Publications

The acquisition of biodiversity data is of prime importance to perform an efficient ecosystem management and ensure the sustainable provisioning of marine ecosystem services. Recent efforts are enforcing environmental genomic methodologies, especially environmental DNA (eDNA) metabarcoding, as a way forward to document biodiversity in a faster and cost‐effective way. Currently implemented biomonitoring regulations, such as the Marine Strategy Framework Directive (MSFD), rely on benthic macroinvertebrate indicator taxa to compute biotic indices (BIs) values and derive an ecological quality assessment. Recent work demonstrated that targeting those macroinvertebrates remains challenging, because of various technical and biological biases. Instead, bacterial communities’ profiles depicted by eDNA metabarcoding data have been shown to mirror macroinvertebrate communities’ variation and can be used to accurately predict the BI values using supervised machine learning (SML). Other studies showed that functional profiles, as obtained by metagenomic or metatranscriptomic approaches, vary along pollution gradient in aquatic ecosystems, demonstrating their potential as powerful indicators. Here, a 16S bacterial dataset collected in the vicinity of aquaculture sites, impacted by organic enrichment of the sea bottom, was used to generate two set of features consisting in either OTU profiles (taxonomic turnover) or predicted gene content using the tax4fun tool (functional turnover) that uses taxonomic annotations to infer functional capabilities based on evolutionary models. Both datasets were leading to accurate predictive models, with comparative performance. These results indicate that both taxonomic and functional turnovers of bacterial communities encompass powerful indicators that could be leveraged by marine biomonitoring programs.

Geographic isolation substantially contributes to species endemism on oceanic islands when speciation involves the colonisation of a new island. However, less is understood about the drivers of speciation within islands. What is lacking is a general understanding of the geographic scale of gene flow limitation within islands, and thus the spatial scale and drivers of geographical speciation within insular contexts. Using a community of beetle species, we show that when dispersal ability and climate tolerance are restricted, microclimatic variation over distances of only a few kilometres can maintain strong geographic isolation extending back several millions of years. Further to this, we demonstrate congruent diversification with gene flow across species, mediated by Quaternary climate oscillations that have facilitated a dynamic of isolation and secondary contact. The unprecedented scale of parallel species responses to a common environmental driver for evolutionary change has profound consequences for understanding past and future species responses to climate variation.

The freshwater polyp provides a potent model system for investigating the conditions that promote wound healing, reactivation of a developmental process and, ultimately, regeneration of an amputated body part. polyps can also be dissociated to the single cell level and can regenerate a complete body axis from aggregates, behaving as natural organoids. In recent years, the ability to exploit has been expanded with the advent of new live-imaging approaches, genetic manipulations that include stable transgenesis, gene silencing and genome editing, and the accumulation of high-throughput omics data. In this Primer, we provide an overview of as a model system for studying regeneration, highlighting recent results that question the classical self-enhancement and long-range inhibition model supposed to drive regeneration. We underscore the need for integrative explanations incorporating biochemical as well as mechanical signalling.

Foraminiferal assemblages are a ubiquitous and abundant component of the deep-sea benthos, even in the deepest ocean trenches. While their distribution seems not constrained over large geographical distance, the current knowledge of foraminifera in trench is solely based on morphological observations. In this study, we document the first DNA metabarcoding dataset from a deep-sea trench focusing specifically on benthic foraminifera. Here we show that, consistent with previous molecular studies of abyssal fauna, trench foraminifera include diverse sequences of yet unknown species captured only by their molecular traces in the sediment. The molecular assemblages of foraminifera significantly differed along a depth gradient of almost 5000 m in the Kuril-Kamchatka trench. The deepest stations at nearly 9500 m were composed of unique phylotypes that were not identified in shallower stations, which means that these assemblages are unlikely the result of a sinking effect from shallower depths. Finally, both sides of the trench harbored very different communities, which could imply that the trench constitutes a physical barrier for the dispersion of some deep-sea foraminiferal species.

