Identification of confiscated pangolin for conservation purposes  through molecular approach

Wirdateti, .; Nugraha, Taufiq Purna; Yulianto, -; Semiadi, Gono

doi:10.11609/jott.7572.14.6.21127-21139

Cited by 2 publications

(2 citation statements)

References 39 publications

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“…First, the assembled mtDNA genomes were aligned with reference mtDNA genomes available on NCBI using global alignment algorithms implemented in Geneious. Only reference genomes from wild pangolins of known origin were included (Gaubert et al, 2018 ; Hassanin et al, 2015 ; Hu, Hao, et al, 2020 ; Mason et al, 2019 ; Nash et al, 2018 ; Wirdateti et al, 2022 ; Table S1 ); however, the documented origin of some samples may not be precise and/or accurate in some cases (see Figure 1 ). Second, stop codons and any overlapping regions between genes were removed (as these regions are under complex selective constraints).…”

Section: Methodsmentioning

confidence: 99%

Phylogeography of the Sunda pangolin, Manis javanica: Implications for taxonomy, conservation management and wildlife forensics

Sitam,

Salgado‐Lynn,

Denel

et al. 2023

Ecology and Evolution

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The Sunda pangolin (Manis javanica) is the most widely distributed Asian pangolin species, occurring across much of Southeast Asia and in southern China. It is classified as Critically Endangered and is one of the most trafficked mammals in the world, which not only negatively impacts wild Sunda pangolin populations but also poses a potential disease risk to other species, including humans and livestock. Here, we aimed to investigate the species' phylogeography across its distribution to improve our understanding of the species' evolutionary history, elucidate any taxonomic uncertainties and enhance the species' conservation genetic management and potential wildlife forensics applications. We sequenced mtDNA genomes from 23 wild Sunda pangolins of known provenance originating from Malaysia to fill sampling gaps in previous studies, particularly in Borneo. To conduct phylogenetic and population genetic analyses of Sunda pangolins across their range, we integrated these newly generated mitochondrial genomes with previously generated mtDNA and nuclear DNA data sets (RAD‐seq SNP data). We identified an evolutionarily distinct mtDNA lineage in north Borneo, estimated to be ~1.6 million years divergent from lineages in west/south Borneo and the mainland, comparable to the divergence time from the Palawan pangolin. There appeared to be mitonuclear discordance, with no apparent genetic structure across Borneo based on analysis of nuclear SNPs. These findings are consistent with the ‘out of Borneo hypothesis’, whereby Sunda pangolins diversified in Borneo before subsequently migrating throughout Sundaland, and/or a secondary contact scenario between mainland and Borneo. We have elucidated possible taxonomic issues in the Sunda/Palawan pangolin complex and highlight the critical need for additional georeferenced samples to accurately apportion its range‐wide genetic variation into appropriate taxonomic and conservation units. Additionally, these data have improved forensic identification testing involving these species and permit the implementation of geographic provenance testing in some scenarios.

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Section: Methodsmentioning

confidence: 99%

Phylogeography of the Sunda pangolin, Manis javanica: Implications for taxonomy, conservation management and wildlife forensics

Sitam,

Salgado‐Lynn,

Denel

et al. 2023

Ecology and Evolution

View full text Add to dashboard Cite

show abstract

“…First, the assembled mtDNA genomes were aligned with reference mtDNA genomes available on NCBI using global alignment algorithms implemented in Geneious. Only reference genomes from wild pangolins of known origin were included (Gaubert et al, 2018;Hassanin et al, 2015;Hu, Hao, et al, 2020;Mason et al, 2019;Nash et al, 2018;Wirdateti et al, 2022;Table S1); however, the documented origin of some samples may not be precise and/or accurate in some cases (see Figure 1). Second, stop codons and any overlapping regions between genes were removed (as these regions are under complex selective constraints).…”

Section: Phylogenetic and Molecular Dating Analysismentioning

confidence: 99%

Phylogeography of the Sunda pangolin, Manis javanica: implications for taxonomy, conservation management and wildlife forensics

Sitam¹,

Salgado-Lynn

Denel

et al. 2023

Preprint

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Aim: The Sunda pangolin (Manis javanica) is the most widely distributed Asian pangolin species. It is one of the most trafficked mammals in the world, which not only negatively impacts wild Sunda pangolin populations, but also poses a potential disease risk to other species, including humans and livestock. Despite the imminent threat to the species’ survival and its prevalence in the wildlife trade, the phylogeography and evolution of the Sunda pangolin is not well understood. We aimed to investigate the species’ phylogeography across its distribution to improve our understanding of the species’ evolutionary history, elucidate any taxonomic uncertainties and enhance the species’ conservation genetic management and wildlife forensics applications. Location: Southeast Asia and southern China. Methods: We sequenced mtDNA genomes from 23 wild Sunda pangolins from Borneo and Peninsular Malaysia. We used these data in conjunction with previous generated mtDNA and nuclear datasets from across the species’ range to perform various phylogenetic and population genetic analyses. Results: We identified an evolutionarily distinct mtDNA lineage in north Borneo, which was estimated to be ~1.6 million years divergent from lineages in west/south Borneo and the mainland, comparable to the divergence time of the Palawan pangolin. There appeared to be mitonuclear discordance, with no apparent genetic structure across Borneo based on analysis of nuclear SNPs. Main conclusions: These findings are consistent with the ‘out of Borneo hypothesis’, whereby Sunda pangolins diversified in Borneo before subsequently migrating throughout Sundaland, and/or a secondary contact scenario between mainland and Borneo. We have elucidated possible taxonomic issues in the Sunda/Palawan pangolin complex, and highlight the critical need for additional georeferenced samples to accurately apportion its range-wide genetic variation into appropriate taxonomic and conservation units. Additionally, these data have improved forensic species identification testing involving these species and permit the implementation of geographic provenance testing in some scenarios.

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Identification of confiscated pangolin for conservation purposes through molecular approach

Cited by 2 publications

References 39 publications

Phylogeography of the Sunda pangolin, Manis javanica: Implications for taxonomy, conservation management and wildlife forensics

Phylogeography of the Sunda pangolin, Manis javanica: Implications for taxonomy, conservation management and wildlife forensics

Phylogeography of the Sunda pangolin, Manis javanica: implications for taxonomy, conservation management and wildlife forensics

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