Publications

The protist genus Gromia was first described in 1835 by Dujardin and while gromiids are prominent in the marine environment, Gromia oviformis was, for a long time, the only valid species regularly recorded. To date, 16 species that are morphologically and/or genetically distinct have been described. While recent studies are documenting their diversity and their ecological importance, G. oviformis has been the sole gromiid species identified in the Black Sea, although unnamed Gromia species have also been recorded. We collected sediment samples from the Romanian continental shelf at varying depths (48 - 58 m) to study the morphological and genetic diversity of gromiids in this part of the Black Sea. Three new species, Gromia bugnae sp. nov., Gromia dianae sp. nov. and Gromia fabi sp. nov., were identified based on an integrative taxonomic approach, thus bringing the total described gromiid species to 19. Analysis of partial SSU rRNA gene sequences confirms that these are distinct species. Additionally, an undescribed species is represented by a sequence from the northern part of the Black Sea (Sevastopol, Kazachya Bay). The study provides further evidence of the diversity of gromiids in the Black Sea and underlines the importance of this little-known group in marginal seas.

Preserving natural genetic diversity and ecological function of wild species is a central goal in conservation biology. As such, anthropogenic hybridization is considered a threat to wild populations, as it can lead to changes in the genetic makeup of wild species and even to the extinction of wild genomes. In European wildcats, the genetic and ecological impacts of gene flow from domestic cats are mostly unknown at the species scale. However, in small and isolated populations, it is known to include genetic swamping of wild genomes. In this context, it is crucial to better understand the dynamics of hybridization across the species range, to inform and implement management measures that maintain the genetic diversity and integrity of the European wildcat. In the present paper, we aim to provide an overview of the current scientific understanding of anthropogenic hybridization in European wildcats, to clarify important aspects regarding the evaluation of hybridization given the available methodologies, and to propose guidelines for management and research priorities.

As part of the worldwide effort to better characterize HLA diversity in populations, we have studied the population of Québec in Canada. This province has been defined by a complex history with multiple founder effects and migration patterns. We analyzed the typing data of 3806 individuals registered in Héma-Québec's Registry, which covered most administrative regions in Québec. Typing information was resolved at the second field level of resolution by next-generation sequencing (NGS) or by Sanger sequencing. We used the HLA-net.eu GENE[RATE] tools to estimate allele and two-locus haplotype frequencies for HLA-A, -B, -C, -DRB1, -DQB1, and -DPB1, as well as Hardy-Weinberg equilibrium (HWE), selective neutrality, and linkage disequilibrium. The chord genetic distance was also calculated between administrative regions and was visualized using non-metric multidimensional scaling (NMDS) analysis. While most individual regions were in HWE, HWE was rejected for the province considered as a whole. Some regions exhibited signatures of selection, mostly toward an excess of heterozygotes. Allele and haplotype frequencies revealed outlier regions that strongly differed from the other regions. NMDS plots also showed differences between regions. The administrative regions of the province of Québec displayed heterogeneity in their HLA profiles. This heterogeneity was attributable to differing allele and haplotype specificities by region. In particular, regions 02-Saguenay-Lac-Saint-Jean and 01-Bas-St-Laurent diverged from the rest of the regions. The urban regions 06-Montréal and 13-Laval were very diversified in their HLA profiles. Together, these results will help optimize donor recruitment strategies in Québec.

Since the split of the coelacanth lineage from other osteichthyans 420 million years ago, the morphological disparity of this clade has remained remarkably stable. Only few outliers with peculiar body shape stood out over the evolutionary history, but they were phylogenetically and stratigraphically independent of each other. Here, we report the discovery of a new clade of ancient latimeriid coelacanths representing a small flock of species present in the Western Tethys between 242 and 241 million years ago. Among the four species, two show highly derived anatomy. A new genus shows reversal to plesiomorphic conditions in its skull and caudal fin organisation. The new genus and its sister Foreyia have anatomical modules that moved from the general coelacanth Bauplau either in the same direction or in opposite direction that affect proportions of the body, opercle and fins. Comparisons with extant genetic models shows that changes of the regulatory network of the Hedgehog signal gene family may account for most of the altered anatomy. This unexpected, short and confined new clade represents the only known example of a burst of morphological disparity over the long history of coelacanths at a recovery period after the Permian-Triassic Mass Extinction.

