Population Genetic Structure and Colonisation History of the Tool-Using New Caledonian Crow

New Caledonian crows exhibit considerable variation in tool making between populations. Here, we present the first study of the species’ genetic structure over its geographical distribution. We collected feathers from crows on mainland Grande Terre, the inshore island of Toupéti, and the nearby island of Maré where it is believed birds were introduced after European colonisation. We used nine microsatellite markers to establish the genotypes of 136 crows from these islands and classical population genetic tools as well as Approximate Bayesian Computations to explore the distribution of genetic diversity. We found that New Caledonian crows most likely separate into three main distinct clusters: Grande Terre, Toupéti and Maré. Furthermore, Toupéti and Maré crows represent a subset of the genetic diversity observed on Grande Terre, confirming their mainland origin. The genetic data are compatible with a colonisation of Maré taking place after European colonisation around 1900. Importantly, we observed (1) moderate, but significant, genetic differentiation across Grande Terre, and (2) that the degree of differentiation between populations on the mainland increases with geographic distance. These data indicate that despite individual crows’ potential ability to disperse over large distances, most gene flow occurs over short distances. The temporal and spatial patterns described provide a basis for further hypothesis testing and investigation of the geographical variation observed in the tool skills of these crows

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Structuration génétique de populations introduites de rats Rattus rattus (Berkenhout, 1769) et Rattus norvegicus (Linné, 1758) en milieu insulaire (l'outil génétique au service de l'étude des invasions biologiques et de l'aide à leur gestion)

PARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

Characterization of eight polymorphic microsatellites in the shrew Crocidura suaveolens and its application to the study of insular populations of the French Atlantic coast

International audienc

Characterization of eight polymorphic microsatellites in the shrew Crocidura suaveolens and its application to the study of insular populations of the French Atlantic coast

International audienc

Phylogeography and diversification of the Dead Sea Sparrow ( Passer moabiticus ) in Iran: insights from a multilocus approach

International audienc

Study of Temperature and Wear Variations of Aluminium in General Dry Sliding Contact

The present research focuses on the study of temperature and wear variations of aluminium in general dry sliding contact conditions. The main aim of this research is to develop a simulation methodology in order to calculate temperature and wear variations of different materials (here: aluminium on cast iron) in general dry sliding contacts. The developed simulation methodology is based on an uncoupled thermo-mechanical and wear analysis. The widely spread finite element software Abaqus is used for the numerical investigations. For calibration and validation, experimental investigations are performed with a pin-on-disc test bench. A comparison between the experimental and the numerical results is presented and discussed. The experimental results are in close greement with the numerical results. For the considered test case (rotational velocity of the disc=300 rpm and load on the pin=110 N) the numerical analysis predicts a maximum temperature of 63°C in comparison to 65°C in the experiment. For the considered test case (rotational velocity of the disc=600 rpm and load on the pin=150 N) the simulation predicts a maximum temperature of 93°C in comparison to 97°C in the experiment. The study concludes that the developed simulation methodology is accurate and can be used to calculate temperature and wear variations of different materials in general dry sliding contact

Impact of quarrying on genetic diversity: an approach across landscapes and over time

International audienceLand conversion is one of the major global changes that threaten population viability. As with many industrial activities, quarrying highly modifies land cover, destroying previous habitats but also creating new conditions potentially supporting functioning and connectivity of pioneer species. Using a multi-landscape and -temporal approach, we assessed the impact of quarrying on the genetic diversity of two amphibians with contrasted ecological constraints: the common toad (Bufo bufo) and the natterjack toad (Bufo calamita), favouring vegetated and pioneer environments, respectively. The study was conducted across six areas of ca. 250 km(2) each. Mixed effect models were used to determine which landscape features affect the genetic diversity of the two species. These analyses were performed at three time points (1940s, 1970s and 2000s). Genetic diversity of B. bufo was found to increase with the area of semi-wooded and herbaceous vegetation, and decrease with the area of roads and urbanized areas. Genetic diversity of B. calamita increased with the area of bare ground and of quarries, and decreased with the area of dense woods. We found no effect of quarrying on B. bufo, unlike for B. calamita in which genetic diversity was favoured by quarrying at all three time-points. Despite having similar generation times, B. bufo's diversity was best explained by 1940s landscape and that of B. calamita by 2000s landscape. This study enlightens the genetic conservation value of quarries for pioneer species and the possible delays between landscape changes and their effects on the populations of some, but not all, species