Lineages to landscapes: Mitogenomic insights and climate refugia informing proactive conservation of the Endangered Tricarinate Hill Turtle (Melanochelys tricarinata) in the Indian Subcontinent
Open accessPreprint — published as 10.1038/s41598-025-26890-5
Abstract
The Tricarinate Hill Turtle Melanochelys tricarinata , endemic to the Indian subcontinent, is classified as ‘Endangered’ due to anthropogenic pressures and climate change. The present study adopts a parallel approach by characterizing the complete mitogenome and evaluating current and future habitat suitability. The mitogenome, spanning 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 key regulatory elements, including 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 geoemydid taxa, and identified it as an ancestral lineage to Sacalia , Notochelys , Heosemys , and Cyclemys . The ensemble model identified suitable habitats under both current and future climate scenarios. Under present scenario, approximately 374,657 km² of suitable habitat was delineated within the training extent with a mean corridor connectivity of 0.377, which was reduced to 238,039 km² when restricted to existing forest cover. The future projections indicate a potential loss of up to 40% in suitable habitat area due to climate change, accompanied by increased fragmentation, reduced patch size, and decreased connectivity. Thus, this study provides comprehensive insights into the 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.
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Lintermans, M., Lutz, M. L., Whiterod, N. S., Gruber, B., Hammer, M. P., Kennard, M. J., Morgan, D. L., Raadik, T. A., Unmack, P. J., Brooks, S. G., et al. (2024) · Biological Conservation · doi:10.1016/j.biocon.2024.110843 · Cited by 22 · see citing works
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Self-citationKundu, S., Mukherjee, T., Kamalakannan, M., Barhadiya, G., Ghosh, C., & Kim, H. (2023) · PeerJ · doi:10.7717/peerj.15975 · Cited by 19 · see citing works
Self-citationOrganization and variation of mitochondrial DNA control region in pleurodiran turtles
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Structural Variation of the Turtle Mitochondrial Control Region
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Pet and turtle: DNA barcoding identified twelve Geoemydid species in northeast India
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Self-citationClimate change affects the early‐life history of a freshwater turtle in a severely drying region
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Elevating human dimensions of amphibian and reptile conservation, a USA perspective
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Self-citationDavidian, A., Dyomin, A. G., Galkina, S., Makarova, N. E., Dmitriev, S. E., & Gaginskaya, E. R. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab324 · Cited by 12 · see citing works
Do Freshwater Turtles Use Rainfall to Increase Nest Success?
Geller, G. A., Doody, J. S., Clulow, S., & Duncan, R. P. (2022) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2022.852175 · Cited by 12 · see citing works
Phylogenetics for Wildlife Conservation
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Phylogenomics reconciles molecular data with the rich fossil record on the origin of living turtles
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Melanochelys trijuga (Schweigger 1812) – Indian Black Turtle
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Population Viability Analysis for Two Species of Imperiled Freshwater Turtles
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On the underappreciated role of scavengers in freshwater ecosystems
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Self-citationTurtle and tortoise mitogenomes under contrasting positive selection pressure
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Melanochelys tricarinata: Horne, B.D., Praschag, P., Choudhury, B.C. & Singh, S.
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RNA Transcription and Control of Gene Expression
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Flagged first, then by citations
1 of the 134 references couldn’t be matched to a known paper.
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Nawani, S., Sureshgopi, D., Raveendran, A. B., Singh, H., Bashir, A., Mondol, S., & Das, A. (2026) · Genes · doi:10.3390/genes17101242
- Authors
- Abedin, I., Putra, A., Kang, H.-E., Singh, A., Singh, S., Jung, W.-K., Kim, H.-W., & Kundu, S.
- Affiliations
- Dibru-Saikhowa Conservation Society
- Pukyong National University (KR)
- Turtle Survival Alliance Foundation India
- Corresponding author
- Kim, Hyun-Woo
- Kundu, Shantanu
- ORCID
- Venue
- Scientific Reports
- Published
- 2025-07-22
- Volume
- 15
- Issue
- 1
- Pages
- 42751-42751
- ISSN
- 2045-2322 (ISSN-L)
- PMC
- PMC12663409
- OpenAlex
- W4416782840
- Cited by
- 1
- References
- 134
- Citations by year
- 2026: 1
- FWCI
- 0.64
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Scientific Reports (publishedVersion, cc-by-nc-nd)
- Research Square (acceptedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Ministry of Education
- Topics
- Physical Sciences › Environmental Science › Nature and Landscape Conservation › Turtle Biology and Conservation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- mitochondrial genome, mitochondrial DNA, phylogeny, divergence time estimation, climate refugia, habitat suitability, habitat fragmentation, genetic connectivity, conservation status, endangered turtles, Indian subcontinent, protected areas, anthropogenic threats, habitat degradation, Oligocene
- MeSH terms
- Refugium, Animals, Bayes Theorem, Climate, Conservation of Natural Resources, India, Phylogeny, Turtles, Ecosystem, Genome, Mitochondrial, Endangered Species
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