Editing Coywolf (section)

===Red wolves and eastern wolves===
[[File:Bartel USFWS pdza rw8.jpg|thumb|A [[Red wolf]]]]
The taxonomy of the red and eastern wolf of the [[Southeastern United States]] and the [[Great Lakes]] regions, respectively, has been long debated, with various schools of thought advocating that they represent either unique species or results of varying degrees of gray wolf × coyote admixture.

In May 2011, an examination of 48,000&nbsp;[[single nucleotide polymorphisms]] in red wolves, eastern wolves, gray wolves, and dogs indicated that the red and eastern wolves were hybrid species, with the red wolf being 76% coyote and 20% gray wolf, and the eastern wolf being 58% gray wolf and 42% coyote, finding no evidence of being distinct species in either.<ref name=VonHolt>{{cite journal |last=von Holt |first=B.M. |display-authors=etal |title=A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids |journal=Genome Res |date=12 May 2011 |pmid=21566151 |doi=10.1101/gr.116301.110 |pmc=3149496 |volume=21 |issue=8 |pages=1294–305}}</ref> The study was criticized for having used red wolves with recent coyote ancestry,<ref name=Beeland>{{cite book |title=The Secret World of Red Wolves |author=Beeland, T. DeLene |year=2013 |publisher=University of North Carolina Press |location=Chapel Hill, NC |isbn= 9781469601991 }}</ref> and a reanalysis in 2012 indicated that it suffered from insufficient sampling.<ref name=Rutledge2>{{cite journal |title=RAD sequencing and genomic simulations resolve hybrid origins within North American ''Canis'' |journal=Biology Letters |date=July 2015 |volume=11 |issue=7 |pages=20150303 |doi=10.1098/rsbl.2015.0303 |pmid=26156129 |pmc=4528444|last1=Rutledge |first1=L. Y |last2=Devillard |first2=S |last3=Boone |first3=J. Q |last4=Hohenlohe |first4=P. A |last5=White |first5=B. N }}</ref> 

A comprehensive review in 2012 further argued that the study's dog samples were unrepresentative of the species' global diversity, having been limited to boxers and poodles, and that the red wolf samples came from modern rather than historical specimens.<ref name=Chambers>{{cite journal |title=An account of the taxonomy of North American wolves from morphological and genetic analyses |year=2012 |journal=North American Fauna |volume=77 |pages=1–67 |doi=10.3996/nafa.77.0001 |last1=Chambers |first1=Steven M. |last2=Fain |first2=Steven R. |last3=Fazio |first3=Bud |last4=Amaral |first4=Michael |doi-access=free }}</ref> The review was itself criticized by a panel of scientists selected for an independent peer review of its findings by the [[USFWS]], which noted that the study's conclusion that the eastern wolf was a full species was based on insufficient evidence — just two unique nonrecombining markers.<ref name=nceas>{{cite web |author=Dumbacher, J. |url=https://downloads.regulations.gov/FWS-HQ-ES-2013-0073-49839/content.pdf |title=Review of Proposed Rule Regarding Status of the Wolf Under the Endangered Species Act |department=NCEAS |publisher=U.S. Fish & Wildlife Service |date=January 2014}}</ref>

In 2016, a [[Whole genome sequencing|whole-genome]] DNA study suggested that all of the North American canids, both wolves and coyotes, diverged from a common ancestor 6,000–117,000&nbsp;years ago. The whole-genome sequence analysis shows that two endemic species of North American wolf, the red wolf and eastern wolf, are [[Genetic admixture|admixtures]] of the coyote and gray wolf.<ref>{{cite journal |doi=10.1126/sciadv.1501714 |pmid=29713682 |pmc=5919777 |title=Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf |journal=Science Advances |volume=2 |issue=7 |pages=e1501714 |year=2016 |last1=von Holdt |first1=B.M. |last2=Cahill |first2=J. A. |last3=Fan |first3=Z. |last4=Gronau |first4=I. |last5=Robinson |first5=J. |last6=Pollinger |first6=J.P. |last7=Shapiro |first7=B. |last8=Wall |first8=J. |last9=Wayne |first9=R.K. |display-authors=6 |bibcode=2016SciA....2E1714V}}</ref><ref>{{cite journal |doi= 10.1126/science.aag0699 |title=How do you save a wolf that's not really a wolf? |journal=Science |year=2016 |last=Morell |first=Virginia}}</ref>

