CJ Battey

CJ Battey







I'm an evolutionary biologist who studies how species' genomes are shaped by patterns of individual movement like dispersal and seasonal migration. Some of my recent work uses genome sequence data to identify cryptic species of migratory birds, link breeding and wintering ranges of declining North American songbirds, and document recent range shifts in Anna's Hummingbirds.

I'm currently a postdoctoral research associate in the Kern Lab at the University of Oregon Institute for Ecology and Evolution, where I'm working on applying machine learning methods to estimate life history parameters like dispersal distance and population density from genetic data. I did my PhD in the Klicka Lab at the University of Washington Department of Biology and the Burke Museum of Natural History, where my dissertation was focused on the impacts of seasonal migration on genetic diversity in birds.

Scroll down for more info on my research, links to code, and pictures of animals.


Population Genetics

Most of my work involves implementing and developing population genetic models to estimate how long ago populations split from each other, how often they exchange migrants, or how big their past populations were. I'm particularly interested in how geography and dispersal interact to shape genetic variation and the capacity for local adaptation (see more in the migration section), and in understanding the limits of information available in DNA sequence data. In practice this involves a mix of sample collection in the field, labwork to prepare DNA for sequencing, and a lot of bioinformatic analysis (mostly R, some python, bash as needed). I spend most of my time attempting to think through how the assumptions of theoretical models interact with the reality of empirical data collection to shape reasonable interpretations of model inferences.

Recently I've been working with my labmate Ethan Linck on an analysis of how minor-allele frequency filters (a common way of cleaning sequence data) can alter inferences from genetic clusering algorithms (preprint here). We have a few other ideas for incorporating uncertainty in visualization techniques in the works too (hopefully up this summer). I also developed a set of interactive simulation apps for undergraduate classes that allow students to build intution for how selection, migration, and drift interact to cause differences in allele frequencies among populations (drift simulator, selective sweep simulator).

Seasonal Migration

Around 30% of bird species migrate seasonally between different habitats, and similar migratory behaviors are found in (among others) butterflies, insects, fish, mammals, snakes, flatworms, fruit flies, and people. My dissertation research is focused on understanding how this process impacts speciation and the capacity for local adaptation in birds. Historically most migratory species were thought to be genetically homogenous, because spatial mixing of genotypes between years should spread genetic variation widely across the range. My research on vireos (pdf), buntings (pdf), and hummingbirds (working on it) has found that a strong correlation between geographic and genetic distance (i.e. "isolation by distance") is instead found even in small bodied species that migrate without family groups, suggesting effective gene flow across the range is relatively low despite the species' large annual movements. Introgression among strongly divergent lineages is frequently observed at range boundaries, but at least in the species I have studied rarely spreads to the center of the range. This combination of IBD and persistent hybrid clines suggests that selection plays an important role in maintaining population differentiation in migratory birds.

How does the interaction of gene flow, drift, and selection shape variation across the genome of migratory species? How much information about past demographics or selective regimes can be reliably inferred from genomic data? I'm currently working on a set of simulation studies and a whole-genome sequence analysis in order to address these questions in the Rufous/Allen's Hummingbird Species Complex.

Range Shifts

"All species ranges are the result of successful past range expansions" - Keitt et al. 2001, Am Nat.

I'm interested in how species ranges change over time, and how human modification of the landscape has shaped their evolution over the last hundred years. Recently I've analyzed two cases (both currently in review): a drop in elevation ranges in Puerto Rican Anolis lizards likely caused by forest regrowth on former agricultural lands during industrialization, and the dramatic northern range expansion of the Anna's Hummingbird caused by introduced plants and hummingbird feeders.


For recent updates see my github

Popgen Shiny Apps:

driftR: an interactive population genetic simulation website that allows students to explore the impacts of genetic drift, selection, migration, mutation, and population sizes on a variety of summary statistics.


adaptR: simulate selective sweeps and other processes with varying selection over time.


structurePlotter: plot output of genotype clustering algorithms with fancy color selection and a permutation algorithm to deal with label switching.



