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

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.

Genetic Characterization and Alternative Preservation Ways of Locally Adapted Sheep Breeds: Cases of Private and Public Sheep Sectors in Tunisia and Italy

“…Measuring genetic diversity in locally adapted and native sheep animal breeds using neutral and maternal molecular markers is essential to setting up conservation strategies [ 39 , 52 , 53 , 54 ]. In fact, filling the knowledge gap on the genomic characterization of sheep resources is a prerequisite for the effective implementation of genetic improvement programs, especially in developing countries’ conditions [ 55 ], such as in the Tunisian case.…”

The name of the game: palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in eastern and southern Africa

“…Caprines probably spread from eastern to southern Africa along a ‘tsetse-free’ corridor from Kenya and southern Tanzania through Zambia to Botswana [21,22]. Genomic similarities of sheep and goat breeds reinforce the hypothesis of substantial contacts between the two regions [20,23]. Although tracing the routes taken by the first caprines on the continent remains a challenge, genomic and linguistic evidence argues in favour of stronger relations between eastern and southern caprine and human populations than between those in other areas, such as western Africa [24–30].…”