CJ Battey

CJ Battey








Visualizing Population Structure with Variational Autoencoders
C. J. Battey, Gabrielle C. Coffing, and Andrew D. Kern. 2021.
G3. https://doi.org/10.1093/g3journal/jkaa036.

Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii
Chris S Clarkson, Alistair Miles, Nicholas J Harding, Eric R Lucas, C J Battey, Jorge Edouardo Amaya-Romero, Jorge Cano, Abdoulaye Diabate, Edi Constant, Davis C Nwakanma, Musa Jawara, John Essandoh, Joao Dinis, Gilbert Le Goff, Vincent Robert, Arlete D Troco, Carlo Costantini, Kyanne R Rohatgi, Nohal Elissa, Boubacar Coulibaly, Janet Midega, Charles Mbogo, Henry D Mawejje, Jim Stalker, Kirk A Rockett, Eleanor Drury, Daniel Mead, Anna E Jeffreys, Christina Hubbart, Kate Rowlands, Alison T Isaacs, Dushyanth Jyothi, Cinzia Malangone, Maryam Kamali, Christa Henrichs, Victoria Simpson, Diego Ayala, Nora J Besansky, Austin Burt, Beniamino Caputo, Alessandra della Torre, Michael Fontaine, H. Charles J Godfray, Matthew W Hahn, Andrew D Kern, Mara K N Lawniczak, Samantha O'Loughlin, Joao Pinto, Michelle M Riehle, Igor Sharakhov, Daniel R Schrider, Kenneth D Vernick, Bradley J White, Martin J Donnelly, Dominic P Kwiatkowski. 2019.
Genome Res. Published in Advance September 28, 2020.
We present a new data resource of 1,142 full genomes from the Anopheles gambiae/coluzzii species complex. I contributed the isolation by distance analysis shown in Figure 4.

Predicting Geographic Location from Genetic Variation with Deep Neural Networks.
C. J. Battey,Peter Ralph, and Andrew Kern. 2019. In Press, eLife. https://elifesciences.org/articles/54507
We describe a deep learning method for estimating sample locations from genotypes, and demonstrate its use in Anopheles mosquitoes, Plasmodium parasites, and humans.

Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data
C. J. Battey, Peter L. Ralph, Andrew D. Kern. 2020. GENETICS May 1, 2020 vol. 215 no. 1 193-214; https://doi.org/10.1534/genetics.120.303143
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.

Evidence of linked selection on the Z chromosome of hybridizing hummingbirds
C. J. Battey (2020) Evolution. doi:10.1111/evo.13888

unformatted ms
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.

Ecological Release of the Anna's Hummingbird during a Northern Range Expansion
Battey, C. J.. 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.

Minor allele frequency thresholds strongly affect population structure inference with genomic datasets
Ethan Linck and C. J. Battey (2019). 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.

A Migratory Divide in the Painted Bunting (Passerina ciris)
C. J. Battey, Ethan B. Linck, Kevin L. Epperly, Cooper French, David L. Slager, Paul W. Sykes, and John Klicka. 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.

Cryptic Speciation and Gene Flow in a Migratory Songbird Species Complex: Insights from the Red-Eyed Vireo (Vireo olivaceus)
C. J. Battey & John Klicka. 2017. 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.

A multilocus phylogeny of a major New World avian radiation: The Vireonidae
Slager, D. L., Battey, C. J., Robert W. Bryson Jr., Gary Voelker, John Klicka. 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.


On the relative ease of speciation with periodic gene flow
Ethan Linck & C. J. Battey. 2019. 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.

Why Montane Anolis Lizards are Moving Downhill While Puerto Rico Warms
Battey , C. J., Luisa M. Otero, George C. Gorman, Paul E. Hertz, Bradford C. Lister, Andres Garcia, Patricia A. Burrowes, and Raymond B. Huey. 2019. 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



Locator (supervised machine learning of sample locations from unphased genotypes)

Popvae (a variational autoencoder for visualizing population structure from genotypes)

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.


LDsim: simulate and plot visualizations of pairs of alleles in a small population. Designed for teaching intro lessons about linkage and linkage disequilibrium.


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.




Academic C. V.




CJ Battey
Computational Biologist
Myriad Genetics
San Francisco, California