A diagnostic assay discriminating between two major Ovis aries mitochondrial DNA haplogroups

Maternal Relationships among Ancient and Modern Southern African Sheep: Newly Discovered Mitochondrial Haplogroups

Simple Summary

The genetic diversity of southern African sheep remains under-studied. We present here the complete mitochondrial genomes of archaeological southern African sheep, as well as the genomes from three indigenous southern African breeds—Damara, Namaqua Afrikaner, and Ronderib Afrikaner. We show that southern African sheep exhibit limited genetic diversity which is consistent with our understanding of their migration south from northernmost Africa. Intriguingly, many of the modern sheep show close relationships with the archaeological sheep, implying an ancestor-descendant relationship. Similarly, the sheep that do not exhibit a close relationship with the archaeological sheep nonetheless cluster closely with each other and do not show a close relationship with European and Asian sheep. This suggests that they too are descendants of indigenous sheep and not the product of historic introductions of exotic breeds.

Abstract

We investigated the genetic diversity and historic relationships among southern African sheep as well as the relationships between them and sheep outside the continent by sourcing both archaeological and modern sheep samples. Archaeological sheep samples derived from the site Die Kelders 1, near Cape Town, date to approximately 1500 years ago. The modern samples were taken as ear snips from Damara, Namaqua Afrikaner, and Ronderib Afrikaner sheep on a farm in Prieska in the Northern Cape. Illumina sequencing libraries were constructed for both ancient and modern specimens. Ancient specimens were enriched for the mitochondrial genome using an in-solution hybridization protocol and modern specimens were subjected to shotgun sequencing. Sequences were mapped to the Ovis aries reference genome, assigned to haplogroups and subhaplogroups, and used to calculate a phylogenetic tree using previously published, geographically dispersed mitochondrial genome sheep sequences. Genetic diversity statistics show that southern African sheep have lower diversity than sheep in other regions. Phylogenetic analysis reveals that many modern southern African sheep are likely descended from prehistoric indigenous sheep populations and not from sheep imported from Europe during the historic period.

Mitochondrial DNA sequence analysis of the Mexican Creole sheep (Ovis aries) reveals a narrow Iberian maternal origin

The Creole sheep in America is supposed to have originated specifically from the Iberian Peninsula and introduced by the Spaniards during the colonization. However, it is not clear their genetic relationship with Iberian breeds. The genetic origin and diversity of the Mexican Creole sheep (MCS) were investigated by mitochondrial DNA control region nucleotide sequences. DNA sequence from 33 MCS samples from three regions of México revealed 21 different haplotypes. Phylogenetic analysis including European and Iberian sheep haplotypes showed that the MCS population belongs to a differentiated and defined genetic lineage. This finding suggests that the MCS populations may be the result of a founder effect originating from a discrete Iberian population. MCS haplotypes were related to haplotypes found in the Churro Trunk and the Entrefino Trunk groups of Iberian breeds, supporting historical reports. In the Mexican genetic branch, there were also haplotypes reported from Lacaune and Awassi sheep breeds. Although it is uncertain whether a particular breed was involved as a founder of the MCS, these populations have a common phylogenetic origin.

Molecular analysis of wild and domestic sheep questions current nomenclature and provides evidence for domestication from two different subspecies

Complete mitochondrial DNA (mtDNA) control regions (CR) were sequenced and analysed in order to investigate wild sheep taxonomy and the origin of domestic sheep (Ovis aries). The dataset for phylogenetic analyses includes 63 unique CR sequences from wild sheep of the mouflon (O. musimon, O. orientalis), urial (O. vignei), argali (O. ammon) and bighorn (O. canadensis) groups, and from domestic sheep of Asia, Europe and New Zealand. Domestic sheep occurred in two clearly separated branches with mouflon (O. musimon) mixed into one of the domestic sheep clusters. Genetic distances and molecular datings based on O. canadensis CR and mtDNA protein-coding sequences provide strong evidence for domestications from two mouflon subspecies. Other wild sheep sequences are in two additional well-separated branches. Ovis ammon collium and O. ammon nigrimontana are joined with a specimen from the transkaspian Ust-Urt plateau currently named O. vignei arkal. Ovis ammon ammon, O. ammon darwini and O. vignei bochariensis represent a separate clade and the earliest divergence from the mouflon group. Therefore, O. musimon, O. vignei bochariensis and Ust-Urt sheep are not members of a 'moufloniform' or O. orientalis species, but belong to different clades. Furthermore, Ust-Urt sheep could be a hybrid population or an O. ammon subspecies closely related to O. ammon nigrimontana.