Editing Coyote (section)

===Evolution===
{{Cladogram|align=right|title=[[Phylogenetic tree]] of the [[Canina (subtribe)|wolf-like canids]] with timing in millions of years{{refn|group=lower-alpha|name=mtdna_seq_desc|For a full set of supporting references refer to the note (a) in the phylotree at [[Evolution of the wolf#Wolf-like canids]]}}
|cladogram={{clade | style = font-size:85%;line-height:80%;width:400px;
 |label1=[[Caninae]] 3.5 [[Megaannum|Ma]]
 |1={{clade
  |label1=3.0
  |1={{clade
   |label1=2.5
   |1={{clade
    |label1=2.0
    |1={{clade
     |label1=0.96
     |1={{clade
       |label1=0.6
       |1={{clade
        |label1=0.38
        |1={{clade
         |1={{clade
          |1={{clade
           |1=[[Dog|Domestic dog]] <span style="{{MirrorH}}">[[File:202104 Dog.svg|50 px]]</span>
           |2=[[Wolf|Gray wolf]] [[File:Dogs, jackals, wolves, and foxes (Plate I).jpg|50 px]]
}}
}}
         |2='''Coyote''' [[File:Dogs, jackals, wolves, and foxes (Plate IX).jpg|50 px]]
}}
        |2=[[African wolf]] [[File:Dogs, jackals, wolves, and foxes (Plate XI).jpg|50 px]]
}}
       |2=[[Golden jackal]] [[File:Dogs, jackals, wolves, and foxes (Plate X).jpg|50 px]]
}}
      |2=[[Ethiopian wolf]] [[File:Dogs, jackals, wolves, and foxes (Plate VI).jpg|50 px]]
}}
     |2=[[Dhole]] [[File:Dogs, jackals, wolves, and foxes (Plate XLI).jpg|50 px]]
}}
     |2=[[African wild dog]] [[File:Dogs, jackals, wolves, and foxes (Plate XLIV).jpg|50 px]]
}}
  |2={{clade
   |1={{clade
    |1=[[Side-striped jackal]] [[File:Dogs, jackals, wolves, and foxes (Plate XIII).jpg|50 px]]
    |2=[[Black-backed jackal]] [[File:Dogs, jackals, wolves, and foxes (Plate XII).jpg|50 px]]
}}
    |label1=2.6
}}
}}
}}
}}

====Fossil record====
{{See also|Evolution of the wolf#Fossil record}}

[[Xiaoming Wang (paleontologist)|Xiaoming Wang]] and [[Richard H. Tedford]], one of the foremost [[Author citation (zoology)|authorities]] on carnivore evolution,<ref>{{cite magazine|title=Natural History: Canid Family Ties |year=2008|magazine=The Magazine of the American Museum of Natural History|url=https://archive.org/stream/naturalhistory11706unse#page/22|page=22|volume=117|number=6|publisher=American Museum of Natural History|location=New York}}</ref> proposed that the genus ''Canis'' was the descendant of the coyote-like ''[[Eucyon davisi]]'' and its remains first appeared in the [[Miocene]] 6{{nbsp}}million years ago (Mya) in the southwestern US and Mexico. By the [[Pliocene]] (5{{nbsp}}Mya), the larger ''[[Canis lepophagus]]''<ref name=fossilworks1/> appeared in the same region and by the [[early Pleistocene]] (1{{nbsp}}Mya) ''C.{{nbsp}}latrans'' (the coyote) was in existence. They proposed that the progression from ''Eucyon davisi'' to ''C.{{nbsp}}lepophagus'' to the coyote was linear evolution.{{sfn|Wang|Tedford|2008|p=58}} 

''C.{{nbsp}}latrans'' and ''C.{{nbsp}}aureus'' are closely related to ''[[Canis edwardii|C.{{nbsp}}edwardii]]'', a species that appeared earliest spanning the mid-[[Blancan]] ([[late Pliocene]]) to the close of the [[Irvingtonian]] (late Pleistocene), and coyote remains indistinguishable from ''C.&nbsp;latrans'' were contemporaneous with ''C.{{nbsp}}edwardii'' in North America.{{sfn|Tedford|Wang|Taylor|2009|pp=175, 180}} Johnston describes ''C.{{nbsp}}lepophagus'' as having a more slender skull and skeleton than the modern coyote.{{sfn|Johnston|1938|p=385}} Ronald Nowak found that the early populations had small, delicate, narrowly proportioned skulls that resemble small coyotes and appear to be ancestral to ''C.&nbsp;latrans''.{{sfn|Nowak|2003|p=241}}

''C. lepophagus'' was similar in weight to modern coyotes, but had shorter limb bones that indicate a less [[cursorial]] lifestyle. The coyote represents a more primitive form of ''Canis'' than the gray wolf, as shown by its relatively small size and its comparatively narrow skull and jaws, which lack the grasping power necessary to hold the large prey in which wolves specialize. This is further corroborated by the coyote's [[sagittal crest]], which is low or totally flattened, thus indicating a weaker bite than the wolves. The coyote, unlike the wolf, is not a specialized carnivore, as shown by the larger chewing surfaces on the [[molar (tooth)|molars]], reflecting the species' relative dependence on vegetable matter. In these respects, the coyote resembles the fox-like progenitors of the genus more so than the wolf.<ref name=nowak1978/>

