Heritage Cases

Caprini is a widespread clade of bovids (antelopes and relatives) that includes goats, sheep, and relatives such as musk ox, takin, and serow. This is a highly successful clade widespread across Eurasia and North America and largely adapted to mountainous habitats. The only extant (wild, not domesticated) African caprins are the nubian and walia ibexes (Capra nubiana and C. walia) and the barbary sheep (Ammotragus lervia). Otherwise, the total absence of caprins from sub-Saharan Africa today is quite remarkable in comparison to their distribution and diversity in Eurasia. The fossil record, however, tells a different story. Caprin fossils, though rare, are known from Plio-Pleistocene sites across eastern and southern Africa. For example, Gentry (1996) described a 3 Ma species of takin (Budorcas churcheri) from Hadar in Ethiopia; takins are today restricted to the Himalayas. Presuming a link to cold-adapted Eurasian lineages, Vrba (1995) used the fossil record of Caprins to propose pulses of faunal immigration of Eurasian taxa into Africa during times of global cooling and sea-level lowering in the Plio-Pleistocene. More recently, one of us (Bibi et al., 2012) described a 2 Ma fossil Capra from Ethiopia, and questioned whether the fossil record of African caprins truly represents – as Vrba had proposed – short-lived faunal immigrations from Eurasia, or whether African fossil caprini represented long-lived endemic lineages, all now extinct. Because the African fossil caprin record is quite sparse, very little is known about the many (often unnamed) species; often too little, in fact, to draw substantive conclusions of relationships based on morphological analyses. The caprin material from the Western Cape (Boomplaas Cave) now provides us with the opportunity to conclusively test the origins and geographic relationships of at least one lineage of extinct African caprin using ancient DNA evidence. In fact the South African record provides some of the most completely preserved material of African caprins, namely the species Makapania broomi, which is known from the late Pliocene of Makapansgat, and which may have affinities with an extinct Pliocene European species (Gentry, 1970). One of us (Brink, 1999) described occurrences of caprin remains resembling those of Makapania from late Quaternary sites in South Africa, extending the geographic and temporal range of this clade to the southern tip of the continent. Another one of us (Faith, 2013) showed that in the Boomplaas Cave fauna, this extinct caprin survived until the early Holocene. The relatively young age and good preservation of the Boomplaas Cave caprin teeth make them ideal candidates for ancient DNA extraction and analysis (Shapiro & Hofreiter, 2014). By determining which extant caprin is the closest relative to the extinct species at Boomplaas Cave we aim to clarify the mystery surrounding the phylogenetic relationship of these specimens. Fossil species such as Makapania broomi have traditionally been referred to the ‘Ovibovini’, a paraphyletic assemblage of large caprins (today takin and musk ox). Ancient DNA promises to finally solve the riddle of an African caprin’s evolutionary origins, and to shed light on African-Eurasian faunal exchanges in a time preceding today’s human-modified landscapes. New methods in ancient DNA extraction (Dabney et al., 2013) offer previously unforeseen possibilities in the scientific investigation of these specimens than was ever previously possible. Aim of the project We aim to successfully extract and sequence DNA sequences of the extinct caprin species from late Pleistocene and early Holocene levels at Boomplaas Cave. We aim to test the following hypotheses: 1. Does the Boomplaas caprin represent a long-lived African lineage, now extinct, or was it a relatively recent faunal immigrant from Eurasia? Implicit in this hypothesis is also the long-term status of faunal exchange (gene flow) between Eurasia and Africa. 2. Does the demographic history of the extinct caprin indicate it was already in decline prior to its early Holocene extinction? Or was extinction a rapid and sudden event? This ties into broader hypotheses of climatic (long-term) vs. human (rapid) causes for late Pleistocene-Holocene large mammal extinctions. Our proposed sampling techniques are well-proven and stem from our extensive experience in sampling, laboratory techniques and published methods and protocols (e.g. Dabney et al., 2013; Gansauge & Meyer 2013; Barlow et al., 2016; Paijmans et al., 2016). It has been shown in previous years that DNA in ancient and historical samples is best preserved in dense bone (e.g. Pinhasi et al., 2015) and tooth roots with cementum (Damgaard et al., 2015). Hence, we propose these for sampling. All material will be processed at the University Potsdam in the Evolutionary Adaptive Genomics group (headed by Prof. Dr. Michael Hofreiter) where dedicated ancient DNA facilities are present. These facilities include several isolated laboratories dedicated to the extraction and manipulation of degraded genetic material. The Evolutionary Adaptive Genomics Group is highly experienced in successfully processing and analysing ancient DNA samples and the specific challenges that can arise with them. A selection of relevant papers and reviews that show our expertise in this research field include: Hofreiter (2014), Elsner et al. (2014), Shapiro & Hofreiter (2014), Campbell & Hofreiter (2015), Paijmans et al. (2016) and Wecek et al. (2016). Our proposed research would produce the first genomic study about an extinct caprin species from Sub-Saharan Africa. To successfully conduct this research it is not only necessary to possess a high level of expertise in obtaining and analyzing ancient DNA but it requires as well palaeontological knowledge to interpret the generated results. Therefore we have incorporated experienced palaeogeneticists (Prof. Dr. Michael Hofreiter, Evolutionary Adaptive Genomics Group) as well as palaeontologists who specialized in African bovids and caprins in particular (e.g. Brink, 1999; Bibi et al. 2012; Faith 2013). Please see as well the uploaded detailed project description (including a detailed sample list with pictures, our work program, significance and implications for future research and profiles of past experience).