Bushmeat genetics: setting up a reference framework for the DNA typing of African forest bushmeat

Barcoding Brazilian mammals to monitor biological diversity and threats: Trends, perspectives, and knowledge gaps

DNA barcoding and environmental DNA (eDNA) represent significant advances for biomonitoring the world's biodiversity and its threats. However, these methods are highly dependent on the presence of species sequences on molecular databases. Brazil is one of the world's largest and most biologically diverse countries. However, many knowledge gaps still exist for describing, identifying, and monitoring of mammalian biodiversity using molecular methods. We aimed to unravel the patterns of the presence of Brazilian mammal species on molecular databases to improve our understanding of how effectively it would be to monitor them using DNA barcoding and environmental DNA, and contribute to mammalian conservation. We foundt many gaps in molecular databases, with many taxa being poorly represented, particularly from Amazonia, the order Lagomorpha, and arboreal, gomivorous, near extinct, and illegally traded species. Moreover, our analyses revealed that species description year was the most important factor determining the probability of a species to being sequenced. Primates are the group with the highest number of species considered a priority for sequencing due to their high level of combined threats. We highlight where investments are needed to fill knowledge gaps and increase the representativity of species on molecular databases to enable a better monitoring ability of Brazilian mammals encompassing different traits using DNA barcoding and environmental DNA.

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.

Insights into the Geographical Origins of the Cabo Verde Green Monkey

The green monkey Chlorocebus sabaeus, L. 1766, native to West Africa, was introduced to the Cabo Verde Archipelago in the 16th century. Historical sources suggest that, due to the importance of Cabo Verde as a commercial entrepôt in the Atlantic slave trade, establishing the precise place of origin of this introduced species is challenging. Non-invasive fecal samples were collected from feral and captive green monkey individuals in Cabo Verde. Two mitochondrial fragments, HVRI and cyt b, were used to confirm the taxonomic identification of the species and to tentatively determine the geographic origin of introduction to the archipelago from the African continent. By comparing the new sequences of this study to previously published ones, it was shown that Cabo Verde individuals have unique haplotypes in the HVRI, while also showing affinities to several populations from north-western coastal Africa in the cyt b, suggesting probable multiple sources of introduction and an undetermined most probable origin. The latter is consistent with historical information, but may also have resulted from solely using mtDNA as a genetic marker and the dispersal characteristics of the species. The limitations of the methodology are discussed and future directions of research are suggested.

Examining the international bushmeat traffic in Belgium: A threat to conservation and public health

The carriage of bushmeat into the European Union is an infringement of EU Animal Health and Wildlife Trade legislation and poses a threat to biodiversity and public health. To explore the nature and scale of the international bushmeat trade, seized leaking luggage and passengers arriving at Brussels Zaventem airport from sub-Saharan Africa between 2017 and 2018 were searched for "meat" (bushmeat and livestock) by border control authorities. Visual identification, radiography and genetic analysis were applied to derive information from seized specimens, including at least ten CITES-listed species. We estimate that an average of 3.9 t of bushmeat is smuggled monthly through Brussels. The average consignment of meat seized per passenger was 2.8 kg and 4 kg of bushmeat or domestic livestock meat, respectively. The international trafficking of bushmeat is evidently active, yet penalties are rarely enforced; hence we provide suggestions to simplify law enforcement procedures.

Detection of a novel Babesia sp. in Amblyomma javanense, an ectoparasite of Sunda pangolins

BACKGROUND

Babesia is a protozoal, tick-borne parasite that can cause life-threatening disease in humans, wildlife and domestic animals worldwide. However, in Southeast Asia, little is known about the prevalence and diversity of Babesia species present in wildlife and the tick vectors responsible for its transmission. Recently, a novel Babesia species was reported in confiscated Sunda pangolins (Manis javanica) in Thailand. To investigate the presence of this parasite in Singapore, we conducted a molecular survey of Babesia spp. in free-roaming Sunda pangolins and their main ectoparasite, the Amblyomma javanense tick.

METHODS

Ticks and tissue samples were opportunistically collected from live and dead Sunda pangolins and screened using a PCR assay targeting the 18S rRNA gene of Babesia spp. DNA barcoding of the cytochrome oxidase subunit I (COI) mitochondrial gene was used to confirm the species of ticks that were Babesia positive.