Teleosts form the largest clade among the extant actinopterygians, some extinct forms of which are still poorly positioned in the phylogeny. The Tselfatiiformes and Araripichthyidae are such examples. A newly discovered genus and species from the Cenomanian of Haqel, Lebanon, is described, and its systematic affinities are discussed. It shares several characteristics (deep and compressed body with elongated and high dorsal and anal fins, edentulous maxilla, and sinusoidal vertebral column) with both the Tselfatiiformes and Araripichthys, making it difficult to place within the teleosts. It shares with Abisaadichthys, among the tselfatiiforms’ family Protobramidae, an autogenous retroarticular, and with Araripichthys premaxillae with a long ascending process, well-developed maxillary articular condyle and two supramaxillae. Moreover, it shows some unique characteristics (a thin maxilla with two large supramaxillae, fused articular and angular bones, mandibular sensory canal opening on the external side of the anguloarticular, first dorsal pterygiophore having the same enlarged semi-circular plate as the first anal pterygiophore) justifying its generic status. Comments on some of the protobramids are presented, and the necessity for phylogenetic analysis to place the Tselfatiiformes, Araripichthys and Ypsiloichthys within the teleosts is outlined.

Most previous accounts summarising the biogeography and species durations of smaller calcareous benthic foraminifera have been based on literature reviews or on a massive North American database that had been taxonomically standardised. In this review we limit consideration to extant and fossil families or genera (from nearshore, open shelf, and deep-sea environments) with modern reviews that have standardised their global morphotaxonomy and where available, are complimented by molecular studies. We confirm previous studies that indicate most shelf species have limited geographic ranges and the majority of deep-water species are widespread and cosmopolitan or nearly so. In our intertidal and inner shelf groups only one species (molecular and morphological), Ammonia veneta, has a cosmopolitan distribution, although four warm-water morphospecies, of Ammonia and Rugobolivinella, have or had distributions that spanned more than one ocean in equatorial latitudes. The majority of both warm- and cool-water species in these groups are regionally or locally-restricted endemics (92% of Bolivinellidae, 100% of Tubulogenerina, 73% of Ammoniidae). The biogeographic distribution of the two rarer, warm-water groups (Bolivinellidae, Tubulogenerina) changed dramatically through the Cenozoic with the Paleocene–Eocene North American–European distribution of Bolivinellidae switching to purely Indo-Pacific by the Pliocene–Quaternary. In our shelf–upper bathyal groups (Notorotaliiidae, Plectofrondiculariidae), two genera have been restricted to the Southern Hemisphere since their Eocene originations with their greatest diversity throughout in New Zealand and Australia, respectively. The dominantly cold-water notorotaliid genus Buccella has a biogeographic distribution largely restricted to the Arctic Ocean and both coasts of North and South America. Most notorotaliid species are locally or regionally endemic (100% of Notorotalia, Parrellina, Porosorotalia, 75% of Buccella). At least 50–60% of species in five extinct mid-bathyal–abyssal families are cosmopolitan and have been throughout the Cenozoic since their originations. The majority of these deep-sea species with more-restricted distributions are rare, and many could possibly be more widespread with further extensive study. This review found that the shortest mean species durations (4–5 myrs) occur in two groups of rather rare, tropical–subtropical inner-shelf foraminifera with many locally endemic species. In cooler and progressively deeper water environments the mean species durations increase to 7–11 myrs for temperate shelf–bathyal taxa (Notorotaliidae), 20 myrs for an extinct mid-shelf to bathyal family (Plectofrondiculariidae) and 41–50 myrs for five extinct mid-bathyal–abyssal families (Chrysalogoniidae, Ellipsoidinidae, Glandulonodosariidae, Pleurostomellidae, Stilostomellidae). One species in each of four of these deep-water families had a species duration of 150–120 myrs.

