Little variation, lots of repetition: mitogenomic diversity in African wild dogs

African wild dogs (Lycaon pictus) are the sole representative of their genus, and form an ancestral lineage most closely related to Asian dholes (Cuon alpinus) and Ethiopian wolves (Canis simensis). They suffered tremendous demographic losses over the past decades and have low levels of mitochondrial (mtDNA) variation, previously measured with a 381 bp segment of the Control region (CR). In this study, we did a whole mitochondrial genome (mitogenomes) comparison of 20 wild dogs from South Africa and Zimbabwe. We questioned (i) whether low levels of mtDNA diversity (typically seen in the CR) are also observed in other regions of the mitogenome, (ii) how mitogenomic diversity in wild dogs compares to other species, and (iii) how mitogenomic lineages have diverged across time. We found that mtDNA diversity was low across the genome, with 5 unique haplotypes across 16,829-17,531 bp (and only 11 CR haplotypes across their entire range), and a nucleotide diversity (π) of 0.0009, which is much lower than most other animal species. We also found an imperfect tandem repeat ('ACACATACGT') at the flanks of the CR, with a total length that extends much further than typically observed in animals, varying between 43-989 bp among individuals. Because the CR is noncoding, this may have occurred due to DNA slippage in a lack of selective constraints. The low number of haplotypes may be the effect of historic population contractions and recent demographic losses, which wild dogs are known to have experienced.