RESULTS

A total of 296 ticks and 40 tissue samples were obtained from 21 Sunda pangolins throughout the 1-year study period. Babesia DNA was detected in five A. javanense ticks (minimum infection rate = 1.7%) and in nine different pangolins (52.9%) located across the country. Phylogenetic analysis revealed that the Babesia 18S sequences obtained from these samples grouped into a single monophyletic clade together with those derived from Sunda pangolins in Thailand and that this evolutionarily distinct species is basal to the Babesia sensu stricto clade, which encompasses a range of Babesia species that infect both domestic and wildlife vertebrate hosts.

CONCLUSIONS

This is the first report documenting the detection of a Babesia species in A. javanense ticks, the main ectoparasite of Sunda pangolins. While our results showed that A. javanense can carry this novel Babesia sp., additional confirmatory studies are required to demonstrate vector competency. Further studies are also necessary to investigate the role of other transmission pathways given the low infection rate of ticks in relation to the high infection rate of Sunda pangolins. Although it appears that this novel Babesia sp. is of little to no pathogenicity to Sunda pangolins, its potential to cause disease in other animals or humans cannot be ruled out.

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.

Is social media the new wet market? Social media platforms facilitate the online sale of bushmeat in West Africa

Social media provides a platform for wildlife crime syndicates to access a global consumer-driven market. Whilst studies have uncovered the online trade in wildlife, the availability of wild meat (bushmeat) has not been assessed. To investigate the sale of wild meat online, we analysed 563 posts published between 2018 and 2022 from six West African Facebook pages selected using predetermined search criteria. Across 1511 images and 18 videos, we visually identified 25 bushmeat species-level taxa including mammals (six Rodentia, five Artiodactyla, three Carnivora, two Pholidota, one Primate, two Lagomorpha, one Hyracoidea), birds (three Galliformes) and reptiles (two Squamata), predominately advertised as smoked (63%) or fresh (30%) whole carcasses or portions. Among the species identified, 16% feature a status of concern on the International Union for Conservation of Nature (IUCN) Red List (Near Threatened to Endangered), 16% are listed on the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES; Appendix I and II) and 24% are either fully or partially protected by local legislation. Images were commonly used as propaganda rather than to display inventory, where additional taxa protected from game hunting in West Africa, such as hornbill, were exclusively listed in captions. The advertisement of these protected and vulnerable species on the surface web indicates weak local and international legislative enforcement. Comparatively, when the same search criteria were applied to the deep web browser Tor no results were generated, reinforcing the idea that bushmeat vendors have no need to hide their activities online. Despite local and international trade restrictions, the taxa advertised feature similarities with bushmeat seizures reported in Europe, alluding to the interconnectedness of the trade facilitated by social media. We conclude that enhanced policy enforcement is essential to combat the online sale of bushmeat and mitigate the potential biodiversity and public health impacts.

A phylogeographic assessment of South African greater cane rats (Thryonomys swinderianus): Preliminary insights

The greater cane rat (Thryonomys swinderianus) is an African rodent with a wide Sub-Saharan distribution range. This species is viewed as an important protein source in many African countries. These rodents are also regularly viewed as a pest species who frequently raid croplands in agricultural settings. No phylogenetic work has to date been published on T. swinderianus from southern Africa. This paper therefore reports the first phylogenetic assessment on the species across the South African distribution range. Thirty samples were sourced from local museum collections, with one direct submission by a member of the public who found a rodent carcass identified as T. swinderianus west of its known distribution range in the Eastern Cape Province of South Africa. Two mitochondrial loci previously used in West African studies of this species were used in the current study to asses T. swinderianus population genetic diversity and phylogenetic structure across the South African distribution. A comparison to sequence data from West Africa was also performed. A divergence time estimation was conducted to further investigate the evolutionary history of the South African sub-population. Similar genetic diversity estimates were observed for the South African sub-population when compared to the West African datasets. Specimens from the eastern parts of South Africa showed higher genetic diversity estimates, possibly indicative of an initial colonisation site from eastern Africa. Two distinct phylogenetic clades were identified by Bayesian inference, forming distinct West African and South African groups. The divergence estimates showed similar ages for the T. swinderianus most recent common ancestor (MRCA) as previously reported. The MRCA estimates for the South African group identified a possible middle to late Pleistocene migratory event from eastern African into southern Africa. Further fine scale sampling across the African distribution range is however needed to provide more accurate assessments for future conservation management planning for the different sub-populations, as needed.

