vonHoldt Lab

Evolutionary Genomics and Ecological Epigenomics

Peer-reviewed Publications

For a complete list of published work, please see my NCBI's Bibliography [link].


D Tandon, K Ressler, D Petticord, A Papa, J Jiranek, R Wilkinson, RY Kartzinel, EA Ostrander, N Burney, C Borden, MAR Udell, BM vonHoldt (2019) Homozygosity for mobile element insertions associated with WBSCR17 could predict success in assistance dog training programs. Genes 10(6), 439 [abstract]

EA Ostrander, G-D Wang, G Larson, BM vonHoldt, BW Davis, V Jagannathan, C Hitte, RK Wayne, Y-P ZHang, Dog10K Consortium (2019) Dog10K: An international sequencing effort to advance studies of canine domestication, phenotypes, and health. National Science Review DOI: https://doi.org/10.1093/nsr/nwz049 [abstract]

A DeCandia*, C Henger*, A Krause**, L Gormezano, M Weckel, C Nagy, J Munshi-South, B vonHoldt (2019) Genetics of urban colonization: Neutral and adaptive variation in coyotes (Canis latrans) inhabiting the New York metropolitan area. Journal of Urban Ecology 5(1), 1-12 (*authors contributed equally; **high school intern) [abstract]

J Hinton, E Heppenheimer, K West, D Caudill, M Karlin, J Kilgo, J Mayer, K Miller, M Walch, B vonHoldt, M Chamberlain (2019) Geographic patterns in morphometric and genetic variation for coyote populations with emphasis in the southeastern United States. Ecology and Evolution 9(6), 3389-3404 [abstract]

A DeCandia, K Brzeski, E Heppenheimer, C Caro*, G Camenisch, P Wandeler, C Driscoll, B vonHoldt (2019) Urban colonization through multiple genetic lenses: The city-fox phenomenon revisited. Ecology and Evolution 9(4), 2046-2060 [abstract]

M Cavedon, C Coubili, E Heppenheimer, B vonHoldt, S Mariani, M Hebbelwhite, T Hegel, D Hervieux, R Serrouya, R Steenweg, B Weckworth, M Musiani (20019) Genes, environment and balancing selection in behaviorally bimodal populations: the caribou case. Molecular Ecology 28, 1946-1963 [abstract]

S Hendricks, R Schweizer, R Harrigan, J Pollinger, R Brown, P Paquet, C Darimont, J Adams, L Waits, B vonHoldt, P Hohenlohe, R Wayne (2019) 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 122(2), 133-149 [abstract]

E Heppenheimer, KE Brzeski, JW Hinton, BR Patterson, LY Rutledge, JF Benson, T Wheeldon, SR Fain, PA Hohenlohe, R Kays, BN White, MJ Chamberlain, BM vonHoldt (2018) High genomic diversity and candidate genes under selection associated with range expansion in eastern coyote (Canis latrans) populations. Ecology & Evolution. 8(24), 12641-12655 [abstract]

ER Bastounes, HM Rando, JL Johnson, LN Trut, BN Sacks, CA Driscoll, B vonHoldt, AV Kukekova (2018) Four structural variants associated with human-directed sociability in dogs are not found in tame red foxes (Vulpes vulpes). Animal Genetics 50(1), 116-118 [abstract]

E Heppenheimer*, KE Brzeski*, R Wooten, W Waddell, LY Rutledge, MJ Chamberlain, DR Stahler, JW Hinton, BM vonHoldt (2018) Rediscovery of red wolf ghost alleles in a canid population along the American Gulf Coast. Genes 9(12), 618 (* authors contributed equally) [abstract]

E Heppenheimer*, RJ Harrigan*, LY Rutledge, K-P Koepfli, AL DeCandia, KE Brzeski, JF Benson, T Wheeldon, BR Patterson, R Kays, PA Hohenlohe, BM vonHoldt (2018) Population genomic analysis of North American eastern wolves (Canis lycaon) supports their conservation priority status. Genes 9(12), 606 (* authors contributed equally) [abstract]

BM vonHoldt*, RY Kartzinel*, CD Huber, VL Underwood, Y Zhen, K Ruegg, KE Lohmueller, TB Smith (2018) Growth factor gene IGF1 is associated with bill size in an African finch (Pyrenestes ostrinus). Nature Communications 9, 4855 (* authors contributed equally) [abstract]

B vonHoldt, SS Ji, ML Aardema, DR Stahler, MAR Udell, JS Sinsheimer (2018) Activity of genes with functions in human Williams-Beuren Syndrome are impacted by mobile element insertions in the gray wolf genome. Genome Biology & Evolution. 10(6), 1546-1553 [ abstract]

