Determining species identity from confiscated pangolin remains using DNA barcoding

Population structure and demographic history of two highly-trafficked species of pangolin in the Congo Basin

African pangolins are hunted for their meat and for use in local traditional medicine, as well as for their scales, which are trafficked internationally, especially to growing Asian markets. Pangolin's population genetic structure can be used to trace the geographic origins of trafficked scales, but substantial sampling gaps across pangolins' ranges hinder these efforts. In this study, we documented population structure and dynamics in the two species of African pangolin, the white-bellied pangolin (Phataginus tricuspis) and the giant pangolin (Smutsia gigantea) in the underexplored Republic of Congo. Using the mitochondrial control region and two nuclear markers (beta-fibrinogen and titin), we identified high genetic diversity in both species. We document a distinct mitochondrial lineage of the white-bellied pangolin, which was most likely shaped by river barriers together with dynamics of forest refugia related to the climatic shifts during the Pleistocene. We detected population growth in the white-bellied pangolin coinciding with a dry period during the Pleistocene, suggesting some ability for this typically forest-dwelling species to persist under diverse environmental conditions. Using landscape genetics, we found all but one of the pangolins we sampled at bush meat markets originated locally. A single individual appeared to have been imported to Congo from Cameroon. These findings significantly contribute to our understanding of pangolin population biology and local trade dynamics. In addition, our data from a previously unstudied part of pangolins' ranges will help us to better understand international wildlife trafficking patterns and to target conservation and protection strategies for these highly vulnerable species.

Evolution and conservation genetics of pangolins

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.

Genomic analysis reveals a cryptic pangolin species

Eight extant species of pangolins are currently recognized. Recent studies found that two mitochondrial haplotypes identified in confiscations in Hong Kong could not be assigned to any known pangolin species, implying the existence of a species. Here, we report that two additional mitochondrial haplotypes identified in independent confiscations from Yunnan align with the putative species haplotypes supporting the existence of this mysterious species/population. To verify the new species scenario we performed a comprehensive analysis of scale characteristics and 138 whole genomes representing all recognized pangolin species and the cryptic new species, 98 of which were generated here. Our morphometric results clearly attributed this cryptic species to Asian pangolins (Manis sp.) and the genomic data provide robust and compelling evidence that it is a pangolin species distinct from those recognized previously, which separated from the Philippine pangolin and Malayan pangolin over 5 Mya. Our study provides a solid genomic basis for its formal recognition as the ninth pangolin species or the fifth Asian one, supporting a new taxonomic classification of pangolins. The effects of glacial climate changes and recent anthropogenic activities driven by illegal trade are inferred to have caused its population decline with the genomic signatures showing low genetic diversity, a high level of inbreeding, and high genetic load. Our finding greatly expands current knowledge of pangolin diversity and evolution and has vital implications for conservation efforts to prevent the extinction of this enigmatic and endangered species from the wild.

Whole-genome resequencing of Chinese pangolins reveals a population structure and provides insights into their conservation

Poaching and trafficking have a substantial negative impact on the population growth and range expansion of the Chinese pangolin (Manis pentadactyla). However, recently reported activities of Chinese pangolins in several sites of Guangdong province in China indicate a promising sign for the recovery of this threatened species. Here, we re-sequence genomes of 15 individuals and perform comprehensive population genomics analyses with previously published 22 individuals. These Chinese pangolins are found to be divided into three distinct populations. Multiple lines of evidence indicate the existence of a newly discovered population (CPA) comprises entirely of individuals from Guangdong province. The other two populations (CPB and CPC) have previously been documented. The genetic differentiation of the CPA and CPC is extremely large (FST = 0.541), which is larger than many subspecies-level differentiations. Even for the closer CPA and CPB, their differentiation (FST = 0.101) is still comparable with the population-level differentiation of many endangered species. Further analysis reveals that the CPA and CPB populations separate 2.5-4.0 thousand years ago (kya), and on the other hand, CPA and CPC diverge around 25-40 kya. The CPA population harbors more runs of homozygosity (ROHs) than the CPB and CPC populations, indicating that inbreeding is more prevalent in the CPA population. Although the CPC population has less mutational load than CPA and CPB populations, we predict that several Loss of Function (LoF) mutations will be translocated into the CPA or CPB populations by using the CPC as a donor population for genetic rescue. Our findings imply that the conservation of Chinese pangolins is challenging, and implementing genetic rescue among the three groups should be done with extreme caution.

