Publications

Publications

Genome-wide ultraconserved elements resolve phylogenetic relationships and biogeographic history among Neotropical leaf-nosed bats in the genus Anoura (Phyllostomidae).


Calderon-Acevedo CA, Bagley JC, Muchhala N Molecular Phylogenetics and Evolution. 2021.
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Two new species of Hypostomus suckermouth-armored catfishes (Teleostei: Loricariidae) from central Brazil.


Soares YFF, Aquino PPU, Bagley JC, Langeani F, Colli GR Journal of Fish Biology. 2021.
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Adaptive evolution in a conifer hybrid zone is driven by a mosaic of introgressed and standing genetic variants.


Menon M, Bagley JC, Page G, Whipple AV, Schoettle AW, Still C, et al. Communications Biology. 2021.
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Utility of targeted sequence capture for phylogenomics in rapid, recent angiosperm radiations: Neotropical Burmeistera bellflowers as a case study.


Bagley JC, Uribe-Convers S, Carlsen M, Muchhala N. Molecular Phylogenetics and Evolution. 2020.
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Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides).


Bagley JC, Uribe-Convers S, Carlsen M, Muchhala N. Molecular Phylogenetics and Evolution. 2020.
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Tracing the footprints of a moving hybrid zone under a demographic history of speciation with gene flow.


Menon M, Landguth E, Saenz AL, Bagley JC, Schoettle A, Wehenkel CA, Cushman S, Waring K, Eckert AJ. Evolutionary Applications. 2019.
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The role of hybridization during ecological divergence between southwestern white pine, Pinus strobiformis, and limber pine, P. flexilis.


Menon M, Bagley JC, Friedline C, Whipple A, Schoettle A, Sáenz AL, Wehenkel CA, Flores-Renteria LH, Sneizko R, Cushman S, Waring K, Eckert AJ Molecular Ecology. 2018.
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New species of Enyalius (Squamata: Leiosauridae) endemic to the Brazilian Cerrado, with comments on how to improve the practice of taxonomy.


Breitman MF, Domingos FMCB, Bagley JC, Wiederhecker HC, Ferrari TB, Cavalcante VHGL, et al. Herpetologica. 2018.
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Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils.


Bagley JC, Mayden RL, Harris PM. PeerJ. 2018.
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Testing hypotheses of diversification in Panamanian frogs and freshwater fishes using hierarchical approximate Bayesian computation with model averaging.


Bagley JC, Mayden RL, Harris PM. Diversity. 2018.
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DNA barcode and minibarcode identification of freshwater fishes from Cerrado headwater streams in central Brazil.


Bagley JC, Aquino PPU, Breitman MF, Hrbek T, Langeani F, Colli GR. Journal of Fish Biology. 2019.
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Strategies for improving approximate Bayesian computation tests for synchronous diversification.


Overcast I, Bagley JC, Hickerson MJ. BMC Evolutionary Biology. 2017.
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Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences.


Ceríaco LM, Gutiérrez EE, Dubois A, et al. (Appendix 1 of Supporting Signatories including JC Bagley). Zootaxa. 2016.
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Phylogeography and species delimitation in convict cichlids (Cichlidae: Amatitlania): implications for taxonomy and Plio–Pleistocene evolutionary history in Central America.


Bagley JC, Matamoros WA, McMahan CD, Tobler M, Chakrabarty P, Johnson JB. Biological Journal of the Linnean Society. 2016.
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Assessing species boundaries in a morphologically conserved group of Neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae).


Bagley JC, Alda F, Breitman MF, van den Berghe EP, Bermingham E, Johnson JB. PLoS One. 2015.
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Reproductive mode evolution in lizards revisited: updated analyses examining geographic, climatic and phylogenetic effects support the cold-climate hypothesis.


Watson CM, Makowsky R, Bagley JC. Journal of Evolutionary Biology. 2014.
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Testing for shared biogeographic history in the lower Central American freshwater fish assemblage using comparative phylogeography: concerted, independent, or multiple evolutionary responses?


Bagley JC, Johnson JB. Ecology and Evolution. 2014.
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Phylogeography of the lower Central American Neotropics: diversification between two continents and between two seas.


Bagley JC, Johnson JB. Biological Reviews. 2014.
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Understanding the diversification of Central American freshwater fishes using comparative phylogeography and species delimitation.


Bagley JC. Ph.D. Dissertation, Brigham Young University. 2014.
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Paleoclimatic modeling and phylogeography of least killifish, Heterandria formosa: insights into Pleistocene expansion-contraction dynamics and evolutionary history of North American Coastal Plain freshwater biota.


Bagley JC, Sandel M, Travis J, Lozano-Vilano M de L, Johnson JB. BMC Evolutionary Biology. 2013.
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Molecular phylogeny and phylogeography of the Australian freshwater fish genus Galaxiella (Teleostei: Galaxiidae), with an emphasis on dwarf galaxias (G. pusilla).


Unmack PJ, Bagley JC, Adams MD, Hammer MD, Johnson JB. PLoS One. 2012.
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Ecological drivers of life-history evolution. In: Ecology and Evolution of Poeciliid Fishes.


Johnson JB, Bagley JC. University of Chicago Press, Chicago, IL. 2011.
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Congeneric phylogeographical sampling reveals polyphyly and novel biodiversity within black basses (Centrarchidae: Micropterus).


Bagley JC, Mayden RL, Roe KJ, Holznagel W, Harris PM. Biological Journal of the Linnean Society. 2011.
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The Respiratory System. In: Biology: The Study of Life (eds Rasco J, Lackey K).


Thompson M, Bagley JC, Rasco J, Lackey K, Cox M. Kendall/Hunt Publishing. 2007.
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