High altitude represents some of the most extreme environments worldwide. The genetic changes underlying adaptation to such environments have been recently identified in multiple animals but remain unknown in horses. Here, we sequence the complete genome of 138 domestic horses encompassing a whole altitudinal range across China to uncover the genetic basis for adaptation to high-altitude hypoxia. Our genome data set includes 65 lowland animals across ten Chinese native breeds, 61 horses living at least 3,300 m above sea level across seven locations along Qinghai-Tibetan Plateau, as well as 7 Thoroughbred and 5 Przewalski's horses added for comparison. We find that Tibetan horses do not descend from Przewalski's horses but were most likely introduced from a distinct horse lineage, following the emergence of pastoral nomadism in Northwestern China ∼3,700 years ago. We identify that the endothelial PAS domain protein 1 gene (EPAS1, also HIF2A) shows the strongest signature for positive selection in the Tibetan horse genome. Two missense mutations at this locus appear strongly associated with blood physiological parameters facilitating blood circulation as well as oxygen transportation and consumption in hypoxic conditions. Functional validation through protein mutagenesis shows that these mutations increase EPAS1 stability and its hetero dimerization affinity to ARNT (HIF1B). Our study demonstrates that missense mutations in the EPAS1 gene provided key evolutionary molecular adaptation to Tibetan horses living in high-altitude hypoxic environments. It reveals possible targets for genomic selection programs aimed at increasing hypoxia tolerance in livestock and provides a textbook example of evolutionary convergence across independent mammal lineages.

A quest to collect live specimens of the well-known foraminifer Ammonia beccarii for sequencing has led to the recognition of five molecular species in Europe all related to it, but no live A. beccarii itself. The five molecular species all clump together in one clade (T3) of the Ammonia phylogenetic tree. All are characterized by large size, ornament on the umbilical side and a deep spiral, sutural fissure on the spiral side (beccarii morphogroup). All five molecular species can be discriminated based on distinct morphological differences as Ammonia batava (North Sea, northeast Atlantic, west Mediterranean Sea), A. corallinarum (northeast Atlantic, west Mediterranean Sea), A. pawlowskii n. sp. (Mediterranean Sea, west Indian Ocean), A. falsobeccarii (North Sea, east Atlantic seaboard, Mediterranean Sea, Persian Gulf), and A. neobeccarii (Mediterranean and Black seas). Using morphological characters, a further four species are recognized in the beccarii morphogroup for which no sequences are presently available: A. beccarii (Mediterranean Sea, northeast Atlantic), A. batava compacta (west Atlantic seaboard), A. debenayi n. sp. (west Indian Ocean), A. venecpeyreae n. sp. (west Mediterranean Sea, Gulf of Aden). One species, A. japonica (China, Japan, South Korea), for which sequences have been obtained, is included in the beccarii morphogroup based on morphological characteristics but differs genetically from the beccarii group. Another species, similar to A. falsobeccarii with secondary sutural openings on the spiral side but probably not part of the beccarii morphogroup because it lacks the spiral sutural canal typical of the group, is described as new – A. langeri (Indian Ocean, East Indies, south Australia). A growth series of A. beccarii topotypes from Rimini, north Adriatic Sea, is illustrated to aid in its recognition and a neotype designated and illustrated. Extinct fossil members of the beccarii morphogroup include A. ikebei, A. inflata, A. italica, A. nakazatoensis, A. punctatogranosa, A. reyi, A. togopiliensis, A. viennensis, and A. voorthuyseni.

The HoxD cluster is critical for vertebrate limb development. Enhancers located in both the telomeric and centromeric gene deserts flanking the cluster regulate the transcription of HoxD genes. In rare patients, duplications, balanced translocations or inversions misregulating HOXD genes are responsible for mesomelic dysplasia of the upper and lower limbs. By aCGH, whole-genome mate-pair sequencing, long-range PCR and fiber fluorescent in situ hybridization, we studied patients from two families displaying mesomelic dysplasia limited to the upper limbs. We identified microduplications including the HOXD cluster and showed that microduplications were in an inverted orientation and inserted between the HOXD cluster and the telomeric enhancers. Our results highlight the existence of an autosomal dominant condition consisting of isolated ulnar dysplasia caused by microduplications inserted between the HOXD cluster and the telomeric enhancers. The duplications likely disconnect the HOXD9 to HOXD11 genes from their regulatory sequences. This presumptive loss-of-function may have contributed to the phenotype. In both cases, however, these rearrangements brought HOXD13 closer to telomeric enhancers, suggesting that the alterations derive from the dominant-negative effect of this digit-specific protein when ectopically expressed during the early development of forearms, through the disruption of topologically associating domain structure at the HOXD locus.

