CJ Battey

CJ Battey







I'm a PhD Candidate in the Klicka Lab at the University of Washington Department of Biology and the Burke Museum of Natural History. I study how species' population sizes and ranges respond to large-scale changes in their environment, and how genetic variation is partitioned across landscapes. Some of my recent work uses genome sequence data to describe cryptic species of migratory birds and to map the wintering ranges of declining North American songbirds.

My current focus is on using comparative genomic data to understand how hummingbirds colonized temperate North America. At a contemporary level, I'm working with colleagues to assess how genetic variation changes when human land-use shifts cause species to colonize novel habitats; focusing on the recent range expansions of the Rufous and Anna's Hummingbirds as a case study. At deeper timescales, we're using genome-sequence data to compare the timing and extent of shifts in population size over the last c. 200,000 years across 30 species of hummingbird occupying distinct biogeographic regions.

I also work on open-source software for dealing with genetic and geographic data analysis in R, TA a bunch of different undergraduate classes, and spend too much time trying to take good pictures of animals. Click around up top to read more about my research or see some pictures of my past fieldwork.


A Migratory Divide in the Painted Bunting (Passerina ciris)

*Our new paper using genetics to map migration in a songbird was just published in The American Naturalist (pdf here).

In the Painted Bunting (Passerina ciris), a North American songbird, populations on the Atlantic coast and interior southern United States are known to be allopatric during the breeding season, but efforts to map connectivity with wintering ranges have been largely inconclusive. Using genomic and morphological data from museum specimens and banded birds, we found evidence of three genetically differentiated Painted Bunting populations with distinct wintering ranges and molt-migration phenologies. In addition to confirming that the Atlantic coast population remains allopatric throughout the annual cycle, we identified an unexpected migratory divide within the interior breeding range. Populations breeding in Louisiana winter on the Yucatán Peninsula, and are parapatric with other interior populations that winter in mainland Mexico and Central America. Across the interior breeding range, genetic ancestry is also associated with variation in wing length, suggesting that selection may be promoting morphological divergence in populations with different migration strategies.

Our manuscript was recently accepted at The American Naturalist and is currently being prepped for publication, but you can read the pre-print version here.

Population Genomics of Hummingbird Range Shifts: Diversity and Gene Flow at an Expanding Range Edge

In 1924 the famous California naturalist and biogeographer Joseph Grinnell described the Anna's Hummingbird (Calypte anna) as a bird of the Baja Peninsula and southern chaparral, breeding as far north as San Francisco with a few individuals dispersing up to near the Oregon border by the end of summer. Today Anna's Hummingbirds are a common urban bird in Seattle and Vancouver (BC), with regular post-breeding dispersal as far as southern Alaska. Last Spring UW's ornithology class found a female incubating chicks next to Lake Union in early March, and as I write this in mid-January I can see two male Anna's Hummingbirds fighting over the feeder in my neighbor's yard. The species has gone from vanishingly rare to ubiquitous in developed areas around Puget Sound in just 50 years, with most of the increase in the last two decades.

Over the same period Seattle's other common hummingbird (the Rufous Hummingbird, Selasphorus rufus, has also experienced a major range shift. Historically wintering in central Mexico, the species now occurs regularly throughout the winter on the US Gulf Coast - a shift of roughly a thousand miles. These range shifts probably have a number of causes - invasive and ornamental plantings, climate change, and hummingbird feeders, to name a few - but the process is likely to become increasingly common among many species in the coming century. The range shifts seen in the Anna's and Rufous Hummingbirds are some of the most dramatic observed in any species, and are relatively well-documented in survey records. This abundance of data allows us to study the population-level dynamics of a colonization and expansion process that many species are likely to undergo in the coming years.

In order to better understand the dynamics and impacts of range shifts on genetic diversity in bird populations, I am collecting tissue samples of Anna's and Rufous Hummingbirds from both core and novel ranges and applying a statistical modeling technique called approximate Bayesian computation (ABC) to compare different demographic models for how species colonize new areas. Do long-distance dispersal events and subsequent founder effects restrict the diversity of novel habitats? Or does gene flow with historic range cores cause edge populations to reflect the standing diversity of the whole range? How do heritable migratory orientations impact range expansions? Where did these range-shifted populations come from in the first place? My study should help us to better understand some of the basic natural history of these species, and can help us develop models for how we expect populations to behave as human impacts on the earth's landscape and climate increase over the next century.

This project recently received NSF funding for expanded sampling of the Anna's Hummingbird, and I expect to have preliminary data in a few months. Stay tuned!

The Genetics of Timing and Orientation in Migratory Hummingbird

The Rufous Hummingbird (Selasphorus rufus) makes the longest migratory journey of any hummingbird, with some individuals flying a circuit of over 7,000 miles between central Mexico and southern Alaska. The species is near-ubiquitous in riparian forests across the Northwest during breeding season, but during their southward fall migration they are concentrated in the two western mountain ranges that provide the most abundant wildflower blooms for quick refueling: the Sierra Nevada and the Rockies. We know from previous (excellent) work by Dr. Lynn Carpenter that Rufous Hummingbirds roughly double their body weight during migratory stopovers in the Sierra Nevada - implying that they lose half their body weight during the first half of their migration. With that kind of physiologic stress, these birds probably have very little wiggle room in finding a good spot to refuel on their way south. So, if you're a fledgeling hummingbird born in Alaska about to head south on a 3500 mile solo journey (both parents leave the nest site before chicks start migration), how do you know where to go?

