Publications

The effectiveness of environmental protection measures is based on the early identification and diagnosis of anthropogenic pressures. Similarly, restoration actions require precise monitoring of changes in the ecological quality of ecosystems, in order to highlight their effectiveness. Monitoring the ecological quality relies on bioindicators, which are organisms revealing the pressures exerted on the environment through the composition of their communities. Their implementation, based on the morphological identification of species, is expensive because it requires time and experts in taxonomy. Recent genomic tools should provide access to reliable and high-throughput environmental monitoring by directly inferring the composition of bioindicators' communities from their DNA (metabarcoding). The French-Swiss program SYNAQUA (INTERREG France-Switzerland 2017-2019) proposes to use and validate the tools of environmental genomic for biomonitoring and aims ultimately at their implementation in the regulatory bio-surveillance. SYNAQUA will test the metabarcoding approach focusing on two bioindicators, diatoms, and aquatic oligochaetes, which are used in freshwater biomonitoring in France and Switzerland. To go towards the renewal of current biomonitoring practices, SYNAQUA will (1) bring together different actors: scientists, environmental managers, consulting firms, and biotechnological companies, (2) apply this approach on a large scale to demonstrate its relevance, (3) propose robust and reliable tools, and (4) raise public awareness and train the various actors likely to use these new tools. Biomonitoring approaches based on such environmental genomic tools should address the European need for reliable, higher-throughput monitoring to improve the protection of aquatic environments under multiple pressures, guide their restoration, and follow their evolution.

Dugaldia emmilta is a teleostean fish found in the late Albian Toolebuc Formation in Queensland, Australia. In the original description, D. emmilta was attributed to the Neoteleostei because of the presence of a tripartite occipital condyle, and the species was postulated to have a basal position among neoteleosteans because of the presence of several plesiomorphic characters. A reexamination of the holotype, together with the description of two new specimens, indicates that D. emmilta is an ichthyodectiform fish. A phylogenetic analysis resolves this species as the sister to Ogunichthys + Ichthyodectoidei. This species shows unusual features for an ichthyodectiform, in particular the shape of the mandible and the arrangement of the teeth on the lower jaw. Jaw mechanics in ichthyodectiforms are peculiar because they allow a significant lateral enlargement. In Dugaldia, a similar disposition is present but is exaggerated by specific features of the maxilla and the mandible. Comparisons with the sarcastic fringehead (Neoclinus blanchardi), a living blenny that shows a ‘gaping display,’ reveal that Dugaldia was likely able to exhibit extreme lateral mouth enlargement.

Ichthyoliths (fossil fish microremains) from geological core samples are commonly recorded and where present allow dating and contribute to the knowledge of the evolution of fish faunas through time (see, for instance, Sibert et al., Citation2014; Sibert and Norris, Citation2015, for the Ocean Drilling Program). However, reports of articulated fish specimens in cores are much rarer due to the limited chance of a core drill returning a small-diameter cylinder of rock encompassing the fossil to the surface. Examples of articulated fishes described from cores include specimens of Permo-Carboniferous actinopterygians near the city of Zurich, Switzerland (Bürgin, Citation1990), as well as a new taxon of a Cenomanian ellimmichthyiform from Alberta, Canada (Hay et al., Citation2007), and two new Eocene cypriniform fishes from Guangdong and Henan, China (Liu, Citation1957; Zhou, Citation1990; Chang and Chen, Citation2008). In this paper, we report the discovery of an ichthyodectiform fish fossil collected during re-evaluation of a core from DSDP Leg 41 Site 367 at the IODP Bremen Core Repository, Germany ( ). The core was recovered from a well drilled in the Cape Verde Basin, ca. 400 km offshore from the West African Atlantic Margin, to test the early basin evolution of the Central Atlantic region (Lancelot et al., Citation1977). The fossil fish was discovered in core 21 section 6 at 699.9 m measured depth, preserved on the bedding surface of a bituminous marl. Reports from the DSDP expedition had previously recorded fish vertebrae in the same subunit, suggesting abundance and/or high preservation rate of fish remains in Central Atlantic waters during the Albian to Cenomanian period (Lancelot et al., Citation1977:fig. 6). Associated calcareous nannofossils indicate an earliest Cenomanian age for the cored interval containing this specimen ().

Conn's Handbook of Models for Human Aging, Second Edition, presents key aspects of biology, nutrition, factors affecting lifespan, methods of age determination, use in research and the disadvantages/advantages of use. Using a multidisciplinary approach, this updated edition is designed as the only comprehensive, current work that covers the diversity in aging models. Chapters on comparative models explore age-related diseases, including Alzheimer's, joint disease, cataracts, cancer and obesity. Also included are new tricks and approaches not available in primary publications. This must-have handbook is an indispensable resource for researchers interested in the mechanisms of aging, gerontologists, health professionals, allied health practitioners and students.

Human-induced habitat changes may lead to the breakdown of reproductive barriers between distantly related species. This phenomenon may result in fertile first-generation hybrids (F ) that exclude the genome of one parental species during gametogenesis, thus disabling introgression. The species extinction risk associated with hybridization with genome exclusion is largely underappreciated because the phenomenon produces only F hybrid phenotype, leading to the misconception that hybrids are sterile and potentially of minor conservation concern. We used a simulation model that integrates the main genetic, demographic, and ecological processes to examine the dynamics of hybridization with genome exclusion. We showed that this mode of hybridization may lead to extremely rapid extinction when the process of genome exclusion is unbalanced between the interbreeding species and when the hybridization rate is not negligible. The coexistence of parental species was possible in some cases of asymmetrical genome exclusion, but show this equilibrium was highly vulnerable to environmental variation. Expanding the exclusive habitat of the species at risk allowed its persistence. Our results highlight the extent of possible extinction risk due to hybridization with genome exclusion and suggest habitat management as a promising conservation strategy. In anticipation of serious threats to biodiversity due to hybridization with genome exclusion, we recommend a detailed assessment of the reproductive status of hybrids in conservation programs. We suggest such assessments include the inspection of genetic content in hybrid gametes.

