Bridgett M. vonHoldt
Wild species can exhibit numerous phenotypes, some of which have been locally adapted, often classified as ecotypes or perhaps subspecies supported by genetic evidence. Any species with a large geographic distribution, often spanning a variety of ecologies (e.g. arid, boreal forest, arctic) can be the focus of exploring how habitat gradients and genetics are correlated, often under the hypothesis focused on genes that are locally adapted. Across said gradients, populations can be highly differentiated with fine-scale genetic structuring and phenotype variation. Analysis of the methylome can provide a unique opportunity to address ecological/evolutionary questions regarding adaptation and response to selection: What degree of natural epigenetic variation exists? Do patterns of methylation segregate with locally adapted populations or overlap with known locally adapted loci? Do transposition-methylation dynamics correlate with fine-scale population structure? How do phenotypes and methylation patterns segregate? Further, I can survey variation in the regulatory genome in relation to specific phenotypes (e.g. body size, skeletal proportions, coat color), social rank (e.g. stress, aggression), demography (e.g. inbreeding), or evolutionary history (e.g. domesticated species, highly inbred or genetically isoalted). (Collaborators: Drs. Daniel Stahler and Douglas Smith of the Yellowstone Wolf Recovery Project; Drs. Robert Wayne, Matteo Pellegrini, and Thomas Smith at UCLA; Dr. Marco Musiani at University of Calgary)
Introgression analysis and admixture mapping
Closely-related species that readily hybridize are often the center of controversy over taxonomic status and priority for conservation management. Ancestry of potentially mixing populations is difficult to resolve when the parental species are closely related. Using a genome-wide approach across a geographic sampling of putatively admixed populations, resolving the ancestry assignment of genomic segments will assist in mapping out not only geographic hybrid zones (e.g. Great Lakes region for wolves and coyotes) but also estimate the timings of the initial admixture event.(Collaborators: Dr. Robert Wayne at UCLA, Dr. Roland Kays at the North Carolina Museum of Natural Sciences)
A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging. PLoS Comput Biol. 2016 ;12(11):e1005183. .
Genetic subdivision and candidate genes under selection in North American grey wolves. Mol Ecol. 2016 ;25(1):380-402. .
Epigenetics in ecology and evolution: what we know and what we need to know. Mol Ecol. 2016 ;25(8):1631-8. .
Mexican Wolves Are a Valid Subspecies and an Appropriate Conservation Target. J Hered. 2015 ;106(4):415-6. .
Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica). Mol Biol Evol. 2012 ;29(10):3193-203. .
A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. Genome Res. 2011 ;21(8):1294-305. .