye, M., A. R. Lemmon, E. Moriarty Lemmon. 2024. Female chorus frogs delay mate choice under suboptimal environmental conditions. Animal Behaviour 209:215 –226. DOI
Cruaud, Astrid; Rasplus, Jean-Yves; Zhang, Junxia; Burks, Roger; Delvare, Gérard; Fusu, Lucian; Gumovsky, Alex; Huber, John T.; Janšta, Petr; Mitroiu, Mircea-Dan; Noyes, John S.; van Noort, Simon; Baker, Austin; Böhmová, Julie; Baur, Hannes; Blaimer, Bonnie B.; Brady, Seán; Bubeníková, Kristýna; Chartois, Marguerite; Copeland, Robert; Dale-Skey Papilloud, Natalie; Dal Molin, Ana; Dominguez, Chrysalin; Gebiola, Marco; Guerrieri, Emilio; Kresslein, Robert L.; Krogmann, Lars; Lemmon, Emily; Murray, Elizabeth A.; Nidelet, Sabine; Nieves-Aldrey, José Luis; Perry, Ryan K.; Peters, Ralph S.; Polaszek, Andrew; Sauné, Laure; Torréns, Javier; Triapitsyn, Serguei; Tselikh, Ekaterina V.; Yoder, Matthew; Lemmon, Alan R.; Woolley, James B.; Heraty, John. 2024. The Chalcidoidea bush of life – a massive radiation blurred by mutational saturation. Cladistics 40:34–63. preprint
Brennan, I., A. R. Lemmon, E. Moriarty Lemmon, C. J. Hoskin, S. Donnellan, S. Keogh. 2024. Populating a continent: phylogenomics reveal the timing of Australian frog diversification. Systematic Biology 73:1-11. preprint
Karimi, N., C. P. Krieg, D. Spalink, A. R. Lemmon, E. Moriarty Lemmon, E. Eifler, A. I. Hernandez, P. W. Chana, A. Rodriguez, J. B. Landis, S. R. Strickler, C. D. Specht, and T. J. Givnish. 2024. Chromosomal evolution, environmental heterogeneity, and immigration drive spatial patterns of species richness in Calochortus (Liliaceae). Proc. Natl. Acad. Sci. USA 121:e2305228121. DOI
Stukel, M., A. R. Porczak, E. L. R. Gordon, J. Vailionis, D. Haji, T. R. Buckley, A. R. Lemmon, E. Moriarty Lemmon, C. Simon. 2024. Phylogenomics improves the phylogenetic resolution and provides strong evidence of mito-nuclear discordance in two genera of a New Zealand cicada (Hemiptera: Cicadidae) species radiation. Systematic Entomology 49:237–257. DOI
Frandsen, P. B., R. W. Holzenthal, M. Espeland, J. Breinholt, J. A Thomas Thorpe, S. Simon, A. Y. Kawahara, D. Plotkin, S. Hotaling, Y. Li, C Riley Nelson, O. Niehuis, C. Mayer, L. Podsiadlowski, A. Donath, B. Misof, E. Moriarty Lemmon, A. R. Lemmon, J. C. Morse, S. Liu, S. U. Pauls, and X. Zhou. 2024. Phylogenomics recovers multiple origins of portable case making in caddisflies (Insecta: Trichoptera), nature's underwater architects. Proceedings of the Royal Society B 291:20240514. preprint
Watts, E. F., B. P. Waldron, M. M. Hantak, E. Moriarty Lemmon, A. R. Lemmon, S. R. Kuchta. 2024. Cryptic species within a cryptic species? Species delimitation in the Cumberland Plateau Salamander, Plethodon kentucki. Herpetologica 80:189–198. DOI
Kuchta, S. R., B. P. Waldron, E. F. Watts, A. R. Lemmon, E. Moriarty Lemmon. 2024. Population structure and species delimitation in the Wehrle's salamander complex. Herpetologica 80:165–176. DOI
Gvozdik, V., M. Dolinay, A. G. Zassi-Boulou, A. R. Lemmon, E. Moriarty Lemmon. 2024. Central African dwarf crocodiles found in syntopy are comparably divergent to South American dwarf caimans. Biology Letters 20:20230448. DOI
Skeels, A., H. Sauquet, A. Mast, P. Weston, P. Olde, Z. Reynolds, J. Fenker, A. Lemmon, E. Moriarty Lemmon, M. Cardillo. Sources of gene tree discordance and their implications for systematics and evolution of a megadiverse Australian plant radiation (subtribe Hakeinae, Proteaceae). Bulletin of the Society of Systematic Biologists 3,. DOI
2023
Benitez-Villasenor, A., C. Granados Mendoza, S. Wanke, M. Penafiel Cevallos, M. Efrain Freire, E. Moriarty Lemmon, A. R. Lemmon, S. Magallon. 2023. The use of Anchored Hybrid Enrichment data to resolve higher-level phylogenetic relationships: A proof-of-concept applied to Asterales (Eudicotyledoneae; Angiosperms). Molecular Phylogenetics and Evolution 181:107714. DOI
Anderson, C. B, O. Ospina, P. Beerli, A. R. Lemmon, and E. Moriarty Lemmon. 2023. The population genetics of speciation by cascade reinforcement. Ecology and Evolution 13:e9773. DOI
Xie, J. P. Del Tredici, M. LaPorte, A. Bekmetjev, A. R. Lemmon, E. Moriarty Lemmon, W. Gong, Y. Tang, J. Li. 2023. Phylogenetic relationships of Tilia (Malvaceae) inferred from multiple nuclear loci and plastid genomes. International Journal of Plant Sciences 184:56–67. DOI
Booker, W. W., E. Moriarty Lemmon, A. R. Lemmon, M. B. Ptacek, A. T. B. Hassinger, J. Schul, H. C. Gerhardt. 2023. Diversification of a polyploid complex: the biogeography and acoustic communication evolution of the North American gray treefrogs throughout the Quaternary. Molecular Ecology 32:4863–4879. preprint
Mossop, K., A. R. Lemmon, E. Moriarty Lemmon, R. Eytan, M. Adams, P. Unmack, K. Smith Date, H. Morales, M. Hammer, B. Wong, D. G. Chapple. 2023. Phylogenomics and biogeography of arid-adapted Chlamydogobius goby fishes. Molecular Phylogenetics and Evolution 182:107757. DOI
Pauls, S. U., W. Graf, A. E. Hjalmarsson, A. R. Lemmon, E. Moriarty Lemmon, M. Petersen, S. Viticek, P. B. Frandsen. 2023. Gill structure linked to ecological and species diversification in a clade of caddisflies. Arthropod Systematics & Phylogeny 81:917–929. DOI
Semple, J.C., H. McMinn-Sauder, M. Stover, A. R. Lemmon, E. Moriarty Lemmon, J. Beck. 2023. Goldenrod herbariomics: Hybrid-sequence capture reveals the phylogeny of Solidago (Asteraceae). American Journal of Botany 110:e16164. DOI
