Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences - a case study in the tree genus Milicia

Background: Species delimitation in closely related plant taxa can be challenging because (i) reproductive barriers are not always congruent with morphological differentiation, (ii) use of plastid sequences might lead to misinterpretation, (iii) rare species might not be sampled. We revisited molecular-based species delimitation in the African genus Milicia, currently divided into M. regia (West Africa) and M. excelsa (from West to East Africa). We used 435 samples collected in West, Central and East Africa. We genotyped SNP and SSR loci to identify genetic clusters, and sequenced two plastid regions (psbA-trnH, trnC-ycf6) and a nuclear gene (At103) to confirm species’ divergence and compare species delimitation methods. We also examined whether ecological niche differentiation was congruent with sampled genetic structure. Results: West African M. regia, West African and East African M. excelsa samples constituted three well distinct genetic clusters according to SNPs and SSRs. In Central Africa, two genetic clusters were consistently inferred by both types of markers, while a few scattered samples, sympatric with the preceding clusters but exhibiting leaf traits of M. regia, were grouped with the West African M. regia cluster based on SNPs or formed a distinct cluster based on SSRs. SSR results were confirmed by sequence data from the nuclear region At103 which revealed three distinct ‘Fields For Recombination’ corresponding to (i) West African M. regia, (ii) Central African samples with leaf traits of M. regia, and (iii) all M. excelsa samples. None of the plastid sequences provide indication of distinct clades of the three species-like units. Niche modelling techniques yielded a significant correlation between niche overlap and genetic distance. Conclusions: Our genetic data suggest that three species of Milicia could be recognized. It is surprising that the occurrence of two species in Central Africa was not reported for this well-known timber tree. Globally, our work highlights the importance of collecting samples in a systematic way and the need for combining different nuclear markers when dealing with species complexes. Recognizing cryptic species is particularly crucial for economically exploited species because some hidden taxa might actually be endangered as they are merged with more abundant species

Prevalence of oropharyngeal beta-lactamase-producing Capnocytophaga spp. in pediatric oncology patients over a ten-year period

BACKGROUND: The aim of this study was to evaluate the prevalence of beta-lactamase-producing Capnocytophaga isolates in young children hospitalized in the Pediatric Oncology Department of Hôpital Sud (Rennes, France) over a ten-year period (1993–2002). METHODS: In neutropenic children, a periodic survey of the oral cavity allows a predictive evaluation of the risk of systemic infections by Capnocytophaga spp. In 449 children with cancer, 3,053 samples were collected by oral swabbing and plated on TBBP agar. The susceptibility of Capnocytophaga isolates to five beta-lactams was determined. RESULTS: A total of 440 strains of Capnocytophaga spp. were isolated, 309 (70%) of which were beta-lactamase producers. The beta-lactamase-producing strains were all resistant to cefazolin, 86% to amoxicillin, and 63% to ceftazidime. The proportion of strains resistant to third-generation cephalosporins remained high throughout the ten-year study, while susceptibility to imipenem and amoxicillin combined with clavulanic acid was always conserved. CONCLUSION: These results highlight the risk of antibiotic failure in Capnocytophaga infections and the importance of monitoring immunosuppressed patients and testing for antibiotic susceptibility and beta-lactamase production

Seroprevalence of malaria in inhabitants of the urban zone of Antananarivo, Madagascar

BACKGROUND: Antananarivo, the capital of Madagascar, is located at an altitude of over 1,200 m. The environment at this altitude is not particularly favourable to malaria transmission, but malaria nonetheless remains a major public health problem. The aim of this study was to evaluate exposure to malaria in the urban population of Antananarivo, by measuring the specific seroprevalence of Plasmodium falciparum. METHODS: Serological studies specific for P. falciparum were carried out with an indirect fluorescent antibody test (IFAT). In a representative population of Antananarivo, 1,059 healthy volunteers were interviewed and serum samples were taken. RESULTS: The seroprevalence of IgG+IgA+IgM was 56.1% and that of IgM was 5.9%. The major risk factor associated with a positive IgG+IgA+IgM IFAT was travel outside Antananarivo, whether in the central highlands or on the coast. The abundance of rice fields in certain urban districts was not associated with a higher seroprevalence. CONCLUSION: Malaria transmission levels are low in Antananarivo, but seroprevalence is high. Humans come into contact with the parasite primarily when travelling outside the city. Further studies are required to identify indigenous risk factors and intra-city variations more clearly

