Our research

We are ecologists and evolutionary biologists and our research focuses on integrating genomics, ecological/field data, and computer modeling to address problems in molecular ecology, distributional ecology, conservation, and biodiversity science. Our research answers basic and applied questions about the ecology and evolution of freshwater and terrestrial organisms and can broadly be divided into two categories: (1) Evolutionary Processes and (2) Applied Ecology. Our research on evolutionary processes focuses on biodiversity ‘hotspots’ (e.g. defined here) and takes us across the Americas, from the southeastern US to Central America and South America. Our applied research focuses on three sub-areas: (i) ecological niche modeling (ENM) of ecological requirements (niches) to predict species past, present, and future distributions, including species responses (e.g. distributional shifts) to climate change and human impacts; (ii) conservation genomics of threatened and endangered species; and (iii) biological assessment (e.g. biomonitoring) and community ecology of the diverse fish assemblages of Alabama and the southeastern US.

Current research projects in the “Bagley Lab” of ecology and evolution at JSU center on ecological niche modeling, conservation genomics, phylogeography, phylogenomics, speciation/hybridization, and local adaptation genomics of North American and Neotropical plants and freshwater fishes and are described in more detail below. While our main area of organismal expertise is ichthyology and most projects focus on fishes, projects are diverse, ranging from Andean bellflowers to central Brazilian fishes.

1. Evolutionary processes

Comparative phylogeography and phylogeographic meta-analyses

We study phylogeography (evolutionary and geographic histories of genetic lineages within and among closely related species) at the single-species and comparative levels. In this field, we are working on novel empirical studies of freshwater fish phylogeography in North America and Brazil based on high-throughput sequence data (e.g. ddRAD-seq, DArT-seq), as well as synthetic comparative reviews of published phylogeographical literature in the context of regional ecological and geological settings. We also have a new ongoing project in collaboration with Fernando Alda’s lab at the University of Tennessee-Chattanooga that is focused on combining georeferenced legacy phylogeographic data (DNA sequence data, esp. mtDNA, available from online repositories) with environmental data to conduct regional and global meta-analyses of fish phylogeography. This exciting project is made possible through our collaboration on PhylogatR, a project funded through an NSF grant to Bryan Carstens and Tara Pelletier.


Single-species phylogeography and demography

Whereas comparative phylogeography (mentioned above) can tell us about broad-scale patterns of evolution of species in a region, comparative studies rely on scaling up from many studies of individual species. These single-species phylogeography studies each tell us about the spatial-demographic histories of a different species or group (including metazoa and viruses). We have been working on phylogeography of terrestrial and aquatic ecosystems of temperate and Neotropical areas for around 15 years. While Dr. Bagley’s dissertation work focused on phylogeography and species delimitation in Central American freshwater fishes, our work looking at the histories of individual species has focused more recently on individual forest trees such as quaking aspen (Populus tremuloides) and pines (genus Pinus), and now that we are located back in Alabama our lab focus is shifting primarily to using phylogeography approaches combined with ecological niche modeling to understand evolutionary processes in species from the North American southeast (a known aquatic biodiversity ‘hotspot’). We also have quite a bit of data on the phylogeography of fishes from the Brazilian Cerrado ‘hotspot’ that we are working to publish.

Quaking aspen phylogeography and population structure (Bagley et al. 2020).

Phylogenomics & species delimitation

Lab research in systematics and taxonomy primarily focuses on discovering and determining evolutionary relationships among species, and clarifying species limits, through analyses of DNA sequence data and morphological characters. Hypotheses of phylogenetic relationships are reconstructed based on broad taxon and character sampling using maximum-likelihood and Bayesian inference analyses, relaxed molecular clocks, clock-partitioning schemes, and tip- and fossil-calibrated models (e.g. fossilized birth-death process). Our work also seeks to describe new biodiversity to improve biodiversity accounting. This work focuses on understanding diversification and the evolution of adaptive traits (e.g. reproductive mode) in monophyletic clades of temperate and Neotropical plants (bellflowers, pines), freshwater fishes, and squamate reptiles. Recent papers focused on

  • Describing two new species of suckermouth armored catfishes (Loricariidae) from central Brazil
  • Phylogenomics of recent, rapid angiosperm radiations with Andean-centered distributions, using Burmeistera (Campanulaceae) as a case study
  • Tailless leaf-nosed Anoura bats that pollinate Burmeistera bellflowers
  • Integrating molecules, morphology, and fossils to infer relationships among North American ‘sucker’ fishes (Catostomidae)

Burmeistera time tree and phylogenetic informativeness (Bagley et al. 2020).