Dissecting the illegal pangolin trade in China: An insight from seizures data reports

Wildlife trafficking poses a major threat to global biodiversity. Species such as pangolins are particularly vulnerable and trade continues almost unabated despite numerous interventions aimed at eradicating illegal wildlife trade. Despite restrictions on the pangolin trade, thousands of pangolins continue to be intercepted annually. We focused on China because of the recent delisting of pangolins from the Chinese pharmacopeia, and their removal from healthcare insurance, despite deeply ingrained traditions of having pangolins for ethno-medicinal use. We collated pangolin interception data from public online media seizure reports to characterize the pangolin trade within China, and found that a total of 326 independent seizures equivalent to 143,130 pangolins (31,676 individuals and 222,908 kg of scale) were reported in 26 provinces. Pangolin domestic seizures are greatest in the southern cities of Dehong, Fangchenggang, and Guangzhou. Also, we found 17 countries within the global pangolins range which were the major source of the pangolin shipments to China. The number of arrests and convictions was much lower than the number of pangolin incidents reported. Our results show a significant increase in the volume of scales and number of live pangolin seizures after amended endangered species law came into effect in 2018, and recorded the highest number of individual pangolin interceptions. China has shown increasing wildlife seizures over time, owing partly to emergent trends in the international wildlife trade as well as increasing global demand for ethnomedicine. The future eradication of illegal wildlife trade in China is dependent not only on stringent border control and offender prosecution but also the; removal of other threatened species from the pharmacopeia and healthcare insurance which includes wildlife derivatives. Furthermore, our work highlights importance of current policy intervention to combat the pangolin trade within China, and the need for further interventions both within China and in export countries.

Comparative study of gut microbiota from captive and confiscated-rescued wild pangolins

Pangolins are among the most critically endangered animals due to widespread poaching and worldwide trafficking. Captive breeding is considered to be one way to protect them and increase the sizes of their populations. However, comparative studies of captive and wild pangolins in the context of gut microbiota are rare. Here, the gut microbiome of captive and confiscated-rescued wild pangolins is compared, and the effects of different periods of captivity and captivity with and without antibiotic treatment are considered. We show that different diets and periods of captivity, as well as the application of antibiotic therapy, can alter gut community composition and abundance in pangolins. Compared to wild pangolins, captive pangolins have an increased capacity for chitin and cellulose/hemicellulose degradation, fatty acid metabolism, and short-chain fatty acid synthesis, but a reduced ability to metabolize exogenous substances. In addition to increasing the ability of the gut microbiota to metabolize nutrients in captivity, captive breeding imposes some risks for survival by resulting in a greater abundance of antibiotic resistance genes and virulence factors in captive pangolins than in wild pangolins. Our study is important for the development of guidelines for pangolin conservation, including health assessment, disease prevention, and rehabilitation of wild pangolin populations.

Scales of our lives: Sex identification of Temminck's pangolin (Smutsia temminckii) using scales retrieved out of the illegal wildlife trade

Pangolins are the most trafficked wild mammals, with their scales in high demand. Scales are often the only part of the animal confiscated from the trade, but they represent accessible material for forensic investigations, including for sexing. This study aimed to develop a sexing tool for Temminck's pangolin, using scales for hormone quantification. Scales from males and females were liquidised using keratinase and the resulting suspension analysed for progestagen and androgen metabolite (scPM and scAM) concentrations. Scale PM and scAM concentrations were compared between sexes, while overall median values for scPM and scAM, as well as a ratio of scPM to scAM (P/A) were used as boundary values for sex identification. Neither scPM nor scAM concentrations were significantly different between the sexes and concentrations of a juvenile and sub-adult male overlapped with females, possibly indicating later sexual maturity in males. Boundary values for scAM concentrations and the P/A ratio predicted sex with 100% accuracy for females and 78% for males, while the accuracies for the scPM boundary value were lower. When only adult individuals are considered, scAM and P/A ratio boundaries are 100% accurate for both sexes. Therefore, scale hormone ratios show promise as a sex identification tool for Temminck's pangolin, particularly applicable in forensic investigations on the pangolin trade.

