Associated Faculty, Ecology and Evolutionary Biology and the Lewis-Sigler Institute for Integrative Genomics

Contact

vonholdt@princeton.edu
609-258-7021
Moffett Laboratory, 328
vonHoldt Lab

Research Area

Genetics & Genomics

Research Focus

Genomics of hybrid zones and ecological epigenetics



Research
Selected Publications

Ecological 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)




Rubbi L, Zhang H, Feng J, He C, Kurnia P, Ratan P, et al. The effects of age, sex, weight, and breed on canid methylomes. Epigenetics. 2022 ;:1-16. PubMed
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vonHoldt BM, Hinton JW, Shutt AC, Murphy SM, Karlin ML, Adams JR, et al. 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. PubMed
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Plassais J, vonHoldt BM, Parker HG, Carmagnini A, Dubos N, Papa I, et al. 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. PubMed
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DeCandia AL, Cassidy KA, Stahler DR, Stahler EA, vonHoldt BM. Social environment and genetics underlie body site-specific microbiomes of Yellowstone National Park gray wolves (). Ecol Evol. 2021 ;11(14):9472-9488. PubMed
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vonHoldt BM, Brzeski KE, Aardema ML, Schell CJ, Rutledge LY, Fain SR, et al. Persistence and expansion of cryptic endangered red wolf genomic ancestry along the American Gulf coast. Mol Ecol. 2021 ;. PubMed
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Carroll C, Rohlf DJ, vonHoldt BM, Treves A, Hendricks SA. Wolf Delisting Challenges Demonstrate Need for an Improved Framework for Conserving Intraspecific Variation under the Endangered Species Act. Bioscience. 2021 ;71(1):73-84. PubMed
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DeCandia AL, Schrom EC, Brandell EE, Stahler DR, vonHoldt BM. 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. PubMed
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Bredemeyer KR, Seabury CM, Stickney MJ, McCarrey JR, vonHoldt BM, Murphy WJ. Rapid Macrosatellite Evolution Promotes X-Linked Hybrid Male Sterility in a Feline Interspecies Cross. Mol Biol Evol. 2021 ;38(12):5588-5609. PubMed
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Taron UH, Salado I, Escobar-Rodríguez M, Westbury MV, Butschkau S, Paijmans JLA, et al.. A sliver of the past: The decimation of the genetic diversity of the Mexican wolf. Mol Ecol. 2021 ;30(23):6340-6354. PubMed
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Johnston RA, Rheinwald JG, vonHoldt BM, Stahler DR, Lowry W, Tung J, et al. K Locus Effects in Gray Wolves: Experimental Assessment of TLR3 Signaling and the Gene Expression Response to Canine Distemper Virus. J Hered. 2021 ;112(5):458-468. PubMed
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Salomons H, Smith KCM, Callahan-Beckel M, Callahan M, Levy K, Kennedy BS, et al. Cooperative Communication with Humans Evolved to Emerge Early in Domestic Dogs. Curr Biol. 2021 ;31(14):3137-3144.e11. PubMed
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Aardema ML, vonHoldt BM, Fritz ML, Davis SR. Global evaluation of taxonomic relationships and admixture within the Culex pipiens complex of mosquitoes. Parasit Vectors. 2020 ;13(1):8. PubMed
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vonHoldt BM, Aardema ML. Updating the Bibliography of Interbreeding among Canis in North America. J Hered. 2020 ;111(3):249-262. PubMed
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Heppenheimer E, Brzeski KE, Hinton JW, Chamberlain MJ, Robinson J, Wayne RK, et al. A Genome-Wide Perspective on the Persistence of Red Wolf Ancestry in Southeastern Canids. J Hered. 2020 ;111(3):277-286. PubMed
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vonHoldt BM, DeCandia AL, Heppenheimer E, Janowitz-Koch I, Shi R, Zhou H, et al. Heritability of interpack aggression in a wild pedigreed population of North American grey wolves. Mol Ecol. 2020 ;29(10):1764-1775. PubMed
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DeCandia AL, Brenner LJ, King JL, vonHoldt BM. Ear mite infection is associated with altered microbial communities in genetically depauperate Santa Catalina Island foxes (Urocyon littoralis catalinae). Mol Ecol. 2020 ;29(8):1463-1475. PubMed
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DeCandia AL, Leverett KN, vonHoldt BM. 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. PubMed
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Ostrander EA, Wang G-D, Larson G, vonHoldt BM, Davis BW, Jagannathan V, et al. Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health. Natl Sci Rev. 2019 ;6(4):810-824. PubMed
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Wang G-D, Larson G, Kidd JM, vonHoldt BM, Ostrander EA, Zhang Y-P. Dog10K: the International Consortium of Canine Genome Sequencing. Natl Sci Rev. 2019 ;6(4):611-613. PubMed
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DeCandia AL, Brzeski KE, Heppenheimer E, Caro CV, Camenisch G, Wandeler P, et al. Urban colonization through multiple genetic lenses: The city-fox phenomenon revisited. Ecol Evol. 2019 ;9(4):2046-2060. PubMed
