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Although the maned wolf displays many fox-like characteristics, it is not closely related to foxes. It lacks the elliptical pupils found distinctively in foxes. The maned wolf’s evolutionary relationship to the other members of the canid family makes it a unique animal.

Electrophoretic studies did not link Chrysocyon with any of the other living canids studied. One conclusion of this study is that the maned wolf is the only species among the large South American canids that survived the late Pleistocene extinction. Fossils of the maned wolf from the Holocene and the late Pleistocene have been excavated from the Brazilian Highlands.

A 2003 study on the brain anatomy of several canids placed the maned wolf together with the Falkland Islands wolf and with pseudo-foxes of the genus Pseudalopex. One study based on DNA evidence showed that the extinct genus Dusicyon, comprising the Falkland Islands wolf and its mainland relative, was the most closely related species to the maned wolf in historical times, and that about seven million years ago it shared a common ancestor with that genus. A 2015 study reported genetic signatures in maned wolves that are indicative of population expansion followed by contraction that took place during Pleistocene interglaciations about 24,000 years before present.

The maned wolf is not closely related to any other living canid. It is not a fox, wolf, coyote, dog, or jackal, but a distinct canid, though, based only on morphological similarities, it previously had been placed in the Canis and Vulpes genera. Its closest living relative is the bush dog (genus Speothos), and it has a more distant relationship to other South American canines (the short-eared dog, the crab-eating fox, and the zorros or Lycalopex).
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Evolution of the wolf
An attempt to explore admixture between Taimyr-1 and gray wolves produced unreliable results.

As the Taimyr wolf had contributed to the genetic makeup of the Arctic breeds, a later study suggested that descendants of the Taimyr wolf survived until dogs were domesticated in Europe and arrived at high latitudes where they mixed with local wolves, and these both contributed to the modern Arctic breeds. Based on the most widely accepted oldest zooarchaeological dog remains, domestic dogs most likely arrived at high latitudes within the last 15,000 years. The mutation rates calibrated from both the Taimyr wolf and the Newgrange dog genomes suggest that modern wolf and dog populations diverged from a common ancestor between 20,000–60,000 YBP. This indicates that either dogs were domesticated much earlier than their first appearance in the archaeological record, or they arrived in the Arctic early, or both.[156]

The finding of a second wolf specimen from the same area (“Taimry-2”) and dated to 42,000 YBP has also been sequenced but yielded only mitochondrial DNA.[157]

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