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

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Science Advances  27 Jul 2016:
Vol. 2, no. 7, e1501714
DOI: 10.1126/sciadv.1501714

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  • RE: A response to Kays
    • Bridgett vonHoldt, Assistant Professor, Princeton University
    • Other Contributors:
      • James Cahill, Graduate student, UC Santa Cruz
      • Ilan Gronau, Professor, Efi Arazi School of Computer Science, Herzliya Interdisciplinary Center
      • Annabel Beichman, Graduate student, UC Los Angeles
      • Kirk E Lohmueller, Assistant Professor, UC Los Angeles
      • John P Pollinger, Staff scientist, UC Los Angeles
      • Jeff Wall, Assistant Professor, UC San Francisco
      • Beth Shapiro, Professor, UC Santa Cruz
      • Robert Wayne, Professor, UC Los Angeles

    Dr. Kays invokes a mitochondrial DNA (mtDNA) capture hypothesis to explain potential discordances between mtDNA haplotype and complete genome sequence data. However, the presence of a divergent mtDNA haplotype is not evidence enough to support the mtDNA capture hypothesis or the existence of a separate species. Caution is warranted when interpreting results from mtDNA sequences as they derive from a single non-recombining locus that only represents matrilineal dynamics and may be affected by natural selection (e.g. 1). It is well known that gene genealogies are highly variable due to the randomness inherent in the coalescent process (e.g. 2-4). In other words, a single demographic model can and will generate very different genealogies. Divergence and recent branches within a genealogy are not surprising and are even expected. Further, this dichotomy becomes more pronounced with large ancestral population sizes (N), as the variance in the time to the most recent common ancestor is of the order N2 (3-5).

    Gray wolves and coyotes are known to have had a large ancestral population size (e.g. effective size 30,000-45,000 for wolves, 6). Therefore, coalescent processes can generate divergent lineages as well as clusters of closely related mtDNA haplotypes. A divergent lineage, if examined in isolation, could be misinterpreted as support for a distinct species if mtDNA sampling was geographically restricted. The divergent and controversial “Algonquin” or eastern wolf (Canis...

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    Competing Interests: None declared.
  • A hypothesis for the disagreement between nuclear and mitochondrial DNA of North American Canis
    • Roland Kays, Scientist, North Carolina Museum of Natural Sciences and North Carolina State University

    The whole-genome analysis of VonHoldt et al. (1) provides the most complete picture to date of North American Canis autosomes, finding no history for long independent, species level evolutionary histories for the red wolf (Canis rufus) or eastern wolf (C. lycaon), suggesting instead that both have a modern origin through hybridization between wolves (C. lupus) and coyotes (C. latrans). This compelling nuclear DNA evidence leaves one mystery yet unsolved - why do many eastern canids have a unique mitochondrial haplotype that does not match extant coyotes or wolves?
    This 'lycaon-type' haplotype was the most compelling evidence used to argue that eastern wolves should be recognized as a unique species (2) because it is similar to coyotes, yet different enough (3%) to suggest ~500K years of divergence between the two. Thus, the eastern wolf was proposed as a sister species to the coyote, evolving into a larger, deer-eating predator in eastern forests. Samples from historic and fossil eastern wolves have likewise returned mtDNA haplotypes similar to this lycaon-type (3) or to coyotes (4, 5), further supporting the coyote sister species hypothesis. Red wolves also have coyote-like mtDNA (6). Thus while the nuclear genome results of VonHoldt et al. (1) support a two species model for North American Canids (C. lupus & latrans), the mtDNA patterns support a three or four species model (adding C. lycaon and/or rufus).

    I suggest that the discordance be...

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    Competing Interests: None declared.