AL DeCandia, AP Dobson, BM vonHoldt (2018) Toward an integrative molecular approach to wildlife disease. Conservation Biology 32(4), 798-807 [abstract]

M Pilot, C Greco, BM vonHoldt, E Randi, W Jedrzejewski, VE Sidorovich, M Konopinski, EA Ostrander, RK Wayne (2018) Widespread, long-term admixture between grey wolves and domestic dogs across Eurasia and its implications for the conservation status of hybrids. Evolutionary Applications 11(5), 662-680 [abstract]

SA Hendricks, S Koblmuller, R Harrigan, J Leonard, R Schweizer, B vonHoldt, R Kays,R Wayne (2017) Defense of an Expanded Historical Range for the Mexican Wolf: A Response to Heffelfinger et al. J Wildlife Management and Wildlife Monographs 81(8), 1331-1333. [abstract]

E Heppenheimer, DS Cosio*, KE Brzeski, C Caudill, K Van Why, MJ Chamberlain, JW Hinton, B vonHoldt (2017) Demographic history influences spatial patterns of genetic diversity in recently expanded coyote (Canis latrans) populations. Heredity 120(3), 183-195 (* undergraduate coauthor) [abstract]

B vonHoldt, Z Fan, D Ortega-Del Vecchyo, RK Wayne (2016) EPAS1 variants in high altitude Tibtan wolves were selectively introgressed into highland dogs. PeerJ 5, e3522 [abstract]

B vonHoldt, J Cahill, I Gronau, B Shapiro, J Wall, RK Wayne (2017) Technical Comment: Response to Hohenlohe et al. Science Advances 3(6), e1701233. [abstract]

B vonHoldt, E Shuldiner*, I Janowitz Koch, R Kartzinel, L Brubaker, S Wanser, D Stahler, C Wynne, M Udell (2017) Structural variants underlie hyper-sociability: A novel theory of dog domestication. Science Advances 3, e1700398 (* undergraduate coauthor; contributed equally with first author) [abstract]

BM vonHoldt, KE Brzeski, DS Wilcove, LY Rutledge (2017) Redefining the role of admixture and genomics in species conservation. Conservation Letters 11(2), 1-6 [abstract]

B vonHoldt, E Heppenheimer, V Petrenko, P Croonquist, LY Rutledge (2017) Ancestry-specific methylation patterns in admixed offspring from an experimental coyote and gray wolf cross. J Heredity 108(4), 341-348 [abstract]

M Thompson, B vonHoldt, S Horvath, M Pellegrini (2017) An epigenetic aging clock for dogs and wolves. Aging 9(3), 1055-1068. [abstract]

S Snir, B vonHoldt, M Pellegrini (2016) A statistical framework to identify deviation from time linearity in epigenetic aging. PLOS Computational Biology. 12(11), e1005183 [abstract]

B vonHoldt, J Cahill, Z Fan, I Gronau, J Robinson, JP Pollinger, B Shapiro, J Wall, RK Wayne (2016) Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf. Science Advances 2, e1501714. [abstract]

R Mariano, B vonHoldt (2016) The canine X chromosome is a sink for canine endogenous retrovirus transposition and is targeted by DNA methylation. Gene Reports 4, 169-176 [abstract]

BM vonHoldt, RW Kays, JP Pollinger, RK Wayne (2016) Admixture mapping identifies introgressed genomic regions in North American canids. Mol Ecol 25(11), 2443-2453 [abstract]

P Charruau, R Johnston, DR Stahler, A Lea, N Snyder-Mackler, DW Smith, B vonHoldt, et al. (2016) Pervasive effects of aging on gene expression in wild wolves. Mol Biol Evol 33(8), 1967-1978. [abstract]

KJF Verhoeven, B vonHoldt, VL Sork (2016) Epigenetics in ecology and evolution: What we know and what we need to know. Mol Ecol 25(8), 1631-1638 (invited commentary) [abstract]

J Robinson, D Ortega Del Vecchyo, Z Fan, B vonHoldt, et al. (2016) Genomic flat-lining in the endangered island fox (Urocyon littoralis). Current Biology 26, 1-7 [abstract]

I Janowitz Koch, MM Clark, MJ Thompson, et al. (2016) The concerted impact of domestication and transposon insertions on methylation patterns between dogs and gray wolves. Mol Ecol 25(8), 1838-1855 [abstract]

RM Schweizer, BM vonHoldt, JC Knowles, et al. (2015) Genetic subdivision and candidate genes under selection in North American gray wolves. Mol Ecol 25(1), 380-402 [abstract]

