Research

My research focuses on using and developing genetics-driven approaches (among others) and computational tools to understand the processes shaping the diversity, distributions, and adaptive evolution of species through space and time. I am also interested in applying the inferences and tools of evolutionary genetics to the conservation of threatened and endangered species. Under these general themes, my research focuses on advancing our understanding of the ecology and evolution of natural populations of animals and plants in four key areas, which naturally overlap:

1. Evolutionary Genetics2. Systematics3. Evolutionary Ecology4. Conservation Genomics

1. Evolutionary Genetics

My research advances our knowledge of evolutionary genetics through studies of phylogeography, phylogenetic analysis (including phylogenetic comparative biology), and the process of speciation (e.g. speciation with gene flow). Phylogeography studies test historical biogeographical hypotheses of vicariance, dispersal, and community assembly. Comparative projects synthesize data from multiple co-distributed species and integrate various fields, including computational biology, population genomics, ecology, geology, and species distribution modeling. Phylogenetic studies illuminate the evolutionary history of species and their trait variation.

Related publications

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 (in review) The role of hybridization during ecological divergence of southwestern white pine, Pinus strobiformis, and limber pine, P. flexilis. Molecular Ecology.

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.

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

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. Early View online. doi: 10.1111/bij.12845; Dryad data doi: http://dx.doi.org/10.5061/dryad.r1d8q.

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

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

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.

2. Systematics

My systematics and taxonomy studies discover and determine evolutionary relationships among species, and then seek to describe new biodiversity. This research focuses on diversification and systematics of freshwater fishes and lizards in biodiversity hotspots of a) the Central and South American Neotropics and b) North America.

Related publications

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.

Bagley JC, Harris PM, Mayden, RL (in review) Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils. Molecular Phylogenetics and Evolution.

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. Early View online. doi: 10.1111/bij.12845; Dryad data doi: http://dx.doi.org/10.5061/dryad.r1d8q.

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

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.

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.

3. Evolutionary Ecology

I am generating genome-wide datasets for investigating the patterns and responses of species to abiotic environmental gradients. Here, I am particularly interested in patterns of tree adaptation to elevational gradients, in the face of ongoing/future climate change. I am also interested in effects of natural selection on life history strategies in livebearing fishes.

Related publications & presentations

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 (in review) The role of hybridization during ecological divergence of southwestern white pine, Pinus strobiformis, and limber pine, P. flexilis. Molecular Ecology.

Bagley JC, Menon M, Friedline C, Whipple A, Schoettle A, Sáenz AL, Wehenkel CA, McGarvey D, Flores-Renteria LH, Sneizko R, Cushman S, Waring K, Eckert AJ (2017) Population genomics and paleoclimatic modeling support speciation with gene flow, not genomic islands of differentiation, in sky-island populations of southwestern white pine. Evolution Meeting 2017, Portland, OR, June 23–27. (International Meeting; Poster Presentation)

Menon M, Bagley JC, Friedline C, Whipple A, Schoettle A, Sáenz AL, Wehenkel CA, McGarvey D, Flores-Renteria LH, Sneizko R, Cushman S, Waring K, Eckert AJ (2017) What’s in a name? Ecological speciation in southwestern white pine. Evolution Meeting 2017, Portland, OR, June 23–27. (International Meeting; Oral Presentation)

4. Conservation Genomics

I am interested in using high-throughput sequencing to address basic and applied questions of relevance to plant and animal conservation. This work focuses on measuring the genetic diversity of wild populations and predicting potential effects of habitat fragmentation, climate change, and other threats to species persistence. I am also interested in conducting molecular and experimental studies of genetic rescue, including the genomic consequences of gene flow into inbred populations. Last, I am interested in the negative and positive effects of hybridization in managed populations.

Related projects

Bagley JC, Aquino PPU, Breitman MF, Langeani F, Colli GR, Hrbek T (on-going) Conservation Genomics of the Highly Endemic and Threatened Annual Killifish, Pirá-Brasília (Simpsonichthys boitonei), from Central Brazil.