Bridgett M. vonHoldt

Contact
vonholdt@princeton.eduResearch Area
Genetics & GenomicsResearch Focus
Genomics of hybrid zones and ecological epigeneticsEcological Epigenomics
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)
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Changes in the rearing environment cause reorganization of molecular networks associated with DNA methylation. J Anim Ecol. 2023 ;92(3):648-664. .
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Coyotes in New York City Carry Variable Genomic Dog Ancestry and Influence Their Interactions with Humans. Genes (Basel). 2022 ;13(9). .
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Disease outbreaks select for mate choice and coat color in wolves. Science. 2022 ;378(6617):300-303. .
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Genetic diversity and family groups detected in a coyote population with red wolf ancestry on Galveston Island, Texas. BMC Ecol Evol. 2022 ;22(1):134. .
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Persistence and expansion of cryptic endangered red wolf genomic ancestry along the American Gulf coast. Mol Ecol. 2022 ;31(21):5440-5454. .
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The effects of age, sex, weight, and breed on canid methylomes. Epigenetics. 2022 ;17(11):1497-1512. .
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Reviving ghost alleles: Genetically admixed coyotes along the American Gulf Coast are critical for saving the endangered red wolf. Sci Adv. 2022 ;8(26):eabn7731. .
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Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids. Curr Biol. 2022 ;32(4):889-897.e9. .
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Cooperative Communication with Humans Evolved to Emerge Early in Domestic Dogs. Curr Biol. 2021 ;31(14):3137-3144.e11. .
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Social environment and genetics underlie body site-specific microbiomes of Yellowstone National Park gray wolves (). Ecol Evol. 2021 ;11(14):9472-9488. .
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Sarcoptic mange severity is associated with reduced genomic variation and evidence of selection in Yellowstone National Park wolves (). Evol Appl. 2021 ;14(2):429-445. .
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Rapid Macrosatellite Evolution Promotes X-Linked Hybrid Male Sterility in a Feline Interspecies Cross. Mol Biol Evol. 2021 ;38(12):5588-5609. .
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A sliver of the past: The decimation of the genetic diversity of the Mexican wolf. Mol Ecol. 2021 ;30(23):6340-6354. .
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Updating the Bibliography of Interbreeding among Canis in North America. J Hered. 2020 ;111(3):249-262. .
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A Genome-Wide Perspective on the Persistence of Red Wolf Ancestry in Southeastern Canids. J Hered. 2020 ;111(3):277-286. .
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Heritability of interpack aggression in a wild pedigreed population of North American grey wolves. Mol Ecol. 2020 ;29(10):1764-1775. .
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Global evaluation of taxonomic relationships and admixture within the Culex pipiens complex of mosquitoes. Parasit Vectors. 2020 ;13(1):8. .
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Of microbes and mange: consistent changes in the skin microbiome of three canid species infected with Sarcoptes scabiei mites. Parasit Vectors. 2019 ;12(1):488. .
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Highly heritable and functionally relevant breed differences in dog behaviour. Proc Biol Sci. 2019 ;286(1912):20190716. .
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Homozygosity for Mobile Element Insertions Associated with Could Predict Success in Assistance Dog Training Programs. Genes (Basel). 2019 ;10(6). .
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Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health. Natl Sci Rev. 2019 ;6(4):810-824. .
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Dog10K: the International Consortium of Canine Genome Sequencing. Natl Sci Rev. 2019 ;6(4):611-613. .
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Urban colonization through multiple genetic lenses: The city-fox phenomenon revisited. Ecol Evol. 2019 ;9(4):2046-2060. .
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Natural re-colonization and admixture of wolves (Canis lupus) in the US Pacific Northwest: challenges for the protection and management of rare and endangered taxa. Heredity (Edinb). 2019 ;122(2):133-149. .
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Growth factor gene IGF1 is associated with bill size in the black-bellied seedcracker Pyrenestes ostrinus. Nat Commun. 2018 ;9(1):4855. .
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Activity of Genes with Functions in Human Williams-Beuren Syndrome Is Impacted by Mobile Element Insertions in the Gray Wolf Genome. Genome Biol Evol. 2018 ;10(6):1546-1553. .
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Rediscovery of Red Wolf Ghost Alleles in a Canid Population Along the American Gulf Coast. Genes (Basel). 2018 ;9(12). .
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High genomic diversity and candidate genes under selection associated with range expansion in eastern coyote () populations. Ecol Evol. 2018 ;8(24):12641-12655. .
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Toward an integrative molecular approach to wildlife disease. Conserv Biol. 2018 ;32(4):798-807. .
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Response to Hohenlohe . Sci Adv. 2017 ;3(6):e1701233. .
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A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging. PLoS Comput Biol. 2016 ;12(11):e1005183. .
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Genomic Flatlining in the Endangered Island Fox. Curr Biol. 2016 ;26(9):1183-9. .
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Admixture mapping identifies introgressed genomic regions in North American canids. Mol Ecol. 2016 ;25(11):2443-53. .
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Genetic subdivision and candidate genes under selection in North American grey wolves. Mol Ecol. 2016 ;25(1):380-402. .
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Pervasive Effects of Aging on Gene Expression in Wild Wolves. Mol Biol Evol. 2016 ;33(8):1967-78. .
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Epigenetics in ecology and evolution: what we know and what we need to know. Mol Ecol. 2016 ;25(8):1631-8. .
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The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves. Mol Ecol. 2016 ;25(8):1838-55. .
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Mexican Wolves Are a Valid Subspecies and an Appropriate Conservation Target. J Hered. 2015 ;106(4):415-6. .
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Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica). Mol Biol Evol. 2012 ;29(10):3193-203. .
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A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. Genome Res. 2011 ;21(8):1294-305. .