Using multiple markers to elucidate the ancient, historical and modern relationships among North American Arctic dog breeds.

Throughout most of the Americas, post-colonial dogs largely erased the genetic signatures of pre-historical dogs. However, the North American Arctic harbors dogs that are potentially descended from pre-historical ancestors, as well as those affected by post-colonial translocations and admixtures. In particular, Inuit dogs from Canada and Greenland are thought to descend from dogs associated with Thule peoples, who relied on them for transportation ca. 1000 years ago. Whether Thule dogs reflected an earlier colonization by Paleoeskimo dogs ca. 4500 years ago is unknown. During the Alaskan Gold Rush, additional sled dogs, possibly of post-colonial derivation, the Alaskan Husky, Malamute and Siberian Husky, were used in the Arctic. The genealogical relationships among and origins of these breeds are unknown. Here we use autosomal, paternal and maternal DNA markers to (1) test the hypothesis that Inuit dogs have retained their indigenous ancestry, (2) characterize their relationship to one another and to other Arctic breeds, and (3) estimate the age of North American indigenous matrilines and patrilines. On the basis of the agreement of all three markers we determined that Inuit dogs have maintained their indigenous nature, and that they likely derive from Thule dogs. In addition, we provide support for previous research that the Inuit dogs from Canada and Greenland dog should not be distinguished as two breeds. The Alaskan Husky displayed evidence of European introgression, in contrast to the Malamute and Siberian Husky, which appear to have maintained most of their ancient Siberian ancestry.

Next-generation sequencing workflow for assembly of nonmodel mitogenomes exemplified with North Pacific albatrosses (Phoebastria spp.).

Use of complete mitochondrial genomes (mitogenomes) can greatly increase the resolution achievable in phylogeographic and historical demographic studies. Using next-generation sequencing methods, it is now feasible to efficiently sequence mitogenomes of large numbers of individuals once a reference mitogenome is available. However, assembling the initial mitogenomes of nonmodel organisms can present challenges, for example, in birds, where mtDNA is often subject to gene rearrangements and duplications. We developed a workflow based on Illumina paired-end, whole-genome shotgun sequencing, which we used to generate complete 19-kilobase mitogenomes for each of three species of North Pacific albatross, a group of birds known to carry a tandem duplication. Although this duplication had been described previously, our procedure did not depend on this prior knowledge, nor did it require a closely related reference mitogenome (e.g. a mammalian mitogenome was sufficient). We employed an iterative process including de novo assembly, reference-guided assembly and gap closing, which enabled us to detect duplications, determine gene order and identify sequence for primer positioning to resolve any mitogenome ambiguity (via minimal targeted Sanger sequencing). We present full mtDNA annotations, including 22 tRNAs, 2 rRNAs, 13 protein-coding genes, a control region and a duplicated feature for all three species. Pairwise comparisons supported previous hypotheses regarding the phylogenetic relationships within this group and occurrence of a shared tandem duplication. The resulting mitogenome sequences will enable rapid, high-throughput NGS mitogenome sequencing of North Pacific albatrosses via direct reference-guided assembly. Moreover, our approach to assembling mitogenomes should be applicable to any taxon.

Genetic characterization of healthy and sebaceous adenitis affected Standard Poodles from the United States and the United Kingdom.

The degree of heterogeneity associated with geographic origin and sebaceous adenitis (SA) status in Standard Poodles from the United States (US) and the United Kingdom (UK) was assessed. Healthy and SA-affected Standard Poodles from the US and the UK shared a major mitochondrial DNA (mtDNA) haplotype and a single Y chromosome haplotype. However, minor mtDNA haplotypes and frequencies were somewhat different between US and UK dogs and were significantly less associated with SA than major haplotypes across both populations. The US and UK populations exhibited recent divergence from a common gene pool, based on allele frequencies of 24 highly polymorphic short tandem repeats and principle coordinates and cluster analyses of genotype frequencies. However, there was no differentiation between SA affected and unaffected dogs. Over 90% of US and UK Poodles shared a common dog leukocyte antigen (DLA) class II haplotype, but showed some differentiation in minor haplotype frequency. No difference was observed in haplotype heterozygosity between SA affected and unaffected dogs from the same country and no disease association for SA was found within the DLA region by a high density single nucleotide polymorphism (SNP) scan. Zygosity mapping in the DLA region of Poodles indicated much lower site-specific diversity than in an outbred population of street dogs from Bali, Indonesia, reflecting the degree that breed associated historical bottlenecks have reduced diversity in a polymorphic region of the genome. This study shows possible pitfalls in more extensive genome-wide association studies, such as case and control numbers, population stratification, the involvement of multiple genes, and/or the possibility that SA susceptibility is fixed or nearly fixed within the breed, which can reduce power to detect genetic associations.

