Publications

We describe Aschemonella monile Gooday and Holzmann sp. nov. from the Clarion–Clipperton Zone (CCZ, abyssal eastern equatorial Pacific), a region characterized by commercially significant concentrations of polymetallic nodules. The new species is the most abundant xenophyophore (giant agglutinated foraminifera) in our main sampling area (12–14°N; 116°30′–117°26′W). Additional specimens originate from the central CCZ, and from a third area, ~900 km NW of the main area, where A. monile numerically dominates the megabenthos in photographic surveys of the seafloor (average densities 1.54 individuals/m2; peak densities > 3 individuals/m2). Aschemonella monile is much larger (≥ 7 cm in length) than previously described species of the genus, with a test comprising an irregular sequence of self-contained, partly overlapping ‘segments’, creating a multichambered structure. A similar, much rarer species from the main study area, described here as Aschemonella aspera Gooday and Holzmann sp. nov., has an unsegmented test with a very rough, coarsely agglutinated wall. Genetic data suggest that A. monile is distinct from A. aspera and most closely related to a group comprising Rhizammina algaeformis and Aschemonella ramuliformis. Both new species have delicate tests that are often attached to nodule surfaces, making them particularly vulnerable to seafloor disturbances.

We evaluated benthic bacterial communities as bioindicators in environmental impact assessments of salmon aquaculture, a rapidly growing sector of seafood industry. Sediment samples (n=72) were collected from below salmon cages towards distant reference sites. Bacterial community profiles inferred from DNA metabarcodes were compared to reference data from standard macrofauna biomonitoring surveys of the same samples. Deltaproteobacteria were predominant in immediate vicinity of the salmon cages. Along the transect, significant shifts in bacterial community structures were observed with Gammaproteobacteria dominating the less-impacted sites. Alpha- and beta-diversity measures of bacterial communities correlated significantly with macrofauna diversity metrics and with five ecological status indices. Benthic bacterial communities mirror the reaction of macrofauna bioindicators to environmental disturbances caused by salmon farming. The implementation of bacterial eDNA metabarcoding in future Strategic Framework Directives is an alternative cost-effective high-throughput biomonitoring solution, providing a basis for management strategies in a matter of days rather than months.

The circadian pacemaker circuit orchestrates rhythmic behavioral and physiological outputs coordinated with environmental cues, such as day/night cycles. The molecular clock within each pacemaker neuron generates circadian rhythms in gene expression, which underlie the rhythmic neuronal functions essential to the operation of the circuit. Investigation of the properties of the individual molecular oscillators in different subclasses of pacemaker neurons and their interaction with neuronal signaling yields a better understanding of the circadian pacemaker circuit. Here, we present a time-lapse fluorescent microscopy approach developed to monitor the molecular clockwork in clock neurons of cultured Drosophila larval brain. This method allows the multi-day recording of the rhythms of genetically encoded fluorescent circadian reporters at single-cell resolution. This setup can be combined with pharmacological manipulations to closely analyze real-time response of the molecular clock to various compounds. Beyond circadian rhythms, this multipurpose method in combination with powerful Drosophila genetic techniques offers the possibility to study diverse neuronal or molecular processes in live brain tissue.

Analyzing genetic variation through time and space is important to identify key evolutionary and ecological processes in populations. However, using contemporary genetic data to infer the dynamics of genetic diversity may be at risk of a bias, as inferences are performed from a set of extant populations, setting aside unavailable, rare, or now extinct lineages. Here, we took advantage of new developments in next-generation sequencing to analyze the spatial and temporal genetic dynamics of the grasshopper , a steppic Southwestern-Palearctic species. We applied a recently developed hybridization capture (hyRAD) protocol that allows retrieving orthologous sequences even from degraded DNA characteristic of museum specimens. We identified single nucleotide polymorphisms in 68 historical and 51 modern samples in order to (i) unravel the spatial genetic structure across part of the species distribution and (ii) assess the loss of genetic diversity over the past century in Swiss populations. Our results revealed (i) the presence of three potential glacial refugia spread across the European continent and converging spatially in the Alpine area. In addition, and despite a limited population sample size, our results indicate (ii) a loss of allelic richness in contemporary Swiss populations compared to historical populations, whereas levels of expected heterozygosities were not significantly different. This observation is compatible with an increase in the bottleneck magnitude experienced by central European populations of following human-mediated land-use change impacting steppic habitats. Our results confirm that application of hyRAD to museum samples produces valuable information to study genetic processes across time and space.

