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Gu T, Hu J, Yu L. Evolution and conservation genetics of pangolins. Integr Zool 2024; 19:426-441. [PMID: 38146613 DOI: 10.1111/1749-4877.12796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Pangolins (Pholidota, Manidae) are classified as an evolutionarily distinct and globally endangered mammal due to their unique morphology (nail-like scales and a myrmecophagous diet) and being the victim of heavy poaching and worldwide trafficking. As such, pangolins serve as a textbook example for studying the special phenotypic evolutionary adaptations and conservation genetics of an endangered species. Recent years have demonstrated significant advancements in the fields of molecular genetics and genomics, which have translated to a series of important research achievements and breakthroughs concerning the evolution and conservation genetics of pangolins. This review comprehensively presents the hitherto advances in phylogeny, adaptive evolution, conservation genetics, and conservation genomics that are related to pangolins, which will provide an ample understanding of their diversity, molecular adaptation mechanisms, and evolutionary potentials. In addition, we highlight the priority of investigating species/population diversity among pangolins and suggest several avenues of research that are highly relevant for future pangolin conservation.
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Affiliation(s)
- Tongtong Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
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Gossé KJ, Gonedelé‐Bi S, Dufour S, Danquah E, Gaubert P. Conservation genetics of the white-bellied pangolin in West Africa: A story of lineage admixture, declining demography, and wide sourcing by urban bushmeat markets. Ecol Evol 2024; 14:e11031. [PMID: 38435007 PMCID: PMC10905243 DOI: 10.1002/ece3.11031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 03/05/2024] Open
Abstract
During the last 40 years, the volumes of African pangolins feeding the illegal wildlife trade have dramatically increased. We conducted a conservation genetics survey of the most traded African species, the white bellied pangolin (WBP; Phataginus tricuspis), across three West African countries including Guinea, Côte d'Ivoire, and Ghana. Our study combining mitochondrial DNA sequencing and microsatellite genotyping is the first to reveal a wide pattern of admixture between two of the six mitochondrial lineages as previously delimited within WBP. We found a signature of isolation by distance but a lack of population genetic structuring, supporting the idea that WBP may have underestimated dispersal abilities. Levels of genetic diversity were low in West African lineages (WAfr and Gha) compared to Central Africa, reinforcing the picture of genetic pauperization shared by West African WBP. We observed a 85%-98% decline in the effective population size of WBP occurring c. 3200 to 400 ya, with current numbers (520-590) at the lower end of the conservative thresholds for minimum viable population size. The microsatellite markers were powerful enough to differentiate between individuals and identify replicated samples, confirming the utility of this approach in tracing the pangolin trade. Genetic diversity estimates confirmed that Yopougon, the main bushmeat market from Abidjan (Côte d'Ivoire), was fed by a large trade network as confirmed by vendors reporting 10 different sources situated 62-459 km away from the market. We conclude that WBP distributed in the Upper Guinean Block should be considered a single management unit of high conservation concern, as impacted by genetic diversity erosion, drastic decline in effective population size, and wide range sourcing for feeding urban bushmeat markets. Given the genetic admixture pattern detected within WBP from West Africa, we advocate for a multi-locus strategy to trace the international trade of the species.
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Affiliation(s)
- Koffi Jules Gossé
- Laboratoire de Biotechnologie, Agriculture et Valorisation des Ressources Biologiques, UFR BiosciencesUniversité Félix Houphouët‐BoignyAbidjanCôte d'Ivoire
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INPUniversité Toulouse 3 – Paul Sabatier (UT3)ToulouseFrance
| | - Sery Gonedelé‐Bi
- Laboratoire de Biotechnologie, Agriculture et Valorisation des Ressources Biologiques, UFR BiosciencesUniversité Félix Houphouët‐BoignyAbidjanCôte d'Ivoire
| | | | - Emmanuel Danquah
- Department of Wildlife and Range Management, Faculty of Renewable Natural ResourcesKwame Nkrumah University of Science and TechnologyKumasiGhana
| | - Philippe Gaubert
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INPUniversité Toulouse 3 – Paul Sabatier (UT3)ToulouseFrance
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR)Universidade do Porto, Terminal de Cruzeiros do Porto de LeixõesPortoPortugal
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Heighton SP, Allio R, Murienne J, Salmona J, Meng H, Scornavacca C, Bastos ADS, Njiokou F, Pietersen DW, Tilak MK, Luo SJ, Delsuc F, Gaubert P. Pangolin Genomes Offer Key Insights and Resources for the World's Most Trafficked Wild Mammals. Mol Biol Evol 2023; 40:msad190. [PMID: 37794645 PMCID: PMC10551234 DOI: 10.1093/molbev/msad190] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023] Open
Abstract
Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and purported medicinal properties. Despite their conservation concern, knowledge of their evolution is limited by a paucity of genomic data. We aim to produce exhaustive genomic resources that include 3,238 orthologous genes and whole-genome polymorphisms to assess the evolution of all eight extant pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera and highlighted the existence of an undescribed species closely related to Southeast Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of Southeast Asian pangolins, provide new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental versus island populations and species lineages, suggesting that conservation planning should consider intraspecific patterns. With the expected loss of genomic diversity from recent, extensive trafficking not yet realized in pangolins, we recommend that populations be genetically surveyed to anticipate any deleterious impact of the illegal trade. Finally, we produce a complete set of genomic resources that will be integral for future conservation management and forensic endeavors for pangolins, including tracing their illegal trade. These comprise the completion of whole-genomes for pangolins through the hybrid assembly of the first reference genome for the giant pangolin (Smutsia gigantea) and new draft genomes (∼43x-77x) for four additional species, as well as a database of orthologous genes with over 3.4 million polymorphic sites.
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Affiliation(s)
- Sean P Heighton
- Laboratoire Evolution et Diversité Biologique (EDB)— IRD-UPS-CNRS, Université Toulouse III, Toulouse, France
| | - Rémi Allio
- Institut des Sciences de l'Évolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique (EDB)— IRD-UPS-CNRS, Université Toulouse III, Toulouse, France
| | - Jordi Salmona
- Laboratoire Evolution et Diversité Biologique (EDB)— IRD-UPS-CNRS, Université Toulouse III, Toulouse, France
| | - Hao Meng
- The State Key Laboratory of Protein and Plant Gene Research of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Céline Scornavacca
- Institut des Sciences de l'Évolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Armanda D S Bastos
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Pretoria, South Africa
| | - Flobert Njiokou
- Laboratoire de Parasitologie et Ecologie, Faculté des Sciences, Université de Yaoundé I, Yaoundé, Cameroon
| | - Darren W Pietersen
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Pretoria, South Africa
| | - Marie-Ka Tilak
- Institut des Sciences de l'Évolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Frédéric Delsuc
- Institut des Sciences de l'Évolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique (EDB)— IRD-UPS-CNRS, Université Toulouse III, Toulouse, France
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade 16 do Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal
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Gossé KJ, Gonedelé-Bi S, Justy F, Chaber AL, Kramoko B, Gaubert P. DNA-typing surveillance of the bushmeat in Côte d'Ivoire: a multi-faceted tool for wildlife trade management in West Africa. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01474-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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