A long‐standing Pleistocene refugium in southern Africa and a mosaic of refugia in East Africa: insights from mtDNA and the common eland antelope

Abstract

Aim Previous genetic studies of African savanna ungulates have indicated Pleistocene refugial areas in East and southern Africa, and recent palynological, palaeovegetation and fossil studies have suggested the presence of a long-standing refugium in the south and a mosaic of refugia in the east. Phylogeographic analysis of the common eland antelope, Taurotragus oryx (Bovidae), was used to assess these hypotheses and the existence of genetic signatures of Pleistocene climate change.Location The sub-Saharan savanna biome of East and southern Africa.Methods Mitochondrial DNA control-region fragments (414 bp) from 122 individuals of common eland were analysed to elucidate the phylogeography, genetic diversity, spatial population structuring, historical migration and demographic history of the species. The phylogeographic split among major genetic lineages was dated using Bayesian coalescent-based methods and a calibrated fossil root of 1.6 Ma for the split between the common eland and the giant eland, Taurotragus derbianus.Results Two major phylogeographic lineages comprising East and southern African localities, respectively, were separated by a net nucleotide distance of 4.7%. A third intermediate lineage comprised only three haplotypes, from Zimbabwe in southern Africa. The estimated mutation rate of 0.097 Myr )1 revealed a more recent common ancestor for the eastern lineage (0.21 Ma; 0.07-0.37) than for the southern lineage (0.35 Ma; 0.10-0.62). Compared with the latter, the eastern lineage showed pronounced geographic structuring, lower overall nucleotide diversity, higher population differentiation, and isolation-bydistance among populations. Main conclusionsThe data support the hypothesis of Pleistocene refugia occurring in East and southern Africa. In agreement with palynological, palaeovegetation and fossil studies, our data strongly support the presence of a longer-standing population in the south and a mosaic of Pleistocene refugia in the east, verifying the efficacy of genetic tools in addressing such questions. The more recent origin of the common eland inhabiting East Africa could result from colonization following extinction from the region. Only two other dated African ungulate phylogenies have been published, applying different methods, and the similarity of dates obtained from the three distinct approaches indicates a significant event c. 200 ka, which left a strong genetic signature across a range of ungulate taxa.

Genetic analysis of southern African gemsbok (Oryx gazella) reveals high variability, distinct lineages and strong divergence from the East African Oryx beisa

“…Our gemsbok sample showed values from about 1.2 to 2.5% which, again, is in accordance with earlier findings for other African bovids (e.g. kudu Tragelaphus strepsiceros: 1.0%, impala Aepyceros melampus: 2.2%, beisa: 1.6-8.1%, eland Taurotragus oryx: 0.5-3.6%, values taken from Nersting and Arctander, 2001;Masembe et al, 2006;Lorenzen et al, 2010).…”

“…Arctander et al, 1996;Alpers et al, 2004;Grobler et al, 2005;Masembe et al, 2006;Lorenzen et al, 2010;Zachos et al, 2010 and references in these studies). Our results are in line with these findings: we found one new haplotype for every 2.5 individuals, and haplotype diversity (0.94 overall and site-specific values ranging from 0.74 to 0.92) is within the range known from other African bovids such as the kob (Kobus kob: 0.72, Birungi and Arctander, 2000) and the African buffalo (Syncerus caffer: 0.91, Simonsen et al, 1998).…”

“…Simonsen et al, 1998;Birungi and Arctander, 2000;Lorenzen et al, 2010;Zachos et al, 2010 and references therein). The first goal of our study was therefore to determine levels of diversity in the gemsbok.…”

Plio-Pleistocene history and phylogeography of Acacia senegal in dry woodlands and savannahs of sub-Saharan tropical Africa: evidence of early colonisation and recent range expansion

“…For example, contraction and expansion of the Sahara desert in Central and West Africa, and interaction of climate with the Great Rift Valley and the elevated topographies of East and Southern Africa produced wide altitudinal ranges forming a complex mosaic of landscapes and localised climate regimes that functioned as refugia during extreme climate conditions (Plana, 2004;Lorenzen et al, 2010).…”

“…However, the ecological distribution of the baobab tree only partially matches that of the dry woodlands and savannahs, and the shea tree has a limited distribution in the SudanoSahelian zone. In contrast to plants, there are numerous studies of vertebrates that show development of intraspecific differentiation that coincides with formation of the woodland and savannah biomes in Africa (Jacobs, 2004), for example, plains zebra, Equus quagga (Lorenzen et al, 2008) and common eland antelope, Taurotragus oryx (Lorenzen et al, 2010).…”