Evaluation of DNA and collagen preservation in Late Pleistocene and Holocene bovid fossils from South Africa

Abstract

Few palaeogenetic studies have been conducted in southern Africa, potentially due to the expectation of very poor biomolecular preservation and the lack of published exploratory studies evaluating this. Thus, we set out to test the preservation of DNA and collagen in skeletal remains over the last ∼110,000 years in South Africa. We collected 320 Late Pleistocene and Holocene fossil teeth and bones from six bovid species, covering six fossil sites and generated digital records (3D models, photographs, and GBIF occurrences) before destructive sampling. We evaluated DNA preservation in 144 specimens and collagen in 54 of these. DNA was preserved in 45% and collagen in 35% of specimens. These were mostly Holocene in age (<11,700 years old), except for four Late Pleistocene specimens dating between ∼50,000 and 12,000 years old harbouring authentic ancient DNA. Geological age was an important explanatory variable in DNA and collagen preservation, but a poor predictor of mean read length. In addition to age, fossil site was a significant explanatory variable in endogenous DNA content, and in the interaction between DNA and collagen preservation, which were also significantly correlated. Thus, collagen content could potentially be used as a predictor of DNA preservation, but only within individual sites. Single-stranded libraries incorporated up to 6.7-fold more endogenous DNA and had higher complexity than double-stranded libraries. We show that palaeogenetic studies on fauna at lower latitudes are possible, and we conclude with recommendations we deem important to consider to maximise the success of such studies.