The analysis of mitochondrial data indicates the existence of population substructure in Karayaka sheep

In the current study, we investigated the existence of population substructure in the Karayaka sheep breed from Turkey. A fragment of the mitochondrial D-loop region has been successfully sequenced in 69 Karayaka sheep sampled in the districts of Çarsamba, Bafra and Ladik. Though the B haplogroup was the most abundant in these three subpopulations, haplogroup frequencies and nucleotide diversities were remarkably different. The analysis of molecular variance (AMOVA) showed the existence of a significant (P-value = 0.019) between-subpopulations component representing 5.14% of the total variation. Moreover, phylogenetic analyses showed that the fixation index (FST) and the GammaST genetic distance between Karayaka subpopulations are similar to those observed between certain Turkish sheep breeds. We conclude that there is a significant population substructure in Karayaka sheep. Since breeds do not behave as single panmictic populations, this result could probably be extrapolated to other ovine breeds. Noteworthy, population substructure can have adverse effects on the maintenance of breed diversity and it is an important confounder effect in genome-wide-association studies.