In some species of songbird, captive breeding experiments have shown that migratory orientation is heritable, and it seems to be passed on in a bizarrely straightforward way. If you breed a Eurasian Black-cap that migrates southeast with one that migrates southwest, their offspring will try to migrate straight south (Helbig 1991). Splits in migratory orientation like this have been found to be associated with population divergence and putative sympatric speciation in some species (e.g. Eurasian Black-cap Sylvia atricapilla, Swainson's Thrush Catharus ustulatus), but no one knows whether the same pattern occurs in hummingbirds, and our understanding of the particular mechanisms of heritable migratory preference is still in its infancy. My project aims to test for genetic divergence in Rufous Hummingbirds migrating along different routes, to associate migratory routes with breeding areas, and to use sequencing data from across the breeding range to describe the biogeography and demographic history of the species.

Right now I'm preparing DNA sequencing libraries from hummingbird tissues from natural history museums around the country, and working on optimizing DNA extractions from feathers to expand sampling in regions where populations are declining. This winter I'll be generating and analyzing sequence data to try to map migratory connectivity in the species (which breeding ranges uses which routes) and testing for significant divergences in genes associated with migratory orientation and timing in other groups of birds. In the meantime I've been working up a few different ways of using citizen-science data to visualize the cool looped migratory routes of the species (see the gif in the top right and maps below - both depict annual changes in report frequency for S. rufus in eBird data).

*data via eBird: eBird Basic Dataset. Version: EBD_relFeb-2014. Cornell Lab of Ornithology, Ithaca, New York. February 2014.

Range Expansion and Reticulate Evolution in the Great-Tailed/Boat-Tailed Grackle

The great-tailed (Quiscalus mexicanus) and boat-tailed (Quiscalus major) grackles are large noisy blackbirds native to Mexico/Central America and the northern Gulf Coast/Florida, respectively. If you've ever been in a K-Mart parking lot in Houston and felt weirdly nervous about the swarms of croaking glossy birds that look a little like small crows - those were grackles. Great-tails are common anywhere humans live in their range. Boat-tails tend to be restricted to the general vicinity of coastal marshes. They look the same, except that boat-tails have yellow eyes and great-tails have dark eyes (weirdly, the difference in eye color is only consistent in the areas where the two species coexist).

Over the course of the last century both species have expanded their ranges northwards into the United States, and great-tailed grackles are now among the most common birds in developed areas from Texas to southern California. I'm looking at the genetics of these closely related species (actually "this", but we'll get there) as they expand northwards because the recent range expansions are a rare opportunity to observe secondary contact between long-isolated lineages - one of the key stages in the process of speciation.

DNA sequenced from grackle feathers suggests that the great-tailed and boat-tailed grackles form a paraphyletic species complex rather than two good species - that is, that some great-tailed grackles are actually more closely related to the boat-tailed grackle than to other great-tails. Specifically a molecular phylogeny built with the Bayesian MCMC program BEAST analyzing sequences from the ND2 mitochondrial gene of grackles from across their range shows that the population of great-tailed grackles native to western Mexico (from Sinaloa north) diverged from the clade including both all other great-tailed grackles and the boat-tailed grackles about 900,000 years ago. Here's a simplified phylogenetic tree:

Each circle is a bird we sequenced, color-coded by clade (lineage, basically). Over in the southwestern US up into Nevada and parts of southern California you can see where the two clades are mixing, and apparently interbreeding freely. The weird thing is that boat-tailed grackles and great-tailed grackles almost never interbreed (almost). So we have an old divergence resulting in what appears to be little ecological differentiation and no apparent reproductive isolation between the two great-tailed clades; and a relatively recent divergence leading to lots of reproductive isolation and both ecological and morphological divergence between the eastern great-tails and the boat-tailed grackle. Pretty weird.

There are a lot of questions to explore in the system, and I'm working in a few directions. First, I'm using niche modeling to examine the relative amounts of ecological divergence between lineages. Second, I'm conducting some classic population-genetics and newer ancenstral-area-reconstruction analyses to take a more detailed look at the historical exchange of genes among grackles in Mexico, which is where most of the action seems to be in the deep divergences of the group. Last, I'm hoping to get a study together to see if the two clades of great-tailed grackles with a new zone of secondary contact in the western US are actually interbreeding freely. More to come.


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.


structurePlotter: a GUI for plotting the results of genotype clustering algorithms (STRUCTURE, fastSTRUCTURE, admixture, TESS, etc).


R scripts for dealing with RADseq data analysis, mapping occurrence data, climatic niche modeling, etc. are up on my


Download PDF



C. J. Battey, 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.

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.

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.


Linck, Ethan B. & Battey, C. J. Minor Allele Frequency Thresholds Strongly Affect Population Structure Inference with Genomic Datasets. 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., 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 Review. 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., 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