Gvozdik, V., T. Necas, D. Jablonski, E. Moriarty Lemmon, A. R. Lemmon, D. Jandzik, J. Moravec. 2023. Phylogenomics of Anguis and Pseudopus (Squamata, Anguidae) provides evidence for Balkan-Apennine mitochondrial capture associated with the Messinian event. Molecular Phylogenetics and Evolution 180:107674. DOI
Nydam, M. L., A. R. Lemmon, E. Moriarty Lemmon, K. Ziegler, C. S. Cohen, L. A. Palomino-Alvarez and C. Gissi. 2023. Phylogenomics of botryllid ascidians and implications for the evolution of allorecognition. Frontiers in Ecology and Evolution 11:1214191. DOI
Knyshov, A., E. R. L. Gordon, P. K. Masonick, S. Castillo, D. Forero, R. Hoey-Chamberlain, W. S. Hwang, K. P. Johnson, A. R. Lemmon, E. Moriarty Lemmon, S. Standring, J. Zhang, C. Weirauch. 2023. Chromosome-aware phylogenomics of Assassin Bugs (Hemiptera: Reduvioidea) elucidates ancient gene conflict. Molecular Biology and Evolution 40:msad168. preprint
Espeland, M., N. Chazot, F. L. Condamine, A. R. Lemmon, E. Moriarty Lemmon, E. Pringle, A. Heath, S. Collins, W. Tiren, M. Mutiso, D. C. Lees, S. Fisher, R. Murphy, S. Woodhall, R. Tropek, S. S. Ahlborn, K. Cockburn, J. Dobson, T. Bouyer, Z. A. Kaliszewska, C. C. M. Baker, G. Talavera, R. Vila, A. J. Gardiner, M. Williams, D. J. Martins, S. Safian, D. A. Edge, N. E. Pierce. 2023. Rapid radiation of ant parasitic butterflies during the Miocene aridification of Africa. Ecology and Evolution 13: e10046. DOI
2022
Booker W. W., E. Moriarty Lemmon, A. R. Lemmon, M. B. Ptacek, A. T. B. Hassinger, J. Schul, H. C. Gerhardt. 2022. The complex history of genome duplication and hybridization in North American gray treefrogs. Molecular Biology and Evolution 39:msab316. preprint
Haji, D., J. Vailionis, M. Stukel, E. Gordon, E. Moriarty Lemmon, A. R. Lemmon, & C. Simon. 2022. Lack of host phylogenetic structure in the gut bacterial communities of New Zealand cicadas and their interspecific hybrids. Scientific Reports 12:20559. DOI
Marchan, D. F., S. W. James, A. R. Lemmon, E. Moriarty Lemmon, M. Novo, J. Dominguez, D. J. Diaz Cosin, D. Trigo. 2022. A strong backbone for an invertebrate group: anchored phylogenomics improves the resolution of genus-level relationships within the Lumbricidae (Annelida, Crassiclitellata). Organisms Diversity & Evolution 22:915–924. DOI
Pyron, R. A., D. A. Beamer, C. R. Holzheuser, E. Moriarty Lemmon, A. R. Lemmon, A. H. Wynn, K. A. O'Connell. 2022. Contextualizing enigmatic extinctions using genomic DNA from fluid-preserved museum specimens of Desmognathus salamanders. Conservation Genetics 23:375–386. DOI
Pyron, R. A., K. A. O'Connell, E. Moriarty Lemmon, A. R. Lemmon, D. A. Beamer. 2022. Candidate-species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones. Ecology and Evolution 12:e8574. DOI
Hernández-Gutiérrez, R., C. Van Den Berg, C. Granados Mendoza, M. Peñafiel Ceballos, E. Freire M., E. Moriarty Lemmon, A. R. Lemmon, S. Magallón. 2022. Localized phylogenetic discordance among nuclear loci due to incomplete lineage sorting and introgression in the family of cotton and cacao (Malvaceae). Frontiers in Plant Science 13:850521. DOI
Piller, K., E. Parker, A. R. Lemmon, E. Moriarty Lemmon. 2022. Investigating the utility of Anchored Hybrid data to resolve the relationships among the Killifishes (Actinopterygii: Cyprinodontiformes), a globally distributed group of fishes. Molecular Phylogenetics and Evolution 173:107482. DOI
Singh, P., I. Irisarri, J. Torres-Dowdall, G. G. Thallinger, H. Svardal, E. Moriarty Lemmon, A. R. Lemmon, S. Koblmüller, A. Meyer, and C. Sturmbauer. 2022. Phylogenomics of trophically diverse cichlids disentangles processes driving adaptive radiation and repeated trophic transitions. Ecology and Evolution 12:e9077. DOI
Duncan, G. D., C. D. Schlicting, F. Forest, A. G. Ellis, A. R. Lemmon, E. Moriarty Lemmon, G. Verboom. 2022. A new sectional classification of Lachenalia (Asparagaceae) based on a multilocus DNA phylogeny. Taxon 71:563–586. DOI
Owen, D. L., D. C. Marshall, E. J. Wade, R. Meister, G. Goemans, K. Kunte, M. Moulds, K. Hill, M. Villet, T. H. Pham, M. Kortyna, E. Moriarty Lemmon, A. R. Lemmon, C. Simon. 2022. Detecting and removing sample contamination in an anchored phylogenomic analysis: an example using Cicadidae. Systematic Biology 71:1504-1523. DOI
Zhang, J., J. Heraty, C. Darling, R. Kresslein, A. Baker, J. Torréns, J.-Y. Rasplus, A. R. Lemmon, E. Moriarty Lemmon. 2022. Anchored phylogenomics and a revised classification of the Planidial larva clade of jewel wasps (Hymenoptera: Chalcidoidea). Systematic Entomology 47:329–353. DOI
Sabbag, A. Fares, M. T. C. Thome, M. L. Lyra, C. A. Brasileiro, E. Moriarty Lemmon, A. R. Lemmon, and C. F. B. Haddad. 2022. Sympatric and independently evolving lineages in the Thoropa miliaris—T. taophora species complex (Anura: Cycloramphidae). Molecular Phylogenetics and Evolution 166:107220. DOI
2021
Deng, X.L., A. Favre, E. Moriarty Lemmon, A. R. Lemmon, S. U. Pauls. 2021. Gene flow and diversification in Himalopsyche martynovi species complex (Trichoptera: Ryacophilidae) in the Hengduan Mountains. Biology 2021:816. DOI
Ospina, O. Lemmon, A. R. Lemmon, M. Dye, C. Zdyrski, S. Holland, D. Stribling, M. L. Kortyna, E. Moriarty Lemmon. 2021. Neurogenomic divergence during speciation by reinforcement of mating behaviors in chorus frogs (Pseudacris). BMC Genomics 22:1-23. DOI
