Phylogeography of the heavily poached African common pangolin (Pholidota, Manis tricuspis) reveals six cryptic lineages as traceable signatures of Pleistocene diversification

Genetic tracing of the illegal trade of the white-bellied pangolin (Phataginus tricuspis) in western Central Africa

The white-bellied pangolin is subject to intense trafficking, feeding both local and international trade networks. In order to assess its population genetics and trace its domestic trade, we genotyped 562 pangolins from local to large bushmeat markets in western central Africa. We show that the two lineages described from the study region (WCA and Gab) were overlapping in ranges, with limited introgression in southern Cameroon. There was a lack of genetic differentiation across WCA and a significant signature of isolation-by-distance possibly due to unsuspected dispersal capacities involving a Wahlund effect. We detected a c. 74.1-82.5% decline in the effective population size of WCA during the Middle Holocene. Private allele frequency tracing approach indicated up to 600 km sourcing distance by large urban markets from Cameroon, including Equatorial Guinea. The 20 species-specific microsatellite loci provided individual-level genotyping resolution and should be considered as valuable resources for future forensic applications. Because admixture was detected between lineages, we recommend a multi-locus approach for tracing the pangolin trade. The Yaoundé market was the main hub of the trade in the region, and thus should receive specific monitoring to mitigate pangolins' domestic trafficking. Our study also highlighted the weak implementation of CITES regulations at European borders.

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.

Uncovering the magnitude of African pangolin poaching with extensive nanopore DNA genotyping of seized scales

Trade in pangolins is illegal, and yet tons of their scales and products are seized at various ports. These large seizures are challenging to process and comprehensively genotype for upstream provenance tracing and species identification for prosecution. We implemented a scalable DNA barcoding pipeline in which rapid DNA extraction and MinION sequencing were used to genotype a substantial proportion of pangolin scales subsampled from 2 record shipments seized in Singapore in 2019 (37.5 t). We used reference sequences to match the scales to phylogeographical regions of origin. In total, we identified 2346 cytochrome b (cytb) barcodes of white-bellied (Phataginus tricuspis) (from 1091 scales), black-bellied (Phataginus tetradactyla) (227 scales), and giant (Smutsia gigantea) (1028 scales) pangolins. Haplotype diversity was higher for P. tricuspis scales (121 haplotypes, 66 novel) than that for P. tetradactyla (22 haplotypes, 15 novel) and S. gigantea (25 haplotypes, 21 novel) scales. Of the novel haplotypes, 74.2% were likely from western and west-central Africa, suggesting potential resurgence of poaching and newly exploited populations in these regions. Our results illustrate the utility of extensively subsampling large seizures and outline an efficient molecular approach for rapid genetic screening that should be accessible to most forensic laboratories and enforcement agencies.

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

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.

Pangolin Genomes Offer Key Insights and Resources for the World's Most Trafficked Wild Mammals

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.

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.

Geography vs. past climate: the drivers of population genetic structure of the Himalayan langur

Background

Contemporary species distribution, genetic diversity and evolutionary history in many taxa are shaped by both historical and current climate as well as topography. The Himalayas show a huge variation in topography and climatic conditions across its entire range, and have experienced major climatic fluctuations in the past. However, very little is known regarding how this heterogenous landscape has moulded the distribution of Himalayan fauna. A recent study examined the effect of these historical events on the genetic diversity of the Himalayan langurs in Nepal Himalaya. However, this study did not include the samples from the Indian Himalayan region (IHR). Therefore, here we revisit the questions addressed in the previous study with a near complete sampling from the IHR, along with the samples from the Nepal Himalaya. We used the mitochondrial Cytochrome-b (Cyt-b, 746 bp) region combined with multiple phylogeographic analyses and palaeodistribution modelling.

Results

Our dataset contained 144 sequences from the IHR as well as the Nepal Himalaya. Phylogenetic analysis showed a low divergent western clade nested within high divergent group of eastern lineages and in the network analysis we identified 22 haplotypes over the entire distribution range of the Himalayan langurs. Samples from the Nepal Himalaya showed geographically structured haplotypes corresponding to different river barriers, whereas samples from IHR showed star-like topology with no structure. Our statistical phylogeography analysis using diyABC supported the model of east to west colonisation of these langurs with founder event during colonisation. Analysis of demographic history showed that the effective population size of the Himalayan langurs decreased at the onset of last glacial maximum (LGM) and started increasing post LGM. The palaeodistribution modelling showed that the extent of suitable habitat shifted from low elevation central Nepal, and adjoining parts of north India, during LGM to the western Himalaya at present.