Population structure and evolutionary history of the greater cane rat (Thryonomys swinderianus) from the Guinean Forests of West Africa

Grasscutter (Thryonomys swinderianus) is a large-body old world rodent found in sub-Saharan Africa. The body size and the unique taste of the meat of this major crop pest have made it a target of intense hunting and a potential consideration as a micro-livestock. However, there is insufficient knowledge on the genetic diversity of its populations across African Guinean forests. Herein, we investigated the genetic diversity, population structures and evolutionary history of seven Nigerian wild grasscutter populations together with individuals from Cameroon, Republic of Benin, and Ghana, using five mitochondrial fragments, including D-loop and cytochrome b (CYTB). D-loop haplotype diversity ranged from 0.571 (± 0.149) in Republic of Benin to 0.921 (± 0.013) in Ghana. Within Nigeria, the haplotype diversity ranged from 0.659 (± 0.059) in Cross River to 0.837 (± 0.075) in Ondo subpopulation. The fixation index (F_ST), haplotype frequency distribution and analysis of molecular variance revealed varying levels of population structures across populations. No significant signature of population contraction was detected in the grasscutter populations. Evolutionary analyses of CYTB suggests that South African population might have diverged from other populations about 6.1 (2.6-10.18, 95% CI) MYA. Taken together, this study reveals the population status and evolutionary history of grasscutter populations in the region.

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.

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.

Addressing the illegal wildlife trade in the European Union as a public health issue to draw decision makers attention

The European Union is one of the most important markets for the trafficking of endangered species and a major transit point for illegal wildlife trade. The latter is not only one of the most important anthropogenic drivers of biodiversity loss, it also represents a growing risk for public health. Indeed, wildlife trade exposes humans to a plethora of severe emerging infectious diseases, some of which have contributed to the most dramatic global pandemics humankind has endured. Illegal wildlife trade is often considered as a problem of developing countries but it is first and foremost an international global business with a trade flow from developing to developed countries. The devastating effects of the ongoing SARS-CoV-2 outbreak should thus be an unassailable argument for European decision makers to change paradigm. Rather than deploying efforts and money to combat novel pathogens, mitigating the risk of spreading emerging infectious diseases should be addressed and be part of any sustainable socioeconomic development plan. Stricter control procedures at borders and policies should be enforced. Additionally, strengthening research in wildlife forensic science and developing a network of forensic laboratories should be the cornerstone of the European Union plan to tackle the illegal wildlife trade. Such proactive approach, that should further figure in the EU-Wildlife Action Plan, could produce a win-win situation: the curb of illegal wildlife trade would subsequently diminish the likelihood of importing new zoonotic diseases in the European Union.

Molecular species identification of bushmeat recovered from the Serengeti ecosystem in Tanzania

Bushmeat harvesting and consumption represents a potential risk for the spillover of endemic zoonotic pathogens, yet remains a common practice in many parts of the world. Given that the harvesting and selling of bushmeat is illegal in Tanzania and other parts of Africa, the supply chain is informal and may include hunters, whole-sellers, retailers, and individual resellers who typically sell bushmeat in small pieces. These pieces are often further processed, obscuring species-identifying morphological characteristics, contributing to incomplete or mistaken knowledge of species of origin and potentially confounding assessments of pathogen spillover risk and bushmeat offtake. The current investigation sought to identify the species of origin and assess the concordance between seller-reported and laboratory-confirmed species of origin of bushmeat harvested from in and around the Serengeti National Park in Tanzania. After obtaining necessary permits, the species of origin of a total of 151 bushmeat samples purchased from known intermediaries from 2016 to 2018 were characterized by PCR and sequence analysis of the cytochrome B (CytB) gene. Based on these sequence analyses, 30%, 95% Confidence Interval (CI: 24.4–38.6) of bushmeat samples were misidentified by sellers. Misreporting amongst the top five source species (wildebeest, buffalo, impala, zebra, and giraffe) ranged from 20% (CI: 11.4–33.2) for samples reported as wildebeest to 47% (CI: 22.2–72.7) for samples reported as zebra although there was no systematic bias in reporting. Our findings suggest that while misreporting errors are unlikely to confound wildlife offtake estimates for bushmeat consumption within the Serengeti ecosystem, the role of misreporting bias on the risk of spillover events of endemic zoonotic infections from bushmeat requires further investigation.