Nicolas, V., O. Mikula, L. A. Lavrenchenko, R. Sumbera, V. Bartakova, A. Bryjova, Y. Meheretu, E. Verheyen, A. D. Missoup, A. R. Lemmon, E. Moriarty Lemmon, J. Bryja. 2021. Phylogenomics of African radiation of Praomyini (Muridae: Murinae) rodents: first fully resolved phylogeny, evolutionary history and delimitation of extant genera. Molecular Phylogenetics and Evolution 107263. DOI
Dolinay, M., T. Necas, B. M. Zimkus, A. Schmitz, E. B. Fokam, E. Moriarty Lemmon, A. R. Lemmon, V. Gvozdik. 2021. Gene flow in phylogenomics: Sequence capture resolves species limits and biogeography of Afromontane forest endemic frogs from the Cameroon Highlands. Molecular Phylogenetics and Evolution 163:107258. preprint
Warwick, A., L. Barrow, M. Smith, D. Means, A. R. Lemmon, E. Moriarty Lemmon. 2021. Signatures of north-eastern expansion and multiple refugia: genomic phylogeography of the Pine Barrens TreeFrog, Hyla andersonii, (Anura: Hylidae). Biological Journal of the Linnean Society 133:120–134. DOI
Bybee, S. M., V. J. Kalkman, R. J. Erickson, P. B. Frandsen, J. W. Breinholt, A. Suvorov, Klaas-Douwe B. Dijkstra, A. Cordero-Rivera, J. H. Skevington, J. C. Abbott, M. Sanchez Herrera, A. R. Lemmon, E. Moriarty Lemmon, J. L. Ware. 2021. Phylogeny and classification of Odonata using targeted genomics. Molecular Phylogenetics and Evolution 160:107115. DOI
Mikula, O., V. Nicolas, R. Šumbera, A. Konečný, C. Denys, E. Verheyen, A. Bryjová, A.R. Lemmon, E. Moriarty Lemmon, J. Bryja. 2021. Nuclear phylogenomics, but not mitogenomics, resolves the most successful late Miocene radiation of African rodents (Rodentia: Muridae: Arvicanthini). Molecular Phylogenetics and Evolution 157:107069. DOI
Hurt, C., K. Hultgren, A. Anker, A. Lemmon, E. Moriarty Lemmon, H. Bracken-Grissom. 2021. First worldwide molecular phylogeny of the morphologically and ecologically hyperdiversified snapping shrimp genus Alpheus (Malacostraca: Decapoda). Molecular Phylogenetics and Evolution 158:107080. DOI
Percequillo, A. R., J. Rodrigues do Prado, E. F. de Abreu-Júnior, J. Dalapicolla, A. C. Pavana, E. de Almeida Chiquito, P. Brennand, S. J. Steppan, A. R. Lemmon, E. Moriarty Lemmon, M. Wilkinson. 2021. Tempo and mode of evolution of Oryzomyine rodents (Rodentia, Cricetidae, Sigmodontinae): a phylogenomic approach. Molecular Phylogenetics and Evolution 159:107120. DOI
Koch, E. L., H. Morales, J. Larsson, A. M. Westram, R. Faria, A. R. Lemmon, E. Moriarty Lemmon, K. Johannesson, R. K. Butlin. 2021. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters 5:196–213. DOI
Natusch D. J. D., D. Esquerré, J. A. Lyons, A. Hamidy, A. R. Lemmon, E. Moriarty Lemmon, A. Riyanto, J. S. Keogh, S. Donnellan. 2021. Phylogenomics, biogeography, and taxonomic revision of New Guinean pythons (Pythonidae, Leiopython) harvested for international trade. Molecular Phylogenetics and Evolution 158:106960. DOI
Cai, L., Z. Xi, E. Moriarty Lemmon, A. R. Lemmon, A. Mast, C. E. Buddenhagen, L. Liu, C. C. Davis. 2021. The perfect storm: gene tree estimation error, incomplete lineage sorting, and ancient gene flow explain the most recalcitrant angiosperm clade, Malpighiales. Systematic Biology 70:491–507. preprint
Brennan, I. G., A. R. Lemmon, E. Moriarty Lemmon, D. M. Portik, V. Weijola, L. Welton, S. C. Donnellan, J. S. Keogh. 2021. Phylogenomics of monitor lizards and the role of competition in dictating body size disparity. Systematic Biology 70:120–132. preprint
Rose, J. P., C. A. Patrocinio Toledo, E. Moriarty Lemmon, A. R. Lemmon, and K. J. Sytsma. 2021. Out of sight, out of mind: widespread nuclear and plastid-nuclear discordance in the flowering plant genus Polemonium (Polemoniaceae) suggests widespread historical gene flow despite limited nuclear signal. Systematic Biology 70:162–180. DOI
Hime, P. et al. 2021. Phylogenomics reveals ancient gene tree discordance in the Amphibian Tree of Life. Systematic Biology 70:49–66. DOI
2020
Esquerré, D., S. Donnellan, I. G. Brennan, A. R. Lemmon, E. Moriarty Lemmon, H. Zaher, F. Grazziotin, J. Scott Keogh. 2020. Phylogenomics, biogeography and morphometrics reveal rapid phenotypic evolution in pythons after crossing Wallace's line. Systematic Biology 69:1039–1051. DOI
Ospina, O.E., L. Tieu, J.J. Apodaca, E. Moriarty Lemmon. 2020. Hidden diversity in the Mountain chorus frog (Pseudacris brachyphona) and the diagnosis of a new species of chorus frog in the Southeastern United States. Copeia 108:778–795. DOI
Ochoa, A., M. Broe, E. Moriarty Lemmon, A.R. Lemmon, D.R. Rokyta, H.L. Gibbs. 2020. Drift, selection, and adaptive variation in small populations of a threatened rattlesnake. Molecular Ecology 29:2612–2625. DOI
Favre, A., J. S. Pringle, J. Heckenhauer, E. Kozuharova, Q. Gao, E. Moriarty Lemmon, A. R. Lemmon, H. Sun, N. Tkach, S. Gebauer, S.-S. Sun, P.-C. Fu. 2020. Phylogenetic relationships and sectional delineation within Gentiana (Gentianaceae). Taxon 69:1221–1238. DOI
Gray, D.A., D.B. Weissman, J.A. Cole, E. Moriarty Lemmon, A.R. Lemmon. 2020. Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment. Zootaxa 4750:328–348. DOI
Novikova, P.Y., I. G. Brennan, W. Booker, M. Mahony, P. Doughty, A. R. Lemmon, E. Moriarty Lemmon, L. Yant, Y. Van de Peer, J. S. Keogh, S. C. Donnellan. 2020. Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus. PLoS Genetics 16:e1008769. DOI
Pyron, R. A., E. Moriarty Lemmon, A. R. Lemmon, D. A. Beamer. 2020. Ancient reticulation, recent introgression, and phylogenomic incongruence among candidate species in Dusky Salamanders (Desmognathus). Molecular Phylogenetics and Evolution 146:106751. DOI