In 2017 a group of canid researchers challenged the 2016 whole-genome DNA study's finding that the red wolf and the eastern wolf were the result of recent coyote–gray wolf hybridization. The group asserts the three-year [[generation time]] used to calculate the divergence periods between different species was lower than empirical estimates of 4.7&nbsp;years. The group also found deficiencies in the previous study's selection of specimens (two representative coyotes were from areas where recent coyote and gray wolf mixing with eastern wolves is known to have occurred), the lack of certainty in the ancestry of the selected Algonquin wolves, and the grouping of Great Lakes and Algonquin wolves together as eastern wolves, despite opposing genetic evidence.  As well, they asserted the 2016 study ignored the fact that there is no evidence of hybridization between coyotes and gray wolves.<ref>{{cite journal |doi=10.1126/sciadv.1602250 |pmid=28630899 |pmc=5462499 |year=2017 |last1=Hohenlohe |first1=Paul A. |last2=Rutledge |first2=Linda Y. |last3=Waits |first3=Lisette P. |last4=Andrews |first4=Kimberly R. |last5=Adams |first5=Jennifer R. |last6=Hinton |first6=Joseph W. |last7=Nowak |first7=Ronald M. |last8=Patterson |first8=Brent R. |last9=Whydeven |first9=Adrian P. |last10=Wilson |first10=Paul A. |last11=White |first11=Brad N. |title=Comment on "Whole-genome sequence analysis shows two endemic species of North American wolf are admixtures of the coyote and gray wolf" |journal=Science Advances |volume=3 |issue=6 |pages=e1602250|bibcode=2017SciA....3E2250H }}</ref>

The group also questioned the conclusions of genetic differentiation analysis in the study stating that results showing Great Lakes, Algonquin and red wolves, plus eastern coyotes differentiated from gray and Eurasian wolves were actually more consistent with an ancient hybridization or a distinct cladogenic origin for the red and Algonquin wolves than of a recent hybrid origin. The group further asserted that the levels of unique alleles for red and Algonquin wolves found the 2017 study were high enough to reveal a high degree of evolutionary distinctness. Therefore, the group argues that both the red wolf and the eastern wolf remain genetically distinct North American taxa.<ref>{{cite journal |doi=10.1126/sciadv.1602250 |pmid=28630899 |pmc=5462499 |year=2017 |last1=Hohenlohe |first1=Paul A. |last2=Rutledge |first2=Linda Y. |last3=Waits |first3=Lisette P. |last4=Andrews |first4=Kimberly R. |last5=Adams |first5=Jennifer R. |last6=Hinton |first6=Joseph W. |last7=Nowak |first7=Ronald M. |last8=Patterson |first8=Brent R. |last9=Whydeven |first9=Adrian P. |last10=Wilson |first10=Paul A. |last11=White |first11=Brad N. |title=Comment on "Whole-genome sequence analysis shows two endemic species of North American wolf are admixtures of the coyote and gray wolf" |journal=Science Advances |volume=3 |issue=6 |pages=e1602250|bibcode=2017SciA....3E2250H }}</ref> This was rebutted by the authors of the earlier study.<ref>{{cite journal |doi=10.1126/sciadv.1701233 |pmid=28630935 |pmc=5462503 |year=2017 |last1=von Holdt |first1=B.M. |last2=Cahill |first2=J. A. |last3=Gronau |first3=I. |last4=Shapiro |first4=B. |last5=Wall |first5=J. |last6=Wayne |first6=R.K. |title=Response to Hohenlohe et al. |journal=Science Advances |volume=3 |issue=6 |pages=e1701233|bibcode=2017SciA....3E1233V }}</ref>

