Elucidating the Evolutionary History of the Critically Endangered Batagur baska Using Complete Mitogenome

Background/Objectives: Batagur baska is a critically endangered turtle, primarily found in the estuaries and tidal regions of large rivers. B. baska has experienced extensive population declines across most of its range, with no confirmed wild populations remaining. This study aims to generate and characterize a complete mitogenome of B. baska, as well as assess its phylogeny and evolutionary history Methods: Eight mitochondrial genome were generated using next-generation sequencing (NGS). The dataset was used to assess phylogenetic position using Bayesian and Maximum Likelihood approaches, as well as to estimate divergence times. Results: The assembled mitogenomes (16,731, 16,715, 16,662, 16,654, 16,642, 16,582, 16,540, 16,527 bp) comprises 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes, along with a fully resolved non-coding control region. The genome exhibits a typical vertebrate organization with a nucleotide composition heavily biased toward A + T content, consistent with other Geoemydidae turtles. This mitochondrial genome data is combined with existing genetic information to evaluate the species’ phylogenetic position. The Bayesian and Maximum likelihood phylogenetic analysis confirmed a close genetic relationship between B. baska and B. affinis. Divergence time estimation analyses indicated that the lineage leading to B. baska diverged at approximately 9.12 million years ago (Ma) (95% HPD: 5.11–13.24 Ma), supporting a Miocene origin. Comparative analyses of the newly generated and previously published mitogenomes identified nucleotide variation, synonymous and nonsynonymous substitutions, and indels, present new mitogenome variation not known before. Conclusions: The research provides a complete mitochondrial genome for the species, offering robust phylogenetic and divergence time estimates. This mitogenomic resource also provides a baseline for future population levels which is required to guide potential breeding programs and reintroduction efforts, as well as for long-term monitoring.