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Phylogeography of the Sunda pangolin, Manis javanica: implications for taxonomy, conservation management and wildlife forensics
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  • Frankie Sitam,
  • Milena Salgado-Lynn,
  • Azroie Denel,
  • Elisa Panjang,
  • Ross McEwing,
  • Amanda Lightson,
  • Rob Ogden,
  • Nur Alwanie Maruji,
  • Nurhartini Kamalia Yahya,
  • Cosmas Ngau,
  • Noor Azleen Mohd Kulaimi,
  • Hartini Ithnin,
  • Jeffrine Rovie-Ryan,
  • Mohd Soffian Abu Bakar,
  • Kyle Ewart
Frankie Sitam
National Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks (DWNP/ PERHILITAN)
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Milena Salgado-Lynn
Danau Girang Field Centre
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Azroie Denel
Sarawak Forestry Corporation
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Elisa Panjang
Danau Girang Field Centre
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Ross McEwing
United Nations Office on Drugs and Crime (UNODC) ROSEAP
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Amanda Lightson
TRACE Wildlife Forensic Network
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Rob Ogden
TRACE Wildlife Forensic Network
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Nur Alwanie Maruji
Wildlife Health, Genetic and Forensic Laboratory (WHGFL)
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Nurhartini Kamalia Yahya
Danau Girang Field Centre
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Cosmas Ngau
National Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks (DWNP/ PERHILITAN)
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Noor Azleen Mohd Kulaimi
National Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks (DWNP/ PERHILITAN)
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Hartini Ithnin
National Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks (DWNP/ PERHILITAN)
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Jeffrine Rovie-Ryan
Universiti Malaysia Sarawak
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Mohd Soffian Abu Bakar
Sabah Wildlife Department
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Kyle Ewart
TRACE Wildlife Forensic Network

Corresponding Author:[email protected]

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Abstract

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.
07 Mar 2023Submitted to Ecology and Evolution
08 Mar 2023Submission Checks Completed
08 Mar 2023Assigned to Editor
11 Mar 2023Reviewer(s) Assigned
12 May 2023Review(s) Completed, Editorial Evaluation Pending
15 May 2023Editorial Decision: Revise Minor
30 Jun 20231st Revision Received
06 Jul 2023Submission Checks Completed
06 Jul 2023Assigned to Editor
06 Jul 2023Review(s) Completed, Editorial Evaluation Pending
12 Jul 2023Editorial Decision: Accept