RJ Fredrickson, PW Hedrick, RK Wayne, et al. (2015) Mexican wolves are a valid subspecies and an appropriate conservation target. J Heredity 106(6), 415-416 [abstract]

RHS Kraus, B vonHoldt<, B Cocchiararo, et al. (2015) A SNP-based approach for rapid and cost-effective genetic wolf monitoring in Europe based on non invasively collected samples. Mol Ecol Resources 15, 295-305 [abstract]

Y Afanador, J Velez-Valentiin, R Valentiin-de la Rosa, et al. (2014) Isolation and characterization of microsatellite loci in the critically endangered Puerto Rican parrot (Amazona vittata). Conserv Genet 6(4), 885-889 [abstract]

M Pilot, C Greco, B vonHoldt, et al. (2014) Genome-wide signatures of population bottlenecks and diversifying selection in European wolves. Heredity 112, 428-442 [abstract]

OC Bedoya-Reina, A Ratan, R Burhans et al. (2013) Galaxy tools to student genome diversity. Gigascience 2, 17 [abstract]

Y Li, B vonHoldt, A Reynolds, et al. (2013) Artificial selection on brain-expressed genes during the domestication of dog. Mol Biol Evol 30, 1867-1876 [abstract]

DM Karyadi, E Karlins, B Decker, et al. (2013) A copy number variant at the KITLG locus likely confers risk for canine squamous cell carcinoma of the digit. PLoS Genetics 9 (3), e1003409 [abstract]

B vonHoldt, J Pollinger, D Earl, et al. (2012) Identification of recent hybridization between gray wolves and domesticated dogs by SNP genotyping. Mammalian Genome 12 (1-2), 80-88 [abstract]

DR Stahler, DR MacNulty, RK Wayne, et al. (2012) The adaptive value of morphological, behavioral, and life history traits in reproductive female wolves. J Animal EcolDOI: 10.1111/j.1365-2656.2012.02039.x [ abstract]

B vonHoldt, S Takuno, B Gaut (2012) Recent LTR retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa japonica). Mol Biol Evol29(10), 3193-3203 [abstract]

RK Wayne, B vonHoldt (2012) Evolutionary genomics of dog domestication. Mamm Genome 23, 3-18 [abstract]

H Huson, B vonHoldt, M Rimbault, et al. (2012) Selection for breed-specific ancestry targets a mutation in the MYO9 gene associated to heat tolerance within performing Alaskan sled dogs. Mamm Genome 23, 178-194 [abstract]

T Coulson, DR MacNulty, DR Stahler, et al. (2011) Modeling effects of environmental change on wolf population dynamics, trait evolution and life history. Science 334, 1275-1278 [abstract]

D Earl, B vonHoldt (2011) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Con Gen Resources 4(2), 359-361 [abstract]

E Geffen, M Kam, R Hefner, et al. (2011) Kin encounter rate and inbreeding avoidance in canids. Mol Ecol 20(24), 5348-5358 [abstract]

B vonHoldt, J Pollinger, D Earl, et al. (2011) A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. Genome Res 21, 1294-1305 [abstract]

B vonHoldt, D Stahler, J Pollinger, et al. (2010) A novel assessment of population structure and gene flow in grey wolf populations of the Northern Rocky Mountains of the United States. Mol Ecol 19, 4412-4427 [abstract]

AR Boyko, P Quignon, L Li, et al. (2010) A simple genetic architecture underlies quantitative traits in dogs. PLoS Biol 8(8), e1000451 [abstract]

I Jankovic, B vonHoldt, N Rosenberg (2010) Heterozygosity of the Yellowstone wolves. Mol Ecol 19, 3246-3249 [abstract]

B vonHoldt, E Han, J Pollinger, et al. (2010) Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464, 898-903 [abstract]

E Cadieu, M Neff, P Quignon, et al. (2009) Coat Variation in Domestic Dog is Goverened by Variants in Three Genes. Science 326, 150-153 [abstract]

H Parker, B vonHoldt, P Quignon, et al. (2009) An expressed Fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs. Science 325(5943), 995-998 [abstract]

T Anderson, B vonHoldt, S Candille, et al. (2009) Molecular and evolutionary history of melanism in North American gray wolves. Science 323(5919), 1339-1343 [abstract]

B vonHoldt, D Stahler, D Smith, et al. (2008) The genealogy and genetic viability of the reintroduced Yellowstone grey wolves. Mol Ecol 17, 252-274 [abstract]

B vonHoldt, E Ostrander (2006) Preview: The singular history of a canine transmissible tumor. Cell 126, 445-447 [abstract]