Prey Preference of Snow Leopard (Panthera uncia) in South Gobi, Mongolia

International audienceAccurate information about the diet of large carnivores that are elusive and inhabit inaccessible terrain, is required to properly design conservation strategies. Predation on livestock and retaliatory killing of predators have become serious issues throughout the range of the snow leopard. Several feeding ecology studies of snow leopards have been conducted using classical approaches. These techniques have inherent limitations in their ability to properly identify both snow leopard feces and prey taxa. To examine the frequency of livestock prey and nearly-threatened argali in the diet of the snow leopard, we employed the recently developed DNA-based diet approach to study a snow leopard population located in the Tost Mountains, South Gobi, Mongolia. After DNA was extracted from the feces, a region of ~100 bp long from mitochondrial 12S rRNA gene was amplified, making use of universal primers for vertebrates and a blocking oligonucleotide specific to snow leopard DNA. The amplicons were then sequenced using a next-generation sequencing platform. We observed a total of five different prey items from 81 fecal samples. Siberian ibex predominated the diet (in 70.4% of the feces), followed by domestic goat (17.3%) and argali sheep (8.6%). The major part of the diet was comprised of large ungulates (in 98.8% of the feces) including wild ungulates (79%) and domestic livestock (19.7%). The findings of the present study will help to understand the feeding ecology of the snow leopard, as well as to address the conservation and management issues pertaining to this wild cat

Sheep Genome Functional Annotation Reveals Proximal Regulatory Elements Contributed to The Evolution of Modern Breeds

Domestication fundamentally reshaped animal morphology, physiology and behaviour, offering the opportunity to investigate the molecular processes driving evolutionary change. Here we assess sheep domestication and artificial selection by comparing genome sequence from 43 modern breeds (Ovis aries) and their Asian mouflon ancestor (O. orientalis) to identify selection sweeps. Next, we provide a comparative functional annotation of the sheep genome, validated using experimental ChIP-Seq of sheep tissue. Using these annotations, we evaluate the impact of selection and domestication on regulatory sequences and find that sweeps are significantly enriched for protein coding genes, proximal regulatory elements of genes and genome features associated with active transcription. Finally, we find individual sites displaying strong allele frequency divergence are enriched for the same regulatory features. Our data demonstrate that remodelling of gene expression is likely to have been one of the evolutionary forces that drove phenotypic diversification of this common livestock species

VarGoats: first results of an international 1000-genome project

National audienc

Vast panmixia in the widely distributed blue shark (Prionace glauca)

International audiencePrionace glaucais thought to be one of the most common and studied pelagic sharks, and yet few is known about its population structure. Blue sharks are fished, mainly as bycatch, across their nearly worldwide (except at polar latitudes), distribution area. The estimated removal of 20 million individuals per year by fisheries classifies blue sharks as near threatened (IUCN, 2009). However, the lack of knowledge of population size and structure, the high fecundity and early maturation of P. glaucaas well as its apparent stable catch rate make it difficult to forecast the long term consequences of such a huge removal on this top-down predator itself, and on its trophic network. Tags studies identified stocks in North Atlantic and in Pacific Ocean with few migrants capable of ten thousand kilometers travels and previous genetic studies concluded to panmixia at the scale of the Pacific Ocean. Here we will present worldwide genetic results on mitochondrial and nuclear DNA with 258 blue shark samples from eight regions

Skin swabbing as a new efficient DNA sampling technique in amphibians, and 14 new microsatellite markers in the alpine newt (Ichthyosaura alpestris)

International audienceThis study introduces a novel DNA sampling method in amphibians using skin swabs. We assessed the relevancy of skin swabs relevancy for genetic studies by amplifying a set of 17 microsatellite markers in the alpine newt Ichthyosaura alpestris, including 14 new polymorphic loci, and a set of 11 microsatellite markers in Hyla arborea, from DNA collected with buccal swabs (the standard swab method), dorsal skin swabs and ventral skin swabs. We tested for quality and quantity of collected DNA with each method by comparing electrophoresis migration patterns. The consistency between genotypes obtained from skin swabs and buccal swabs was assessed. Dorsal swabs performed better than ventral swabs in both species, possibly due to differences in skin structure. Skin swabbing proved to be a useful alternative to buccal swabbing for small or vulnerable animals: by drastically limiting handling, this method may improve the trade-off between the scientific value of collected data, individual welfare and species conservation. In addition, the 14 new polymorphic microsatellites for the alpine newt will increase the power of genetic studies in this species. In four populations from France (n = 19-25), the number of alleles per locus varied from 2 to 16 and expected heterozygosities ranged from 0.04 to 0.91. Presence of null alleles was detected in two markers and two pairs displayed gametic disequilibrium. No locus appeared to be sex-linked

