Philippe Gaubert

Philippe Gaubert
Institute of Research for Development | IRD · Laboratoire Evolution et Diversité Biologique (EDB), Université Paul Sabatier, Toulouse, France

PhD

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252
Publications
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Publications

Publications (252)
Article
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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 con...
Article
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 world's most endangered marine mammals, through an unprecedented dataset enc...
Article
Full-text available
African wild pigs have a contentious evolutionary and biogeographic history. Until recently, desert warthog (Phacochoerus aethiopicus) and common warthog (P. africanus) were considered a single species. Molecular evidence surprisingly suggested they diverged at least 4.4 million years ago, and possibly outside of Africa. We sequenced the first whol...
Article
Full-text available
Although the bushmeat trade is a significant component of the Anthropocene crisis in the tropics, the reliability of species-level identification is generally lacking from bushmeat surveys. We conducted a comprehensive study of 23 bushmeat markets in Cameroon and one seizure from a French airport using a multi-gene DNA-typing approach and a dedicat...
Article
Full-text available
Illegal hunting of wildlife is one of the major issues in tropical ecosystems, especially when it occurs in highly degraded habitats with forest cover fragmentation. In this study, we assessed the impact of bushmeat hunting in a large forest patch (the Lama Natural Forest; LNF) and 11 nearby forest islands, using Traditional Ecological Knowledge fr...
Article
Full-text available
Aim: Comprehensive, global information on species' occurrences is an essential biodiversity variable and central to a range of applications in ecology, evolution, biogeography and conservation. Expert range maps often represent a species' only available distributional information and play an increasing role in conservation assessments and macroeco...
Article
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, Dendro...
Article
Full-text available
We are an international group of biological scientists, conservationists, and environmentalists who have been closely following the plight and conservation of pangolins over a number of years. Pangolins comprise the mammalian Order Pholidota, which contains eight living species found in diverse habitats in Africa (4 species) and Asia (4 species), w...
Preprint
Full-text available
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 world's most endangered marine mammals, through an unprecedented dataset enc...
Preprint
Full-text available
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 stri...
Article
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The gray wolf (Canis lupus) expanded its range across Holarctic regions during the late Pleistocene. Consequently, most gray wolves share recent (<100 kya) maternal origins corresponding to a widespread Holarctic clade. However, two deeply divergent (200-700 kya) mitochondrial clades are restricted, respectively, to the Indian subcontinent and the...
Article
Zootaxa came as a new and innovative publication medium for taxonomy, amidst a scenario of devaluation of this important biological science. After 20 years, it has ascertained itself as one of the main journals in animal taxonomy. However, the contribution of the journal to the taxonomy of Mammalia (mammals), one of the most studied groups of anima...
Article
Full-text available
Health risks associated to the use of tropical wildlife have so far been envisioned through the lens of zoonotic pathogens spread by the bushmeat trade, putting aside the equally vibrant network of traditional medicine markets (TMMs). We collected information on the preservative techniques used for animal body parts from TMMs in Benin through a sem...
Article
Full-text available
The Mediterranean monk seal Monachus monachus is one of the most threatened marine mammals, with only 600–700 individuals restricted to three populations off the coast of Western Sahara and Madeira (North Atlantic) and between Greece and Turkey (eastern Mediterranean). Its original range was from the Black Sea (eastern Mediterranean) to Gambia (wes...
Article
Full-text available
Conservationists can benefit from encompassing research, social, and economic aspects of conservation issues to produce holistic conservation guidelines. Pangolins have become a taxon of conservation eminence as they continue to be poached and trafficked to extinction, and have been mislabeled as potential intermediary hosts of SARS-CoV-2 which is...
Article
Full-text available
Background Pangolins are trafficked in unsustainable volumes to feed both local and global trade networks for their meat and the medicinal properties of their derivatives, including scales. We focus on a West African country (Benin) to assess the medicinal and spiritual values of pangolins among different ethnic groups and identify the cohort of bu...
Article
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Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America¹, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our res...
Article
The Mediterranean monk seal (Monachus monachus) is one of the world’s most endangered marine mammals. Centuries of human persecution along with recent expansion of the fishing industry and intensive shoreline development, have isolated Mediterranean monk seals into small populations in the eastern Mediterranean Basin and eastern North Atlantic. We...
Article
Despite the known genetic permeability among wolf-like canids, there is currently no evidence of gene flow between the recently acknowledged African wolf (Canis lupaster) and domestic dogs (C. lupus familiaris). We genotyped African wolves across their range, together with African domestic dogs and ‘reference’ grey wolves (C. l. lupus; not occurrin...
