Microsatellite markers for the yam bean <em>Pachyrhizus</em> (Fabaceae)

Premise of the study: Microsatellite loci were developed for the understudied root crop yam bean (Pachyrhizus spp.) to investigate intraspecific diversity and interspecific relationships within the genus Pachyrhizus. Methods and Results: Seventeen nuclear simple sequence repeat (SSR) markers with perfect di- and trinucleotide repeats were developed from 454 pyrosequencing of SSR-enriched genomic libraries. Loci were characterized in P. ahipa and wild and cultivated populations of four closely related species. All loci successfully cross-amplified and showed high levels of polymorphism, with number of alleles ranging from three to 12 and expected heterozygosity ranging from 0.095 to 0.831 across the genus. Conclusions: By enabling rapid assessment of genetic diversity in three native neotropical crops, P. ahipa, P. erosus, and P. tuberosus, and two wild relatives, P. ferrugineus and P. panamensis, these markers will allow exploration of the genetic diversity and evolutionary history of the genus Pachyrhizus

Genetic variation in a North African rodent pest, Meriones shawi: microsatellite polymorphism

Meriones shawi is an ubiquitous and endemic rodent in northern African. This species is considered as an economically important pest because it often damages crops. Moreover, the gerbillines are known to function as reservoirs for a variety of serious human epidemic diseases. Ten polymorphic microsatellite loci were identified using 454 GS-FLX Titanium pyrosequencing and a multiplex PCR assay was developed. The utility of these markers was evaluated in 30 individuals from three different Moroccan populations. Number of alleles per locus ranged from 2 to 7, with observed and expected heterozygosities ranging from 0.033 to 0.967 and from 0.033 to 0.729, respectively. Departures from Hardy-Weinberg equilibrium were observed at two loci. These markers will be useful resources for future population genetics studies for this rodent and pest-borne disease management.Key words: Meriones shawi, gerbil, rodent-borne disease, microsatellite, polymorphism

Genetic Variation in a North African Rodent Pest, Meriones shawi : Microsatellite Polymorphism

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Species boundaries in European and Macaronesian &lt;I&gt;Porella&lt;/I&gt; L. (Jungermanniales, Porellaceae)

Il est difficile de reconnaître les espèces du genre Porella, connu pour sa grande plasticité phénotypique. Des analyses génétiques et morphologiques ont été réalisées sur un grand échantillonnage d\u27espèces européennes et macaronésiennes (328 colonies collectées dans 150 localités environ) afin de i) définir les entités génétiques et ii) trouver les meilleurs caractères permettant leur identification. Neuf espèces sont ainsi reconnues, dont P. platyphylloidea avec des colonies du Canada incluses pour comparaison. La plupart des colonies de Porella sont multiclonales ; elles présentent du polymorphisme intra- et interspécifique et des mélanges de thalles mâles et femelles. Au niveau intraspécifique, le niveau de variabilité génétique observé est élevé, spécialement chez P. canariensis, P. obtusata et P. platyphylla. Enfin, une clé révisée des espèces est donnée.The genus Porella is known for high phenotypic plasticity and rather ill defined species boundaries. Genetic and morphological data are analyzed for a broad sample of European and Macaronesian species (328 colonies collected in about 150 localities) in order to i) separate genetic entities and ii) identify the morphological characters that best define these entities. Nine species are recognized, including P. platyphylloidea from Canada, included for comparison. Many Porella colonies are multiclonal, attested by diversity found within colonies with intraspecific and interspecific polymorphisms, but also by male and female individuals found growing intermixed. At the intraspecific level, high levels of genetic variation are found, especially for P. canariensis, P. obtusata and P. platyphylla. Finally a revised key of the species is proposed.</p

Usages agricoles, apports continentaux et dynamique temporelle des taxons eucaryotes dans une zone de transition critique marine du Petit Cul-de-Sac Marin (Guadeloupe)

International audienceA first study by Pierre Sabatier and colleagues (co-funded by the OHM Littoral Caraïbe, APR 2018 and 2019) analyzed core sediments from both Guadeloupe and Martinique (French West Indies), and showed that the widespread use of a non-specific systemic herbicide (glyphosate) at the end of the years 1990 has induced an unprecedented rise in soil erosion and a major release of persistent chlordecone pesticides that were trapped in banana field soils. We have now studied the implications of these agricultural usages and environmental consequences on the dynamics of the eukaryotic biodiversity using a metabarcoding approach. We show that both the OTU richness and the diversity were significantly higher in samples corresponding to the period 2001-2017 which is characterized by a fast sedimentation rate (FSR), compared to the period 1950-2000 which is characterized by a slow sedimentation rate (SSR). Temporal analyses demonstrated that during the FSR period the relative read abundances of several classes were significant increasing over time while over were decreasing. On the contrary the same classes demonstrated a relative stability over the second half of the 20th century. Combined to temporal analyses of the alpha and beta diversity we could capture the ongoing temporal changes in eukaryotic community composition in a way that probably reflects the ecological processes and the ecosystem functions that are involved. Overall, our results show a correlation between concentration of pollutants from agricultural usages, modifications of the land erosion processes and compositional reorganizations over the two last decades in a critical transition zone located close to the most anthropized area of GuadeloupeDes premières études de Pierre Sabatier et ses collègues (cofinancées par l'OHM Littoral Caraïbe, APR 2018 et 2019) qui ont analysé des carottes de sédiments à la fois en Guadeloupe et en Martinique (Antilles Françaises), ont montré que l'utilisation généralisée d'un herbicide systémique non spécifique (le glyphosate) à la fin des années 1990 a induit une augmentation sans précédent de l'érosion des sols et une libération importante de pesticides persistants de type chlordécone qui étaient piégés dans les sols des champs de bananes. Nous avons maintenant étudié les implications de ces usages agricoles et des conséquences environnementales sur la dynamique de la biodiversité eucaryote en utilisant une approche de métabarcodage. Nous montrons que la richesse en OTU et la diversité sont significativement plus élevées dans les échantillons correspondant à la période 2001-2017 qui est caractérisée par un taux de sédimentation rapide (FSR), par rapport à la période 1950-2000 qui est caractérisée par un taux de sédimentation lent (SSR). Des analyses temporelles ont démontré que durant la période FSR, les abondances relatives en lecture de plusieurs classes augmentaient significativement dans le temps alors que pour d’autres classes nous observions une diminution. A l’inverse, ces mêmes classes présentent une stabilité relative au cours de la seconde moitié du 20ème siècle. En combinant des analyses temporelles de la diversité alpha et bêta, nous avons pu capturer des changements temporels dans la composition des assemblages eucaryotes d'une manière qui reflète probablement les processus écologiques et les fonctions de l'écosystème qui sont impliqués. Globalement, nos résultats montrent une corrélation entre la concentration de polluants issus des usages agricoles, les modifications des processus d'érosion des sols et les réorganisations de la composition au cours des deux dernières décennies dans une zone de transition critique située à proximité de la zone la plus anthropisée de la Guadeloupe