Chasing a ghost: notes on the present distribution and conservation of the sooty mangabey (Cercocebus atys) in Guinea-Bissau, West Africa

The West-African sooty mangabey (Cercocebus atys) is threatened by habitat loss, hunting for meat consumption, and mortality during crop-foraging events. The species’ overall demographic trend is unknown. Presence and distribution in Guinea-Bissau, a country neighbored by Senegal and Republic of Guinea, was confirmed in 1946 but the species was declared extinct in 1989 and not observed in subsequent countrywide expeditions. Narratives of its presence across southern Guinea-Bissau are scattered in reports and occurrence in the eastern part was reported in 2017, but the limits of its distribution are currently unknown. Here, we present recent geo-referenced visual and molecular-based records of the sooty mangabey for three protected areas in southern Guinea-Bissau collected as part of a region-wide survey. Individuals were observed in Cufada Lagoons Natural Park (2015) and Dulombi National Park (NP) (2016) and photographed in Boé NP (2007, 2015 and 2020). Thirty-six samples collected in Boé NP (2017) were identified as sooty mangabey using a 402 base pair fragment of the mitochondrial cytochrome b gene. Our work suggests a wider distribution in Guinea-Bissau than previously described, augments knowledge of the populations’ current habitat use and threats, and has implications for efforts to conserve the species in West Africa. Considering the sooty mangabey as the reservoir of the simian immunodeficiency virus that led to the human variant, HIV-2, confirmation that the Guinea-Bissau population is not extinct may lead to a better understanding of early viral jump to humans and consequent epidemic spread, specifically of the HIV-2 Subgroup A. We highlight the need for extra conservation measures by Guinea-Bissau authorities.

Morphometric and genetic differentiation among populations of flat-headed cusimanse (Crossarchus platycephalus) in Nigeria

Geographic barriers can partition genetic diversity among populations and drive evolutionary divergence between populations, promoting the speciation process and affecting conservation goals. We integrated morphological and genomic data to assess the distribution of variation in the flat-headed cusimanse (Crossarchus platycephalus), a species of least conservation concern, on either side of the River Niger in Nigeria. Ecological disturbances affect the conservation status of many other animals in this region. The two populations were differentiated in the snout and fore limbs, with greater morphological diversity in the western population. We used Restriction site Associated DNA sequencing (RAD-seq) and identified two genotypic clusters in a STRUCTURE analysis. Individuals from the eastern population are almost entirely assigned to one cluster, whereas genotypes from the western population are a mixture of the two clusters. The population from west of the River Niger also had higher heterozygosity. The morphological and population genetic data are therefore in agreement that the population from west of the River Niger is more diverse than the eastern population, and the eastern population contains a subset of the genetic variation found in the western population. Our results demonstrate that combining morphological and genotypic measures of diversity can provide a congruent picture of the distribution of intraspecific variation. The results also suggest that future work should explore the role of the River Niger as a natural barrier to migration in Nigeria.

Investigating zoonotic infection barriers to ape Plasmodium parasites using faecal DNA analysis

African apes are endemically infected with numerous Plasmodium spp. including close relatives of human Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale, and Plasmodium malariae. Although these ape parasites are not believed to pose a zoonotic threat, their ability to colonise humans has not been fully explored. In particular, it remains unknown whether ape parasites are able to initiate exo-erythrocytic replication in human hepatocytes following the bite of an infective mosquito. Since animal studies have shown that liver stage infection can result in the excretion of parasite nucleic acids into the bile, we screened faecal samples from 504 rural Cameroonians for Plasmodium DNA. Using pan-Laverania as well as P. malariae- and P. vivax-specific primer sets, we amplified human P. falciparum (n = 14), P. malariae (n = 1), and P. ovale wallikeri (n = 1) mitochondrial sequences from faecal DNA of 15 individuals. However, despite using an intensified PCR screening approach we failed to detect ape Laverania, ape P. vivax or ape P. malariae parasites in these same subjects. One faecal sample from a hunter-gatherer contained a sequence closely related to the porcupine parasite Plasmodium atheruri. Since this same faecal sample also contained porcupine mitochondrial DNA, but a matching blood sample was Plasmodium-negative, it is likely that this hunter-gatherer consumed Plasmodium-infected bushmeat. Faecal Plasmodium detection was not secondary to intestinal bleeding and/or infection with gastrointestinal parasites, but indicative of blood parasitaemia. Quantitative PCR identified 26-fold more parasite DNA in the blood of faecal Plasmodium-positive than faecal Plasmodium-negative individuals (P = 0.01). However, among blood-positive individuals only 10% - 20% had detectable Plasmodium sequences in their stool. Thus, faecal screening of rural Cameroonians failed to uncover abortive ape Plasmodium infections, but detected infection with human parasites, albeit with reduced sensitivity compared with blood analysis.