Dowdy, N.J., S. Keating, A.R. Lemmon, E. Moriarty Lemmon, W.E. Conner, C. H. Scott Chiavlo, S.J. Weller, R.B. Simmons, M. Sisson, J.M. Zaspel. 2020. A deeper meaning for shallow-scale phylogenomic studies: Nested Anchored Hybrid Enrichment offers great promise for resolving the tiger moth Tree Of Life (Insecta: Lepidoptera: Erebidae). Systematic Entomology 45:874–893. DOI
Wu, Yuan-He, et al., E. Moriarty Lemmon. 2020. A combined approach of mitochondrial DNA and anchored nuclear phylogenomics sheds light on unrecognized diversity, phylogeny, and historical biogeography of the torrent frogs, genus Amolops (Anura: Ranidae). Molecular Phylogenetics and Evolution 148:106789. DOI
Natusch, D., A. Hamidy, S. Keogh, A. R. Lemmon, S. Donnellan, A. Riyanto, E. Moriarty Lemmon, D. Esquerré, J. A. Lyons. 2020. Species delimitation and systematics of the green pythons (Morelia viridis complex) of Melanesia and Australia. Molecular Phylogenetics and Evolution 142:106640. DOI
Garcia-R, J.C., E. Moriarty Lemmon, A.R. Lemmon, N. French. 2020. Phylogenomic reconstruction sheds light on new relationships and timescale of rails (Aves: Rallidae) evolution. Diversity 12:70. DOI
Mendoza, C. Granados, M. Jost, E. Hagsater, S. Magallon, D. van den Berg, E. Moriarty Lemmon, A. R. Lemmon, G. A. Salazar, S. Wanke. 2020. Target nuclear and off-target plastid hybrid enrichment data inform a range of evolutionary depths in the orchid genus Epidendrum. Frontiers in Plant Science 10:1761. DOI
Chen, J.-M., E. Prendini, Y.-H. Wu, B.-L. Zhang, C. Suwannapoom, H.-M. Chen, J.-Q. Jin, E. Moriarty Lemmon, A. R. Lemmon, B. L. Stuart, C. J. Raxworthy, R. W. Murphy, Z.-Y. Yuan, J. Che. 2020. An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frogs (Anura: Rhacophoridae). Molecular Phylogenetics and Evolution 145:106724. DOI
Banker, S. E., Alan R. Lemmon, A. Bigelow Hassinger, M. Dye, S. D. Holland, M. L. Kortyna, H. Ralicki, E. Moriarty Lemmon. 2020. Hierarchical Hybrid Enrichment: multi-tiered genomic data collection across evolutionary scales, with application to chorus frogs (Pseudacris). Systematic Biology 69:756–773. DOI
Baker, A., J. Heraty, J. Mottern, J. Zhang, H. Hines, A. R. Lemmon, and E. Moriarty Lemmon. 2020. Inverse dispersal patterns in a group of ant parasitoids (Hymenoptera: Eucharitidae: Oraseminae) and their ant hosts. Systematic Entomology 45:1-19. DOI
2019
Simon, C., E. R. L. Gordon, M. S. Moulds, J. A. Cole, D. Haji, A. R. Lemmon, E. Moriarty Lemmon, M. Kortyna, K. Nazario, E. J. Wade, R. C. Meister, G. Goemans, S. M. Chiswell, P. Pessacq, C. Veloso, J. P. McCutcheon, P. Lukasik. 2019. Off-target capture data, endosymbiont genes and morphology reveal a relict lineage sister to all other singing cicadas. Biological Journal of the Linnean Society 128:865–886. DOI
Li, Jianhua, M. Stukel, P. Bussies, K. Skinner, A. Lemmon, E. Moriarty Lemmon, K. Brown, A. Bekmetjev, N. Swenson. 2019. Maple phylogeny and biogeography inferred from phylogenomic data. Journal of systematics and Evolution 57:594–606. DOI
Martin, G. J., K. F. Stanger-Hall, M. A. Branham, L. F. L. Da Silveira, S. E. Lower, D. W. Hall, X.-Y. Li, A. R. Lemmon, E. Moriarty Lemmon, S. M. Bybee. 2019. Higher-level phylogeny and reclassification of Lampyridae (Coleoptera: Elateroidea). Insect Systematics and Diversity 3:11. DOI
Garcia-Porta, J., I. Irisarri, M. Kirchner, A. Rodríguez, S. Kirchhof, J. L. Brown, A. MacLeod, A. P. Turner, F. Ahmadzadeh, G. Albaladejo, J. Crnobrnja-Isailovic, I. de la Riva, A. Fawzi, P. Galán, B. Göçmen, D. J. Harris, O. Jiménez-Robles, U. Joger, O. Jovanović Glavaš, M. Karış, G. Koziel, S. Künzel, M. Lyra, D. Miles, M. J. Nogales Hidalgo, M. Anıl Oğuz, P. Pafilis, L. Rancilhac, N. Rodríguez, B. Rodríguez Concepción, E. Sanchez, D. Salvi, T. Slimani, A. S'khifa, A. Turk Qashqaei, A. Žagar, A. Lemmon, E. Moriarty Lemmon, M. Angel Carretero, S. Carranza, H. Philippe, B. Sinervo, J. Müller, M. Vences, K. C. Wollenberg Valero. 2019. Environmental temperatures shape thermal physiology as well as diversification and genome-wide substitution rates in lizards. Nature Communications 10:4077. DOI
Phillips, A.J., A. Dornburg, K. Zapfe, F. E. Anderson, S. W. James, C. Erseus, E. Moriarty Lemmon, A. R. Lemmon, and B. W. Williams. 2019. Phylogenetic analysis of a putative missing link sparks reinterpretation of leech evolution. Genome Biology and Evolution 11:3082–3093. DOI
Buys, M.H., R.C. Winkworth, P.J. de Lange, P.G. Wilson, N. Mitchell, A.R. Lemmon, E. Moriarty Lemmon, S. Holland, J.R. Cherry, J. Klapste. 2019. The phylogenomics of diversification on an island: applying Anchored Hybrid Enrichment to New Zealand Leptospermum scoparium (Myrtaceae). Botanical Journal of the Linnean Society 191:1–17. DOI
Burbrink, F.T., S. Ruane, A. Kuhn, N. Rabibisoa, B. Randriamahatantsoa, A. P. Raselimanana, M. S. M. Andrianarimalala, J. Cadle, A.R. Lemmon, E. Moriarty Lemmon, R. A. Nussbaum, L. Jones, R. Pearson, C. J. Raxworthy. 2019. The origins and diversification of the exceptionally rich gemsnakes (Colubroidea: Lamprophiidae: Pseudoxyrhophiinae) in Madagascar. Systematic Biology 68:918–936. DOI
Crowl, A. A., P. S. Manos, J. D. McVay, A. R. Lemmon, E. Moriarty Lemmon, A. L. Hipp. 2019. Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus) using anchored enrichment. New Phytologist 226:1158–1170. DOI