The developing vertebrate limb has long proved as an excellent system for studying the mechanisms involved in pattern formation and morphogenesis and more recently in transcriptional regulation and morphological evolution. To elucidate the stage-specific expression profiles of the components of the developing limb, we have generated the temporal transcriptome of the limb progenitors and of the overlying ectoderm separately. Our study has uncovered a collinear activation of Hoxc genes in the limb ectoderm that we have validated by in situ hybridization. However, while members of the HoxA and HoxD clusters show complex and dynamic patterns of expression during limb development that correlate with the morphology of the different limb segments, no specific function for the HoxC or HoxB clusters has been identified ( 1 - 3 ). To investigate the function of Hoxc genes in the limb ectoderm, we have reexamined the HoxC cluster null mice. Remarkably, and despite exhibiting normal terminal phalanges, these mice didn't form claws (anonychia). Morphological and immunohistochemical analysis identified a failure in the differentiation of the main components of the nail/claw organ. To unravel the transcriptional regulation of Hoxc genes in the limb ectoderm, we used the ATACseq technique. Using this approach, we identified two putative regulatory regions which activity was tested in mouse transgenic enhancer assays. It is currently considered that Hox genes have played a key role in the evolution of morphological traits, probably associated with changes in their regulatory landscapes ( 4 ). Given that the form and size of the distal limb integumentary organ (nail, claw or hoof) correlates with that of the distal phalanx and that the development of hooves was a major innovation in the evolution of a cursorial lifestyle, we are also exploring the possible implication of Hoxc genes in the nail/claw/hoof transition. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Vanhoeffenella is a common deep-sea monothalamous foraminifer, some species of which have a unique eye-like test morphology. Owing to its world-wide distribution, it has been recorded numerous times since the "heroic age" of the deep-sea exploration in the early 20th century. So far, only 4 species have been described, and no attempts have been made to estimate the real diversity of this peculiar genus. Over the last fifteen years, we have collected specimens of Vanhoeffenella from various deep-sea areas, providing the basis for an integrative taxonomy and biogeography of this genus. Here, we clarify the phylogenetic position of Vanhoeffenella and give an account of its diversity in the Atlantic, Arctic and Southern Oceans (the Weddell Sea) as revealed by genetic marker (SSU rDNA) and morphology. Our study shows that Vanhoeffenella branches within Clade F of monothalamids and incorporates at least 10 putative species. Some could be distinguished by either morphological or molecular features, but only the integrative taxonomic approach provides a robust way to assess their diversity. We examine the new material of the type species (V. gaussi Rhumbler), redescribe the poorly-known V. oculus Earland and describe formally a fifth species, V. dilatata sp. nov.

The African parasitoid wasp Cotesia sesamiae is a generalist species structured in locally adapted populations showing differences in host range. The recent discovery of Cotesia typhae, a specialist, sister species to C. sesamiae, provides a good framework to study the genetic determinants of parasitoid host range. To investigate the genomic bases of divergence between these populations and species, we used a targeted sequencing approach on 24 samples. We targeted the bracovirus genomic region encoding virulence genes involved in the interaction with the lepidopteran hosts of the wasps. High sequencing coverage was obtained for all samples, allowing the study of genetic variation between wasp populations and species. By combining population genetic estimations, such as nucleotide diversity (π), relative differentiation (FST) and absolute divergence (dxy), with branch‐site dN/dS measures, we identified six of 98 bracovirus genes showing significant divergence and evidence of positive selection. These genes, belonging to different gene families, are potentially involved in host adaptation and in the specialization process. Fine‐scale analyses of genetic variation also revealed mutations and large deletions in certain genes inducing pseudogenization and loss of function. The image emerging from these results is that adaptation mediated by bracovirus genes happens through selection of particularly adaptive alleles and loss of nonadaptive genes. These results highlight the central role of the bracovirus in the molecular interactions between the wasps and their hosts and in the evolutionary processes of specialization.

We had previously reported a mouse line carrying the Atypical female courtship (HoxD) allele, where an ectopic accumulation of Hoxd10 transcripts was observed in a sparse population of cells in the adult isocortex, as a result of a partial deletion of the HoxD gene cluster. Female mice carrying this allele displayed an exacerbated paracopulatory behavior, culminating in a severe mutilation of the studs' external genitals. To unequivocally demonstrate that this intriguing phenotype was indeed caused by an illegitimate function of the HOXD10 protein, we use CRISPR/Cas9 technology to induce a microdeletion into the homeobox of the Hoxd10 gene in cis with the HoxDallele.

Promiscuous mating and sperm competition often induce arms races between the sexes with detrimental outcomes for females. However, ants with multiply-inseminated queens have only a single time-window for sperm competition and queens are predicted to gain control over the outcome of sperm storage quickly. The seminal fluid of Acromyrmex leaf-cutting ants reduces the viability of rival sperm, but how confrontations between unrelated ejaculates affect sperm storage remains unknown.