Biology subjects

Gaubert, P.

Publications and source records attributed to Gaubert, P..

9 recordsLinked to original sources

bioRxiv2025

From deserts to forests: sequencing of the giant forest hog completes the genomic history of the African Suids

The giant forest hog (GFH, Hylochoerus meinertzhageni), the largest and most elusive wild pig, is found in a disjunct range across equatorial Africa, primarily inhabiting forests and woodlands. It is the only remaining African suid species without whole-genome data. The GFH is currently classified into three subspecies, differing in skull morphology and size. Here, we present the first whole-genome data of nine GFHs; one from Guinea and eight Uganda, representing the two geographically most distant subspecies. This genomic evidence allowed us to resolve the previously uncertain placement of the GFH among African suids as a sister group to the warthogs (Phacochoerus spp.). Also, we found a deep evolutionary split between the two GFH populations resulting in a level of genetic differentiation (FST > 0.75), which is similar to or higher than values observed among species of African wild pigs. The GFH likely diverged from warthogs around 4.6 Mya while the two study populations of GFH diverged at least 0.5 Mya and, subsequently, experienced very dissimilar demographic trajectories. The individual from Guinea had half of the heterozygosity level of the Uganda population, and lower value compared to all the African suids, probably as a result of the long term low Ne and isolation. Due to the close affinity of GFH with the African rainforest biotic zone, our findings have implications for understanding the history of habitat change in Africa. They also indicate a very deep and previously underappreciated evolutionary divergence within the GFH that may have implications for its conservation.

genomics↗

bioRxiv2025

Advancing global DNA-referencing of bushmeat in African tropical forests: a tool for identifying trade hotspots and dynamics in western and central Africa

The bushmeat trade in Africa is a largely unregulated activity that drives the unsustainable exploitation of wild terrestrial vertebrates--an issue often coined the bushmeat crisis. We build on a four-gene mitochondrial DNA-typing approach to develop an unprecedented reference database framework for effectively tracing the bushmeat trade in tropical Africa. Our dataset comprises over 2,500 samples collected over a 13-yr period across 10 African countries and two European airports. Relying on an expert analytical pipeline and [~]8,700 nucleotide sequences, we identified 96% of samples to the species-level. In contrast, we estimated that conventional two-gene approaches would have yielded 18-26% erroneous or inconclusive taxonomic assignments. DNA-typing refined > 50% of field identifications, with refinement reaching 92-95% for highly processed carcasses seized in Europe. Leveraging expanded taxonomic representation, we empirically refined the genetic species thresholds applied to bushmeat and provide a reproducible pipeline for using our expert reference database from NCBI. Overall, we identified 133 species--mostly mammals--with one-third listed as of conservation concern, and uncovered cryptic diversity evidence within several taxa. Our results also demonstrated the value of community ecology indexes for large-scale monitoring of the bushmeat trade. While national markets generally mirrored regional biodiversity patterns across tropical Africa, Benin emerged as a notable outlier and a key wildlife trade hotspot. We advocate for the integration of community ecology frameworks into surveillance efforts to guide more effective, regionally tailored mitigation strategies. Continued, standardized sampling is essential to broaden taxonomic coverage and enhance detection of cryptic biodiversity in genetic bushmeat monitoring.

genetics↗

bioRxiv2024

A wide diversity of viruses detected in African mammals involved in the wild meat supply chain

The processes involved in acquiring, trading, preparing, and consuming wild meat pose significant risks for the emergence of zoonotic infectious diseases. Several major viral outbreaks have been directly linked to the wild meat supply chain, yet our knowledge of the virome in many mammals involved in this chain remains limited and disproportionately focused on certain mammalian taxa and pathogens. This report presents the findings of a metagenomic viral screening of 99 specimens belonging to 27 wild African mammal species and one domesticated species, all traded for their meat. The study focuses on tissue and swab samples collected from various regions in the Democratic Republic of the Congo and in Brussels, Belgium. A total of fifteen virus strains were detected, belonging to the families Arteriviridae, Retroviridae and Sedoreoviridae (primates), Picobirnaviridae (primates and rodents), Picornaviridae (rodents), Hepadnaviridae (hyrax), Orthoherpesviridae (artiodactylid and carnivore) and Spinareoviridae (carnivore). Several strains were detected in mammalian hosts for the first time, expanding their host range and genetic diversity. Of note is the presence of viruses genetically related to recognised zoonotic pathogens, i.e., human picobirnavirus (Orthopicobirnavirus hominis) (primates and rodents), simian foamy viruses (Simiispumavirus) (primates), and rotavirus A (Rotavirus alphagastroenteritidis) (primates). The presence of these viruses in primates is concerning as non-human primates are phylogenetically closely related to humans, which can facilitate interspecies viral transmission. These findings underscore the high diversity of mammalian viruses and the potential risk of human infection through cross-species transmission during the close interactions with wildlife in the wild meat supply chain.