Burbrink, F. T., F. G. Grazziotin, R. R. A. Pyron, D. Cundall, S. Donnellan, F. Irish, J. S. Keogh, F. Kraus, R. W. Murphy, B. Noonan, S. Ruane, C. J. Raxworthy, A. R. Lemmon, E. Moriarty Lemmon, H. Zaher. 2019. Interrogating genomic-scale data for Squamata (lizards, snakes, and amphisbaenians) shows no support for key traditional morphological relationships. Systematic Biology 69:502–520. DOI
Wolfe, J. M., J. W. Breinholt, K. A. Crandall, A. R. Lemmon, E. Moriarty Lemmon, T. E. Timm, M. E. Siddall, H. D. Bracken-Grissom. 2019. A phylogenomic framework, evolutionary timeline, and genomic resources for comparative studies of decapod crustaceans. Proceedings of the Royal Society B 286:20190079. preprint
Mason, A., F. Grazziotin, R. R. A. Pyron, H. Zaher, A. R. Lemmon, E. Moriarty Lemmon, C. Parkinson. 2019. Reticulate evolution in Nuclear Middle America causes discordance in the phylogeny of palm-pitvipers (Viperidae: Bothriechis). Journal of Biogeography 46:833–844. DOI
Kriebel R., B.T. Drew, C.P. Drummond; J.G. González-Gallegos; F. Celep, M. M. Mahdjoub, J.P. Rose, C.-L. Xiang, G.-X. Hu, J.B. Walker, E. Moriarty Lemmon, A.R. Lemmon, K.J. Sytsma. 2019. Tracking temporal shifts in area, biomes, and pollinators in the radiation of salvia (Sages, Lamiaceae) across continents: leveraging Anchored Hybrid Enrichment and targeted sequence data. American Journal of Botany 106:573–597. DOI
Li, J.-H., P. Del Tredici, A.R. Lemmon, E. Moriarty Lemmon, Y. Zhao, C. Fu. 2019. Allopatric speciation in Asia contributed to the diversity anomaly between eastern Asia and eastern North America: Evidence from anchored phylogenomics of Stewartia (Theaceae). International Journal of Plant Science 180:768–777. DOI
Machado, R.J.P., J.P. Gillung, S.L. Winterton, I.J. Garzon, A.R. Lemmon, E. Moriarty Lemmon, J.D. Oswald. 2019. Owlflies are derived antlions: anchored phylogenomics and a revised phylogenetic classification of the family Myrmeleontidae (Insecta: Neuroptera). Systematic Entomology 44:418–450. DOI
Faria, R., A. M. Westram, P. Chaube1, H. Morales, T. Larsson, A. Lemmon, E. Moriarty Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, R. Butlin. 2019. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology 28:1375-1393. DOI
Yuan, Z.-Y., B. -L. Zhang, C. J. Raxworthy, D. W. Weisrock, P. M. Hime, J. Jin, A. R. Lemmon, E. Moriarty Lemmon, S. D. Holland, M. Kortyna, W. Zhou, M.-S. Peng, J. Che, E. Prendini. 2019. Natatanuran frogs used the Indian Plate to step-stone disperse and radiate across the Indian Ocean. National Science Review 6:10-14. DOI
2018
Margres, M.J., A.H. Patton, K.P. Wray, A. Hassinger, M. Ward, E. Moriarty Lemmon, A. Lemmon, D.R. Rokyta. 2018. Tipping the scales: the migration-selection balance leans toward selection in snake venoms. Molecular Biology and Evolution 36:271–282. DOI
Kuntner M., C.A. Hamilton, R.-C. Cheng, M. Gregorič, N. Lupše, T. Lokovšek, E. Moriarty Lemmon, A.R. Lemmon, I. Agnarsson, J.A. Coddington, J.E. Bond. 2018. Golden Orbweavers ignore biological rules: phylogenomic and comparative analyses unravel a complex evolution of sexual size dimorphism. Systematic Biology 68:555–572. preprint
Taheri, S. S.W. James, V. Roy, T. Decaëns, B.W. Williams, F. Anderson, R. Rougerie, C.-H. Chang, G.G. Brown, L. Cunha, D.W.G. Stanton, E. Da Silva, J-H. Chen, A. R. Lemmon, E. Moriarty Lemmon, M. Bartz, D. Baretta, I. Barois, E. Lapied, M. Coulis, L. Dupont. 2018. Complex taxonomy of the 'brush tail' peregrine earthworm Pontoscolex corethrurus. Molecular Phylogenetics and Evolution 124:60-70. DOI
Caparroz, R., A. Vaz Rocha, G. S. Cabanne, P. Tubaro, A. Aleixo, E. Moriarty Lemmon, A. Lemmon. 2018. Mitogenomes of two neotropical bird species and the multiple independent origin of mitochondrial gene orders in Passeriformes. Molecular Biology Reports 45:279–285. DOI
Taucce P.P.G., M.J. Hickerson, C. Canedo, C.F.B. Haddad, A.R. Lemmon, E. Moriarty Lemmon, M. Vences, M. Lyra. 2018. The mitochondrial genomes of five frog species of the Neotropical genus Ischnocnema (Anura: Brachycephaloidea: Brachycephalidae). Mitochondrial DNA Part B: Resources 3:917-919. DOI
Percy, D. M., A. Crampton-Platt, S. Sveinsson, A. R. Lemmon, E. Moriarty Lemmon, D. Ouvrard, D. Burckhardt. 2018. Resolving the psyllid tree of life: a phylogeny of the superfamily Psylloidea (Hemiptera). Systematic Entomology 43:762–776. DOI
Johnson, A. J., D. D. McKenna, B. H. Jordal, A. I. Cognato, S. M. Smith, A. R. Lemmon, E. Moriarty Lemmon, J. Hulcr. 2018. Phylogenomics clarifies repeated evolutionary origins of inbreeding and fungus farming in bark beetles (Curculionidae, Scolytinae). Molecular Phylogenetics and Evolution 127:229–238. DOI
Irisarri, I., C. Sturmbauer, S. Pooja, P. Franchini, F. Henning, J. T. Dowdall, S. Koblmuller, G. Thallinger, E. Moriarty Lemmon, A. Lemmon, C. Fischer, A. Meyer. 2018. Anchored phylogenomics uncovers deep inter-tribal hybridizations in the Lake Tanganyika cichlid radiation and highlights adaptive loci shaping species' ecology. Nature Communications 9:3159. DOI
Bogarín, D., O. Alejandro Pérez-Escobar, D. Groenenberg, S. D. Holland, A. P. Karremans, E. Moriarty Lemmon, A. R Lemmon, F. Pupulin, E. Smets, B. Gravendeel. 2018. Anchored Hybrid Enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex. Molecular Phylogenetics and Evolution 129:27 –47. DOI