Download PDF



Linck, E. and Battey, C. (2019), Minor allele frequency thresholds strongly affect population structure inference with genomic datasets. Mol Ecol Resour. Accepted Author Manuscript. doi:10.1111/1755-0998.12995. preprint: bioRxiv 188623; doi: https://doi.org/10.1101/188623
We show that genotype clustering alogirthms like STRUCTURE fail when singletons are included in the analysis, and predictably lose power to discriminate populations when the minimum minor allele count is greater than 2.

Battey, C. J., Ethan B. Linck, Kevin L. Epperly, Cooper French, David L. Slager, Paul W. Sykes, and John Klicka, "A Migratory Divide in the Painted Bunting (Passerina ciris)," The American Naturalist 191, no. 2 (February 2018): 259-268. https://doi.org/10.1086/695439 Appendix_1
We use a combination of genotype clustering, demographic modeling, and wing-length measurements to show that adjacent breeding populations consistently migrate to different wintering grounds in a North American songbird with declining populations.

Battey, C. J. & Klicka, J. 2017. Cryptic Speciation and Gene Flow in a Migratory Songbird Species Complex: Insights from the Red-Eyed Vireo (Vireo olivaceus). Molecular Phylogenetics and Evolution, Available online 12 May 2017, ISSN 1055-7903 https://doi.org/10.1016/j.ympev.2017.05.006
Phylogenetic analyses of nuclear SNP's and mtDNA show that the Red-eyed Vireo (V. olivaceus) as currently recognized includes two species-level lineages that migrate in different directions across the equator.

Slager, D. L., Battey, C. J., Robert W. Bryson Jr., Gary Voelker, John Klicka. A multilocus phylogeny of a major New World avian radiation: The Vireonidae. Molecular Phylogenetics and Evolution, Volume 80, November 2014, Pages 95-104, ISSN 1055-7903 http://dx.doi.org/10.1016/j.ympev.2014.07.021
A nearly complete species-level phylogeny of the Vireonidae based on ND2 and Z-linked DNA finds extensive evidence of cryptic diversity in the tropics and a few striking cases of morphological conservation.


Battey, C. J. Time Lags and Niche Shifts in a Biological Invasion of Hummingbirds. (In Review) bioRXiv, May 29 2018. https://doi.org/10.1101/329615
I document a century of range shifts in the Anna's Hummingbird and show that recent exponential growth in the Pacific Northwest is the product of a series of range and climatic niche expansions that started in the early 20th century using a combination of demographic and niche modeling.

Battey, C. J., Luisa M. Otero, George C. Gorman, Paul E. Hertz, Bradford C. Lister, Andres Garcia, Patricia A. Burrowes, and Raymond B. Huey. Why montane Puerto Rican lizards are moving downhill while the climate warms. In Revision. Appendix_1
Puerto Rico is warming up, leading to predictions that montane lizards will be forced to move uphill. We analyzed 50 years of specimen records to show that montane lizards instead moved downhill since the 1970's, likely due to extensive regeneration of low-altitude forests following an economic shift from agriculture to industry.


Battey, C. J., Linck EB, Epperly KL, French C, Slager DL, Sykes PW, Klicka J. Data from: A migratory divide in the Painted Bunting (Passerina ciris). September 5, 2017. https://doi.org/10.5061/dryad.cp40s

Battey, C. J., Klicka J. Data from: Cryptic speciation and gene flow in a migratory songbird species complex: insights from the red-eyed vireo (Vireo olivaceus). May 15, 2017. https://doi.org/10.5061/dryad.9b6p8


Battey, C. J. "Migration Increases Niche Breadth in North American Hummingbirds." Electronic Journal of Applied Multivariate Statistics 8 (2015): 1-10.
I show that migratory hummingbirds are not tracking a single climatic niche through the year by comparing observed climate variability with hypothetical "resident" strategies of species staying on the breeding or wintering grounds.

Battey, C. J., T. Ross. Impacts of Habitat Restoration and Status of Avian Communities in Seattle City Parks. May 2015. Seattle Audubon Society: http://www.seattleaudubon.org/sas/About/Science/CitizenScience/NeighborhoodBirdProj ect.aspx


A random subset of recent pictures. Find more on my tumblr



CJ Battey
PhD Candidate, Klicka Lab
University of Washington Dept. of Biology
548 Kincaid Hall, Box 351800
Seattle, WA 98195-1800