Phylogeny and Patterns of Diversity of Goat mtDNA Haplogroup A Revealed by Resequencing Complete Mitogenomes.

We sequenced to near completion the entire mtDNA of 28 Sardinian goats, selected to represent the widest possible
diversity of the most widespread mitochondrial evolutionary lineage, haplogroup (Hg) A. These specimens were reporters of
the diversity in the island but also elsewhere, as inferred from their affiliation to each of 11 clades defined by D-loop
variation. Two reference sequences completed the dataset. Overall, 206 variations were found in the full set of 30
sequences, of which 23 were protein-coding non-synonymous single nucleotide substitutions. Many polymorphic sites
within Hg A were informative for the reconstruction of its internal phylogeny. Bayesian and network clustering revealed a
general similarity over the entire molecule of sequences previously assigned to the same D-loop clade, indicating
evolutionarily meaningful lineages. Two major sister groupings emerged within Hg A, which parallel distinct geographical
distributions of D-loop clades in extant stocks. The pattern of variation in protein-coding genes revealed an overwhelming
role of purifying selection, with the quota of surviving variants approaching neutrality. However, a simple model of
relaxation of selection for the bulk of variants here reported should be rejected. Non-synonymous diversity of Hg’s A, B and
C denoted that a proportion of variants not greater than that allowed in the wild was given the opportunity to spread into
domesticated stocks. Our results also confirmed that a remarkable proportion of pre-existing Hg A diversity became
incorporated into domestic stocks. Our results confirm clade A11 as a well differentiated and ancient lineage peculiar of
Sardinia