Fine-scale population genetic structure of arctic foxes (Vulpes lagopus) in the High Arctic

Abstract Objective The arctic fox (Vulpes lagopus) is a circumpolar species inhabiting all accessible Arctic tundra habitats. The species forms a panmictic population over areas connected by sea ice, but recently, kin clustering and population differentiation were detected even in regions where sea ice was present. The purpose of this study was to examine the genetic structure of a population in the High Arctic using a robust panel of highly polymorphic microsatellites. Results We analyzed the genotypes of 210 individuals from Bylot Island, Nunavut, Canada, using 15 microsatellite loci. No pattern of isolation-by-distance was detected, but a spatial principal component analysis (sPCA) revealed the presence of genetic subdivisions. Overall, the sPCA revealed two spatially distinct genetic clusters corresponding to the northern and southern parts of the study area, plus another subdivision within each of these two clusters. The north–south genetic differentiation partly matched the distribution of a snow goose colony, which could reflect a preference for settling into familiar ecological environments. Secondary clusters may result from higher-order social structures (neighbourhoods) that use landscape features to delimit their borders. The cryptic genetic subdivisions found in our population may highlight ecological processes deserving further investigations in arctic foxes at larger, regional spatial scales

Deep-sea wood-eating limpets of the genus Pectinodonta Dall, 1882 (Mollusca: Gastropoda: Patellogastropoda: Pectinodontidae) from the tropical West Pacific

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Barcoding type specimens helps to identify synonyms and an unnamed new species in Eumunida Smith, 1883 (Decapoda : Eumunididae)

13 páginas, 2 figuras, 3 tablas.The primary purpose of DNA-barcoding projects is to generate an efficient expertise and identification tool. This is an important challenge to the taxonomy of the 21st century, as the demand increases and the expert capacity does not. However, identifying specimens using DNA-barcodes requires a preliminary analysis to relate molecular clusters to available scientific names. Through a case study of the genus Eumunida (Decapoda : Eumunididae), we illustrate how naming molecule-based units, and thus providing an accurate DNA-based identification tool, is facilitated by sequencing type specimens. Using both morphological and unlinked molecular markers (COI and 28S genes), we analysed 230 specimens from 12 geographic areas, covering two-thirds of the known diversity of the genus, including type specimens of 13 species. Most hypotheses of species delimitation are validated, as they correspond to molecular units linked to only one taxonomic name (and vice versa). However, a putative cryptic species is also revealed and three entities previously named as distinct species may in fact belong to a single one, and thus need to be synonymised. Our analyses, which integrate the current naming rules, enhance the a-taxonomy of the genus and provide an effective identification tool based on DNA-barcodes. They illustrate the abilityThis work was supported by the ‘Consortium National de Recherche en Génomique’, and the ‘Service de Systematique Moléculaire’ of the Muséum National d’Histoire Naturelle (UMS 2700 CNRS-MNHN). It is part of the agreement n 2005/67 between the Genoscope and the Muséum National d’Histoire Naturelle on the project ‘Macrophylogeny of Life’ directed by Guillaume Lecointre. These data fed the MarBol project supported by the Sloan Foundation.Peer reviewe

Temporal pesticide dynamics alter specific eukaryotic taxa in a coastal transition zone

International audienceLand use change and anthropogenic forcing can drastically alter the rates and patterns of sediment transport and modify biodiversity and ecosystem functions in coastal transition zones, such as the coastal ecosystems. Molecular studies of sediment extracted DNAs provide information on currently living organisms within the upper layers or buried from various periods of time, but might also provide knowledge on species dynamics, replacement and turnover. In this study, we evaluated the eukaryotic communities of a marine core that present a shift in soil erosion that was linked to glyphosate usage and correlated to chlordecone resurgence since 2000. We show differences in community composition between samples from the second half of the last century and those from the last two decades. Temporal analyses of the relative abundance, alpha diversity, and beta diversity for the two periods demonstrated different temporal dynamics depending on the considered taxonomic group. In particular, Ascomycetes showed a decrease in abundance over the most recent period associated with changes in community membership but not community structure. Two photosynthetic groups, Bacillariophyceae and Prasinophytes clade VII, showed a different pattern with an increase in abundance since the beginning of the 21st century with a decrease in diversity and evenness to form more heterogeneous communities dominated by a few abundant OTUs. Altogether, our data reveal that agricultural usages such as pesticide use can have long-term and species-dependent implications for microeukaryotic coastal communities on a tropical island