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Genetic analyses of southern African livestock have been limited and primarily focused on agricultural production rather than the reconstruction of prehistory. Attempts to sequence DNA preserved in archaeological remains of domestic stock have been hampered by the discovery of high error rates in the morphological identification of fauna. As such, much DNA sequencing effort that was directed at sequencing southern Africa’s domestic livestock has been expended sequencing wild forms. The few genetic data that are available from both modern and archaeological domestic stock show relatively low genetic diversity in maternally inherited mitochondrial lineages in both sheep and cattle. Analyses of modern stock show, in contrast, that the bi-parentally inherited nuclear genome is relatively diverse. This pattern is perhaps indicative of historic cross-breeding with stock introduced from outside Africa. Critically important to moving forward in our understanding of the prehistory of domesticates in southern Africa is attention to the high error rates in faunal analyses that have been documented both genetically and through ZooMS.