Development and characterization of 20 polymorphic microsatellite markers for the white-bellied pangolin Phataginus tricuspis (Mammalia, Pholidota)

Aguillon, Samantha; Dipita, Alain Din; Lecompte, Émilie; Missoup, Alain Didier; Tindo, Maurice; Gaubert, Philippe

doi:10.1007/s11033-020-05511-6

Cited by 10 publications

(18 citation statements)

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“…The PSMC curves for the two P. tricuspis lineages showed different trends; the Western Central Africa (WCA) lineage presented a stable IICR through time, while the Dahomey Gap (DG) lineage experienced a progressive decline (Figure 3b). These differences are mirrored by their genetic diversity whereby DG contains low levels of genetic diversity and high levels of inbreeding, while WCA has an opposite pattern (Figure 4, see below; Aguillon, et al 2020; Zanvo, et al 2022). Our results for the two different P. tricuspis lineages (Gaubert, et al 2016) included in this study suggest that the demographic history of the species is likely complex, lineage specific, and will require more thorough investigation (notably since the DG sample had limited sequencing depth; Table S1).…”

Section: Resultsmentioning

confidence: 99%

Pangolin genomes offer key insights and resources for the world’s most trafficked wild mammals

Heighton

Allio

Murienne

et al. 2023

Preprint

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Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and medicinal properties. Despite their great 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 pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera of pangolins, and highlighted the existence of an undescribed species closely related to South-East Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of South-East Asian pangolins, provides new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental vs. island populations and species lineages, suggesting that conservation planning should consider intra-specific patterns. With the expected loss of genomic diversity from recent, extensive trafficking not yet been realized in pangolins, we recommend that populations are 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 required for conserving pangolins, including tracing their illegal trade. These include the completion of whole-genomes for pangolins through the first reference genome with long reads 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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Section: Resultsmentioning

confidence: 99%

Pangolin genomes offer key insights and resources for the world’s most trafficked wild mammals

Heighton

Allio

Murienne

et al. 2023

Preprint

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“…Only WCA and Gabon individuals with at least 75% of genotyping success were considered for the analyses (N = 558). The 75% threshold coincides with ≥ 15 microsatellite markers, which triples the minimum number of loci needed to discriminate among WCA individuals (Aguillon et al, 2020).…”

Section: Methodsmentioning

confidence: 90%

“…We amplified 20 microsatellite markers developed from the genome of WBP using four multiplexes (4 to 6 loci) following Aguillon et al (2020). PCR products were run on an ABI 3730 DNA Analyser (Thermo Fisher Scientific) at Genoscreen and GeT-PlaGe ( https://get.genotoul.fr/; INRAE, Toulouse, France).…”

Section: Methodsmentioning

confidence: 99%

“…Using mitochondrial and nuclear DNA sequences, Gaubert et al (2016) delineated six cryptic, divergent and geographically isolated lineages across the species’ range, that were later traced by Zhang et al (2020) from large scale seizures made in Hong Kong. Further development of specific microsatellites markers (Aguillon et al, 2020) and extensive sample collection allowed to trace the WBP trade at the scale of a sub-region, the Dahomey Gap (West Africa), demonstrating 200–300 km trade distances between sourced forest and urban markets (Zanvo et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

“…Despite the original development of microsatellite markers from Cameroonian samples (Aguillon et al, 2020), no extensive genetic studies have yet been conducted on pangolins in the country. Cameroon has a long history of bushmeat consumption and trade (Bahuchet & Ioveva, 1999), and pangolins are commonly offered for sale in bushmeat markets and restaurants (Ingram et al, 2018; Nguyen et al, 2021), even since the advent of the COVID-19 pandemic (Harvey-Carroll et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

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Genetic tracing of the white-bellied pangolin’s trade in western central Africa

Dipita

Missoup

Aguillon

et al. 2023

Preprint

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African pangolins are intensively harvested to feed illegal trade networks. We focused on the conservation genetics of the most trafficked African species, the white-bellied pangolin (WBP; Phataginus tricuspis), through the genotyping of 562 individuals from reference populations and urban bushmeat markets in a vibrant trade hub from western Central Africa. Across Cameroon, Equatorial Guinea and northern Gabon, there was a lack of genetic differentiation and a signature of isolation-by-distance possibly due to unsuspected dispersal capacities involving a Wahlund effect. Despite a high level of genetic diversity compared to western Africa, we detected a 74-83% decline in the effective population size of WBP during the Middle Holocene. Private allele frequency tracing approach indicated up to 600 km sourcing distance by large urban markets from Cameroon, involving transnational trade activities. The 20 microsatellites markers used in this study provided the necessary power to distinguish among all WBP individuals and should be considered a valuable resource for future forensic applications. Because lineage admixture was detected in the study area, we recommend a multi-locus approach for tracing the pangolin trade. The Yaounde market was a major recruiter of genetic diversity in the region, and should receive urgent conservation action to mitigate the pangolin trade.

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Conservation genetics of the white‐bellied pangolin in West Africa: A story of lineage admixture, declining demography, and wide sourcing by urban bushmeat markets

Gossé,

Gonedelé‐Bi,

Dufour

et al. 2024

Ecology and Evolution

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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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Development and characterization of 20 polymorphic microsatellite markers for the white-bellied pangolin Phataginus tricuspis (Mammalia, Pholidota)

Cited by 10 publications

References 47 publications

Pangolin genomes offer key insights and resources for the world’s most trafficked wild mammals

Pangolin genomes offer key insights and resources for the world’s most trafficked wild mammals

Genetic tracing of the white-bellied pangolin’s trade in western central Africa

Conservation genetics of the white‐bellied pangolin in West Africa: A story of lineage admixture, declining demography, and wide sourcing by urban bushmeat markets

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