Biology subjects

vonHoldt, B. M.

Publications and source records attributed to vonHoldt, B. M..

7 recordsLinked to original sources

bioRxiv2024

Introgression across narrow contact zones shapes the genomic landscape of phylogenetic variation in an African bird clade

Genomic analyses of hybrid zones provide excellent opportunities to investigate the consequences of introgression in nature. In combination with phylogenomics analyses, hybrid zone studies may illuminate the role of ancient and contemporary gene flow in shaping variation of phylogenetic signals across the genome, but this avenue has not been explored yet. We combined phylogenomic and geographic cline analyses in a Pogoniulus tinkerbird clade to determine whether contemporary introgression through hybrid zones contributes to gene-tree heterogeneity across the species ranges. We found diverse phylogenetic signals across the genome with the most common topologies supporting monophyly among taxa connected by secondary contact zones. Remarkably, these systematic conflicts were also recovered when selecting only individuals from each taxons core range. Using analyses of derived allele sharing and "recombination aware" phylogenomics, we found that introgression shapes gene-tree heterogeneity, and the species tree most likely supports monophyletic red-fronted tinkerbirds, as recovered in previous reconstructions based on mitochondrial DNA. Furthermore, by fitting geographic clines across two secondary contact zones, we found that introgression rates were lower in genomic regions supporting the putative species tree compared to those supporting the two taxa in contact as monophyletic. This demonstrates that introgression through narrow contact zones shapes gene-tree heterogeneity even in allopatric populations. Finally, we did not find evidence that mitochondria-interacting nuclear genes acted as barrier loci. Our results show that species can withstand important amounts of introgression while maintaining their phenotypic integrity and ecological separation, raising questions regarding the genomic architecture of adaptation and barriers to gene flow.

evolutionary biology↗

bioRxiv2022

Coyotes in New York city carry variable dog genomic ancestry and influence their interactions with humans

Coyotes are ubiquitous on the North American landscape as a result of their recent expansion across the continent. They have been documented in the heart of some of the most urbanized cities, such as Chicago, Los Angeles, and New York City. Here, we explored the genomic composition of coyotes in the New York metropolitan area to investigate if genomic demography and admixture differs from expected for urban-dwelling canids. We identified moderate-to-high estimates of relatedness among coyotes living in Queens and adjacent neighborhoods, suggestive of a relatively small population. Although we found low background levels of domestic dog ancestry across most coyotes in our sample, we identified a male suspected to be a first-generation coyote-dog hybrid, as well as his two putative backcrossed offspring that carried approximately 25% dog ancestry. The male coyote-dog hybrid and one backcrossed offspring each carried two mutations that are known to increase human-directed hypersociability in dogs and gray wolves. An additional, unrelated coyote with little dog ancestry also carries two of these mutations. These genetic patterns suggest that gene flow from domestic dogs may become an increasingly important consideration as coyotes continue to inhabit metropolitan regions.

evolutionary biology↗

bioRxiv2021

Persistence and expansion of cryptic endangered red wolf genomic ancestry along the American Gulf coast

Admixture and introgression play a critical role in adaptation and genetic rescue that has only recently gained a deeper appreciation. Here, we explored the geographic and genomic landscape of cryptic ancestry of the endangered red wolf that persists within the genome of a ubiquitous sister taxon, the coyote, all the while the red wolf has been extinct in the wild since the early 1980s. We assessed admixture across 102,621 SNP loci genotyped in 293 canid genomes. We found support for increased red wolf ancestry along an east-to-west gradient across the southern United States that was associated with historical admixture in the past 100 years. Southwestern Louisiana and southeastern Texas, the geographic zone where the last red wolves were known prior to their extinction in the wild, contained the highest and oldest levels of red wolf ancestry. X-linked regions of low recombination rates were depleted of introgression, relative to the autosomes, suggestive of the large X effect and enrichment with loci involved in maintaining reproductive isolation. Recombination rate was positively correlated with red wolf ancestry across coyote genomes, consistent with theoretical predictions. The geographic and genomic extent of cryptic red wolf ancestry can provide novel and variable genomic resources for the survival of the endangered red wolf.

