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Yes, but this works (as far as I know) for populations diverged for some significant time. As all CSW are actually descendants of one female wolf, and several female GSD, and as the first pairing was done some 50 years ago, you would get results that some percent of CSW population are 100% GSD and other percent of CSW are 100% carpathian wolf, and the percentage of GSD or wolf in the population of CSW would depend only on the relative amount of female lines used, so in theory if only male descendants of the wolf Brita were used, than according to mitochondria only GSD are present, or on the other hand, if only male descendants of the GSD females were used, than we have only wolf mitochondria...
Of course assuming that actually mitochondria from sperm do not play role.
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To get ride of sex biaised inheritance mtDNA is used in combination with nuclear Y-chromosome and autosomal markers. Furthermore microsatellites are VERY more polymorphic than any other makers, this solves the "signifiant time" needed.
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Does anybody know, if there was found any significant difference in overall DNA between wolf and dogs other than genes for skin/coat/eye pigmentation?
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I guess this is not the way to look for, promising ways are modifications of mRNA expression and genetic regulatory networks.