Genetic connectivity across marginal habitats: the elephants of the Namib Desert.

Locally isolated populations in marginal habitats may be genetically distinctive and of heightened conservation concern. Elephants inhabiting the Namib Desert have been reported to show distinctive behavioral and phenotypic adaptations in that severely arid environment. The genetic distinctiveness of Namibian desert elephants relative to other African savanna elephant (Loxodonta africana) populations has not been established. To investigate the genetic structure of elephants in Namibia, we determined the mitochondrial (mt) DNA control region sequences and genotyped 17 microsatellite loci in desert elephants (n = 8) from the Hoanib River catchment and the Hoarusib River catchment. We compared these to the genotypes of elephants (n = 77) from other localities in Namibia. The mtDNA haplotype sequences and frequencies among desert elephants were similar to those of elephants in Etosha National Park, the Huab River catchment, the Ugab River catchment, and central Kunene, although the geographically distant Caprivi Strip had different mtDNA haplotypes. Likewise, analysis of the microsatellite genotypes of desert-dwelling elephants revealed that they were not genetically distinctive from Etosha elephants, and there was no evidence for isolation by distance across the Etosha region. These results, and a review of the historical record, suggest that a high learning capacity and long-distance migrations allowed Namibian elephants to regularly shift their ranges to survive in the face of high variability in climate and in hunting pressure.

Distinguishing forest and savanna African elephants using short nuclear DNA sequences.

A more complete description of African elephant phylogeography would require a method that distinguishes forest and savanna elephants using DNA from low-quality samples. Although mitochondrial DNA is often the marker of choice for species identification, the unusual cytonuclear patterns in African elephants make nuclear markers more reliable. We therefore designed and utilized genetic markers for short nuclear DNA regions that contain fixed nucleotide differences between forest and savanna elephants. We used M13 forward and reverse sequences to increase the total length of PCR amplicons and to improve the quality of sequences for the target DNA. We successfully sequenced fragments of nuclear genes from dung samples of known savanna and forest elephants in the Democratic Republic of Congo, Ethiopia, and Namibia. Elephants at previously unexamined locations were found to have nucleotide character states consistent with their status as savanna or forest elephants. Using these and results from previous studies, we estimated that the short-amplicon nuclear markers could distinguish forest from savanna African elephants with more than 99% accuracy. Nuclear genotyping of museum, dung, or ivory samples will provide better-informed conservation management of Africa's elephants.