Genomics of speciation & local adaptation, with implications for climate change

Understanding how barriers to gene flow arise, and new species boundaries are formed and maintained, is a central goal of evolutionary biology. Yet, the study of ‘speciation’, presents numerous challenges and requires integrative perspectives taking into account geographical factors (biogeography) and range dynamics, niche evolution, reproductive isolation, as well as the evolution of neutral and adaptive genetic variation in the context of demographic history. We have become interested for several years now in the ways in which plant versus animal systems can reveal different aspects of the speciation process.

Our recent and on-going projects on southwestern white pine (Pinus strobiformis) highlight the role of hybridization and extrinsic factors during ecological speciation. We are also using genome scan and environmental association analyses to understand local adaptation to climatic gradients and challenging environments (high elevation) in this system, with important implications for understanding tree responses to climate change. By contrast, some Neotropical fish lineages that Dr. Bagley has studied (e.g. livebearers; Poeciliidae) are more predisposed to speciation through intrinsic pre- or postmating isolation, and exhibit presumed niche conservatism but a high degree of phenotypic variation. We are eager to develop future projects expanding our speciation and adaptation work along these two avenues of research.

Southwestern white pine hybrid zone and genetic structure (Menon et al. 2018).

2. Applied Ecology

Organismally, Dr. Bagley is a professionally trained ichthyologist and he has been studying and publishing on freshwater fishes since 2006 (15 years of experience).

Thus, while the lab has worked on a variety of organisms and many ‘basic’-science questions (projects above), we are also fundamentally interested in conducting applied research into questions of relevance to the biological assessment (e.g. biomonitoring, fisheries research), community ecology, and conservation of the diverse fish assemblages of Alabama and the southeastern US. We are working with state agencies to develop projects in this applied arena. Currently, we are most interested in

  • Applying our expertise in phylogeography and genomics to conservation issues, e.g. see Conservation genomics project(s) below
  • Development of wadeable and non-wadeable Index of Biotic Integrity (IBI) approaches for assessing state/regional waters
  • Environmental niche modeling (ENM) to predict species past, present, and future distributions in response to climate change
  • Environmental DNA (eDNA) metabarcoding of freshwater rivers and streams of Alabama and surrounding areas (e.g. Mobile basin extensions into Mississippi and Georgia)

Conservation genomics

Our expertise in population genomics and molecular and bioinformatics approaches for analyzing next-generation sequencing data places us in an excellent position to apply these cost-effective and informative tools to applied problems in conservation and management. We are initiating a project on conservation genomics of Alabama’s threatened and endangered minnow species, which was recently approved for funding from the Alabama Division of Wildlife and Freshwater Fisheries (DWFF). This project has two parts, one for each species. The species are the Blue Shiner (Cyprinella caerulea), which is restricted to the Coosa River system of the Mobile Basin, and the Cahaba Shiner (Notropis cahabae) native to the Cahaba River basin. Blue Shiner is pictured below (Photo courtesy of Dr. Pat O’Neil, GSA).

Blue Shiner Blue Shiner

Ecological niche modeling (ENM) of species responses to climate change

We are interested in applications of niche theory to questions about the actual and potential distributions of species in the past, present, and future, through ecological niche modeling (ENM) (also see this book). The ENM approach has many applications, and those that we find most exciting include its uses for predicting species responses to global climate change (GCC) and biodiversity assessment/accounting. Currently, Dr. Bagley has an ongoing project with students in his Ecology CURE course and in the Bagley Lab to predict the responses of Alabama’s coastal dune plant species to GCC. We are reconstructing the niches and predicting present and future distributions (under climate and carbon emissions scenarios for year 2070; ~50 years from now) for 14 endemic foredune and backdune species, including charismatic species such as sea oats (Uniola paniculata) as well as taxa that are lesser-known to the general public, such as sea purslane (Sesuvium portulacastrum) and Florida rosemary (Ceratiola ericoides). We are grateful to the JSU Department of Biology and College of Science and Mathematics for funding and support of this project.

ENM results for saltmeadow cordgrass (Sporobolus pumilus).

ENM results for saltmeadow cordgrass (Sporobolus pumilus) predicting the species distribution (suitable habitat) under current (left) and future (right) conditions.