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 e...

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Bibliographic Details
Published in:The Journal of heredity 2011-09, Vol.102 (5), p.610-616
Main Authors: Ishida, Yasuko, Demeke, Yirmed, van Coeverden de Groot, Peter J., Georgiadis, Nicholas J., Leggett, Keith E.A., Fox, Virginia E., Roca, Alfred L.
Format: Article
Language:English
Subjects:
Animals
Base Sequence
Cell Nucleus - genetics
Congo
Conservation
Conservation biology
Deoxyribonucleic acid
DNA
DNA - chemistry
Elephantidae
Elephants
Elephants - classification
Elephants - genetics
Ethiopia
Forensic sciences
Genes, X-Linked
Genetic Variation
Genotype
Male
Namibia
Species Specificity
Systematic biology
Taxonomy
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Summary: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.
ISSN:0022-1503
1465-7333
DOI:10.1093/jhered/esr073