Reconstituer la composition du régime alimentaire des herbivores domestiques au pâturage : l'approche par métabarcoding

National audienceIdentifying the type of grass ingested by grazing stock remains a bottleneck for analyzing the extent to which available grass affects the properties of end animal products. The use of metabarcoding technology, as presented in this document, offers promising perspectives in terms of better understanding the interactions between ingested grass, animals (mainly their eating habits) and end products (and their quality). This experiment was carried out in order to test this technology on the faeces of dairy cattle grazing on grassland with a diversified botanical composition. By sequencing plant DNA fragments found in tested faeces, it was possible to identify the full range of ingested taxons. Twice as many taxons were found in the faeces of cattle grazing on botanically rich grassland with a low stocking rate compared to faeces from cattle grazing on botanically poor grassland with a high stocking rate.Savoir exactement ce que les animaux ont ingéré au pâturage demeure un verrou pour affiner l'analyse entre herbe offerte et caractéristiques du produit animal correspondant. La technique de métabarcoding (dite aussi code-barres ADN), ici présentée, offre des perspectives prometteuses pour la compréhension des interactions entre herbe, animal et produits animaux. Une expérimentation a permis de tester cette technique sur des fèces de vaches laitières pâturant des prairies de composition botanique très contrastée. Par séquençage des fragments d'ADN des plantes retrouvés dans les fèces, nous avons pu identifier l'ensemble des taxons ingérés (au niveau de la famille, du genre ou de l'espèce végétale) et montrer qu'il y avait 2 fois plus de taxons différents dans les fèces des vaches pâturant à faible chargement une prairie diversifiée que dans les fèces des vaches pâturant à fort chargement une prairie moins diversifiée. Cette caractérisation des plantes ingérées au pâturage est un élément de connaissance important pour les études portant sur le comportement alimentaire et les performances des animaux ainsi que sur la qualité des produits

Caractérisation du régime alimentaire des ruminants à partir de l’analyse des produits de la digestion par DNA metabarcoding

National audienceCharacterizing the diet of ruminants at pasture in diversified grasslands is a difficult step that could be realized by using the DNA-based methods recently developed for assessing the composition of environmental samples (i.e. metabarcoding approach). In this study, we performed two experiments to assess the performance of this method. The diet was inferred from rumen and faecal samples after DNA extraction, subsequent amplification of a short fragment of chloroplast DNA with universal primers used for plant DNA identification (trnL approach), and sequencing of the PCR products using HighSeq Illumina system. The first experiment compared the results obtained from replicated extractions and PCRs performed on faecal samples from cattle with a diversified diet, and showed a high reproducibility of the method. The second experiment was designed to assess the semi-quantitative aspects of this approach. Five diets were allocated to five sheep fed ad libitum according to a 5 × 5 Latin square design. The diets were mixtures of green fodder differing by their white clover:ryegrass ratios (i.e., 0:100, 25:75, 50:50, 75:25 and 100:0). The analysis of rumen contents allowed a reliable estimation of the proportion of each species ingested, while the information was much less accurate from faecal samples. Technical and analytical solutions are currently tested in order to improve the quantitative information obtained from faecal samplesLa caractérisation du régime alimentaire des ruminants au pâturage au sein de prairies diversifiées est un verrou méthodologique qui pourrait en partie être levé à l’aide de méthodes basées sur l’analyse de l’ADN présent dans des échantillons environnementaux (métabarcoding). Pour évaluer la fiabilité de cette technique, nous avons mené deux expérimentations au cours desquelles l’ADN issu d’échantillons de contenu du rumen et de fèces a été extrait. Un fragment court d’ADN chloroplastique a été amplifié en utilisant des amorces universelles (approche trnL) et les produits PCR ont été séquencés en utilisant un système HighSeq Illumina. La première expérimentation a consisté à comparer les résultats obtenus à partir d’extractions et de PCRs répétées sur des fèces de bovins alimentés avec un régime diversifié et a permis de valider la reproductibilité de la méthode. La deuxième expérimentation a été conçue pour évaluer les aspects semi-quantitatifs de cette approche. Cinq moutons ont été alimentés ad libitum selon un carré latin 5 × 5 avec cinq mélanges binaires de ray-grass anglais et de trèfle blanc en proportions variables (0:100, 25:75, 50:50, 75:25 et 100:0). Les analyses de contenu du rumen ont permis de quantifier de manière fiable les proportions ingérées de chaque espèce, tandis que l’information issue de l’analyse des fèces était beaucoup moins précise. Des solutions techniques et analytiques sont actuellement examinées pour améliorer la quantification à partir des échantillons fécau