Article
Full-text available
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 tricuspi...
Preprint
Full-text available
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 tricusp...
Article
Full-text available
Although pangolins are considered to be one of the most trafficked wild mammals in the world, their conservation status remains uncertain through most of their ranges, and notably in western Africa. Using local ecological knowledge in combination with direct occurrence evidence, we assessed the distribution and abundance of the white-bellied pangol...
Article
Full-text available
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 th...
Article
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 th...
Technical Report
Full-text available
African Civet is listed as Least Concern because the species has a wide distribution range, is present in a variety of habitats, is relatively common across its range, is present in numerous protected areas, and has a total population believed to be relatively stable. It may, however, be undergoing some localised declines through hunting, including...
Article
Mediterranean monk seals (MMS) are among the most endangered marine mammals on Earth. We screened mitochondrial variability (control region [CR1] and mitogenomes) of the species through a 180‐yr timeframe and extended by 20% (n = 205) the number of samples from a previous investigation, including historical specimens from 1833 to 1975. Although we...
Book
Promoting forensic science in wildlife law enforcement is critical to combatting the illegal trade in pangolins. An understanding of poaching, illegal trade routes, verification of species, identification of protected species in traditional medicines and illegal smuggling of pangolins necessitated the development of capacity to conduct forensic ana...
Book
This chapter provides an authoritative account of the phylogeny and taxonomy of fossil and extant pangolins. Historical discrepancies around the taxonomy of pangolins are discussed, notably in terms of infraordinal classification, while the respective merits of morphological and molecular analyses to solve the phylogenetic relationships among pango...
Data
Table showing the catalog number, species information, average genomic sequencing coverage, identified genetic clusters, location and date of sample collection, and the publication associated with the publicly available data.
Article
Full-text available
The evolutionary history of the wolf-like canids of the genus Canis has been heavily debated, especially regarding the number of distinct species and their relationships at the population and species level [1–6]. We assembled a dataset of 48 resequenced genomes spanning all members of the genus Canis except the black-backed and side-striped jackals...
Article
Full-text available
The Convention on Biological Diversity (CBD) commits its 196 nation parties to conserve biological diversity, use its components sustainably, and share fairly and equitably the benefits from the utilization of genetic resources. The last of these objectives was further codified in the Convention's Nagoya Protocol (NP), which came into effect in 201...
Article
Full-text available
Pangolins, considered the most-trafficked mammals on Earth, are rapidly heading to extinction. Eight extant species of these African and Asian scale-bodied anteaters are commonly recognized, but their evolutionary relationships remain largely unexplored. Here we present the most comprehensive phylogenetic assessment of pangolins, based on genetic v...
Article
Anomaluroidea, commonly known as the “scaly-tailed squirrels,” are an emblematic group of tropical African mammals that includes gliding forms. The family Anomaluridae was until recently represented by three genera: the flying scaly-tailed squirrels (Anomalurus), the flying mouse (Idiurus) and the flightless scaly-tailed squirrels (Zenkerella). Idi...
Article
Full-text available
Natural selection in domestic dogs is of great interest in evolutionary biology since dogs have migrated to every inhabited continent of the world alongside humans, and adapted to diverse environments. Here, we explored their demographic history and genetic basis of adaptation to the tropical African environment using whole genome analyses of 19 Af...
Article
Full-text available
The biogeographic dynamics affecting the Indian subcontinent, East and Southeast Asia during the Plio-Pleistocene has generated complex biodiversity patterns. We assessed the molecular biogeography of the small Indian civet (Viverricula indica) through mitogenome and cytochrome b + control region sequencing of 89 historical and modern samples to (i...
Chapter
The Mediterranean Basin (MB), connected by cultural exchanges since prehistoric times, provides an outstanding framework to study species introductions, notably in mammals. Carnivores are among the most successful mammalian invaders. As such, a number of middle-sized representatives (“mesocarnivores”) such as the domestic cat and mongooses have bee...
Chapter
Full-text available
The Cape Genet is listed as Least Concern because it has a relatively wide range in South Africa, appears to be common, occurs in human-modified habitats, does not face major threats, and is present in several protected areas across its distribution. Population size and trend estimates are not available for most areas, but it is thought that the po...
Chapter
Full-text available
The Small-spotted Genet is listed as Least Concern as this species has a wide distribution within the assessment region, is locally common, and has a very broad habitat tolerance that includes being commensal with human settlements in urban and rural landscapes. Small-spotted Genets are also present in many protected areas across the region.
