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Background: Phylogenetic studies of wild Canis species have relied heavily on the mitochondrial DNA control region (mtDNA CR) to infer species relationships and evolutionary lineages. Previous analyses of the CR provided evidence for a North American evolved eastern wolf (C. lycaon), that is more closely related to red wolves (C. rufus) and coyotes (C. latrans) than grey wolves (C. lupus). Eastern wolf origins, however, continue to be questioned. Therefore, we analyzed mtDNA from 89 wolves and coyotes across North America and Eurasia at 347 base pairs (bp) of the CR and 1067 bp that included the ATPase6 and ATPase8 genes. Phylogenies and divergence estimates were used to clarify the evolutionary history of eastern wolves, and regional comparisons of nonsynonomous to synonomous substitutions (dN/dS) at the ATPase6 and ATPase8 genes were used to elucidate the potential role of selection in shaping mtDNA geographic distribution. Results: We found high concordance across analyses between the mtDNA regions studied. Both had a high percentage of variable sites (CR = 14.6%; ATP = 9.7%) and both phylogenies clustered eastern wolf haplotypes monophyletically within a North American evolved lineage apart from coyotes. Divergence estimates suggest the putative red wolf sequence is more closely related to coyotes (DxyCR = 0.01982 ± 0.00494 SD; DxyATP = 0.00332 ± 0.00097 SD) than the eastern wolf sequences (DxyCR = 0.03047 ± 0.00664 SD; DxyATP = 0.00931 ± 0.00205 SD). Neutrality tests on both genes were indicative of the population expansion of coyotes across eastern North America, and dN/dS ratios suggest a possible role for purifying selection in the evolution of North American lineages. dN/dS ratios were higher in European evolved lineages from northern climates compared to North American evolved lineages from temperate regions, but these differences were not statistically significant. Conclusions: These results demonstrate high concordance between coding and non-coding regions of mtDNA, and provide further evidence that the eastern wolf possessed distinct mtDNA lineages prior to recent coyote introgression. Purifying selection may have influenced North American evolved Canis lineages, but detection of adaptive selection in response to climate is limited by the power of current statistical tests. Increased sampling and development of alternative analytical tools will be necessary to disentangle demographic history from processes of natural selection. [ABSTRACT FROM AUTHOR]

This study examined the genetic nature and relatedness of Canis latrans (Coyotes) in eastern Massachusetts (i.e., eastern Coyotes). We characterized 67 animals at the mitochondrial DNA control region, and 55 of those at 8 microsatellite loci. Structure analysis and factorial correspondence analysis of the microsatellite genotypes indicated that the eastern Coyotes in Massachusetts clustered with other northeastern Canis populations and away from western Coyotes, C. lycaon (Eastern Wolves), and C. lupus (Gray Wolves). They contained mitochondrial haplotypes from both western Coyotes and Eastern Wolves, consistent with their hybrid origin from these two species. There was no evidence of either C. lupus familiaris (Domestic Dog) or Gray Wolf mitochondrial DNA in the animals. These results indicate that the eastern Coyote should more appropriately be termed "Coywolf" to reflect their hybrid (C. latrans x lycaon) origin. Genetic data were also used to assess parental and kinship relationships, and confirmed that family units typically contain an unrelated breeding pair and their offspring. Lastly, a synthesis of knowledge of the eastern Coyote as well as implications for Wolf recovery in the northeast US is provided. [ABSTRACT FROM AUTHOR]