Gray Wolves

Whole-genome sequence analysis shows that two endemic species of North American wolf 

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Gray Wolves

he U.S. Fish and Wildlife Service (USFWS) accepts the species status of both red and eastern wolves, with markedly divergent conservation implications. The red wolf is protected by the U.S. Endangered Species Act (ESA). However, the endangered eastern wolf, which was only recently recognized as a distinct species (814) and is currently restricted to a small portion of its historic range, would not be listed under the current political landscape. Instead, the acceptance of the eastern wolf species has led the USFWS to propose the delisting of the gray wolf. The reasoning for this action is that the historical range of the eastern wolf is hypothesized to include the Great Lakes region and 29 eastern states to the exclusion of the gray wolf (11, 15, 16). Because the geographic range of the gray wolf as originally listed in the 1975 ESA petition included these areas, the USFWS subsequently proposed that the entire original listing was invalid. Essentially, the presence of the eastern wolf, rather than the gray wolf, in the eastern United States would cause the original listing to be annulled. With the exception of the Mexican wolf, the gray wolf would be delisted (lose protection) from its entire North American range under the proposed USFWS rule change (17). These differing consequences of species listing, despite the possibility of similar admixed origin, provide a marked example of how taxonomy can both protect and threaten endangered species under the ESA.

Although there is extensive literature on the red wolf and eastern wolf [for example, (2, 11, 18, 19)], only recently have genome-wide data been analyzed to support an admixed or ancient origin hypothesis. A previous study genotyped and analyzed more than 42,000 single-nucleotide polymorphisms (SNPs) in a large panel of North American and Eurasian wolf-like canids that supported an admixed origin for both red and eastern wolves (5). However, a reanalysis of these data found evidence for a genetic cluster in central Ontario representing the eastern wolf and concluded that the SNP array data may suffer from ascertainment bias (20). A more recent study presented new, ascertainment-free genome-wide SNP data from the eastern wolf and showed through simulation that admixture alone cannot explain the unique positions of the eastern wolf in a principal components analysis (PCA) (21). Here, we use a genome sequencing approach to directly search for regions of unique ancestry in the genomes of red and eastern wolves that cannot be explained by admixture between coyotes and gray wolves. We present 28 sequenced genomes from a diversity of large canids representing Eurasian and North American wolf populations, including North American regions where wolf/coyote admixture is currently absent and regions with suspected admixture. An exhaustive search of wolf genomes from the Great Lakes region including Algonquin Provincial Park, where pure eastern wolves are thought to exist, and from red wolves from the captive breeding colony reveals little unique ancestry and instead demonstrates a distinct geographic pattern of admixture between gray wolves and coyotes. We argue strongly for a less typologically oriented implementation of the ESA that allows interim protection of hybrids while encouraging the restoration of historic patterns of variation through habitat protection.

RESULTS

Genome sequencing

We sequenced 28 canid genomes to varying coverage ranging from 4 to 29-fold and mapped reads to the domestic dog reference genome (Table 1). After filtering for quality and minimum coverage, we retained 5,424,934 SNPs (referred to as 5.4 million SNPs) genotyped across all sequenced genomes. From these data, we estimated that heterozygosity (π) was highest in the Indian wolf (π = 1.71/kb) and lowest in the endangered Mexican wolf (π = 0.48/kb), which is consistent with previous observations of low diversity in the inbred captive Mexican wolf colony (22). We note that the fraction of missing data is negatively correlated with π, although we could not quantify the extent of this effect given the heterogeneous nature of the samples (Table 1).

PLEASE READ THE REST OF THEIR RESULTS BELOW

Source: Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf | Science Advances

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