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

## TL;DR

Pancake tortoises have low genetic diversity and two distinct evolutionary groups, which suggests the need for targeted conservation efforts.

## Contribution

The study reveals cryptic speciation and population divergence in pancake tortoises using mitogenome data.

## Key findings

- Pancake tortoises have extremely low mitogenome nucleotide diversity.
- Northern populations are expanding while central populations are contracting, with poor connectivity.
- A deep genetic split of ~5.74 million years exists between Kenyan and Tanzanian clades.

## Abstract

Pancake tortoise (Malacochersus tornieri), 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 M. tornieri using mitochondrial genomes (mitogenomes) of 60 free-ranging individuals from 11 localities across northern and central Tanzania. M. tornieri 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 M. tornieri and inform conservation management.

•Pancake tortoises exhibit extremely low mitogenomic genetic diversity•Northern populations expanding, central contracting; poor connectivity across Tanzania•Deep split ∼5.74 mya between Kenyan and Tanzanian clades suggests possible cryptic speciation•Findings guide population-specific conservation management and habitat protection

Pancake tortoises exhibit extremely low mitogenomic genetic diversity

Northern populations expanding, central contracting; poor connectivity across Tanzania

Deep split ∼5.74 mya between Kenyan and Tanzanian clades suggests possible cryptic speciation

Findings guide population-specific conservation management and habitat protection

Zoology; Genomics; Evolutionary biology