CJ Battey

CJ Battey







I'm an evolutionary biologist who studies how populations move across landscapes and adapt to varying environments. To do that I build computational tools and statistical pipelines that combine ecological and genetic data both from my own fieldwork and public datasets. Some of my recent work has identified cryptic species of migratory birds, mapped the migratory routes of declining North American songbirds, and documented exponential population growth in hummingbird populations.

I've also developed interactive simulation webapps to help students learn the basics of population genetics, and worked with my collaborator Ethan Linck to study how bioinformatic processing affects inference of population structure from genetic data.

I'm currently a postdoctoral researcher in the Kern Lab at the University of Oregon Institute of Ecology and Evolution, where I'm developing new simulation tools and machine learning methods to improve our ability to identify the genetic basis of trait variation in species that are structured over space, including mosquitoes and humans. 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.


Spatial Population Genetics

Standard models in population genetics are based on randomly mating populations, but real organisms mate with nearby individuals and disperse a limited distance from their parents. In the Kern Lab one of my primary goals has been to develop new simulation and inference tools that let us model genetic variation in continuous space. This is one of the oldest challenges in population genetics, which was *almost* solved by Wright and Malecot in the early twentieth century. Unfortunately their models of isolation by distance are inherently flawed because they fail to account for an important ecological process -- density-dependent population growth -- which prevents individuals from clustering (see Felsenstein's excellent 1975 Am Nat article "A Pain in the Torus: Some Difficulties with Models of Isolation By Distance" for the full details). Working with Andy Kern and Peter Ralph, we have developed new forward-time simulators that allow us to generate chromosome-scale alignments of tens of thousands of individuals evolving in continuous space, and we are using these tools to investigate how inference from genetic data is shaped by spatial processes. The figure at the top of this section shows an early result of our simulator -- mapping how dispersal distance determines the geographic spread of ancestry over time.

This research involves a lot of esoteric modeling and programming, but it has important implications for human health and society. When researchers attempt to connect genomes and traits -- for example, by trying to identify genes responsible for insecticide resistance in mosquitoes or heart disease in humans -- the standard models in use today assume that populations are exposed to similar environments. But when populations are structured over space, this is unlikely to be true. The figure below is a preview of a new study we're working on to show how current methods of correcting genome-wide association studies (GWAS) for population structure can fail when breeding structure and the environment covary over space (preprint coming soon!). We need better methods to model the interaction of geographic population structure and spatial variation in the environment if we are going to understand how genotypes connect to the complex phenotypes that matter to efforts like public health and vector control. That's why we're now developing deep learning methods to co-estimate phenotype associations and population structure, which will be my focus over the next year.

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



Battey, C.J. Ecological Release of the Anna's Hummingbird During a Northern Range Expansion. (in press.) The American Naturalist, April 2019. bioRXiv preprint: https://doi.org/10.1086/704249
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.

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 map migratory connectivity and infer phylogeographic history in a declining North American songbird.

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
We test species limits in a songbird species complexes that migrates both north and south of the equator, and show that austral migrant Red-eyed Vireos are a distinct species.

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.


C. J. Battey, Peter L. Ralph, Andrew D. Kern. Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data bioRxiv 659235; doi: https://doi.org/10.1101/659235
We describe a new continuous space population genetic simulation and use it to study the impacts of limited dispersal on summary statistics, demographic inference, and GWAS.

C. J. Battey Evidence of Linked Selection on the Z Chromosome of Hybridizing Hummingbirds. Under Review.
Whole-genome data documents hybridization in Rufous and Allen's Hummingbirds and indicates a role for linked selection in elevated differentiaton of the Z chromosome.

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 nonrandom subset of recent pictures. Find more on my tumblr



CJ Battey
Postdoctoral Researcher, Kern Lab
University of Oregon Institute of Ecology and Evolution
301 Pacific Hall
Eugene, OR 97402