Chapter
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The Rusty-spotted Genet is listed as Least Concern as, although it is possible that this species may be undergoing some localised declines in a few areas due to road collisions, direct or accidental persecution by farmers, hunting for skins, meat and trophies, and predation by feral/domestic cats and dogs, it has a wide distribution range, occurrin...
Article
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 multi-locus approach for taxonomic delineation and trade tracing of this heavily poached sp...
Article
In the last three decades, the range of the Egyptian mongoose (Herpestes ichneumon) has increased in the Iberian Peninsula. A panel of microsatellites was used to confront the patterns of genetic diversity of the species with the scenario of its recent northward expansion in its Iberian range. Evidence of substructure and significant genetic differ...
Technical Report
Full-text available
Listed as Least Concern because it has a relatively wide distribution, is locally common, and there do not appear to be any major threats to the species.
Technical Report
Full-text available
Listed as Least Concern as although it is possible that they may be undergoing some localised declines in a few areas, they have a wide distribution range, occur in a variety of habitats, and are present in many protected areas on the African continent.
Technical Report
Full-text available
Listed as Data Deficient because there is little current information on the population status and trends of this species, its exact distribution, or possible threats. Although the species has been previously collected or sighted in various habitats and over a wide altitudinal range within its estimated large distribution (ca 500,000 km²), some repo...
Technical Report
Full-text available
Listed as Near Threatened because the species is believed to have undergone a population decline of around 20% over the last 12 years (assuming a generation length of four years) based on estimates of forest loss in its range in the Upper Guinea forests, coupled with the impacts of hunting; such rates are expected to continue for the next three gen...
Technical Report
Full-text available
Listed as Least Concern because the species is common within a relatively wide distribution range in West Africa, and occurs in a variety of habitats. It is not believed to be declining at a rate fast enough to warrant listing in a higher category of threat. However, with the availability of further information, specifically on the adaptability of...
Technical Report
Full-text available
Listed as Least Concern because the species has a relatively wide distribution, is present in a region of mostly intact habitat, and appears to be common. It may be undergoing localised declines in some regions because of hunting and deforestation.
Technical Report
Full-text available
Listed as Least Concern as the species is widespread, common in at least part of its range, and present in many protected areas. There appear to have been some range and population increases in Europe in recent years, but these may be because of better observation and documentation.
Article
For most Ivorian regions quantitative data on the exploitation of bushmeat by local communities are scarce. We studied hunting patterns around Dassioko Sud Forest Reserve, a remnant coastal forest in south-eastern Côte d'Ivoire, through a 6-month survey of nine restaurants, in three villages surrounding the Reserve. We collected quantitative and qu...
Article
Full-text available
The bushmeat trade in West and Central Africa embraces a broad range of ecological, economic, and conservation issues. To date, most studies have focused on the economic and conservation aspects of the bushmeat trade, with less emphasis on the ecological implications of wildlife extraction. Here, we analysed available literature on the bushmeat tra...
Data
Description Table S1 Detailed list of the samples and cytochrome b + control region sequences used in this study. Samples used for the concatenated analysis are highlighted in green. Type specimen appears in red. Museum acronyms: ZSM = Zoologische Staatssammlung München; KFBG = Kadoorie Farm and Botanic Garden, Hong Kong; NHM = Natural History Muse...
Technical Report
Full-text available
African Civet is listed as Least Concern because the species has a wide distribution range, is present in a variety of habitats, is relatively common across its range, is present in numerous protected areas, and has a total population believed to be relatively stable. It may, however, be undergoing some localised declines through hunting, including...
Technical Report
Full-text available
This species is listed as Vulnerable based on a total population of fewer than 10,000 mature individuals (roughly estimated based on a range area of ca. 147,000 km², an average population density highly unlikely to exceed one individual/10 km², and a proportion of mature individuals of 67%) and the likelihood that the species underwent a population...
Technical Report
Full-text available
Crested Genet is listed as Vulnerable based on a total population containing ca. 7,000 mature individuals (roughly estimated based on a range area of ca 100,000 km², an average population density highly unlikely to exceed one individual/10 km², and a proportion of mature individuals of 67%) and the likelihood that the species underwent a population...
Technical Report
Full-text available
This poorly-known species has no reliable information on its current population status or precise limits of distribution. There have been no confirmed records for almost four decades, although search effort for this largely aquatic species has been extremely limited. Its range area is estimated at ca. 224,000 km², which suggests that its extent of...
Technical Report
Full-text available
Listed as Data Deficient because this species is known only from 10 museum specimens, with no confirmed records since 1946, and the habitat requirements and distribution range are not well known. It often has been considered synonymous with other large-spotted genet taxa (especially Pardine Genet Genetta pardina), and the uncertainty surrounding it...