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To download the publications below, click on the Adobe PDF logo following each reference and obtain PDF files from my ResearchGate profile.  However, to comply with copyright laws, I ask that you

  1. please request permission from me by E-mail before downloading PDF’s (also shoot me an E-mail if you have trouble obtaining reprints or pre-prints from ResearchGate),
  2. please limit the use of PDF files to printing of single copies for personal research and study, and
  3. 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.

Peer-reviewed Publications

16.            Menon MG, Bagley JC, Friedline C, Whipple A, Schoettle A, Sáenz AL, Wehenkel CA, Flores-Renteria LH, Sneizko R, Cushman S, Waring K, Eckert AJ (in review) The role of hybridization during ecological divergence between southwestern white pine, Pinus strobiformis, and limber pine, P. flexilis. Molecular Ecology.
15.            Breitman MF, Domingos FMCB, Bagley JC, Wiederhecker HC, Ferrari TB, Cavalcante VHGL, et al. (in review) New species of Enyalius (Squamata: Leiosauridae) endemic to the Brazilian Cerrado, with comments on how to improve the practice of taxonomy. Herpetologica.
14.           Bagley JC, Harris PM, Mayden, RL (in review) Phylogeny, temporal diversification, and conflicting relationships of suckers (Cypriniformes: Catostomidae) inferred from multiple data types and fossil-calibrated divergence dating. Molecular Phylogenetics and Evolution.
13.            Bagley JC, Aquino PPU, Hrbek T, Hernandez S, Langeani F, Colli GR (in revision) Using ddRAD-seq phylogeography to test for genetic effects of headwater river capture in suckermouth armored catfish (Loricariidae: Hypostomus) from the central Brazilian Shield. Molecular Ecology.
12.            Overcast I, Bagley JC, Hickerson, MJ (2017) Practical strategies for improving approximate Bayesian computation tests for synchronous diversification. BMC Evolutionary Biology, 17, 2013.
11.             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. Click to view Early View on BJLS website. doi: coming soon. pdficon_small
10.             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. doi: 10.1371/journal.pone.0121139 pdficon_small

9.             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. doi: 10.1111/jeb.12536 pdficon_small 

8.             Bagley JC, Johnson JB (2014) 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. doi: 10.1002/ece3.1058 [Dissertation Chapter 2]  Follow this link to the journal website where you can download the final ms and supplementary material. pdficon_small

7.          Bagley JC, Johnson JB (2014) Phylogeography of the lower Central American Neotropics: diversification between two continents and between two seas. Biological Reviews, 89(4), 767-790. doi: 10.1111/brv.12076. Published online 3 February 2014. [Dissertation Chapter 1]  Follow this link to the journal website where you can download the final ms and supplementary material. pdficon_small

6.          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:10.1186/1471-2148-13-223 pdficon_small
5.          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. doi:10.1371/journal.pone.0038433 pdficon_small
4.          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. doi: 10.1111/j.1095-8312.2011.01720.x pdficon_small
Peer-reviewed Book Chapters
3.          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. Buy Book on Amazon (This chapter was peer-reviewed.) pdficon_small

2.          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

Peer-reviewed Short Communications / Opinions:
1.          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. doi: 10.11646/zootaxa.4196.3.9.
Spotted bass M punctulatus