Conclusion

The current genetic diversity and distribution of Himalayan langurs in the Nepal Himalaya has been shaped by river barriers, whereas the rivers in the IHR had relatively less time to act as a strong genetic barrier after the recent colonisation event. Further, the post LGM expansion could have had confounding effect on Himalayan langur population structure in both Nepal Himalaya and IHR.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02054-1.

Can DNA help trace the local trade of pangolins? Conservation genetics of white-bellied pangolins from the Dahomey Gap (West Africa)

Background

African pangolins are currently experiencing unprecedented levels of harvesting, feeding both local demands and the illegal international trade. So far, the lack of knowledge on the population genetics of African pangolins has hampered any attempts at assessing their demographic status and tracing their trade at the local scale. We conducted a pioneer study on the genetic tracing of the African pangolin trade in the Dahomey Gap (DG). We sequenced and genotyped 189 white-bellied pangolins from 18 forests and 12 wildlife markets using one mitochondrial fragment and 20 microsatellite loci.

Results

Tree-based assignment procedure showed that the pangolin trade is endemic to the DG region, as it was strictly fed by the the Dahomey Gap lineage (DGL). DGL populations were characterized by low levels of genetic diversity, an overall absence of equilibrium, important inbreeding levels, and lack of geographic structure. We identified a 92–98% decline in DGL effective population size 200–500 ya—concomitant with major political transformations along the ‘Slave Coast’—leading to contemporaneous estimates being inferior to minimum viable population size (< 500). Genetic tracing suggested that wildlife markets from the DG sourced pangolins through the entire DGL range. Our loci provided the necessary power to distinguish among all the genotyped pangolins, tracing the dispatch of a same individual on the markets and within local communities. We developed an approach combining rarefaction analysis of private allele frequencies with cross-validation of observed data that traced five traded pangolins to their forest origin, c. 200–300 km away from the markets.

Conclusions

Although the genetic toolkit that we designed from traditional markers can prove helpful to trace the illegal trade in pangolins, our tracing ability was limited by the lack of population structure within the DGL. Given the deleterious combination of genetic, demographic, and trade-related factors affecting DGL populations, the conservation status of white-bellied pangolins in the DG should be urgently re-evaluated.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01971-5.

Ancient volcanos as species pumps: A case study of freshwater amphipods in Northeast Asia

Volcano-tectonic processes have been viewed as primary drivers in the formation of present-day diversity. Volcanos associated with mountain uplifts drive allopatric speciation through vicariance and may impact the surrounding areas like species pump or species attractor. However, the application of these hypotheses to aquatic fauna has rarely been tested explicitly. We tested these hypotheses in the Changbai Mountains (Mts), which are one of the most typical, active volcanic ranges in Northeast (NE) Asia with a long and turbulent geological history. The Gammarus nekkensis species complex of amphipod crustaceans, widely distributed throughout NE Asia with poor dispersal abilities and a long evolutionary history, is a suitable model for testing hypotheses of species pump or species attractor. Phylogenetic and ancestral range reconstructions demonstrated that the studied amphipod originated from the Changbai Mts ~27 Ma and diverged into eastern (Clade I) and western (Clade II) clades, which corresponds well with the initial volcanic eruption of the Changbai Mts in the Late Oligocene. The subsequent diversifications of subclades CI-3, CII-1a and CII-2a were probably driven by second and third eruptions of the Changbai Mts during the Miocene. In particular, the Changbai lineages had spread to the Russian Far East multiple times since the Early Miocene, and widely colonized the region during the Pleistocene. Our discoveries suggest that the ancient volcanos of the Changbai Mts act as species pumps in NE Asia, resulted in burst of diversification around the Changbai Mts and subsequent dispersals into adjacent regions.