evolutionary biology↗

bioRxiv2020

Experimental assessment of K locus effects on the gray wolf response to virus

In North American gray wolves, black coat color is dominantly inherited via a three base pair coding deletion in the canine beta defensin 3 (CBD103) gene. This three base pair deletion, called the KB allele, was introduced through hybridization with dogs and subsequently underwent a selective sweep that increased its frequency in wild wolves. Despite apparent positive selection, KBB wolves have significantly lower fitness than wolves with the KyB genotype, even though the two genotypes show no observable differences in black coat color. Thus, the KB allele is thought to have pleiotropic effects on as-yet unknown phenotypes. Given the role of skin-expressed CBD103 in innate immunity, we hypothesized that the KB allele influences the gene regulatory response to viral infection. To test this hypothesis, we developed a panel of primary epidermal keratinocyte cell cultures from 24 wild North American gray wolves (both Kyy and KyB genotypes) and generated immortalized Kyy and CBD103 knockout lines. We assessed the transcriptome-wide responses of wolf keratinocytes to polyinosinic:polycytidylic acid (polyI:C), which mimics infection by a double-stranded RNA virus, and to live canine distemper virus. Keratinocytes with the KyB genotype and with the Kyy genotype had similar gene regulatory responses to viral infection, suggesting that this response does not explain pleiotropic effects of the KB allele on fitness. This study supports the feasibility of using cell culture methods to investigate the phenotypic effects of naturally occurring genetic variation in wild mammals.

evolutionary biology↗

bioRxiv2019

Of Microbes and Mange: Consistent changes in the skin microbiome of three canid species infected with sarcoptic mange

Sarcoptic mange is a highly contagious skin disease caused by the ectoparasitic mite, Sarcoptes scabiei. Although it afflicts over 100 mammal species worldwide, sarcoptic mange remains a disease obscured by variability at the individual, population, and species levels. Amid this variability, it is critical to identify consistent drivers of morbidity, particularly at the skin barrier. We characterized the skin microbiome of three species of North American canids: coyotes (Canis latrans), red foxes (Vulpes vulpes), and gray foxes (Urocyon cinereoargenteus). Comparing mange-infected and uninfected individuals, we found remarkably consistent signatures of microbial dysbiosis associated with mange infection. Across genera, mange-infected canids exhibited reduced microbial diversity, altered community composition, and increased abundance of opportunistic pathogens. The primary bacteria comprising these secondary infections were Staphylococcus pseudintermedius, previously associated with canid ear and skin infections, and Corynebacterium spp, previously found among the gut flora of S. scabiei mites and hematophagous arthropods. Considered together, this evidence suggests that mange infection consistently alters the canid skin microbiome and facilitates secondary bacterial infection. These results provide valuable insights into the pathogenesis of mange at the skin barrier of North American canids and can inspire novel treatment strategies. By further adopting a \"One Health\" framework that considers mites, microbes, and the potential for interspecies transmission, we can better elucidate the patterns and processes underlying this ubiquitous and enigmatic disease.

genetics↗

bioRxiv2019

Microbial dysbiosis and its implications for disease in a genetically depauperate species

THE host-associated microbiome is increasingly recognized as a critical player in health and immunity. When commensal microbial communities are disrupted, dysbiosis can contribute to disease pathogenesis and severity. Santa Catalina Island foxes (Urocyon littoralis catalinae) present an ideal case study for examining dysbiosis in wildlife due to their depauperate genomic structure and extremely high prevalence of ear canal tumors. Although the precise cause is yet unknown, infection with ear mites (Otodectes cynotis) has been linked to chronic inflammation, which is associated with abnormal cell growth and tumor development. Given the paucity of genomic variation in these foxes, other dimensions of molecular diversity, such as commensal microbes, may be critical to host response and adaptation. We therefore characterized the host-associated microbiome across six body sites of Santa Catalina Island foxes, and performed differential abundance testing between healthy and mite-infected ear canals. We found that mite infection was significantly associated with reduced microbial diversity and evenness, with the opportunistic pathogen Staphylococcus pseudintermedius dominating the ear canal community. These results suggest that secondary bacterial infection may contribute to the sustained inflammation associated with tumor development. Uncovering high abundance of S. pseudintermedius provides critical insight into the pathogenesis of this complex system, as the emergence of antibiotic resistant strains remains a concern of the medical, veterinary, and conservation communities. Through use of culture-independent sequencing techniques, this study contributes to the broader effort of applying a more inclusive understanding of molecular diversity to questions within wildlife disease ecology.

genetics↗

bioRxiv2018

Rediscovery of red wolf ghost alleles in a canid population along the American Gulf Coast

Rediscovering species once thought to be extinct or on the edge of extinction is rare. Red wolves have been extinct along the Gulf Coast region since 1980, with their last populations found in coastal Louisiana and Texas. We report the rediscovery of red wolf ghost alleles in a canid population on Galveston Island, Texas. We analyzed over 7,000 SNPs in 60 canid representatives from all legally recognized North American Canis species and two phenotypically ambiguous canids from Galveston Island. We found notably high Bayesian cluster assignments of the Galveston canids to captive red wolves with extensive sharing of red wolf private alleles. Today, the only known extant wild red wolves persist in a reintroduced population in North Carolina, which is dwindling amongst political and taxonomic controversy. Our rediscovery of red wolf ancestry after almost 40 years introduces both positive opportunities for additional conservation action and difficult policy challenges.

genomics↗