Lineages to landscapes: mitogenomic insights and climate refugia informing proactive conservation of the endangered Tricarinate Hill Turtle (Melanochelys tricarinata) in the Indian subcontinent

The Tricarinate Hill Turtle (Melanochelys tricarinata), endemic to the Indian subcontinent, faces significant threats from intensifying anthropogenic pressures and severe habitat degradation. Thus, to facilitate conservation efforts for this endangered species, a comprehensive assessment of its genomics and ecology is imperative. The present study adopts two independent approaches by characterizing the complete mitogenome and evaluating current and future habitat suitability. The mitogenome (16,745 bp) comprises 37 genes, with most protein-coding genes beginning with the canonical ATG start codon. The codon usage analysis revealed that arginine, leucine, and serine are the most frequently used amino acids. The control region contains a termination-associated sequence, four conserved sequence blocks, and two distinct tandem repeat motifs. The phylogenetic assessment using both Bayesian inference and Maximum-likelihood methods consistently placed M. tricarinata in a distinct clade, separate from other geoemydids. The mitogenome-based TimeTree analysis revealed that M. tricarinata diverged from its closest relatives during the Oligocene. The comparative analyses of partial mitochondrial genes revealed substantial divergence between Melanochelys congeners (3.71-5.20% in cox1, 7.99-9.29% in cytb), with low haplotypic diversity in M. tricarinata and high in M. trijuga. The ensemble model identified suitable habitats under both current and future climate scenarios. Under present scenario, approximately 374,657 km² of ideal habitat was delineated within the training extent with a mean corridor connectivity of 0.377, which was reduced to 238,039 km² and mean connectivity of 0.518 when restricted to existing forest cover. Moreover, only 31,450 km² of the suitable habitat for this species falls within Protected Areas, representing just 11.912% of the total identified favorable area. The future projections suggest a potential reduction of up to 40% in suitable habitat area due to climatic changes, accompanied by increased fragmentation, smaller patch sizes, and over 80% decline in connectivity across future scenarios. Thus, this study provides comprehensive insights into the systematic position, evolutionary history and ecological requirements of M. tricarinata, offering a critical scientific foundation to guide effective conservation and management strategies for this imperiled species across its native range.