I am an evolutionary biologist focused on problems in molecular ecology and biodiversity science. My research program primarily focuses on the use of genome-wide SNP and targeted sequence capture data to infer the evolutionary relationships of species and populations, and to understand how historical/ecological processes have shaped the distributions of biodiversity in space and time. My focus on biodiversity leads inevitably to the main target areas for biodiversity worldwide–the Neotropical biodiversity ‘hotspots’ (e.g. defined here), which harbor the majority of Earth’s plant and animal species. My current research topics are diverse, reflecting my diverse interests and skillset, and include projects focused on:

    1. Phylogenomics of rapid angiosperm radiations with Andean-centered distributions, and that of their bat pollinators (Tropical Andes hotspot)
    2. Phylogeography of temperate and Neotropical plants (e.g. forest trees) and freshwater fishes (Brazilian Cerrado and Mesoamerica hotspots), and
    3. Understanding the interplay of speciation, adaptation, and gene flow (hybridization) in outcrossing forest trees that form hybrid zones (North America, South America, China).

Each area of my research program has benefitted from rapid advances in high-throughput sequencing (HTS) methods and bioinformatics tools over the last few years. Bioinformatically, this work is computationally intensive (multiple programming languages and simulation frameworks, plus genetic and ecological niche modeling approaches) and requires handling genome-scale data from species with genomes of widely variable size and complexity (∼1 to >10 gigabases), as well as dealing with polyploidy issues in plants.

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phylogenomics & species delimitation

Burmeistera phylogenomics tanglegram Burmeistera phylogenetic informativeness

My 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 focus on

    –Phylogenomics of recent, rapid angiosperm radiations with Andean-centered distributions, using Burmeistera (Campanulaceae) as a case study
    –Integrative taxonomy and species delimitation in Cerrado lizards.


phylogeography of freshwater & terrestrial ecosystems

Aspen GBS phylogeography

Phylogeography, the study of the geographical distributions of genetic lineages within and among closely related species, has assumed a central role in molecular ecology for inferring the historical and ecological processes influencing present-day biodiversity patterns. Along with collaborators from the U.S., Brazil, and Mexico, I have been involved in a number of projects using single-species and comparative (multispecies) phylogeography approaches to improve our understanding of the diversification, stability, and assembly of North American and Neotropical biotic communities. This work currently focuses on three intriguing systems that present different contexts for understanding evolutionary processes: 1) North American forest trees, and freshwater fish assemblages of the 2) Mesoamerica (Central America) and 3) Brazilian Cerrado biodiversity 'hotspots'.

Here is a more in-depth look at my prior research in phylogeography.


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

ddRADseq population structure example (Menon et al. 2018) genomic cline example (Menon et al. 2018)

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. I have become interested in the ways in which plant versus animal systems can reveal different aspects of the speciation process.

Our current 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 I have 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. I am eager to develop future projects expanding my speciation and adaptation work along these two avenues of research.


code & bioinformatics pipelines

Check my GitHub and software pages to see what I've been coding lately. However, the main software package that I am currently developing is PIrANHA v0.3a2, a useful repository of pipelines and wrapper functions for automating tasks in phylogenetics and phylogeography.


What follows is a slightly dated summary of projects I am involved in, as recently as 2017–2018, which I hope to find time to update soon.

Current Projects Summary from Justin C. Bagley


PhD dissertation research

[coming soon.]