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January 2015 - present
January 2008 - December 2014
Publications
Publications (50)
Human admixture history is rarely a simple process in which distinct populations, previously isolated for a long time, come into contact once to form an admixed population. In this study, we aim to reconstruct the complex admixture histories of the population of São Tomé, an island in the Gulf of Guinea that was the site of the first slave-based pl...
Human populations harbor a high concentration of deleterious genetic variants. Here, we tested the hypothesis that non-random mating practices affect the distribution of these variants, through exposure in the homozygous state, leading to their purging from the population gene pool. To do so, we produced whole-genome sequencing data for two pairs o...
The biogeographic and demographic history of the house mouse, Mus musculus domesticus, has been closely linked to human history since pre-Neolithic times – this species first appeared in the Near East and subsequently dispersed westward with humans into regions with local Mus species. However, if this issue is now well known for the eastern Mediter...
Humans have a long history of transporting and trading plants, contributing to the evolution of domesticated plants. Theobroma cacao originated in the Neotropics from South America. However, little is known about its domestication and use in these regions. In this study, ceramic residues from a large sample of pre-Columbian cultures from South and...
After a long-standing debate, African elephants, listed as Vulnerable on the IUCN Red list of Threatened Species, are now considered by the IUCN as two distinct species: savannah elephants ( Loxodonta africana ) and forest elephants ( Loxodonta cyclotis ), the latter being severely threatened by forest loss, fragmentation and degradation due to agr...
Les fermiers cultivant autour de la forêt de Sebitoli en Ouganda rapportent l'existence d'éléphants de taille et de comportements hétérogènes. Nos travaux conduits dans cette zone forestière, s'appuyant sur des méthodes de génétique et de morphométrie couplée à du machine learning, confirment l’existence de morphotypes différents et génétiquement d...
From the 15th to the 19th century, the Trans-Atlantic Slave-Trade (TAST) influenced the genetic and cultural diversity of numerous populations. We explore genomic and linguistic data from the nine islands of Cabo Verde, the earliest European colony of the era in Africa, a major Slave-Trade platform between the 16th and 19th centuries, and a previou...
From the 15th to the 19th century, the Trans-Atlantic Slave-Trade (TAST) influenced the genetic and cultural diversity of numerous populations. We explore genomic and linguistic data from the nine islands of Cabo Verde, the earliest European colony of the era in Africa, a major Slave-Trade platform between the 16th and 19th centuries, and a previou...
From the 15th to the 19th century, the Trans-Atlantic Slave-Trade (TAST) influenced the genetic and cultural diversity of numerous populations. We explore genomic and linguistic data from the nine islands of Cabo Verde, the earliest European colony of the era in Africa, a major Slave-Trade platform between the 16th and 19th centuries, and a previou...
From the 15th to the 19th century, the Trans-Atlantic Slave-Trade (TAST) influenced the genetic and cultural diversity of numerous populations. We explore genomic and linguistic data from the nine islands of Cabo Verde, the earliest European colony of the era in Africa, a major Slave-Trade platform between the 16th and 19th centuries, and a previou...
From the 15th to the 19th century, the Trans-Atlantic Slave-Trade influenced the genetic and cultural diversity of numerous populations. We explore genomic and linguistic data from the nine islands of Cabo Verde, the earliest European colony of the era in Africa, a major Slave-Trade platform between the 16th and 19th centuries, and a previously uni...
Sedimentary ancient DNA (sedaDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sedaDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising examples are 18S-V9 rRNA (~121–130 base pairs, bp) and diat-...
After a long-standing debate, African elephants are now considered by the IUCN as two distinct species: savannah elephants (Loxodonta africana), listed as endangered on the IUCN Red List of Threatened Species, and forest elephants (Loxodonta cyclotis), critically endangered. Both are severely threatened by forest loss, fragmentation and degradation...
Résumé. Le site paléolithique de Roc-en-Pail a été découvert fortuitement entre 1870 et 1871, en marge de l’exploitation d’une carrière alors que la science préhistorique n’en est encore qu’à ses débuts. Néanmoins, dès sa découverte, les industries lithiques sont rapportées au type du Moustier, en référence aux travaux pionniers d’É. Lartet et H. C...
The paleolithic site at Roc-en-Pail was discovered by chance between 1870 and 1871, in the context of quarrying activities when Prehistoric Science was at its youth. Nevertheless the lithic industries were immediate linked to the Moustier type with reference to the pioneer work of É. Lartet and H. Christy. The site was only latter largely excavated...
Mobile devices for on-field DNA analysis have been used for medical diagnostics at the point-of-care, forensic investigations and environmental surveys, but still have to be validated for ancient DNA studies. We report here on a mobile laboratory that we setup using commercially available devices, including a compact real-time PCR machine, and desc...
We present the complete mitochondrial (mtDNA) genome of the branchiopod Limnadia lenticularis (Linnaeus, 1761). The circular genome is 15,151 bp in size and includes the standard complement of 37 genes (13 protein-coding genes, 22 tRNA genes and two rRNA genes) plus one non-coding region (control region). Genes were encoded on one or the other of b...
In shelled molluscs, assigning valid species names to independent evolutionary lineages can be a difficult task. Most original descriptions are based on empty shells and the high levels of variation in shape, color and pattern in some groups can make the shell a poor proxy for species-level identification. The deep-sea gastropod turbinid genus Bolm...
