In both breeds the frequency spectrum of ancestral polymorphisms is generally flat.
In the modern Finnish breeds, the frequency of G- oY1 was 77%, 57%, and 60% in Finnsheep, Kainuu Grey, and Åland, respectively [see Additional file 4: Table S3], indicating that SNP G- oY1 is frequent in the modern north-European breeds.
In the contemporary native Finnish breeds, the frequency of SNP G- oY1 ranges from 57 to 77% [see Additional file 4: Table S3] and the frequency of SNP G- oY1 is highest in north European, British Islands and central Russian populations [ 12], [see Figure 2 and Additional file 4: Table S3].
We also computed rolling average allele frequencies in both breeds (using the frequency of the allele with the lowest frequency averaged over both breeds) using a five-locus sliding window for both chromosomes and for each pair of averages; we subtracted the mean Angus allele frequency from that for Holstein.
CLJ was not known in this breed before and the frequency of this condition was seemingly increasing.
There are clear differences between breeds in the frequencies of the ROH of various lengths (Fig. 3).
A comparison of the 219 bp sequences obtained from the ancient dog specimens (n = 18) and the contemporary native breeds indicates that the frequency of Hg D is significantly reduced in the ancient data set (0% in the ancient dataset, 33% in the modern dataset, p < 0.001).
Thus, in the first group of breeds the average frequencies of the I-668 and G-660 alleles were 0.08 and 0.61, respectively.
For each chromosome segment we calculated a modified version of Depaulis-Veuille's H-test [ 8], referred to as HAPH, where HAPH =, where p i is the (within breed) frequency of the ith haplotype and N is the total number of haplotypes observed for the breed at the position.