In 2021, an mDNA analysis of modern and extinct North American wolf-like canines indicates that the extinct Late Pleistocene [[Beringian wolf#Range|Beringian wolf]] was the ancestor of the southern wolf [[Clade#Definition|clade]], which includes the [[Mexican wolf]] and the [[Great Plains wolf]]. The Mexican wolf is the most ancestral of the gray wolves that live in North America today. The modern coyote appeared around 10,000 years ago. The most genetically basal coyote mDNA clade pre-dates the [[Last Glacial Maximum]] and is a haplotype that can only be found in the Eastern wolf. This implies that the large, wolf-like [[Pleistocene coyote]] was the ancestor of the Eastern wolf. Further, another ancient haplotype detected in the Eastern wolf can be found only in the Mexican wolf. The authors propose that Pleistocene coyote and Beringian wolf admixture led to the Eastern wolf long before the arrival of the modern coyote and the modern wolf.<ref>{{cite journal |doi=10.1002/ece3.7757 |pmid=34257949 |pmc=8258226 |year=2021 |last1=Wilson |first1=Paul J. |last2=Rutledge |first2=Linda Y. |title=Considering Pleistocene North American wolves and coyotes in the eastern Canis origin story |journal=Ecology and Evolution |volume=11 |issue=13 |pages=9137–9147|bibcode=2021EcoEv..11.9137W }}</ref>

In 2023, a genomic study indicates that eastern wolves have evolved separately from grey wolves for the past 67,000 years and had experienced admixture with coyotes 37,000 years ago. The Great Lakes wolves were the result of admixture between eastern wolves and grey wolves 8,000 years ago. Eastern coyotes were the result of admixture between eastern wolves and "western" coyotes during the last century.<ref>{{cite journal |title=Tracing Eastern Wolf Origins From Whole-Genome Data in Context of Extensive Hybridization |journal=Molecular Biology and Evolution |doi=10.1093/molbev/msad055 |year=2023 |author=Vilaca S.T. |volume=40 |issue=4 |pages=msad055 |pmid=37046402 |pmc=10098045}}</ref>

====Mexican wolf × coyote hybrids====
In a study that analyzed the molecular genetics of coyotes, as well as samples of historical red wolves and [[Mexican wolf|Mexican wolves]] from Texas, a few coyote genetic markers have been found in the historical samples of some isolated Mexican wolf individuals. Likewise, gray wolf Y chromosomes have also been found in a few individual male Texan coyotes.<ref>{{cite journal |doi=10.1371/journal.pone.0003333 |pmid=18841199 |pmc=2556088 |year=2008 |last1=Hailer |first1=F. |last2=Leonard |first2=J.A. |title=Hybridization among three native North American ''Canis'' species in a region of natural sympatry |journal=PLOS ONE |volume=3 |issue=10 |pages=e3333 |bibcode=2008PLoSO...3.3333H|doi-access=free }}</ref> This study suggested that although the Mexican wolf is generally less prone to hybridizations with coyotes, exceptional genetic exchanges with the Texan coyotes may have occurred among individual gray wolves from historical remnants before the population was completely extirpated in Texas. The resulting hybrids would later on melt back into the coyote populations as the wolves disappeared. 

The same study discussed an alternative possibility that the red wolves, which also once overlapped with both species in central Texas, were involved in circuiting the gene flows between the coyotes and gray wolves, much like how the eastern wolf is suspected to have bridged gene flows between gray wolves and coyotes in the Great Lakes region, since direct hybridizations between coyotes and gray wolves is considered rare.

In tests performed on a stuffed carcass of what was initially labelled a [[chupacabra]], mitochondrial DNA analysis conducted by [[Texas State University]] showed that it was a coyote, though subsequent tests revealed that it was a coyote × gray wolf hybrid sired by a male Mexican wolf.<ref>{{cite news |author=Ardizzoni, S. |date=September 1, 2013 |url=http://bionews-tx.com/news/2013/09/01/texas-state-university-researcher-helps-unravel-mystery-of-texas-blue-dog-claimed-to-be-chupacabra/ |title=Texas State University researcher helps unravel mystery of Texas 'blue dog' claimed to be Chupacabra |website=Bio News Texas |access-date=January 23, 2014 |archive-date=March 19, 2014 |archive-url=https://web.archive.org/web/20140319203625/http://bionews-tx.com/news/2013/09/01/texas-state-university-researcher-helps-unravel-mystery-of-texas-blue-dog-claimed-to-be-chupacabra/ |url-status=dead }}</ref>