Editing Red wolf (section)

===== Genetic marker evidence =====
In 1980, a study used [[gel electrophoresis]] to look at fragments of DNA taken from dogs, coyotes, and wolves from the red wolf's core range. The study found that a unique [[allele]] (expression of a [[gene]]) associated with [[Lactate dehydrogenase]] could be found in red wolves, but not dogs and coyotes. The study suggests that this allele survives in the red wolf. The study did not compare gray wolves for the existence of this allele.<ref name=ferrell1980/>

[[Mitochondrial DNA]] (mDNA) passes along the maternal line and can date back thousands of years.<ref name=beeland2013/> In 1991, a study of red wolf mDNA indicates that red wolf [[genotypes]] match those known to belong to the gray wolf or the coyote. The study concluded that the red wolf is either a wolf × coyote hybrid or a species that has hybridized with the wolf and coyote across its entire range. The study proposed that the red wolf is a southeastern occurring subspecies of the gray wolf that has undergone hybridization due to an expanding coyote population; however, being unique and threatened that it should remain protected.<ref name=wayne1991/> This conclusion led to debate for the remainder of the decade.<ref name=gittleman1991/><ref name=nowak1992/><ref name=dowling1992/><ref name=roy1994/><ref name=brewster1995/><ref name=nowak1995/><ref name=nowak1995a/><ref name=roy1996/><ref name=nowak1998/><ref name=wayne1998/><ref name=reich1999/>

{{cladogram
|title=Proposed phylogenetic tree of wolf evolution
|cladogram=
  {{clade
  |label1 = Ancestral Canid{{br}}(1-2 million years ago)
  |1 =
    {{clade
    |1 =
      {{clade
      |1 = [[Coyote]]
      |2 =
        {{clade
        |1 = [[Red wolf]]
        |2 = [[Eastern wolf]]
        }}
      }}
    |label2 = [[Gray wolf]]
    |grouplabel2 = [[Subspecies of Canis lupus|Gray wolf subspecies]]
    |bar2 = grey
    |2 =
      {{clade
      |1 = {{clade}}
      |2 = {{clade}}
      }}
    }}
  }}
}}

In 2000, a study looked at red wolves and [[Eastern wolf|eastern Canadian wolves]]. The study agreed that these two wolves readily hybridize with the coyote. The study used eight [[microsatellites]] (genetic markers taken from across the [[genome]] of a specimen). The phylogenetic tree produced from the genetic sequences showed red wolves and eastern Canadian wolves clustering together. These then clustered next closer with the coyote and away from the gray wolf. A further analysis using mDNA sequences indicated the presence of coyote in both of these two wolves, and that these two wolves had diverged from the coyote 150,000–300,000&nbsp;years ago. No gray wolf sequences were detected in the samples. The study proposes that these findings are inconsistent with the two wolves being subspecies of the gray wolf, that red wolves and eastern Canadian wolves evolved in North America after having diverged from the coyote, and therefore they are more likely to hybridize with coyotes.<ref name=wilson2000/>

In 2009, a study of eastern Canadian wolves using microsatellites, mDNA, and the paternally-inherited [[yDNA]] markers found that the eastern Canadian wolf was a unique [[ecotype]] of the gray wolf that had undergone recent hybridization with other gray wolves and coyotes. It could find no evidence to support the findings of the earlier 2000 study regarding the eastern Canadian wolf. The study did not include the red wolf.<ref name=koblmuller2009/>

In 2011, a study compared the genetic sequences of 48,000&nbsp;[[single nucleotide polymorphisms]] ([[mutations]]) taken from the genomes of canids from around the world. The comparison indicated that the red wolf was about 76% coyote and 24% gray wolf with hybridization having occurred 287–430&nbsp;years ago. The eastern wolf was 58% gray wolf and 42% coyote with hybridization having occurred 546–963&nbsp;years ago. The study rejected the theory of a common ancestry for the red and eastern wolves.<ref name=beeland2013/><ref name=vonholdt2011/> However the next year, a study reviewed a subset of the 2011 study's [[Single-nucleotide polymorphism]] (SNP) data and proposed that its methodology had skewed the results and that the red and eastern wolves are not hybrids but are in fact the same species separate from the gray wolf.<ref name=beeland2013/><ref name=rutledge2012a>{{cite journal |last1=Rutledge |first1=Linda Y. |last2=Wilson |first2=Paul J. |last3=Klütsch |first3=Cornelya F.C. |last4=Patterson |first4=Brent R. |last5=White |first5=Bradley N. |year=2012 |url=http://people.trentu.ca/brentpatterson/index_files/Rutledge%20et%20al%202012%20-%20conservation%20genomics%20in%20perspective.pdf |title=Conservation genomics in perspective: A holistic approach to understanding ''Canis'' evolution in North America |journal=Biological Conservation |volume=155 |pages=186–192 |doi=10.1016/j.biocon.2012.05.017 |bibcode=2012BCons.155..186R |access-date=2013-07-01}}</ref> The 2012 study proposed that there are three true ''Canis'' species in North America: The gray wolf, the western coyote, and the red wolf / eastern wolf. The eastern wolf was represented by the Algonquin wolf. The Great Lakes wolf was found to be a hybrid of the eastern wolf and the gray wolf. Finally, the study found the eastern coyote itself to be yet another a hybrid between the western coyote and the eastern (Algonquin) wolf (for more on eastern North American wolf-coyote hybrids, ''see'' [[coywolf]]).<ref name=rutledge2012a/>

Also in 2011, a scientific [[literature review]] was undertaken to help assess the taxonomy of North American wolves. One of the findings proposed was that the eastern wolf is supported as a separate species by morphological and genetic data. Genetic data supports a close relationship between the eastern and red wolves, but not close enough to support these as one species. It was "likely" that these were the separate descendants of a common ancestor shared with coyotes. This review was published in 2012.<ref name=chambers2012/> In 2014, the [[National Center for Ecological Analysis and Synthesis]] was invited by the [[United States Fish and Wildlife Service]] to provide an independent review of its proposed rule relating to gray wolves. The center's panel findings were that the proposed rule depended heavily upon a single analysis contained in a scientific literature review by Chambers ''et al''. (2011 ),{{citation needed|date=November 2023}} that that study was not universally accepted, that the issue was "not settled", and that the rule does not represent the "best available science".<ref name=dumbacher2014/>

Brzeski ''et al''. (2016)<ref name=brzeski2016/> conducted an mDNA analysis of three ancient (300–1,900&nbsp;years old) wolf-like samples from the southeastern United States found that they grouped with the coyote clade, although their teeth were wolf-like. The study proposed that the specimens were either coyotes and this would mean that coyotes had occupied this region continuously rather than intermittently, a North American evolved red wolf lineage related to coyotes, or an ancient coyote–wolf hybrid. Ancient hybridization between wolves and coyotes would likely have been due to natural events or early human activities, not landscape changes associated with European colonization because of the age of these samples.<ref name=brzeski2016/> Coyote–wolf hybrids may have occupied the southeastern United States for a long time, filling an important niche as a medium-large predator.<ref name=roy1996/><ref name=brzeski2016/>