The nervous system is produced and maintained in adult Hydra through the continuous production of nerve cells and mechanosensory cells (nematocytes or cnidocytes). De novo neurogenesis occurs slowly in intact animals that replace their dying nerve cells, at a faster rate in animals regenerating their head as a complete apical nervous system is built in few days. To dissect the molecular mechanisms that underlie these properties, a precise monitoring of the markers of neurogenesis and nematogenesis is required. Here we describe the conditions for an efficient BrdU-labeling coupled to an immunodetection of neuronal markers, either regulators of neurogenesis, here the homeoprotein prdl-a, or neuropeptides such as RFamide or Hym-355. This method can be performed on whole-mount animals as well as on macerated tissues when cells retain their morphology. Moreover, when antibodies are not available, BrdU-labeling can be combined with the analysis of gene expression by whole-mount in situ hybridization. This co-immunodetection procedure is well adapted to visualize and quantify the dynamics of de novo neurogenesis. Upon continuous BrdU labeling, the repeated measurements of BrdU-labeling indexes in specific cellular populations provide a precise monitoring of nematogenesis as well as neurogenesis, in homeostatic or developmental conditions.

To understand the function of an organ, it is often useful to understand the role of its constituent cell populations. Unfortunately, the rarity of individual cell populations often makes it difficult to obtain enough material for molecular studies. For example, the accessory gland of the Drosophila male reproductive system contains two distinct secretory cell types. The main cells make up 96% of the secretory cells of the gland, while the secondary cells (SC) make up the remaining 4% of cells (about 80 cells per male). Although both cell types produce important components of the seminal fluid, only a few genes are known to be specific to the SCs. The rarity of SCs has, thus far, hindered transcriptomic analysis study of this important cell type. Here, a method is presented that allows for the purification of SCs for RNA extraction and sequencing. The protocol consists in first dissecting glands from flies expressing a SC-specific GFP reporter and then subjecting these glands to protease digestion and mechanical dissociation to obtain individual cells. Following these steps, individual, living, GFP-marked cells are sorted using a fluorescent activated cell sorter (FACS) for RNA purification. This procedure yields SC-specific RNAs from ~40 males per condition for downstream RT-qPCR and/or RNA sequencing in the course of one day. The rapidity and simplicity of the procedure allows for the transcriptomes of many different flies, from different genotypes or environmental conditions, to be determined in a short period of time.

Tooth replacement in vertebrates is extremely diverse, and its study in extinct taxa gives insights into the evolution of the different dental renewal modes. Based on μ-CT scans of a left lower jaw of the extinct fish †Scheenstia (Actinopterygii, Lepisosteiformes), we describe in detail a peculiar tooth replacement mode that is, as far as we could ascertain from the literature, unique among vertebrates. The formation of the replacement teeth comprises a 180° rotation of their acrodin cap that occurs intraosseously within bony crypts, and their setting up appears to be synchronous. We propose a model for the dental renewal process and identify complementary anatomical features visible in the tomography such as the junction between the different tooth-bearing bones (prearticular–coronoid and dentary), as well as cavities corresponding to intraosseous crypts, nervous and/or vascular canals. The location of the cavities and their subsequent identification (e.g. Meckel's cavity, mandibular sensory canal) help us to identify the function of pores visible on the bone surface and understand their relation to internal anatomical features. Finally, recognition of this tooth replacement mode raises the question of whether it is specific to †Scheenstia or related to a particular dentition type and thus potentially occurs in other lineages.