The global magnitude and implications of legal and illegal wildlife trade in China

China is one of the largest consumer markets in the international legal and illegal wildlife trade. An increasing demand for wildlife and wildlife products is threatening biodiversity, both within China and in other countries where wildlife destined for the Chinese market is being sourced. We analysed official data on legal imports of CITES-listed species in five vertebrate classes (mammals, reptiles, amphibians, birds and fish), and on enforcement seizures of illegally traded wildlife, during 1997–2016. This is the first study that collates and analyses publicly available data on China's legal and illegal wildlife trade and considers a broad range of species. Specifically, we estimated the scale and scope of the legal and illegal wildlife trade, quantified the diversity of species involved, and identified the major trading partners, hotspots and routes associated with illegal trade. Our findings show that substantial quantities of wildlife have been extracted globally for the Chinese market: during 1997–2016 over 11.5 million whole-organism equivalents and 5 million kg of derivatives of legally traded wildlife, plus over 130,000 illegally traded animals (alive and dead) and a substantial amount of animal body parts and products, were imported into China. Although measures to reduce demand and alleviate poverty are crucial to curb unsustainable and illegal wildlife trade in the longer term, China's wildlife regulators and enforcers must take urgent measures to disrupt the supply chains from source to market.

Molecular Genetics Supports a Potential Fifth Asian Pangolin Species (Mammalia, Pholidota, Manis)

Recently, two mitochondrial haplotypes, H4 and H8, of Manis sp. were found in two seizures in Hong Kong that do not correspond to Manis javanica, Manis pentadactyla or Manis crassicaudata of Asian pangolin species or any African pangolin species. It was proposed that both haplotypes derived from Manis culionensis, an unknown lineage of M. javanica, or a thus far unidentified Asian pangolin species (Manis sp.). To further investigate these three hypotheses, we used two mitochondrial genes of all eight known extant pangolin species and conducted phylogenetic tree reconstructions, divergence time estimation, and species delimitation analyses. All analyses consistently confirmed that these two haplotypes of Manis sp. constitute a distinct lineage, potentially representing a fifth Asian pangolin species, which originated around the Late Miocene to Early Pliocene (6.95 [4.64-9.85] million years ago). Our study provides genetic support for a potential fifth Asian pangolin species and helps to better understand species diversity of Asian pangolins, which is urgently needed for effective conservation work.

Mitochondrial DNA analysis of critically endangered Chinese Pangolins (Manis pentadactyla) from Nepal

Chinese Pangolins (Manis pentadactyla) are Critically Endangered and one of the most illegally traded mammals globally. We generated first COI sequences from five individuals of this species from Nepal. BLASTn search of our 600 bp sequences at GenBank showed pair-wise identity between 99.17% and 100% to M. pentadactyla. There were three haplotypes and a total of five variable sites among five M. pentadactyla sequences. Neighbor-joining tree revealed that all M. pentadactyla from Nepal clustered into same group further splitting into two sub-groups albeit with low bootstrap value, suggesting potential multiple geographic origins. The K2P distance was 0.3% within group and 0.7% between four sequences from Bhaktapur and Kavrepalanchok districts (Mape2, Mape3, Mape5 and Mape6) and museum sample (Mape10). This study has generated reference samples for M. pentadactyla from Nepal and will be helpful in understanding dynamics of illegal trade of this species and in successful identification of M. pentadactyla from Nepal even in the absence of intact specimens.

