To download the publications below, click on the Adobe PDF logo following each reference and obtain PDF files from the publisher's website or my ResearchGate profile. However, to comply with copyright laws, I ask that you please limit the use of PDF files to printing of single copies for personal research and study, and do not modify the files in any way or use them for commercial purposes.

Thanks. ~ J

Follow this link to see my Google Scholar Citations.

journal articles


Bagley JC, Johnson CC, McGregor SW, Breitman MF, Armbruster JW, Harris PM, O'Neil PE (2023) Marine and freshwater fishes of Alabama: a revised checklist and discussion of taxonomic issues. Zootaxa, 5357(3), 301-341. HTML doi


Bagley JC, Breitman MF, Johnson JB (2022) Length–weight relation for seven Neotropical freshwater fish species (Actinopterygii) endemic to Central America. Acta Ichthyologica et Piscatoria, 2022, 183–187. HTML

Calderón-Acevedo CA, Bagley JC, Muchhala N (2022) Genome-wide ultraconserved elements resolve phylogenetic relationships and biogeographic history among Neotropical leaf-nosed bats in the genus Anoura (Phyllostomidae). Molecular Phylogenetics and Evolution, 167, 107356. Available online 10 November 2021. HTML pdf doi


Soares YFF, Aquino PPU, Bagley JC, Langeani F, Colli GR (2021) Two new species of Hypostomus suckermouth-armored catfishes (Teleostei: Loricariidae) from central Brazil. Journal of Fish Biology. HTML pdf doi


Menon M, Bagley JC, Page G, Whipple AV, Schoettle AW, Still C, Wehenkel C, Waring K, Flores-Rentería L, Cushman SA, Eckert AJ (in revision). Adaptive evolution in a conifer hybrid zone is driven by a mosaic of introgressed and standing genetic variants. Communications Biology.

Bagley JC, Heming NM, Gutiérrez EE, Devisetty UK, Mock KE, Eckert AJ, Strauss SH (2020) Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides). Ecology and Evolution.

Bagley JC, Uribe-Convers S, Carlsen M, Muchhala N (2020) Utility of targeted sequence capture for phylogenomics in rapid, recent angiosperm radiations: Neotropical Burmeistera bellflowers as a case study. Molecular Phylogenetics and Evolution. Available online. doi


Menon M, Landguth E, Saenz AL, Bagley JC, Schoettle A, Wehenkel CA, Cushman S, Waring K, Eckert AJ (2019). Tracing the footprints of a moving hybrid zone under a demographic history of speciation with gene flow. Evolutionary Applications, 1-15. HTML pdf doi

Bagley JC, Aquino PPU, Breitman MF, Hrbek T, Langeani F, Colli GR (2019). DNA barcode and minibarcode identification of freshwater fishes from Cerrado headwater streams in central Brazil. Journal of Fish Biology, 95, 1046-1060. HTML pdf doi


Bagley JC, Hickerson M, Johnson JB (2018) Testing hypotheses of diversification in Panamanian frogs and freshwater fishes using hierarchical approximate Bayesian computation with model averaging. Diversity, 10, 120. HTML pdf doi

Bagley JC, Mayden RL, Harris PM (2018) Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils. PeerJ, 6, e5168. HTML pdf doi

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 (2018) The role of hybridization during ecological divergence between southwestern white pine, Pinus strobiformis, and limber pine, P. flexilis. Molecular Ecology, 27, 1245-1260. pdf doi

Breitman MF, Domingos FMCB, Bagley JC, Wiederhecker HC, Ferrari TB, Cavalcante VHGL, et al. (2018) New species of Enyalius (Squamata: Leiosauridae) endemic to the Brazilian Cerrado, with comments on how to improve the practice of taxonomy. Herpetologica, 74(4), 355-369. HTML pdf doi


Overcast I, Bagley JC, Hickerson, MJ (2017) Strategies for improving approximate Bayesian computation tests for synchronous diversification. BMC Evolutionary Biology, 17, 2013. HTML pdf doi


Bagley JC, Matamoros WA, McMahan CD, Tobler M, Chakrabarty P, Johnson JB (2016) Phylogeography and species delimitation in convict cichlids (Cichlidae: Amatitlania): implications for taxonomy and Plio–Pleistocene evolutionary history in Central America. Biological Journal of the Linnean Society. pdf pdf doi


Bagley JC, Alda F, Breitman MF, van den Berghe EP, Bermingham E, Johnson JB (2015) Assessing species boundaries in a morphologically conserved group of Neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae). PLoS One, 10(4), e0121139. HTML pdf doi


Watson CM, Makowsky R, Bagley JC (2014) Reproductive mode evolution in lizards revisited: updated analyses examining geographic, climatic and phylogenetic effects support the cold-climate hypothesis. Journal of Evolutionary Biology, 27(12), 2767-2780. HTML pdf doi

Bagley JC, Johnson JB (2014b) Testing for shared biogeographic history in the lower Central American freshwater fish assemblage using comparative phylogeography: concerted, independent, or multiple evolutionary responses? Ecology and Evolution, 4(9), 1686-1705. HTML pdf doi

Bagley JC, Johnson JB (2014a) Phylogeography of the lower Central American Neotropics: diversification between two continents and between two seas. Biological Reviews, 89(4), 767-790. HTML pdf doi


Bagley JC, Sandel M, Travis J, Lozano-Vilano M de L, Johnson JB (2013) 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. BMC Evolutionary Biology, 13, 223. doi: HTML pdf doi


Unmack PJ, Bagley JC, Adams MD, Hammer MD, Johnson JB (2012) Molecular phylogeny and phylogeography of the Australian freshwater fish genus Galaxiella (Teleostei: Galaxiidae), with an emphasis on dwarf galaxias (G. pusilla). PLoS One, 7(6), e38433. HTML pdf doi


Bagley JC, Mayden RL, Roe KJ, Holznagel W, Harris PM (2011). Congeneric phylogeographical sampling reveals polyphyly and novel biodiversity within black basses (Centrarchidae: Micropterus). Biological Journal of the Linnean Society, 104(2), 346-363. HTML pdf doi

proceedings and book chapters

Johnson JB, Bagley JC (2011) Ecological drivers of life-history evolution. In: Ecology and evolution of poeciliid fishes. (eds Evans JP, Pilastro A, Schlupp I), pp. 38-49. University of Chicago Press, Chicago, IL. ISBN-10: 0226222748. (NOTE: This chapter was peer-reviewed.) Book pdf

Thompson M, Bagley JC, Rasco J, Lackey K, Cox M (2007) The Respiratory System. In: Biology: The Study of Life (eds Rasco J, Lackey K) Kendall/Hunt Publishing. ISBN-10: 0757556434.


Bagley JC (2014) Understanding the diversification of Central American freshwater fishes using comparative phylogeography and species delimitation. PhD dissertation, Department of Biology, Brigham Young University, Provo, UT. Abstract pdf (653k)

short communications

Ceríaco LM, Gutiérrez EE, Dubois A, et al. (Appendix 1 of Supporting Signatories including JC Bagley) (2016) Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences. Zootaxa, 4196, 435-445. HTML pdf doi doi: 10.11646/zootaxa.4196.3.9.

editorials and letters

[coming soon.]