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Etude théorique et expérimentale de la vibrométrie laser à longue distance par lidar cohérent

La mesure sans contact et à grande distance de vibrations de faible amplitude (de l'ordre du micromètre) est un besoin grandissant dans le monde industriel, tant dans le domaine civil pour étudier l'intégrité de structures, que dans le domaine militaire afin de réaliser l identification de cibles. Les lidars à détection cohérente hétérodyne (ou lidars cohérents) permettent la mesure de vitesse de vibration jusqu à quelques micromètres par seconde, à plusieurs kilomètres, voire plusieurs dizaines de kilomètres de distance. Leur principe est de mesurer le décalage fréquentiel de l onde laser dû à l effet Doppler subi lors de la rétrodiffusion sur une cible vibrante. La problématique scientifique des travaux exposés dans ce mémoire est la conception d'un vibromètre laser capable de mesurer ces faibles vitesses de vibration à grande distance sur des cibles non coopératives. Une étude théorique et expérimentale est menée, concernant, en particulier, les bruits affectant la mesure de vibration par lidar, ainsi que le couplage entre la tache laser et la répartition des modes de vibration sur la surface de la cible. Un simulateur de la mesure, validé en comparant les mesures expérimentales sur une maquette d'avion avec les mesures simulées, permet de déterminer les performances du système. Puis la capacité de mesure des lidars cohérents est démontrée expérimentalement, à partir d'une architecture lidar fibrée à 1,5 micromètre, sur des cibles en vol à 2,5 km, ainsi que par des mesures très basses fréquences sur bâtiments. Enfin, la possibilité de compensation des vibrations propres de la plateforme en vue d'embarquer le vibromètre laser sur un porteur mobile est étudiée.Remote sensing of very low amplitude (few micrometers) vibration at long range is a growing need in the industry, both in the civilian sector to study the integrity of structure, and in the military sector to achieve target identification. Coherent lidars allow the measure of vibration speed around some micrometers per second at a range of several kilometers or even dozens of kilometres. They are based on the measure of the frequency shift due to Doppler effect suffered when backscattering on a moving target occurs. The scientific issue of the work reported in this thesis is to design a laser vibrometer measuring these low vibration speeds of non-cooperative targets at long range. A theoretical and experimental study is conducted, more particularly about the noise affecting the measure, and the coupling between the laser spot and the vibration patterns on the surface of the target. A simulator of the measure, validated by comparing experimental measurements on a model airplane with simulated measurements, is built to determine the system performance. Then the experimental demonstration of the ability of coherent lidar to perform long range and high sensitivity measurements is made on flying targets at 2.5 km, and by very low frequency measures on buildings, using a 1.55 micron all fibered lidar. Finally, the compensation of own platform vibration is studied in order to board the laser vibrometer on a moving carrier.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Geomorphology of the Makgadikgadi Basin (Botswana): Insight Into the Propagation of the East African Rift System

International audienceThe Southwestern Branch of the East African Rift System propagates through the Central and Southern African plateaus and ends in the Okavango Makgadikgadi Zambezi Basin. This basin hosts the Okavango Graben and the Eiseb Graben, considered as the terminus of the Southwestern Branch of the rift. To the southeast, the Makgadikgadi Basin is affected by a series of normal faults forming the Makgadikgadi Rift Zone (MRZ) which regional geodynamic significance remains unclear. Based on fieldwork and geomorphic analysis, we revisited the geomorphological features associated with paleolakes and the fault pattern within the Makgadikgadi Basin to better constrain the dynamics of the MRZ. Fault scarps and offsets along linear dunes show normal‐dip kinematics of faults, indicating a NW‐SE extension direction in the area. Furthermore, lacustrine shorelines in the basin are undeformed, proving that they post‐date the fault activity. The previously published ages of these shorelines demonstrate that the MRZ currently has a low tectonic activity. Integrated in the geodynamic framework of the region, these results suggest that present‐day deformation shifts toward the Okavango Graben north of the MRZ. We therefore propose a “zip‐opening” model to explain the propagation of the Southwestern Branch of the East African Rift System where the tip of the system progressively progresses southwestward, driven by motions of the continental plates

GNSS data from fieldwork in northern Botswana (2021 and 2022 missions)

