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Phylogeny and patterns of diversity of goat mtDNA haplogroup A revealed by resequencing complete mitogenomes

Doro, Maria Grazia and Piras, Daniela and Leoni, Giovanni Giuseppe and Casu, Giuseppina and Vaccargiu, Simona and Parracciani, Debora and Naitana, Salvatore and Pirastu, Mario and Novelletto, Andrea (2014) Phylogeny and patterns of diversity of goat mtDNA haplogroup A revealed by resequencing complete mitogenomes. PLoS One, Vol. 9 (4), e95969. eISSN 1932-6203. Article.

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DOI: 10.1371/journal.pone.0095969

Abstract

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.

Item Type:Article
ID Code:9894
Status:Published
Refereed:Yes
Uncontrolled Keywords:Sardinian goats, mtDNA, mitochondrial evolutionary lineage, haplogroup (Hg) A
Subjects:Area 07 - Scienze agrarie e veterinarie > VET/02 Fisiologia veterinaria
Area 05 - Scienze biologiche > BIO/10 Biochimica
Divisions:001 Università di Sassari > 01-a Nuovi Dipartimenti dal 2012 > Medicina Veterinaria
Publisher:Public Library of Science
eISSN:1932-6203
Copyright Holders:© 2014 Doro et al.
Deposited On:20 Jun 2014 11:16

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