Quantitative estimates of glacial refugia for chimpanzees (Pan troglodytes) since the Last Interglacial (120,000 BP)

Paleoclimate reconstructions have enhanced our understanding of how past climates have shaped present-day biodiversity. We hypothesize that the geographic extent of Pleistocene forest refugia and suitable habitat fluctuated significantly in time during the late Quaternary for chimpanzees (Pan troglodytes). Using bioclimatic variables representing monthly temperature and precipitation estimates, past human population density data, and an extensive database of georeferenced presence points, we built a model of changing habitat suitability for chimpanzees at fine spatio-temporal scales dating back to the Last Interglacial (120,000 BP). Our models cover a spatial resolution of 0.0467° (approximately 5.19 km² grid cells) and a temporal resolution of between 1000 and 4000 years. Using our model, we mapped habitat stability over time using three approaches, comparing our modeled stability estimates to existing knowledge of Afrotropical refugia, as well as contemporary patterns of major keystone tropical food resources used by chimpanzees, figs (Moraceae), and palms (Arecacae). Results show habitat stability congruent with known glacial refugia across Africa, suggesting their extents may have been underestimated for chimpanzees, with potentially up to approximately 60,000 km² of previously unrecognized glacial refugia. The refugia we highlight coincide with higher species richness for figs and palms. Our results provide spatio-temporally explicit insights into the role of refugia across the chimpanzee range, forming the empirical foundation for developing and testing hypotheses about behavioral, ecological, and genetic diversity with additional data. This methodology can be applied to other species and geographic areas when sufficient data are available.

A new species of tree hyrax (Procaviidae: Dendrohyrax) from West Africa and the significance of the Niger–Volta interfluvium in mammalian biogeography

Tree hyraxes (Dendrohyrax) are one of only three genera currently recognized in Procaviidae, the only extant family in the mammalian order Hyracoidea. Their taxonomy and natural history have received little attention in recent decades. All tree hyrax populations of Guineo-Congolian forests of Africa are currently treated as a single species, Dendrohyrax dorsalis, the western tree hyrax, but many other groups of mammals distributed across this large biome have been shown to consist of several different species, each restricted to a distinct biogeographical region. We analysed variation in loud-call structure, pelage colour, skull morphometrics and mitochondrial genomes in populations across much of the range of D. dorsalis. This integrative approach uncovered considerable cryptic variation. The population found between the Niger and Volta Rivers in West Africa is particularly distinctive, and we describe it herein as a new species. Our study highlights the need to revise the taxonomy of the genus Dendrohyrax in light of modern systematics and current understanding of its distribution. It also adds to a growing body of evidence that the Niger–Volta interfluvium has a distinct meso-mammal fauna. Unfortunately, the fauna of this region is under major threat and warrants much greater conservation attention.

WP, Sterkhova VV, Kusamba C, Rödel M, Penner J, Peterson AT, Brown RM. Rivers, not refugia, drove diversification in arboreal, sub-Saharan African snakes

The relative roles of rivers versus refugia in shaping the high levels of species diversity in tropical rainforests have been widely debated for decades. Only recently has it become possible to take an integrative approach to test predictions derived from these hypotheses using genomic sequencing and paleo-species distribution modeling. Herein, we tested the predictions of the classic river, refuge, and river-refuge hypotheses on diversification in the arboreal sub-Saharan African snake genus Toxicodryas. We used dated phylogeographic inferences, population clustering analyses, demographic model selection, and paleo-distribution modeling to conduct a phylogenomic and historical demographic analysis of this genus. Our results revealed significant population genetic structure within both Toxicodryas species, corresponding geographically to river barriers and divergence times from the mid-Miocene to Pliocene. Our demographic analyses supported the interpretation that rivers are indications of strong barriers to gene flow among populations since their divergence. Additionally, we found no support for a major contraction of suitable habitat during the last glacial maximum, allowing us to reject both the refuge and river-refuge hypotheses in favor of the river-barrier hypothesis. Based on conservative interpretations of our species delimitation analyses with the Sanger and ddRAD data sets, two new cryptic species are identified from east-central Africa. This study highlights the complexity of diversification dynamics in the African tropics and the advantages of integrative approaches to studying speciation in tropical regions.

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.

