vonHoldt Lab

Evolutionary Genomics and Ecological Epigenomics

Peer-reviewed Publications

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

E Heppenheimer, KE Brzeski, JW Hinton, MJ Chamberlain, RK Wayne, J Robinson, BM vonHoldt (accepted) A genome-wide perspective on the persistence of red wolf ancestry in southeastern canids. Journal of Heredity

BM vonHoldt, ML Aardema (2020) Updating the bibliography of interbreeding among Canis in North America. Journal of Heredity DOI: 10.1093/jhered/esaa004

BM vonHoldt, AL DeCandia, E Heppenheimer, I Janowitz-Koch, KE Brzeski, KA Cassidy, DR Stahler, JS Sinsheimer (2020) Heritability of inter-pack aggression in a wild pedigreed population of North American grey wolves. Molecular Ecology DOI: 10.1111/mec.15349 [abstract]

ML Aardema, BM vonHoldt, ML Fritz, SR Davis (2020) Global evaluation of taxonomic relationships and admixture within the Culex pipiens complex of mosquitoes. Parasites & Vectors 13(8) [abstract]

AL DeCandia, JL King, BM vonHoldt (2019) Ear mite infection is associated with altered microbial communities in genetically depauperate Santa Catalina Island foxes (Urocyon littoralis catalinae). Molecular Ecology DOI: 10.1111/mec.15325 [abstract]

AL DeCandia, KN Leverett*, BM vonHoldt (2019) Of microbes and mange: consistent changes in the skin microbiome of three canid species infected with Sarcoptes scabies mites. Parasites & Vectors 12, 488 [abstract]

EL MacLean, N Synder-Mackler, BM vonHoldt, JA Serpell (2019) Highly heritable and functionally relevant breed differences in dog behaviour. Proceedings of the Royal Society B Biological Sciences 286(1912) [abstract]

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]