Publications

Based on molecular and morphological characters, we describe a new species of monothalamous foraminifera, Psammophaga secriensia sp. nov., that was sampled from two coastal locations (48 m and 53 m depth) on the Romanian Black Sea continental shelf. Molecular data further confirm its presence in the northeastern part of the Black Sea (Balaklava Bay, 5–10 m depth). Specimens of Psammophaga secriensia sp. nov. are characterized by an elongate to broadly pyriform test and a simple rounded aperture. The wall is translucent and the cytoplasm contains mineral grains of different sizes. The genus Psammophaga, including Psammophaga simplora and several undetermined morphotypes, has been reported from different areas of the Black Sea. Previous research using an integrative taxonomic approach has identified two additional species (Psammophaga zirconia; Psammophaga sp., Gooday et al., 2011) occurring in the Black Sea. Monothalamids are an important part of the meiobenthos in the Black Sea and our results increase the knowledge of foraminiferal diversity in this marginal sea.

Changes in gene expression represent an important source of phenotypic innovation. Yet how such changes emerge and impact the evolution of traits remains elusive. Here, we explore the molecular mechanisms associated with the development of masculinizing ovotestes in female moles. By performing integrative analyses of epigenetic and transcriptional data in mole and mouse, we identified the co-option of SALL1 expression in mole ovotestes formation. Chromosome conformation capture analyses highlight a striking conservation of the 3D organization at the SALL1 locus, but an evolutionary divergence of enhancer activity. Interspecies reporter assays support the capability of mole-specific enhancers to activate transcription in urogenital tissues. Through overexpression experiments in transgenic mice, we further demonstrate the capability of SALL1 to induce kidney-related gene programs, which are a signature of mole ovotestes. Our results highlight the co-option of gene expression, through changes in enhancer activity, as a plausible mechanism for the evolution of traits.

In vertebrates, there are two known mechanisms by which meiotic recombination is directed to the genome: in humans, mice, and other mammals, recombination occurs almost exclusively where the protein PRDM9 binds, while in species lacking an intact , such as birds and canids, recombination rates are elevated near promoter-like features. To test if PRDM9 also directs recombination in non-mammalian vertebrates, we focused on an exemplar species, the corn snake (). Unlike birds, this species possesses a single, intact ortholog. By inferring historical recombination rates along the genome from patterns of linkage disequilibrium and identifying crossovers in pedigrees, we found that PRDM9 specifies the location of recombination events outside of mammals. However, we also detected an independent effect of promoter-like features on recombination, which is more pronounced on macro- than microchromosomes. Thus, our findings reveal that the uses of PRDM9 and promoter-like features are not mutually-exclusive, and instead reflect a tug of war, which varies in strength along the genome and is more lopsided in some species than others.

The physiology and behavior of social organisms correlate with their social environments. However, because social environments are typically confounded by age and physical environments (i.e., spatial location and associated abiotic factors), these correlations are usually difficult to interpret. For example, associations between an individual's social environment and its gene expression patterns may result from both factors being driven by age or behavior. Simultaneous measurement of pertinent variables and quantification of the correlations between these variables can indicate whether relationships are direct (and possibly causal) or indirect. Here, we combine demographic and automated behavioral tracking with a multiomic approach to dissect the correlation structure among the social and physical environment, age, behavior, brain gene expression, and microbiota composition in the carpenter ant Camponotus fellah. Variations in physiology and behavior were most strongly correlated with the social environment. Moreover, seemingly strong correlations between brain gene expression and microbiota composition, physical environment, age, and behavior became weak when controlling for the social environment. Consistent with this, a machine learning analysis revealed that from brain gene expression data, an individual's social environment can be more accurately predicted than any other behavioral metric. These results indicate that social environment is a key regulator of behavior and physiology.

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.