Mitogenomes reveal multiple evolutionary units and low genetic diversity of the critically endangered pancake tortoise Malacochersus tornieri

Pancake tortoise (<i>Malacochersus tornieri</i>), a critically endangered East African endemic, is threatened by habitat destruction and illegal collection. Its fragmented range and isolated populations may have driven genetic differentiation that could inform its conservation. We infer evolutionary histories and population structure of <i>M. tornieri</i> using mitochondrial genomes (mitogenomes) of 60 free-ranging individuals from 11 localities across northern and central Tanzania<i>. M. tornieri</i> has rearranged mitogenome structure, translocation mutations of protein-coding genes, and extremely low mitogenome nucleotide diversity. Northern and central Tanzanian populations exhibit shallow divergence and contrasting demographic histories, with recent expansion in the north and contraction in the central population. This, combined with isolation-by-distance patterns found, suggests poor population connectivity. We found two divergent clades, one in central Tanzania and the other in Kenya, with the latter diverging ∼5.74 million years ago, suggesting possible cryptic speciation. Our findings provide insights into the population status of <i>M. tornieri</i> and inform conservation management.