GNSS data from 2021 and 2022 fieldworks in northern Botswana. Authors: Gaudaré L., Dauteuil O., Jolivet M. Géosciences-Rennes, UMR-CNRS 6118, University of Rennes, 35042 Rennes, Franc

Blowing the rivers: Regional-scale control of the drainage network by wind in northern Kalahari (Africa)

International audienceUnderstanding the impact of aeolian processes on the regional-scale dynamics of fluvial systems in semi-arid regions is a major issue in the framework of climate change. Although the interactions between aeolian and fluvial processes have been studied on a meter to kilometer scale, few studies have upscaled to the regional scale. Using satellite images and SRTM-1 digital elevation models we document the formation of parabolic dunes and foredunes along the main rivers of the southern Angolan Plateau and northern Kalahari Basin (Africa). We demonstrate that these aeolian features derive from interactions between the morphology of the drainage system, the wind pattern, the vegetation cover and the transport capacity of the rivers. As a retro-action phenomenon, the progradation of parabolic dune fields induces tens-of-kilometers shifting in rivers courses in the northern Kalahari basin. The mechanism proposed has implications in terms of fluvial dynamics, river capture, geometry of clastic deposits in basins or source-to-sink budget

Neogene Uplift and Exhumation of Plutonic Bodies in the Beni Bou Ifrour Massif (Nador, northeastern Morocco)

International audienceIn Neogene times, the whole Mediterranean Sea was the center of an intense magmatic activity. This post-collisional magmatism produced a large amount of volcanic edifices through the Alpine belts, together with some intrusives. These plutonic bodies can be associated with skarn-type mineralization, well-known in Elba Island or Serifos Island (Cyclades), where they are generally exhumed by detachment faults. In Morocco, the plutons hosted by the Beni Bou Ifrour massif are connected to the biggest skarn-type iron concentrations of the country (production > 60 Mt, reserves ≈ 25 Mt). The purpose of this work is to explain the late uplift of this massif and subsequent exhumation of the intrusives. As a final product of the Africa-Eurasia plate convergence since ca. 70 Ma, the Rif Mountains constitute the westernmost segment of the Mediterranean Alpine belts. In the oriental part of this range, volcanic summits and Paleozoic to Mesozoic massifs outcrop in the surrounding Mio-Pliocene plains. The Beni Bou Ifrour massif, in the Nador province, consists in a dome-shaped folded Mesozoic series (Domerian to Barremian) affected by a slight epizonal regional metamorphism (ca. 14-12 Ma), dislocated by Neogene NE-SW faults and eventually sealed by upper Miocene transgressive sediments. The hosted intrusives (7.58 ± 0.03 Ma; Duggen et al., 2005) are the plutonic equivalents to the potassic calc-alkaline lavas (andesites mainly) from the surrounding "satellite" volcanic massifs. They turn out to stand in higher topographic position than the younger shoshonitic lavas of the neighboring Gourougou stratovolcano (6.12 ± 0.01 Ma; Duggen et al., 2005). Previous studies have attributed this uplift to the action of normal faults (pull-apart basins; Guillemin & Houzay, 1982), thrusting (Kerchaoui, 1985; 1995) or even of a caldeira resurgence (El Bakkali, 1995). To discriminate against those exhumation mechanisms, field work has been performed, coming along with new cross-sections to illustrate the geometry of the Beni Bou Ifrour massif. A paleomagnetism campaign was conducted, to determine if the plutonic intrusions have been tilted since their emplacement. Apatite fission tracks and 40Ar-39Ar dating allow us to estimate the exhumation age of the igneous bodies, and therefore add chronological constraints to the tectonic model. Geochemical study has also been performed on the magmatic rocks, and added to an extensive dataset (El Bakkali, 1995; Kerchaoui, 1995; Duggen et al., 2005). The existence of a magmatic chamber below the Beni Bou Ifrour dome will thus be discussed. Once established, the tectonic model of the Beni Bou Ifrour massif will help to precise the emplacement of the mineralized bodies and to integrate the iron-skarn metallogenesis within the structural evolution of the Rif orogenic segment

Faut-il cantonner les actifs des sociétés d'assurance-vie ?

Jolivet Benoit, Bellando Jean-Louis, Pestre Gilles. Faut-il cantonner les actifs des sociétés d'assurance-vie ?. In: Revue d'économie financière, n°11, 1989. L’assurance européenne : la grande transformation, sous la direction de Denis Kessler et Benoit Jolivet. pp. 285-304