Global terrapin character-based DNA barcodes: assessment of the mitochondrial COI gene and conservation status revealed a putative cryptic species
Technological and analytical advances to study evolutionary biology, ecology, and conservation of the Southern River Terrapin (Batagur affinis ssp.) are realised through molecular approaches, including DNA barcoding. We evaluated the use of COI DNA barcodes in Malaysia’s Southern River Terrapin popu...
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| Format: | Article |
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Multidisciplinary Digital Publishing Institute
2023
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| Online Access: | http://psasir.upm.edu.my/id/eprint/108113/ |
| _version_ | 1848865076311752704 |
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| author | Mohd Salleh, Mohd Hairul Esa, Yuzine Mohamed, Rozihan |
| author_facet | Mohd Salleh, Mohd Hairul Esa, Yuzine Mohamed, Rozihan |
| author_sort | Mohd Salleh, Mohd Hairul |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | Technological and analytical advances to study evolutionary biology, ecology, and conservation of the Southern River Terrapin (Batagur affinis ssp.) are realised through molecular approaches, including DNA barcoding. We evaluated the use of COI DNA barcodes in Malaysia’s Southern River Terrapin population to better understand the species’ genetic divergence and other genetic characteristics. We evaluated 26 sequences, including four from field specimens of Southern River Terrapins obtained in Bota Kanan, Perak, Malaysia, and Kuala Berang, Terengganu, Malaysia, as well as 22 sequences from global terrapins previously included in the Barcode of Life Database (BOLD) Systems and GenBank. The species are divided into three families: eight Geoemydidae species (18%), three Emydidae species (6%), and one Pelomedusidae species (2%). The IUCN Red List assigned the 12 species of terrapins sampled for this study to the classifications of critically endangered (CR) for 25% of the samples and endangered (EN) for 8% of the samples. With new haplotypes from the world’s terrapins, 16 haplotypes were found. The intraspecific distance values between the COI gene sequences were calculated using the K2P model, which indicated a potential cryptic species between the Northern River Terrapin (Batagur baska) and Southern River Terrapin (Batagur affinis affinis). The Bayesian analysis of the phylogenetic tree also showed both species in the same lineage. The BLASTn search resulted in 100% of the same species of B. affinis as B. baska. The Jalview alignment visualised almost identical sequences between both species. The Southern River Terrapin (B. affinis affinis) from the west coast of Peninsular Malaysia was found to share the same haplotype (Hap_1) as the Northern River Terrapin from India. However, B. affinis edwardmolli from the east coast of Peninsular Malaysia formed Hap_16. The COI analysis found new haplotypes and showed that DNA barcodes are an excellent way to measure the diversity of a population. |
| first_indexed | 2025-11-15T13:58:57Z |
| format | Article |
| id | upm-108113 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-15T13:58:57Z |
| publishDate | 2023 |
| publisher | Multidisciplinary Digital Publishing Institute |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-1081132024-09-24T07:52:11Z http://psasir.upm.edu.my/id/eprint/108113/ Global terrapin character-based DNA barcodes: assessment of the mitochondrial COI gene and conservation status revealed a putative cryptic species Mohd Salleh, Mohd Hairul Esa, Yuzine Mohamed, Rozihan Technological and analytical advances to study evolutionary biology, ecology, and conservation of the Southern River Terrapin (Batagur affinis ssp.) are realised through molecular approaches, including DNA barcoding. We evaluated the use of COI DNA barcodes in Malaysia’s Southern River Terrapin population to better understand the species’ genetic divergence and other genetic characteristics. We evaluated 26 sequences, including four from field specimens of Southern River Terrapins obtained in Bota Kanan, Perak, Malaysia, and Kuala Berang, Terengganu, Malaysia, as well as 22 sequences from global terrapins previously included in the Barcode of Life Database (BOLD) Systems and GenBank. The species are divided into three families: eight Geoemydidae species (18%), three Emydidae species (6%), and one Pelomedusidae species (2%). The IUCN Red List assigned the 12 species of terrapins sampled for this study to the classifications of critically endangered (CR) for 25% of the samples and endangered (EN) for 8% of the samples. With new haplotypes from the world’s terrapins, 16 haplotypes were found. The intraspecific distance values between the COI gene sequences were calculated using the K2P model, which indicated a potential cryptic species between the Northern River Terrapin (Batagur baska) and Southern River Terrapin (Batagur affinis affinis). The Bayesian analysis of the phylogenetic tree also showed both species in the same lineage. The BLASTn search resulted in 100% of the same species of B. affinis as B. baska. The Jalview alignment visualised almost identical sequences between both species. The Southern River Terrapin (B. affinis affinis) from the west coast of Peninsular Malaysia was found to share the same haplotype (Hap_1) as the Northern River Terrapin from India. However, B. affinis edwardmolli from the east coast of Peninsular Malaysia formed Hap_16. The COI analysis found new haplotypes and showed that DNA barcodes are an excellent way to measure the diversity of a population. Multidisciplinary Digital Publishing Institute 2023 Article PeerReviewed Mohd Salleh, Mohd Hairul and Esa, Yuzine and Mohamed, Rozihan (2023) Global terrapin character-based DNA barcodes: assessment of the mitochondrial COI gene and conservation status revealed a putative cryptic species. Animals, 13 (11). art. no. 1720. pp. 1-17. ISSN 2076-2615 https://www.mdpi.com/2076-2615/13/11/1720 10.3390/ani13111720 |
| spellingShingle | Mohd Salleh, Mohd Hairul Esa, Yuzine Mohamed, Rozihan Global terrapin character-based DNA barcodes: assessment of the mitochondrial COI gene and conservation status revealed a putative cryptic species |
| title | Global terrapin character-based DNA barcodes: assessment of the mitochondrial COI gene and conservation status revealed a putative cryptic species |
| title_full | Global terrapin character-based DNA barcodes: assessment of the mitochondrial COI gene and conservation status revealed a putative cryptic species |
| title_fullStr | Global terrapin character-based DNA barcodes: assessment of the mitochondrial COI gene and conservation status revealed a putative cryptic species |
| title_full_unstemmed | Global terrapin character-based DNA barcodes: assessment of the mitochondrial COI gene and conservation status revealed a putative cryptic species |
| title_short | Global terrapin character-based DNA barcodes: assessment of the mitochondrial COI gene and conservation status revealed a putative cryptic species |
| title_sort | global terrapin character-based dna barcodes: assessment of the mitochondrial coi gene and conservation status revealed a putative cryptic species |
| url | http://psasir.upm.edu.my/id/eprint/108113/ http://psasir.upm.edu.my/id/eprint/108113/ http://psasir.upm.edu.my/id/eprint/108113/ |