To date, research on MS in Sardinia has been mainly focusing on the most frequent HLA ancestral haplotype and only on loci A, B, DR [36] [38].
Next we compared the ancestral allele of the core SNP with the first proximate SNP upstream and looked for the most frequent haplotype between the ancestral allele of the core SNP and each of the alleles of the first proximate SNP.
If, for example, 80% of the individuals showed the most frequent haplotype between the ancestral allele and the first proximate SNP upstream, then EHH = 0.80 at that point.
For each TR locus, we determined presence/absence of TR polymorphism, and for each polymorphic locus, we found a modal repeat number (a proxy for the most frequent, and thus likely ancestral, allele).
Repeats ([A/T]n and separately [GT/CA]n) were binned according to the repeat number of the modal (most frequent and hence likely ancestral) allele at each locus.
Considering plastid haplotypes, the most frequent H14 is likely the ancestral, from which H18-H22, 26, 26 have originated.
In statistical parsimony, the most frequent and most connected haplotype is regarded as being ancestral [18].
The major, i.e., most frequent, haplotype in 12 of these segments is the ancestral one (i.e., M=0).
All genotype calls were used and the ancestral allele was taken as the most frequent allele observed in these out-group animals.
Considering the population history of the pigs, we assume that the major wild boar haplotype SUS_PRLR4, even though not the most frequent haplotype is a good candidate for being the ancestral haplotype of the European domestic pig.