Environmental factors associated with Bartonella vinsonii subsp. berkhoffii seropositivity in free-ranging coyotes from northern California.

Bartonella vinsonii subsp. berkhoffii is a newly recognized pathogen of domestic dogs and humans. Coyotes (Canis latrans) are considered an important reservoir of this bacterium in the western United States, but its vectors are still unknown. Our objective was to identify environmental factors associated with Bartonella antibody prevalence in 239 coyotes from northern California, using an enzyme-linked immunosorbent assay. In addition, associations were evaluated between B. v. berkhoffii and two pathogens with known vectors and habitat requirements, Dirofilaria immitis and Anaplasma phagocytophilum. Overall, B. v. berkhoffii seroprevalence was 28% (95% confidence interval [CI], 22.3%, 33.7%) and Bartonella seropositive coyotes were more likely than seronegative coyotes to be positive for Anaplasma phagocytophilum (Odds ratio = 3.3; 95% CI = 1.8, 5.9) and Dirofilaria immitis (Odds ratio = 2.1; 95% CI = 1.2, 3.8). The most likely geographic clusters of Bartonella and Dirofilaria overlapped. Bartonella seropositivity was associated with higher precipitation (p = 0.003) and proximity to the coast (p = 0.007) in univariate analysis. The association with precipitation varied with season, based on a logistic regression model.

Spatial analysis of Yersinia pestis and Bartonella vinsonii subsp. berkhoffii seroprevalence in California coyotes (Canis latrans).

Zoonotic transmission of sylvatic plague caused by Yersinia pestis occurs in California, USA. Human infections with various Bartonella species have been reported recently. Coyotes (Canis latrans) are ubiquitous throughout California and can become infected with both bacterial agents, making the species useful for surveillance purposes. This study examined the geographic distribution of 863 coyotes tested for Y. pestis and Bartonella vinsonii subsp. berkhoffii serologic status to gain insight into the natural history of B. vinsonii subsp. berkhoffii and to characterize the spatial distribution of the two agents. We found 11.7% of specimens positive to Y. pestis and 35.5% positive to B. vinsonii subsp. berkhoffii. The two pathogens had distinct spatial clusters: Y. pestis was more prevalent in eastern portions of the state and B. vinsonii subsp. berkhoffii in coastal regions. Prevalence of Y. pestis increased with increasing elevation, whereas prevalence of B. vinsonii subsp. berkhoffii decreased with increasing elevation. There were differences in the proportions of positive animals on a yearly basis to both pathogens.

Validation for use with coyotes (Canis latrans) of a commercially available enzyme-linked immunosorbent assay for Dirofilaria immitis.

Serological tests offer a potentially powerful tool for monitoring parasites in wildlife populations. However, such tests must be validated before using them with target wildlife populations. We evaluated in coyotes (Canis latrans) the performance of a commercially available serological test used to detect canine heartworm (Dirofilaria immitis) in domestic dogs. We obtained 265 coyote carcasses and serological specimens from 54 additional coyotes from several regions of California, USA. We necropsied coyotes to determine the adult heartworm infection status. Blood was collected at necropsy on filter paper strips and allowed to dry; it was later eluted in a buffer solution, and the supernatant was tested for heartworm. Receiver operating characteristic (ROC) analysis was used to assess discriminatory power of the test and indicated a 93% probability that a randomly selected infected coyote would exhibit a higher enzyme-linked immunosorbent assay (ELISA) value than a randomly selected uninfected coyote. We estimated specificity at 96% (95% CI: 92-98%) for 165 uninfected coyotes and sensitivity at 85% (77-91%) for 100 infected coyotes, results similar to published values for the commercial serological test used with dog serum or plasma. Test performance was similar for filter paper specimens and supernatant of frozen whole blood collected in EDTA tubes (i.e. hemolyzed plasma). We found no difference in test performance among geographic or demographic coyote groups. Our findings support application of the test to filter paper or standard serological specimens for detection of heartworm in coyote populations.

Increasing prevalence of canine heartworm in coyotes from California.

Thirty-seven subadult and adult coyotes (Canis latrans), collected August 1992 through December 1996 from a coastal foothill area in northern California (USA), were examined for adult heartworm (Dirofilaria immitis). During 1992 through 1993, at the end of a 6 yr drought, none of four coyotes examined were infected with heartworms. However, during 1994 through 1996, after the drought had ended, prevalences were 91% in 23 adult coyotes and 40% in 10 subadult coyotes. Heartworm intensity did not differ by sex of coyote, and averaged (+/- SE) 19.4 +/- 3.8 among adults; one subadult had > 238 heartworms. The prevalence and intensity of heartworm infection in coyotes reported here for 1994 through 1996 are the highest reported anywhere in the United States.