The study of the Palaeolithic in Senegal has made considerable progress in the last decade and has provided a renewed vision of the behavioral evolution of prehistoric populations in West Africa. The cultural trajectories within the region seem to be highly variable and bear witness to strong behavioral dynamics, the mechanisms of which still need to be better understood. However, the number of reliable, dated, and stratified sites, as well as the palaeoenvironmental data providing a context for populations in their palaeolandscapes, is still scarce. In order to provide new and solid data, we conducted new archaeological survey in the Niokolo-Koba National Park in south-central Senegal, aiming at a preliminary identification of Pleistocene and early Holocene sedimentary deposits. Here, we report an overview of the newly discovered industries found in different contexts. Most of the 27 identified sites show surface and out-of-context assemblages, but other sites are stratified and have all the criteria to justify the development of a long-term archaeological, geochronological, geomorphological, and palaeobotanical project. The Niokolo-Koba National Park, through which the Gambia River flows, is characterized by an abundance of sources of knappable material and by well-preserved sedimentary sequences. Therefore, archaeological research in the Niokolo-Koba National Park has the potential to provide major milestones in our understanding of the evolutionary dynamics at work in West Africa during the early periods of occupation of the region.

During development, Hox genes are temporally activated according to their relative positions on their clusters, contributing to the proper identities of structures along the rostrocaudal axis. To understand the mechanism underlying this Hox timer, we used mouse embryonic stem cell-derived stembryos. Following Wnt signaling, the process involves transcriptional initiation at the anterior part of the cluster and a concomitant loading of cohesin complexes enriched on the transcribed DNA segments, that is, with an asymmetric distribution favoring the anterior part of the cluster. Chromatin extrusion then occurs with successively more posterior CTCF sites acting as transient insulators, thus generating a progressive time delay in the activation of more posterior-located genes due to long-range contacts with a flanking topologically associating domain. Mutant stembryos support this model and reveal that the presence of evolutionary conserved and regularly spaced intergenic CTCF sites controls the precision and the pace of this temporal mechanism.

Two influential concepts in tissue patterning are Wolpert's positional information and Turing's self-organized reaction-diffusion (RD). The latter establishes the patterning of hair and feathers. Here, our morphological, genetic, and functional-by CRISPR-Cas9-mediated gene disruption-characterization of wild-type versus "scaleless" snakes reveals that the near-perfect hexagonal pattern of snake scales is established through interactions between RD in the skin and somitic positional information. First, we show that ventral scale development is guided by hypaxial somites and, second, that ventral scales and epaxial somites guide the sequential RD patterning of the dorsolateral scales. The RD intrinsic length scale evolved to match somite periodicity, ensuring the alignment of ribs and scales, both of which play a critical role in snake locomotion.

In this study the aim was to resolve the taxonomy of several species of Hübner (Pyraloidea, Crambinae) with previously unrecognised morphological variation. By analysing the DNA barcode (COI-5P) in numerous specimens, the aim was to reconstruct phylogenetic relationships between species, to provide better evidence for synonymies, and to circumscribe their geographical distribution. Using an innovative DNA hybridisation capture protocol, the DNA barcode of the lectotype of (Fabricius, 1794) was partially recovered for comparison with the 229 DNA barcode sequences of specimens available in the Barcode of Life Datasystems, and this firmly establishes the identity of the species. The same protocol was used for the following type specimens: the (Walker, 1859) holotype, thus confirming the synonymy of this name with , the holotype of (Zeller, 1863), , the holotype of Dyar, 1914, newly synonymised with , and a specimen of Dyar, 1913, collected in 1992. In addition, nine specimens of , , Dyar, 1914 and Dyar, 1915, from North to South America were sampled using classical COI amplification and Sanger sequencing. Dyar, described from Bermuda, is the name to be applied to the more widespread North American species formerly identified as . Following morphological study of its holotype, Butler, 1878, is also synonymised with . The name Hübner, 1818, is considered a nomen dubium associated with . The adult morphology is diagnosed and illustrated, and distributions are plotted for , , , and based on slightly more than 800 specimens. For the first time, DNA barcode sequences are provided for the Antillean . This work provides a modified, improved protocol for the efficient hybrid capture enrichment of DNA barcodes from 18 and 19 century type specimens in order to solve taxonomic issues in Lepidoptera.