The adoption of Next-Generation Sequencing (NGS) by the field of DNA barcoding of Metazoa has been hindered by the fit between the classical COI barcode and the Sanger-based sequencing method.
Here we describe a framework for the sequencing and multiplexing of mitogenomes on NGS platforms that implements (I) a universal long-range PCR-based amplifi...
With only one species of pike in Europe (Esox lucius Linnaeus, 1758), Esox systematics was considered settled for decades. However recent taxonomical studies of European pikes led to the discovery of two new species: Esox cisalpinus Bianco & Delmastro, 2011 from Northern and Central Italy, and Esox aquitanicus Denys et al. 2014 in the South-West of...
Morphological (shell) and molecular examination of a large suite of specimens of pleurotomariids from around New Caledonia and the Coral Sea reveals the existence of four species in the complex of Perotrochus caledonicus: Perotrochus deforgesi Metivier, 1990 and P. pseudogranulosus sp. nov. live allopatrically on the plateaus and guyots of the Cora...
Viola elatior (Violaceae) is a Eurasian perennial plant species in which French populations are threatened by anthropogenic pressures. Microsatellite primers were developed to investigate its genetic structure and diversity.
Eight microsatellite markers were isolated using next-generation sequencing. Loci were amplified and screened for 138 individ...
During the past decade, a large number of multi-gene analyses aimed at resolving the phylogenetic relationships within Decapoda. However relationships among families, and even among sub-families, remain poorly defined. Most analyses used an incomplete and opportunistic sampling of species, but also an incomplete and opportunistic gene selection amo...
West Pike’s Story: a dated phylogeography of Esox spp. (Actinopterygii, Esocidae)
Denys GPJ 1*, Hinsinger DD 2, Davesne D 2, Debruyne R 2, Delmastro GB 3, Keith P 1, Persat H 4, Utge J 2, Dettai A 2
1 UMR BOREA MNHN–CNRS 7208–IRD 207–UPMC–UCBN, 57 rue Cuvier CP26, 75005 Paris, France
2 UMR ISYEB 7205 MNHN–CNRS–UPMC–EPHE, 57 rue Cuvier CP26, 75005...
The Mediterranean red algal flora is diverse but current knowledge of its diversity is at best fragmentary. Here, a new species of Kallymenia from Croatia is described based on morphological and molecular data. Members of the genus Kallymenia share similar morphology making their generic identification relatively easy, whereas species level identif...
In 2011, three specimens from an unknown species of tube-nosed bat (genus Murina) were collected in montane moist forest at altitudes between 1117 and 1682 m in the Ngoc Linh Nature Reserve of Vietnam. We sequenced the mitochondrial COI gene from Ngoc Linh bats and performed comparisons with Murina sequences available in the nucleotide databases. T...
Premise of the study: Microsatellite loci were developed for the understudied root crop yam bean (Pachyrhizus spp.) to investigate intraspecific diversity and interspecific relationships within the genus Pachyrhizus.
Methods and Results: Seventeen nuclear simple sequence repeat (SSR) markers with perfect di- and trinucleotide repeats were developed...
The sequencing of the crustacean collection of the MNHN, Paris, constitutes a promising yet very challenging barcoding project. For the collection’s crustacean specimens preserved in ethanol, some of which were collected up to 40 years ago, the conventional COI barcoding procedure of amplification with Folmer primers failed for more than half of th...
The marine invertebrates barcoding effort engaged at the MNHN contributed to many different projects. First, an unprecedented sample of Antarctic crinoids has been barcoded revealing probable cryptic speciation within different taxa. For example, seven sympatric COI lineages can be distinguished within the broadcaster Promachocrinus kerguelensis, a...
Characterizing speciation processes in the sea remains a highly contentious issue because geographic barriers to gene exchange, which are the initial conditions for the allopatric speciation model, are not obvious. Moreover, many benthic marine organisms have long-lived planktonic larvae that allow them to connect distant patches of habitats. We he...
Because they house large biodiversity collections and are also research centres with sequencing facilities, natural history museums are well placed to develop DNA barcoding best practices. The main difficulty is generally the vouchering system: it must ensure that all data produced remain attached to the corresponding specimen, from the field to pu...
Cancellariidae, or nutmeg shells, is a family of marine gastropods that feed on the body fluids and the egg cases of marine animals. The 300 or so living species are distributed worldwide, mostly on soft bottoms, from intertidal to depths of about 1000 m. Although they are a key group for the understanding of neogastropod evolution, they are still...
The life histories of Predaea ollivieri J. Feldmann and P. pusilla (Berthold) J. Feldmann were studied in vitro. In P. ollivieri, carpospore germination was unipolar, and sporophytes were formed of sparsely branched uniseriate filaments. In P. pusilla, carpospore germination was bipolar, and sporophytes were formed of uniseriate filaments consolida...
The objective of this study was to determine the solids separation efficiency of the four swirl separators and the drum filter within one of the water recirculation systems (RAS) of a salmon-smolt hatchery. Water flowrates and concentrations of total suspended solids (TSS) within the RAS were measured weekly over 5 weeks in 2004 and 4 weeks in 2005...
Coastal wetlands are characterized by high biodiversity, which is one of the main criteria considered when establishing protection policies or when proposing adequate management actions. In this study, the crustacean and aquatic insect composition of the Empordà wetlands is described. These two faunal groups contribute highly to the total biodivers...
