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.
Institute of Population Genetics, National Research Council (CNR), Sassari, Italy.
Maria Grazia
MG
Doro
Institute of Population Genetics, National Research Council (CNR), Sassari, Italy; Experimental Zoo-prophylactic Institute of Sardinia, Sassari, Italy.
Daniela
D
Piras
Faculty of Veterinary Sciences, University of Sassari, Sassari, Italy.
Giovanni Giuseppe
GG
Leoni
Institute of Population Genetics, National Research Council (CNR), Sassari, Italy.
Giuseppina
G
Casu
Institute of Population Genetics, National Research Council (CNR), Sassari, Italy.
Simona
S
Vaccargiu
Genetic Park of Ogliastra, Perdasdefogu, Italy.
Debora
D
Parracciani
Faculty of Veterinary Sciences, University of Sassari, Sassari, Italy.
Salvatore
S
Naitana
Institute of Population Genetics, National Research Council (CNR), Sassari, Italy; Genetic Park of Ogliastra, Perdasdefogu, Italy.
Mario
M
Pirastu
Department of Biology, University "Tor Vergata", Rome, Italy.
Andrea
A
Novelletto
D000818:Animals; D004272:DNA, Mitochondrial / Q000235:genetics*; D014644:Genetic Variation; D054629:Genome, Mitochondrial; D006041:Goats / Q000235:genetics*; D006239:Haplotypes; D010802:Phylogeny; D017422:Sequence Analysis, DNA
D004272:DNA, Mitochondrial