Pepper, M., J. Sumner, I. G. Brennan, K. Hodges, A. R. Lemmon, E. Moriarty Lemmon, G. Peterson, D. L. Rabosky, L. Schwarzkopf, I. A. W. Scott, G. Shea, and J. S. Keogh. 2018. Speciation in the mountains and dispersal by rivers: Molecular phylogeny of the Australian Eulamprus water skinks and the biogeography of Eastern Australia. Journal of Biogeography 45:2040–2052. DOI
Piekarski, P., J. M. Carpenter, A. R. Lemmon, E. Moriarty Lemmon, B. J. Sharanowski. 2018. Phylogenomic evidence overturns current conceptions of social evolution in wasps (Vespidae). Molecular Biology and Evolution 35:2097-2109. DOI
Barrow, L. N., A. R. Lemmon, E. Moriarty Lemmon. 2018. Targeted sampling and target capture: Assessing phylogeographic concordance with genome-wide data. Systematic Biology 67:979–996. DOI
Relyea, R., P. R. Stephens, L. N. Barrow, A. R. Blaustein, P. W. Bradley, J. C. Buck, A. Chang, J. P. Collins, B. Crother, J. Earl, S. S. Gervasi, J. T. Hoverman, O. Hyman, E. Moriarty Lemmon, T. M. Luhring, M. Michelson, C. Murray, S. Price, R. D. Semlitsch, A. Sih, A. B. Stoler, N. VandenBroek, A. Warwick, G. Wengert, J. I. Hammond. 2018. Phylogenetic patterns of trait and trait plasticity evolution: Insights from amphibian embryos. Evolution 72:663–678. DOI
Winterton, S., A. R. Lemmon, J. P. Gillung, I. J. Garzon, D. Badano, D. K. Bakkes, L. C.V. Breitkrutz, M. S. Engel, E. Moriarty Lemmon, X. Liu, R. J.P. Machado, J. H. Skevington, J. D. Oswald. 2018. Evolution of lacewings and allied orders using anchored phylogenomics (Neuroptera, Megaloptera, Raphidioptera). Systematic Entomology 43:330–354. DOI
Haddad S., S. Shin, A. R. Lemmon, E. Moriarty Lemmon, P. Svacha, B. Farrell, A. Ślipiński, D. Windsor, and D. D. McKenna. 2018. Anchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles (Cerambycidae). Systematic Entomology 43:68–89. DOI
Léveillé-Bourret, E., J. R. Starr, B. A. Ford, E. Moriarty Lemmon, A. R. Lemmon. 2018. Resolving a rapid radiation using universal enrichment probes for hundreds of nuclear genes in non-model plants (CDS clade, Cyperaceae). Systematic Biology 67:94–112. DOI
Breinholt, J. W., A. R. Lemmon, E. Moriarty Lemmon, L. Xiao, and A. Y. Kawahara. 2018. Resolving relationships among the megadiverse butterflies and moths with a novel pipeline for anchored phylogenomics. Systematic Biology 67:78–93. DOI
Heinicke, M., A. R. Lemmon, E. Moriarty Lemmon, K. McGrath, S. Blair Hedges. 2018. Phylogenomic support for evolutionary relationships of New World direct-developing frogs (Anura: Terraranae). Molecular Phylogenetics and Evolution 118:145–155. DOI
Shin, S., D. Clarke, A. R. Lemmon, E. Moriarty Lemmon, A. Aitken, S. Haddad, B. Farrell, A. Marvaldi, R. Oberprieler, and D. McKenna. 2018. Phylogenomic data yield new and robust insights into the phylogeny and evolution of weevils. Molecular Biology and Evolution 35:823–838. DOI
2017
Maddison, W. P., S. C. Evans, C. A. Hamilton, J. E. Bond, A. R. Lemmon, E. Moriarty Lemmon. 2017. A genome-wide phylogeny of jumping spiders (Araneae: Salticidae), using anchored hybrid enrichment. ZooKeys 695:89 –101. DOI
Margres, M. J., K. P. Wray, A. T. B. Hassinger, M. Ward, J. J. McGivern, E. Moriarty Lemmon, A. R. Lemmon, and D. R. Rokyta. 2017. Quantity, not quality: rapid adaptation in a polygenic trait proceeded exclusively through expression differentiation. Molecular Biology and Evolution 34:3099–3110. DOI
Dietrich, C. H., J. M. Allen, A. R. Lemmon, E. Moriarty Lemmon, D. M. Takiya, O. Evangelista, and K. P. Johnson. 2017. Leafhopper and Treehopper (Hemiptera: Cicadomorpha: Membracoidea) Phylogeny: The Limits of Phylogenomics? Insect Systematics and Diversity 1:57–72. DOI
Lemmon, E. Moriarty and T. Juenger. 2017. Geographic variation in hybridization across a reinforcement contact zone of chorus frogs (Pseudacris). Ecology and Evolution 7:9485–9502. DOI
Shavvon R., S. Osaloo, A. Maassoumii, F. Moharrek, S. Erkul, A. R. Lemmon, E. Moriarty Lemmon, I. Michalak, A. Muellner-Riehl, A. Favre. 2017. Increasing phylogenetic support for explosively radiating taxa: the promise of high-throughput sequencing for Oxytropis (Fabaceae). Journal of Systematics and Evolution 55:385–404. DOI
Barrow, L. N., J. A. Soto-Centeno, A. R. Warwick, A. R. Lemmon, and E. Moriarty Lemmon. 2017. Evaluating suture zones and refugia through comparative phylogeography of amphibians in the Southeastern Coastal Plain. Journal of Biogeography 44:2692–2705. DOI
Wanke, S., C. Granados Mendoza, S. Müller, A. Paizanni Guillén, C. Neinhuis, A. R. Lemmon, E. Moriarty Lemmon, M.-S. Saimain. 2017. Recalcitrant deep and shallow nodes in Aristolochia (Aristolochiaceae) illuminated using anchored hybrid enrichment. Molecular Phylogenetics and Evolution 117:111–123. DOI
Margres, M., A. B. Bigelow, E. Moriarty Lemmon, A. R. Lemmon, D. R. Rokyta. 2017. Selection to increase expression, not sequence diversity precedes gene family origin and expansion. Genetics 206:1569–1580. DOI
Cardillo, M., P. Weston, P. Olde, Z. Reynolds, A. Mast, E. Moriarty Lemmon, A. R. Lemmon, and L. Bromham. 2017. The phylogeny and biogeography of Hakea (Proteaceae) reveals the role of biome shifts in a continental plant radiation. Evolution 71:1925–2135. DOI
Crother, B. I., R. M. Bonett, J. Boundy, F. T. Burbrink, K. de Queiroz, D. R. Frost, R. Highton, J. B. Iverson, E. L. Jockusch, F. Kraus, K. L. Krysko, A. D. Leaché, E. Moriarty Lemmon, R. W. McDiarmid, J. R. Mendelson III, P. A. Meylan, T. W. Reeder, S. Ruane, M. E. Seidel. 2017. Scientific and Standard English Names of Amphibians and Reptiles of North America North of Mexico, with Comments Regarding Confidence in our Understanding, 8th Ed. Edited by John J. Moriarty. Society for the Study of Amphibians and Reptiles Herpetological Circular No. 43. DOI