genomics↗

bioRxiv2023

African bush pigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival

Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old divergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable FST values, and a recent divergence time (<500,000 years). Thus, our study challenges key arguments for splitting Potamochoerus into two species and suggests their speciation might be incomplete. Our findings also indicate that Malagasy bushpigs diverged from southern African populations and underwent a limited bottleneck 1,000-5,000 years ago, concurrent with human arrival in Madagascar. These results shed new light on the evolutionary history of an iconic and widespread African genus and provide insight into the longstanding biogeographic puzzle surrounding the bushpigs presence in Madagascar.

evolutionary biology↗

bioRxiv2023

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, Cote dIvoire and Ghana. Our study combining mitochondrial DNA (mtDNA) sequencing and microsatellites genotyping is the first to reveal a global pattern of admixture between two of the six mitochondrial lineages as previously delimited within WBP. We found a signature of isolation-by-distance and a lack of population genetic structuring, supporting the idea that WBP may have underestimated dispersal abilities. Levels of genetic diversity were low compared to central African lineages, 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 microsatellites 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 (Cote dIvoire), 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.

genetics↗

bioRxiv2023

Genetic tracing of the white-bellied pangolins (Phataginus tricuspis) trade in western central Africa

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, we observed a lack of genetic differentiation and a signature of isolation-by-distance possibly due to unsuspected dispersal capacities involving a Wahlund effect. Despite a higher 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 WBP 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.

genetics↗

bioRxiv2023

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 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.

genomics↗

bioRxiv2021

The antique genetic plight of the Mediterranean monk seal (Monachus monachus)

Disentangling the impact of Late Quaternary climate change from human activities can have crucial implications on the conservation of endangered species. We investigated the population genetics and demography of the Mediterranean monk seal (Monachus monachus), one of the worlds most endangered marine mammals, through an unprecedented dataset encompassing historical (extinct) and extant populations from the eastern North Atlantic to the entire Mediterranean Basin. We show that Cabo Blanco (Western Sahara/Mauritania), Madeira, Western Mediterranean (historical range), and Eastern Mediterranean regions segregate into four populations. This structure is likely the consequence of recent drift, combined with long-term isolation by distance (R2 = 0.7), resulting from prevailing short-distance (< 500 km) and infrequent long-distance dispersal (< 1,500 km). All populations (Madeira especially), show high levels of inbreeding and low levels of genetic diversity, seemingly declining since historical time, but surprisingly not being impacted by the 1997 massive die-off in Cabo Blanco. Approximate Bayesian Computation analyses support scenarios combining local extinctions and a major effective population size decline in all populations during Antiquity. Our results suggest that the early densification of human populations around the Mediterranean Basin coupled with the development of seafaring techniques were the main drivers of the decline of Mediterranean monk seals.

genetics↗

bioRxiv2021

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

We conducted in the Dahomey Gap (DG) a pioneer study on the genetic tracing of the African pangolin trade. We sequenced and genotyped 189 white-bellied pangolins from 18 forests and 12 wildlife markets using one mitochondrial fragment and 20 microsatellites loci. Tree-based assignment procedure showed the endemicity of the pangolin trade, as strictly fed by the lineage endemic to the DG (DGL). DGL populations were characterized by low levels of genetic diversity, an overall absence of equilibrium, inbreeding depression 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 inferior to minimum viable population size. Genetic tracing suggested that wildlife markets from the DG sourced through the entire DGL range. Our loci provided the necessary power to distinguish among all the genotyped pangolins, tracing the dispatch of same individuals on the markets and within local communities. We developed an approach combining rarefaction analysis of private allele frequencies and cross-validation with observed data that could trace five traded pangolins to their forest origin, c. 200-300 km away from the markets. Although the genetic toolkit that we designed from traditional markers can prove helpful to trace the pangolin trade, our tracing ability was limited by the lack of population structure within 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.

genetics↗