Abstract
Simple SummaryThe 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.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.
Highlights
More than 400 million sheep (Ovis aries) representing approximately 170 breeds live in Africa [1], but they are not indigenous to the continent
The modern sheep are dominated by subhaplogroup B1 (n = 42) and include A1b (n = 13), previously unreported in southern African sheep
The low level of genetic diversity in southern African sheep is consistent with models of serial founder effects as sheep populations moved across these diverse ecosystems
Summary
More than 400 million sheep (Ovis aries) representing approximately 170 breeds live in Africa [1], but they are not indigenous to the continent. They were likely domesticated from the European mouflon (Ovis aries musimon) and the Asiatic mouflon (Ovis orientalis) in southwestern Asia about 10,000 years ago [2–6]. Domesticated sheep probably moved westwards across the Mediterranean coast of northern Africa, down the Nile Valley, and across the -wetter Sahara. They reached the Turkana basin by 3000 BCE [13,14]
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