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

Pangolins, or scaly anteaters, have recently been flagshiped as one of the most illegally traded mammals, and as a corollary, as potential intermediate hosts at the origin of the COVID-19 pandemic. In order to improve the traceability of their trade, we developed 20 polymorphic microsatellite loci for the white-bellied pangolin (Phataginus tricuspis), the species most frequently found on African bushmeat markets. We genotyped 24 white-bellied pangolins from the Douala market, Cameroon, originating from the Ebo forest c. 75 km north-east of Douala. The number of alleles per locus ranged from 4 to 12 (mean = 6.95), and mean observed and expected heterozygosities were 0.592 (0.208-0.875) and 0.671 (0.469-0.836), respectively. Genetic diversity was higher than that cross-estimated from microsatellite loci developed for other species of pangolins. Two loci deviated from Hardy-Weinberg equilibrium and two loci showed linkage disequilibrium. Genetic variance (PCoA) was increased with the addition of 13 pangolins of unknown origin, possibly suggesting that the Douala market is fed from differentiated source populations of white-bellied pangolins. Each of the 37 individuals had a unique multilocus genotype. The unbiased probability of identity (uPI) and the probability of identity among siblings (PIsibs) were both very low (uPI = 8.443 e-21; PIsibs = 1.011 e-07). Only five microsatellite loci were needed to reach the conservative value of PIsibs < 0.01, overall indicating a powerful discriminating power of our combined loci. These 20 newly developed microsatellite loci might prove useful in tracing the local-to-global trade of the white-bellied pangolin, and will hopefully contribute to the DNA-assisted implementation of future conservation strategies at reasonable costs.

Genomic consequences of population decline in critically endangered pangolins and their demographic histories

Pangolins are among the most critically endangered animals due to heavy poaching and worldwide trafficking. However, their demographic histories and the genomic consequences of their recent population declines remain unknown. We generated high-quality de novo reference genomes for critically endangered Malayan (Manis javanica, MJ) and Chinese (M. pentadactyla, MP) pangolins and re-sequencing population genomic data from 74 MJs and 23 MPs. We recovered the population identities of illegally traded pangolins and previously unrecognized genetic populations that should be protected as evolutionarily distinct conservation units. Demographic reconstruction suggested environmental changes have resulted in a population size fluctuation of pangolins. Additionally, recent population size declines due to human activities have resulted in an increase in inbreeding and genetic load. Deleterious mutations were enriched in genes related to cancer/diseases and cholesterol homeostasis, which may have increased their susceptibility to diseases and decreased their survival potential to adapt to environmental changes and high-cholesterol diets. This comprehensive study provides not only high-quality pangolin reference genomes, but also valuable information concerning the driving factors of long-term population size fluctuations and the genomic impact of recent population size declines due to human activities, which is essential for pangolin conservation management and global action planning.

Novel detection of provenance in the illegal wildlife trade using elemental data

Despite being the fourth largest criminal market in the world, no forensic tools have been sufficiently developed to accurately determine the legal status of seized animals and their parts. Although legal trading is permissible for farmed or captive-bred animals, many animals are illegally removed from the wild and laundered by masquerading them as captive bred. Here we present high-resolution x-ray fluorescence (XRF) as a non-invasive and cost-effective tool for forensic classification. We tested the efficacy of this technique by using machine learning on a training set of zoo specimens and wild-caught individuals of short-beaked echidnas (Tachyglossus aculeatus), a small insectivorous monotreme in Australia. XRF outperformed stable isotope analysis (δ13C, δ15N), reducing overall classification error below 4%. XRF has the added advantage of providing samples every 200 μm on a single quill, enabling 100% classification accuracy by taking the consensus of votes per quill. This accurate and cost-effective forensic technique could provide a much needed in situ solution for combating the illegal laundering of wildlife, and conversely, assist with certification of legally bred animals.

DNA Barcoding for the Identification and Authentication of Animal Species in Traditional Medicine

Animal-based traditional medicine not only plays a significant role in therapeutic practices worldwide but also provides a potential compound library for drug discovery. However, persistent hunting and illegal trade markedly threaten numerous medicinal animal species, and increasing demand further provokes the emergence of various adulterants. As the conventional methods are difficult and time-consuming to detect processed products or identify animal species with similar morphology, developing novel authentication methods for animal-based traditional medicine represents an urgent need. During the last decade, DNA barcoding offers an accurate and efficient strategy that can identify existing species and discover unknown species via analysis of sequence variation in a standardized region of DNA. Recent studies have shown that DNA barcoding as well as minibarcoding and metabarcoding is capable of identifying animal species and discriminating the authentics from the adulterants in various types of traditional medicines, including raw materials, processed products, and complex preparations. These techniques can also be used to detect the unlabelled and threatened animal species in traditional medicine. Here, we review the recent progress of DNA barcoding for the identification and authentication of animal species used in traditional medicine, which provides a reference for quality control and trade supervision of animal-based traditional medicine.