Threats from wildlife trade: The importance of genetic data in safeguarding the endangered Four-eyed Turtle (Sacalia quadriocellata)

Wildlife trade has been considered one of the largest threats to biodiversity in Southeast Asia. Many vertebrates, such as pangolins, elephants and turtles have been heavily hunted as a result of high demand from emerging markets in China and other countries in the region. In Vietnam, over-exploitation of turtles over several decades to supply the international trade has extirpated numerous populations and driven several species to the brink of extinction. To reverse this trend, conservation measures, such as re-introduction of confiscated or captive-bred animals to their native habitats, should be implemented to recover severely declined local populations. For species with a complex phylogeographic structure, however, it is crucial to understand geographic patterns of genetically-distinct populations to avoid releasing animals of unknown origin to wrong localities. In this study, we investigate the phylogeographic pattern of the Four-eyed Turtle (Sacalia quadriocellata), a widely traded species, which occurs in southern China, northern and central Laos and much of Vietnam, using samples with known localities and those collected from the local trade. Our range-wide phylogenetic and network study, based on the complete mitochondrial cytochrome b gene, recovered at least three major clades and seven subclades within the species range. Amongst these, two subclades, one from northern Annamites, Vietnam and the other from north-eastern Laos, are newly discovered. The fine scale phylogeographic analysis helped us to assign misidentified sequences from GenBank and those from confiscated animals with unknown origin to well-defined geographic populations. The results highlight the importance of incorporating samples collected from the local trade and the wild in genetic analyses to support both ex-situ and in-situ conservation programmes of highly-threatened species in accordance with the IUCN’s One Plan Approach.

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.

Skull shape variation in extant pangolins (Pholidota: Manidae): allometric patterns and systematic implications

Pangolins are among the most endangered groups of mammals, comprising eight extant species delineated into three genera. Despite several studies dedicated to their skeletal anatomy, the potential taxonomic insight from cranial morphological variation in extant Pholidota is yet to be assessed with modern geometric morphometric methods. We present the first comprehensive study on the cranial morphology of extant pangolins and discuss its implications for the taxonomy and evolution of the group. We performed landmark-based morphometric analyses on 241 museum specimens to describe the variation in skull shape in seven of the eight extant species. Our analyses revealed genus- and species-level morphological discrimination, with Asian species (Manis spp.) being grouped together, whereas African pangolins present distinct skull shapes between small (Phataginus spp.) and large (Smutsia spp.) species. Analyses of allometry also identified a set of traits whose allometric trajectories distinguish Asian from African specimens. Finally, we uncovered intraspecific variation in skull shape in white-bellied pangolins (Phataginus tricuspis) that partly corroborates recent DNA-based differentiation among biogeographically distinct populations. Overall, our results shed light on the morphological diversity of the skull of these enigmatic myrmecophagous mammals and confirm the genus-level classification and cryptic diversity within the white-bellied pangolin revealed by molecular phylogenetics.

Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae

BACKGROUND

This study used next generation sequencing to generate the mitogenomes of four African pangolin species; Temminck's ground pangolin (Smutsia temminckii), giant ground pangolin (S. gigantea), white-bellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla).

RESULTS

The results indicate that the mitogenomes of the African pangolins are 16,558 bp for S. temminckii, 16,540 bp for S. gigantea, 16,649 bp for P. tetradactyla and 16,565 bp for P. tricuspis. Phylogenetic comparisons of the African pangolins indicated two lineages with high posterior probabilities providing evidence to support the classification of two genera; Smutsia and Phataginus. The total GC content between African pangolins was observed to be similar between species (36.5% - 37.3%). The most frequent codon was found to be A or C at the 3rd codon position. Significant variations in GC-content and codon usage were observed for several regions between African and Asian pangolin species which may be attributed to mutation pressure and/or natural selection. Lastly, a total of two insertions of 80 bp and 28 bp in size respectively was observed in the control region of the black-bellied pangolin which were absent in the other African pangolin species.

CONCLUSIONS

The current study presents reference mitogenomes of all four African pangolin species and thus expands on the current set of reference genomes available for six of the eight extant pangolin species globally and represents the first phylogenetic analysis with six pangolin species using full mitochondrial genomes. Knowledge of full mitochondrial DNA genomes will assist in providing a better understanding on the evolution of pangolins which will be essential for conservation genetic studies.