Lyra, M., U. Joger, D. Donaire, T. Slimani, E. H. El Mouden, S. Künzel, A. R. Lemmon, E. Moriarty Lemmon, M. Vences. 2017. The mitochondrial genomes of Atlas geckos (Quedenfeldtia): mitogenome assembly from transcriptomes and anchored hybrid enrichment data sets. Mitochondrial DNA Part B Resources. 2:1356-358. DOI
Chen, X., A. R. Lemmon, E. Moriarty Lemmon, R. R. A. Pyron, and F. T. Burbrink. 2017. Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes. Molecular Phylogenetics and Evolution 111:206–218. DOI
Fragoso-Martinez, I., G. A. Salazar, M. M. Gordillo, S. Magallon, L. Sanchez-Reyes, E. Moriarty Lemmon, A. R. Lemmon, F. Sazatornil, and C. Granados Mendoza 2017. A pilot study applying the Plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace: Lamiaceae). Molecular Phylogenetics and Evolution 117:124–134. DOI
Dornburg, A., J. Townsend, W. Brooks, E. Spriggs, R. Eytan, J. Moore, P. Wainwright, A. Lemmon, E. Moriarty Lemmon, T. Near. 2017. New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset. Molecular Phylogenetics and Evolution 110:27–38. DOI
Domingos, F. M. C. B., G. R. Colli, A. R. Lemmon, E. Moriarty Lemmon, L. B. Beheregaray. 2017. In the shadows: Phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus). Molecular Phylogenetics and Evolution 107:455-465. DOI
Mitchell, N., P. O. Lewis, E. Moriarty Lemmon, A. R. Lemmon, K. E. Holsinger. 2017. Anchored phylogenomics resolves the evolutionary relationships in the rapid radiation of Protea L. (Proteaceae). American Journal of Botany 104:102–115. DOI
Nunziata, S., S. Lance, D. Scott, E. Moriarty Lemmon, D. Weisrock. 2017. Genomic data detect corresponding signatures of very recent population size trends in two salamander species impacted by climate change. Molecular Ecology 26:1060–1074. DOI
2016
Stout, C. C., M. Tan, A. R. Lemmon, E. Moriarty Lemmon, J. W. Armbruster. 2016. Resolving Cypriniformes Relationships Using An Anchored Enrichment Approach. BMC Evolutionary Biology 16:244. DOI
Manthey, J. D., M. Tollis, A. R. Lemmon, E. Moriarty Lemmon, S. Boissinot. 2016. Diversification in wild populations of the model organism Anolis carolinensis: a genome-wide phylogeographic investigation using target capture. Ecology and Evolution 6:8115–8125. DOI
Hamilton, C. A., A. R. Lemmon, E. Moriarty Lemmon, J. E. Bond. 2016. Expanding Anchored Hybrid Enrichment to resolve both deep and shallow relationships within the spider Tree of Life. BMC Evolutionary Biology 16:212. DOI
Tucker, D. B., G. R. Colli, L. G. Giugliano, S. B. Hedges, C. R. Hendry, E. Moriarty Lemmon, A. R. Lemmon, J. W. Sites Jr., and R. R. A. Pyron. 2016. Methodological congruence in phylogenomic analyses with morphological support for teiid lizards (Sauria: Teiidae). Molecular Phylogenetics and Evolution 103:75–84. DOI
Young, A. D., A. R. Lemmon, J. H. Skevington, X. Mengual, G. Stahls, M. Reemer, K. Jordaens, S. Kelso, E. Moriarty Lemmon, M. Hauser, M. De Meyer, B. Misof, B. Wiegmann. 2016. The first anchored enrichment dataset produced for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae) and sets the stage for future large-scale phylogenetic analyses. BMC Evolutionary Biology 16:143. DOI
Engebretsen K., L. Barrow, E. Rittenmeyer, J.M. Brown, and E. Moriarty Lemmon. 2016. Quantifying the spatio-temporal dynamics in a chorus frog hybridization zone (Pseudacris) over 30 years. Ecology and Evolution 6:5013–5031. DOI
Pyron, A. R., C. R. Hendry, F. Hsieh, A. R. Lemmon, E. Moriarty Lemmon. 2016. A generalized integrative approach to genomic phylogeography and species delimitation in Brown and Red-bellied snakes (Storeria). Biological Journal of the Linnean Society 177:937–949. DOI
Edwards, S. V., Z. Xi, A. Janke, B. C. Faircloth, J. E. McCormack, T. C. Glenn, B. Zhong, S. Wu, E. Moriarty Lemmon, A. R. Lemmon, A. D. Leache, L. Liu, C. C. Davis. 2016. Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics. Molecular Phylogenetics and Evolution 94:447-462. DOI
Funk, W. C., M. A. Murphy, K. L. Hoke, E. Muths, S. M. Amburgey, E. Moriarty Lemmon, and A. R. Lemmon. 2016. Elevational speciation in action? Restricted gene flow associated with adaptive divergence across an altitudinal gradient. Journal of Evolutionary Biology 29:241-252. DOI
Peloso, P., D. Frost, S. Richards, M. Rodrigues, M. Matsui, C. Raxworthy, S. Donnellan, S. Biju, E. Moriarty Lemmon, A. Lemmon, W. Wheeler. 2016. The impact of Anchored Phylogenomics and taxon sampling on phylogenetic inference in narrowmouthed frogs (Anura, Microhylidae). Cladistics 2015:1-28. DOI
2015
Prum, R. O., J. S. Berv, A. Dornburg, D. J. Field, J. P. Townsend, E. Moriarty Lemmon, and A. R. Lemmon. 2015. A comprehensive phylogeny of birds (Aves) using targeted next generation DNA sequencing. Nature 526:569-573. DOI
Ruane, S., C. J. Raxworthy, A. R. Lemmon, E. Moriarty Lemmon, F. T. Burbrink. 2015. Comparing species-tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: An empirical study on Malagasy pseudoxyrhophiine snakes. BMC Evolutionary Biology 15:221. DOI
Barrow, L. N., A. Bigelow, C. Phillips, E. Moriarty Lemmon. 2015. Phylogeographic inference using Bayesian model comparison across a fragmented chorus frog species complex. Molecular Ecology 24:4739–4758. DOI