The oldest fossils that fall within the range of the modern coyote date to 0.74–0.85 [[Megaannum|Ma]] (million years) in Hamilton Cave, West Virginia; 0.73 Ma in Irvington, California; 0.35–0.48 Ma in Porcupine Cave, Colorado, and in Cumberland Cave, Pennsylvania.{{sfn|Tedford|Wang|Taylor|2009|p=136}} Modern coyotes arose 1,000 years after the [[Quaternary extinction event]].<ref name="meachen2012"/> Compared to their modern [[Holocene]] counterparts, [[Pleistocene coyote]]s (''C.{{nbsp}}l. orcutti'') were larger and more robust, likely in response to larger [[Competition (biology)|competitors]] and prey.<ref name="meachen2012">{{cite journal | doi = 10.1073/pnas.1113788109|pmid=22371581| title = Evolution in coyotes (''Canis latrans'') in response to the megafaunal extinctions| journal = Proceedings of the National Academy of Sciences| volume = 109| issue = 11| pages = 4191–6| year = 2012| last1 = Meachen | first1 = J. A. | last2 = Samuels | first2 = J. X. |issn=1091-6490|oclc=475396714|bibcode=2012PNAS..109.4191M | pmc=3306717| url=http://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1043&context=natlpark|doi-access=free}}</ref> Pleistocene coyotes were likely more specialized carnivores than their descendants, as their teeth were more adapted to shearing meat, showing fewer grinding surfaces suited for processing vegetation.<ref name="meachen2014">{{Cite journal | doi = 10.1371/journal.pone.0116041|pmid=25551387| title = Ecological Changes in Coyotes (''Canis latrans'') in Response to the Ice Age Megafaunal Extinctions| journal = PLOS ONE| volume = 9| issue = 12| page = e116041| year = 2014| last1 = Meachen | first1 = J. A. | last2 = Janowicz | first2 = A. C. | last3 = Avery | first3 = J. E. | last4 = Sadleir | first4 = R. W. |bibcode = 2014PLoSO...9k6041M | pmc=4281224|doi-access=free}}</ref> Their reduction in size occurred within 1,000 years of the Quaternary extinction event, when their large prey died out.<ref name="meachen2012"/> Furthermore, Pleistocene coyotes were unable to exploit the big-game hunting [[Ecological niche|niche]] left vacant after the extinction of the [[dire wolf]] (''Aenocyon{{nbsp}}dirus''), as it was rapidly filled by gray wolves, which likely actively killed off the large coyotes, with [[natural selection]] favoring the modern gracile morph. Coyotes are usually 5-7 feet long.<ref name="meachen2014"/>

====DNA evidence====
[[File:Canis latrans orcutti.png|thumb|A skeleton of a [[Pleistocene coyote]] (''C.{{nbsp}}l. orcutti'')]]

In 1993, a study proposed that the wolves of North America display skull traits more similar to the coyote than wolves from Eurasia.<ref name=goulet1993/> In 2010, a study found that the coyote was a [[lineage (genetic)#Basal lineage|basal]] member of the clade that included the [[Tibetan wolf]], the [[Dog|domestic dog]], the [[Mongolian wolf]] and the [[Eurasian wolf]], with the Tibetan wolf diverging early from wolves and domestic dogs.<ref name=zhang2010/>

In 2016, a [[Whole genome sequencing|whole-genome]] DNA study proposed, based on the assumptions made, that all of the North American wolves and coyotes diverged from a common ancestor about 51,000&nbsp;years ago.<ref name=vonholdt2016/><ref name=virginia2016/> However, the proposed timing of the wolf / coyote divergence conflicts with the discovery of a coyote-like specimen in strata dated to 1&nbsp;Mya.{{sfn|Wang|Tedford|2008|p={{page needed|date=November 2020}}}} The study also indicated that all North American wolves have a significant amount of coyote ancestry and all coyotes some degree of wolf ancestry, and that the red wolf and eastern wolf are highly [[Genetic admixture|admixed]] with different proportions of gray wolf and coyote ancestry.<ref name=vonholdt2016/><ref name=virginia2016/>

Genetic studies relating to wolves or dogs have inferred phylogenetic relationships based on the only reference genome available, that of the Boxer dog. In 2017, the first reference genome of the wolf ''Canis lupus lupus'' was mapped to aid future research.<ref name=gopalakrishnan2017/> In 2018, a study looked at the genomic structure and admixture of North American wolves, wolf-like canids, and coyotes using specimens from across their entire range that mapped the largest dataset of nuclear genome sequences against the wolf reference genome.

The study supports the findings of previous studies that North American gray wolves and wolf-like canids were the result of complex gray wolf and coyote mixing. A polar wolf from Greenland and a coyote from Mexico represented the purest specimens. The coyotes from Alaska, California, Alabama, and Quebec show almost no wolf ancestry. Coyotes from Missouri, Illinois, and Florida exhibit 5–10% wolf ancestry. There was 40% wolf to 60% coyote ancestry in red wolves, 60% wolf to 40% coyote in Eastern timber wolves, and 75% wolf to 25% coyote in the Great Lakes wolves. There was 10% coyote ancestry in Mexican wolves and the Atlantic Coast wolves, 5% in Pacific Coast and Yellowstone wolves, and less than 3% in Canadian archipelago wolves. If a third canid had been involved in the admixture of the North American wolf-like canids, then its genetic signature would have been found in coyotes and wolves, which it has not.<ref name=sinding2018/>

In 2018, [[whole genome sequencing]] was used to compare members of the genus ''Canis''. The study indicates that the common ancestor of the coyote and gray [[wolf]] has genetically [[Genetic admixture|admixed]] with a [[ghost population]] of an extinct, unidentified canid. The "ghost" canid was genetically close to the [[dhole]], and had evolved after the divergence of the [[African wild dog]] from the other canid species. The [[Basal (phylogenetics)|basal]] position of the coyote compared to the wolf is proposed to be due to the coyote retaining more of the mitochondrial genome from the unknown extinct canid.<ref name=gopalakrishnan2018/>