Assessing Monkeypox Virus Prevalence in Small Mammals at the Human-Animal Interface in the Democratic Republic of the Congo

During 2012, 2013 and 2015, we collected small mammals within 25 km of the town of Boende in Tshuapa Province, the Democratic Republic of the Congo. The prevalence of monkeypox virus (MPXV) in this area is unknown; however, cases of human infection were previously confirmed near these collection sites. Samples were collected from 353 mammals (rodents, shrews, pangolins, elephant shrews, a potamogale, and a hyrax). Some rodents and shrews were captured from houses where human monkeypox cases have recently been identified, but most were trapped in forests and agricultural areas near villages. Real-time PCR and ELISA were used to assess evidence of MPXV infection and other Orthopoxvirus (OPXV) infections in these small mammals. Seven (2.0%) of these animal samples were found to be anti-orthopoxvirus immunoglobulin G (IgG) antibody positive (six rodents: two Funisciurus spp.; one Graphiurus lorraineus; one Cricetomys emini; one Heliosciurus sp.; one Oenomys hypoxanthus, and one elephant shrew Petrodromus tetradactylus); no individuals were found positive in PCR-based assays. These results suggest that a variety of animals can be infected with OPXVs, and that epidemiology studies and educational campaigns should focus on animals that people are regularly contacting, including larger rodents used as protein sources.

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.

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

Knowledge on faunal diversification in African rainforests remains scarce. We used phylogeography to assess (i) the role of Pleistocene climatic oscillations in the diversification of the African common pangolin (Manis tricuspis) and (ii) the utility of our multilocus approach for taxonomic delineation and trade tracing of this heavily poached species. We sequenced 101 individuals for two mitochondrial DNA (mtDNA), two nuclear DNA and one Y-borne gene fragments (totalizing 2602 bp). We used a time-calibrated, Bayesian inference phylogenetic framework and conducted character-based, genetic and phylogenetic delineation of species hypotheses within African common pangolins. We identified six geographic lineages partitioned into western Africa, Ghana, the Dahomey Gap, western central Africa, Gabon and central Africa, all diverging during the Middle to Late Pleistocene. MtDNA (cytochrome b + control region) was the sole locus to provide diagnostic characters for each of the six lineages. Tree-based Bayesian delimitation methods using single- and multilocus approaches gave high support for 'species' level recognition of the six African common pangolin lineages. Although the diversification of African common pangolins occurred during Pleistocene cyclical glaciations, causative correlation with traditional rainforest refugia and riverine barriers in Africa was not straightforward. We conclude on the existence of six cryptic lineages within African common pangolins, which might be of major relevance for future conservation strategies. The high discriminative power of the mtDNA markers used in this study should allow an efficient molecular tracing of the regional origin of African common pangolin seizures.

Forensic application of DNA barcoding for identification of illegally traded African pangolin scales

The escalating growth in illegal wildlife trade and anthropogenic habitat changes threaten the survival of pangolin species worldwide. All eight extant species have experienced drastic population size reductions globally with a high extinction risk in Asia. Consequently, forensic services have become critical for law enforcement, with a need for standardised and validated genetic methods for reliable identifications. The seizure of three tonnes of pangolin scales, believed to have originated from Africa, by Hong Kong Customs Authorities provided an opportunity for the application of DNA barcoding in identifying scales. Three mitochondrial DNA gene regions (COI, Cyt b, and D-loop) were amplified for a subsample of the confiscated material and compared with taxonomically verified references. All four African species were recovered as monophyletic with high interspecific uncorrected p-distance estimates (0.048-0.188) among genes. However, only three of four African species (Phataginus tricuspis, Phataginus tetradactyla, and Smutsia gigantea, originating from West and Central Africa) and one of four Asian species (Manis javanica from Southeast Asia) were identified among scales. Although the assignment of unknown scales to specific species was reliable, additional genetic tools and representative reference material are required to determine geographic origins of confiscated pangolin specimens.

Towards a Universal Approach Based on Omics Technologies for the Quality Control of Food

In the last decades, food science has greatly developed, turning from the consideration of food as mere source of energy to a growing awareness on its importance for health and particularly in reducing the risk of diseases. Such vision led to an increasing attention towards the origin and quality of raw materials as well as their derived food products. The continuous advance in molecular biology allowed setting up efficient and universal omics tools to unequivocally identify the origin of food items and their traceability. In this review, we considered the application of a genomics approach known as DNA barcoding in characterizing the composition of foodstuffs and its traceability along the food supply chain. Moreover, metabolomics analytical strategies based on Nuclear Magnetic Resonance (NMR) and Mass Spectroscopy (MS) were discussed as they also work well in evaluating food quality. The combination of both approaches allows us to define a sort of molecular labelling of food that is easily understandable by the operators involved in the food sector: producers, distributors, and consumers. Current technologies based on digital information systems such as web platforms and smartphone apps can facilitate the adoption of such molecular labelling.