Eytan, R., B. Evans, A. Dornburg, A. Lemmon, E. Moriarty Lemmon, P. Wainwright, T. Near. 2015. Are 100 enough? Inferring Acanthomorph teleost phylogeny using Anchored Hybrid Enrichment. BMC Evolutionary Biology 15:113. DOI
Warwick, A., J. Travis, E. Moriarty Lemmon. 2015. Geographic variation in the Pine Barrens treefrog (Hyla andersonii): concordance of genetic, morphometric, and acoustic signal data. Molecular Ecology 24:3281-3298. DOI
Brandley, M., S. Singhal, J. Bragg, C. Jennings, A. R. Lemmon, E. Moriarty Lemmon, C. Moritz. 2015. Evaluating the phylogenetic informativeness of anchored enrichment loci at the tips of the tree of life: an empirical study using Eugongylus group scincid lizards. BMC Evolutionary Biology 15:62. DOI
2014
Pyron, A. R., C. R. Hendry, V. M. Chou, E. Moriarty Lemmon, A. R. Lemmon, F. T. Burbrink. 2014. Effectiveness of Phylogenomic Data and Coalescent Species-Tree Methods for Resolving Difficult Nodes in the Phylogeny of Advanced Snakes (Serpentes: Caenophidia). Molecular Phylogenetics and Evolution 81:221-231. DOI
Warwick, A., J. Travis, E. Moriarty Lemmon. 2014. Development and characterization of 21 microsatellite loci for the Pine Barrens treefrog (Hyla andersonii). Conservation Genetic Resources. DOI
Barrow, L. N., C. A. Phillips, E. Moriarty Lemmon. 2014. Development and characterization of 24 microsatellite loci for the Illinois Chorus Frog (Pseudacris illinoensis) and Strecker's Chorus Frog (P. streckeri). Conservation Genetic Resources. DOI
Malone, J. H., J. Ribado, E. Moriarty Lemmon. 2014. Sensory drive does not explain reproductive character displacement of male acoustic signals in the Upland Chorus Frog (Pseudacris feriarum). Evolution 68:1306–1319. DOI
Barrow, L. N., H. F. Ralicki, S. A. Emme, E. Moriarty Lemmon. 2014. Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing. Molecular Phylogenetics and Evolution 75:78–90. DOI
2013
2012
Lemmon, A. R., S. Emme, E. Moriarty Lemmon. 2012. Anchored hybrid enrichment for massively high-throughput phylogenomics. Systematic Biology 61:727–744. DOI
Lemmon, A. R., E. Moriarty Lemmon. 2012. High-throughput development of informative nuclear markers for shallow-scale phylogenetics and phylogeography. Systematic Biology 61:745–761. DOI
Carstens, B., A. R. Lemmon, and E. Moriarty Lemmon. 2012. The promises and pitfalls of next-generation sequencing data in phylogeography. Systematic Biology 61:713–715. DOI
2011
Rokyta, D. R., K. P. Wray, A. R. Lemmon, E. Moriarty Lemmon, S. B. Caudle. 2011. A high-throughput venom-gland transcriptome for the Eastern Diamondback Rattlesnake (Crotalus adamanteus) and evidence for pervasive positive selection across toxin classes. Toxicon 57:657–671. DOI
Lemmon, E. Moriarty, M. Murphy, and T. E. Juenger. 2011. Identification and characterization of nuclear microsatellite loci for multiple species of chorus frogs (Pseudacris) for population genetic analyses. Conservation Genetics Resources 3:233–237. DOI
2010
Lemmon, E. Moriarty, and A. R. Lemmon. 2010. Reinforcement in chorus frogs: lifetime fitness estimates including intrinsic natural selection and sexual selection against hybrids. Evolution 64:1748–1761. DOI
Brown, J. M., A. R. Lemmon, S. M. Hedke, E. Moriarty Lemmon. 2010. When trees grow too long: investigating the causes of highly inaccurate Bayesian branch length estimates. Systematic Biology 59:145–161. DOI
2009
Lemmon, A. R., J. M. Brown, K. Stanger-Hall, and E. Moriarty Lemmon. 2009. The effect of missing data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Systematic Biology 58:130–145. DOI
Lemmon, E. Moriarty. 2009. Diversification of conspecific signals in sympatry: geographic overlap drives multi-dimensional reproductive character displacement in frogs. Evolution 63:1155–1170. DOI
2008
Lemmon, A. R. and E. Moriarty Lemmon. 2008. A likelihood framework for estimating phylogeographic history on a continuous landscape. Systematic Biology 57:544–561. DOI
Lemmon, E. Moriarty, A. R. Lemmon, J. T. Collins, and D. C. Cannatella. 2008. A new North American chorus frog species (Amphibia: Hylidae: Pseudacris) from the south-central United States. Zootaxa 1675:1–30. DOI
2007
Lemmon, E. Moriarty, A. R. Lemmon, and D. C. Cannatella. 2007. Geological and climatic forces driving speciation in the continentally distributed trilling chorus frogs (Pseudacris). Evolution 61:2086–2103. DOI
Lemmon, E. Moriarty, A. R. Lemmon, J. A. Lee-Yaw, J. T. Collins, and D. C. Cannatella. 2007. Phylogeny-based delimitation of species boundaries and contact zones in the trilling chorus frogs (Pseudacris). Molecular Phylogenetics and Evolution 44:1068–1082. DOI
2005
2004
Moriarty, E. C. and D. C. Cannatella. 2004. Phylogenetic relationships of North American chorus frogs (Pseudacris). Molecular Phylogenetics and Evolution 30:409–420. DOI
Lemmon, A. R. and E. C. Moriarty. 2004. The importance of proper model assumption in Bayesian phylogenetics. Systematic Biology 53:265–277. DOI
2001
Sever, D. M., T. R. Halliday, E. C. Moriarty, and B. Arano. 2001. Sperm storage in the smooth newt (Triturus v. vulgaris) II. Ultrastructure of the spermathecae after the breeding season. Acta Zoologica 82:49–56. DOI
Sever, D. M., E. C. Moriarty, L.C. Rania, and W.C. Hamlett. 2001. Sperm storage in the oviduct of an internally fertilizing frog, Ascaphus truei. Journal of Morphology 248:1–21. DOI
1998