Completed Projects

Completed Projects

[PhD Dissertation] Understanding the Diversification of Central American Freshwater Fishes Using Comparative Phylogeography and Species Delimitation

Collaborators: Jerry Johnson, plus help from other Collaborators, including Maria Florencia Breitman, Eric van den Berghe, Prosanta Chakrabarty, Michael Tobler, and Wilfredo Matamoros

  • I conducted my dissertation research in the Jerry Johnson Lab at Brigham Young University, where I took research in the lab in new directions focused on using comparative phylogeography and coalescent-based species delimitation to understand evolutionary diversification of Central American freshwater fishes. I have described my dissertation research on my Phylogeography page, and I list other information about activities and publications resulting from this work on my CV and Publications pages (see drop-down menus, top of page).

  • Bagley_PhD_diss_BYUScholArchive_screenshotPlease feel free to download a copy of my dissertation from the BYU Scholars Archive ETD service website (click here or on the screenshot of the Scholars Archive page at right). Below, I provide the Abstract of my dissertation for your pursuing, which can help direct your reading to topics of interest.

Dissertation Abstract: 

Phylogeography and molecular phylogenetics have proven remarkably useful for understanding the patterns and processes influencing historical diversification of biotic lineages at and below the species level, as well as delimiting morphologically cryptic species. In this dissertation, I used an integrative approach coupling comparative phylogeography and coalescent-based species delimitation to improve our understanding of the biogeography and species limits of Central American freshwater fishes. In Chapter 1, I conducted a literature review of the contributions of phylogeography to understanding the origins and maintenance of lower Central American biodiversity, in light of the geological and ecological setting. I highlighted emerging phylogeographic patterns, along with the need for improving regional historical biogeographical inference and conservation efforts through statistical and comparative phylogeographic studies. In Chapter 2, I compared mitochondrial phylogeographic patterns among three species of livebearing fishes (Poeciliidae) codistributed in the lower Nicaraguan depression and proximate uplands. I found evidence for mixed spatial and temporal divergences, indicating phylogeographic “pseudocongruence” suggesting that multiple evolutionary responses to historical processes have shaped population structuring of regional freshwater biota, possibly linked to recent community assembly and/or the effects of ecological differences among species on their responses to late Cenozoic environmental events. In Chapter 3, I used coalescent-based species tree and species delimitation analyses of a multilocus dataset to delimit species and infer their evolutionary relationships in the Poecilia sphenops species complex (Poeciliidae), a widespread but morphologically conserved group of fishes. Results indicated that diversity is underestimated and overestimated in different clades by c. ±15% (including candidate species); that lineages diversified since the Miocene; and that some evidence exists for a more probable role of hybridization, rather than incomplete lineage sorting, in shaping observed gene tree discordances. Last, in Chapter 4, I used a comparative phylogeographical analysis of eight codistributed species/genera of freshwater fishes to test for shared evolutionary responses predicted by four drainage-based hypotheses of Neotropical fish diversification. Integrating phylogeographic analyses with paleodistribution modeling revealed incongruent genetic structuring among lineages despite overlapping ancestral Pleistocene distributions, suggesting multiple routes to community assembly. Hypotheses tests using the latest approximate Bayesian computation model averaging methods also supported one pulse of diversification in two lineages diverged in the San Carlos River, but multiple divergences of three lineages across the Sixaola River basin, Costa Rica, correlated to Neogene sea level events and continental shelf width. Results supported complex biogeographical patterns illustrating how species responses to historical drainage-controlling processes have influenced Neotropical fish diversification.


Paleoclimatic modeling and phylogeography of least killifish, Heterandria formosa, from the Gulf-Atlantic Coastal Plain

Collaborators: Mike Sandel, Joe Travis, Jerry Johnson, and Lourdes Lozano-Vilano

  • 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


Congeneric Phylogeography and Novel Biodiversity within Black Basses (Centrarchidae: Micropterus)

Collaborators: Richard Mayden and Phillip Harris

  • Bagley JC, Mayden RL, Roe KJ, Holznagel W, Harris PM (2011). Congeneric phylogeography reveals polyphyly and novel biodiversity within black basses (Centrarchidae: Micropterus). Biological Journal of the Linnean Society, 104, 346-363. doi: 10.1111/j.1095-8312.2011.01720.x.

  • Published work on this research topic came out of my Master’s project conducted in Phil Harris’s lab at the University of Alabama, which is also discussed on my Phylogeography page.