CJ Battey

CJ Battey







I'm a postdoc in the Kern Lab at the University of Oregon Institute of Ecology and Evolution, where I'm developing simulation and inference tools to help us describe and control for spatial structure in population 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 publication PDFs, links to code, and pictures of animals.



C. J. Battey, "Ecological Release of the Anna's Hummingbird during a Northern Range Expansion," The American Naturalist 194, no. 3 (September 2019): 306-315.
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 In Revision
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.

Ethan Linck & C. J. Battey On the relative ease of speciation with periodic gene flow. bioRxiv 758664; doi: https://doi.org/10.1101/758664
We show that speciation is much faster under periodic than constant gene flow, and that these processes can be distinguished (usually) from the site frequency spectrum.

C. J. Battey Evidence of Linked Selection on the Z Chromosome of Hybridizing Hummingbirds. In Revision.
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 Anolis Lizards are Moving Downhill While Puerto Rico Warms. bioRxiv 751941; doi: https://doi.org/10.1101/751941
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



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.



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