Re(4): Why do you want to confirm the existence of mountain lions in New England?
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It is indeed possible to distinguish individual cougars by their DNA. It is much more difficult to determine what population of cougars that individual was born into.

More is probably known about the DNA of Florida panthers than any other population of cougars. In 2008 a deer hunter shot a young male in west-central Alabama. Geneticists were able to identify his father, who lived at the northern edge of panther range in SW Florida.

DNA analysis of the Quabbin skull is not possible because the previous owners had put it in beach. A cougar ulna (lower arm bone) was found later near the site. Both these remains are in the collection of the Museum of Comparative Zoology at Harvard University. It's possible that DNA could be extracted from that ulna. (I measured it, and ulnas from several other cougars, and decided it could be from the same individual.)

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