Nucleotide Variation and Selective Pressure in the Mitochondrial Genome of African Elephants

Among the large mammals of Africa, elephants are probably the worst affected by human activities. Although they have been listed as endangered and protected since 1989, illegal poaching and habitat destruction continue to diminish and isolate remaining populations that are dispersed widely over 37 sub-Saharan African countries. Their populations currently exist in small isolated habitat, and this threatens elephant genetic diversity. Although literature is available on the taxonomy and phylogeny of African elephant, few studies have focused on codon usage on mitochondrial genomes. To analyze nucleotide diversity, selective pressure and demographic history of African elephants, we used the portion of mitochondrial sequences of 102 individuals available in the genome database. Our data indicated a low codon bias index (CBI) and a relatively high effective number of codons (ENC) value in the mitochondrial genome, suggesting that African elephants are less biased in their codon usage preference. The data also support a strong purifying selection in the mitochondrial genome of African elephants. However, few sites are under positive selection in the mitochondrial genome of African elephants, with Loxodonta africana presenting more sites under positive selection compared to L. cyclotis. The present work supports the idea that different evolutionary rate among nucleotide sites in L. africana and L. cyclotis, attributable to differences in the frequency of positive selection and probably different environmental conditions, are the driving forces for the codon usage bias in African elephants. Further studies are needed to investigate the contribution of different subpopulation in the genetic structure and diversity of African elephants.