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MacLean EL, Snyder-Mackler N, vonHoldt BM, Serpell JA. Highly heritable and functionally relevant breed differences in dog behaviour. Proc Biol Sci. 2019 ;286(1912):20190716. PubMed
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Tandon D, Ressler K, Petticord D, Papa A, Jiranek J, Wilkinson R, et al. Homozygosity for Mobile Element Insertions Associated with Could Predict Success in Assistance Dog Training Programs. Genes (Basel). 2019 ;10(6). PubMed
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Hendricks SA, Schweizer RM, Harrigan RJ, Pollinger JP, Paquet PC, Darimont CT, et al. 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. PubMed
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Pilot M, Greco C, vonHoldt BM, Randi E, J?drzejewski W, Sidorovich VE, et al.. Widespread, long-term admixture between grey wolves and domestic dogs across Eurasia and its implications for the conservation status of hybrids. Evol Appl. 2018 ;11(5):662-680. PubMed
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Heppenheimer E, Brzeski KE, Wooten R, Waddell W, Rutledge LY, Chamberlain MJ, et al. Rediscovery of Red Wolf Ghost Alleles in a Canid Population Along the American Gulf Coast. Genes (Basel). 2018 ;9(12). PubMed
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Heppenheimer E, Brzeski KE, Hinton JW, Patterson BR, Rutledge LY, DeCandia AL, et al. High genomic diversity and candidate genes under selection associated with range expansion in eastern coyote () populations. Ecol Evol. 2018 ;8(24):12641-12655. PubMed
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vonHoldt BM, Kartzinel RY, Huber CD, Le Underwood V, Zhen Y, Ruegg K, et al. Growth factor gene IGF1 is associated with bill size in the black-bellied seedcracker Pyrenestes ostrinus. Nat Commun. 2018 ;9(1):4855. PubMed
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DeCandia AL, Dobson AP, vonHoldt BM. Toward an integrative molecular approach to wildlife disease. Conserv Biol. 2018 ;32(4):798-807. PubMed
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vonHoldt BM, Ji SS, Aardema ML, Stahler DR, Udell MAR, Sinsheimer JS. 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. PubMed
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vonHoldt BM, Shuldiner E, Koch IJanowitz, Kartzinel RY, Hogan A, Brubaker L, et al. Structural variants in genes associated with human Williams-Beuren syndrome underlie stereotypical hypersociability in domestic dogs. Sci Adv. 2017 ;3(7):e1700398. PubMed
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vonHoldt BM, Cahill JA, Gronau I, Shapiro B, Wall J, Wayne RK. Response to Hohenlohe . Sci Adv. 2017 ;3(6):e1701233. PubMed
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Snir S, vonHoldt BM, Pellegrini M. A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging. PLoS Comput Biol. 2016 ;12(11):e1005183. PubMed
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vonHoldt BM, Kays R, Pollinger JP, Wayne RK. Admixture mapping identifies introgressed genomic regions in North American canids. Mol Ecol. 2016 ;25(11):2443-53. PubMed
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Koch IJanowitz, Clark MM, Thompson MJ, Deere-Machemer KA, Wang J, Duarte L, et al. The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves. Mol Ecol. 2016 ;25(8):1838-55. PubMed
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Charruau P, Johnston RA, Stahler DR, Lea A, Snyder-Mackler N, Smith DW, et al. Pervasive Effects of Aging on Gene Expression in Wild Wolves. Mol Biol Evol. 2016 ;33(8):1967-78. PubMed
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Robinson JA, Del Vecchyo DOrtega-, Fan Z, Kim BY, vonHoldt BM, Marsden CD, et al. Genomic Flatlining in the Endangered Island Fox. Curr Biol. 2016 ;26(9):1183-9. PubMed
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Verhoeven KJF, vonHoldt BM, Sork VL. Epigenetics in ecology and evolution: what we know and?what we need to know. Mol Ecol. 2016 ;25(8):1631-8. PubMed
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Schweizer RM, vonHoldt BM, Harrigan R, Knowles JC, Musiani M, Coltman D, et al. Genetic subdivision and candidate genes under selection in North American grey wolves. Mol Ecol. 2016 ;25(1):380-402. PubMed
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Fredrickson RJ, Hedrick PW, Wayne RK, vonHoldt BM, Phillips MK. Mexican Wolves Are a Valid Subspecies and an Appropriate Conservation Target. J Hered. 2015 ;106(4):415-6. PubMed
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vonHoldt BM, Takuno S, Gaut BS. Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica). Mol Biol Evol. 2012 ;29(10):3193-203. PubMed
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vonHoldt BM, Pollinger JP, Earl DA, Knowles JC, Boyko AR, Parker H, et al. A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. Genome Res. 2011 ;21(8):1294-305. PubMed
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