Salts of the diazonium coupling agent -phenylenebis(diazonium) form diazonium-terminated conjugated thin films on a variety of conductive and nonconductive surfaces by spontaneous reaction of the coupling agent with the surface. The resulting diazonium-bearing surface can be reacted with various organic and inorganic nucleophiles to form a functionalized surface. These surfaces have been characterized with voltammetry, XPS, infrared and Raman spectroscopy, and atomic force microscopy. Substrates that can be conveniently and quickly modified with this process include ordinary glass, gold, and an intact, fully assembled commercial screen-printed carbon electrode. The scope and convenience of this process make it promising for practical surface modification.

The dispersal of non-native genes due to hybridization is a form of cryptic invasion with growing concern in evolution and conservation. This includes the spread of transgenic genes and antibiotic resistance. To investigate how genes and phenotypes are transmitted, we developed a general model that, for the first time, considers concurrently: multiple loci, quantitative and qualitative gene expression, assortative mating, dominance/recessivity inheritance and density-dependent demographic effects. Selection acting on alleles or genotypes can also be incorporated. Our results reveal that the conclusions about how hybridization threatens a species can be biased if they are based on single-gene models, while considering two or more genes can correct this bias. We also show that demography can amplify or balance the genetic effects, evidencing the need of jointly incorporating both processes. By implementing our model in a real case, we show that mallard ducks introduced in New Zealand benefit from hybridization to replace native grey-ducks. Total displacement can take a few generations and occurs by interspecific competition and by competition between hybrids and natives, demonstrating how hybridization may facilitate biological invasions. We argue that our general model represents a powerful tool for the study of a wide range of biological and societal questions.

Introgression between domestic and wild taxa is a conservation issue because it can lead to the genetic extinction of wild taxa. Understanding the causes of introgression is thus a crucial task for conservation biologists. Here we provide evidence from biparentally, paternally and maternally inherited genetic markers in hybridizing European wildcats (Felis silvestris silvestris) and domestic cats (Felis silvestris catus) that one cause of introgression can be range expansion of the threatened species. We analyzed 68 autosomal, two Y-chromosomal and four mitochondrial diagnostic single nucleotide polymorphisms, and a sequence of 384 base pair of mitochondrial DNA, in 224 wild- and domestic cats from the Jura region of eastern Switzerland and western France. Using Bayesian estimation approaches, we found more gene flow from domestic cats to wildcats than vice versa (0.017 and 0.003 migrants per generation). Introgression of maternally inherited markers was higher than of paternally inherited markers. To test if these observed introgression patterns might be explained by wildcat expansion, we simulated neutral genetic data under various models of hybridization including spatial features such as range expansion. The most likely scenario represented an expansion of wildcats into domestic cat range. We also explored the geographic distribution of wildcats and hybrids. In comparison to wildcats, hybrids were found closer to the edge of the wildcat distribution range. Overall, the patterns we observed are compatible with the hypothesis that introgression is caused by wildcat range expansion, rather than by domestic cat invasion of wildcat habitat. That the threatened European wildcat is expanding is a positive sign, but careful monitoring of introgression and its fitness consequences is needed to ensure that the wildcat does not go genetically extinct in the generations to come.

Hydra tissues are made from three distinct populations of stem cells that continuously cycle and pause in G2 instead of G1. To characterize the role of cell proliferation after mid-gastric bisection, we have (i) used flow cytometry and classical markers to monitor cell cycle modulations, (ii) quantified the transcriptomic regulations of 202 genes associated with cell proliferation during head and foot regeneration, and (iii) compared the impact of anti-proliferative treatments on regeneration efficiency. We confirm two previously reported events: an early mitotic wave in head-regenerating tips, when few cell cycle genes are up-regulated, and an early-late wave of proliferation on the second day, preceded by the up-regulation of 17 cell cycle genes. These regulations appear more intense after mid-gastric bisection than after decapitation, suggesting a position-dependent regulation of cell proliferation during head regeneration. Hydroxyurea, which blocks S-phase progression, delays head regeneration when applied before but not after bisection. This result is consistent with the fact that the Hydra central region is enriched in G2-paused adult stem cells, poised to divide upon injury, thus forming a necessary constitutive pro-blastema. However a prolonged exposure to hydroxyurea does not block regeneration as cells can differentiate apical structures without traversing S-phase, and also escape in few days the hydroxyurea-induced S-phase blockade. Thus Hydra head regeneration, which is a fast event, is highly plastic, relying on large stocks of adult stem cells paused in G2 at amputation time, which immediately divide to proliferate and/or differentiate apical structures even when S-phase is blocked.