Print PageRecently, there have been many evolutionary studies trying to elucidate the relationships between proboscideans. With modern advances in DNA sequencing technologies researchers have been able to obtain entire mitochondrial genome sequences for both the extinct woolly mammoth (Mammuthus primigenius) and the American mastodon (Mammut americanum). Having these complete genomes has helped to resolve higher-order relationships in this clade, but there is still debate about the taxonomy of the African elephant. Phylogenies constructed from nuclear DNA support splitting forest (Loxodonta cyclotis) and savanna elephants (Loxodonta africana) into two species, while studies of mitochondrial DNA show a more complex story that does not support the two-taxon hypothesis. Missing from previous analyses is a complete mitochondrial genome for the forest elephant. Therefore, we sequenced two individual forest elephant mitochondrial genomes, one from West African and one from Central Africa, by extracting DNA from dung and designing 47 sets of overlapping primer pairs to amplify across the entire genome.
Results/Conclusions
The results of our phylogenetic analyses show that the African elephant forms a deeply diverged clade separate from the Asian elephant, and that there is support for species-level differentiation between forest and savanna elephants. While we do see a clear split between savanna and forest elephants, further study of the phylogeography of the West African forest elephant is warranted due to the diversity of habitats (i.e. forest, savanna and desert) found in that region. Additionally, using the phylogeny we have inferred, we conducted an analysis to detect any positive selection that may be acting on the 13 protein-coding genes of the mitochondrial genome. These genes create proteins that make up the complexes of the electron transport chain, thus directly influencing energy production and metabolism. Due to the importance of this process, the proteins involved are under high functional constraint. Given the specialized ecological and morphological differences between forest and savanna elephants, we expected to find a small number of significant amino acid changes between these two taxa. We found one such radical amino acid change in the ND4 gene, which is believed to pump protons across an electrochemical gradient. An amino acid change in this gene could affect the efficiency of pumping protons, which may alter overall metabolic performance in these individuals. Future work includes mapping these amino acids onto protein crystal structures in order to determine whether the specific changes may alter the overall protein structure, hence potentially altering protein function.
