Une évaluation conjointe des performances de quatre méthodes d’estimation de liens de parenté génétique dédiées à l’ADN ancien

La reconstruction des liens de parenté génétique au sein de contextes funéraires est aujourd’hui une analyse de plus en plus répandue, capable dans certains cas de dévoiler un instantané des coutumes, pratiques funéraires et règles de résidence de sociétés du passé. En parallèle, de nombreuses méthodes statistiques permettent désormais d’inférer automatiquement des liens de parenté génétique entre plusieurs échantillons d’ADN ancien. Néanmoins, si ces méthodes revendiquent leur capacité à tr..

GRUPS-rs, a high-performance ancient DNA genetic relatedness estimation software relying on pedigree simulations

International audienceBackground: The study of fine-grain genetic kinship ties (parents, siblings, cousins, etc.) from ancient remains is now gaining significant interest within the field of paleogenetics, as a means of deciphering the social organization of past societies. However, kinship analyses are in practice often quite difficult to apply within paleogenetic studies, and may carry a high degree of uncertainty in the results they provide, especially when applied on low coverage and/or highly degraded samples, or when studying poorly characterized populations. To overcome these challenges, most of the available kinship estimation methods either refrain from inferring ties beyond the second degree (e.g., half-siblings), and/or rely on the use of a cohort of individuals to obtain a satisfactory statistical significance. Thus, the current state of the art remains intrinsically limited when attempting to estimate kinship on a small number of individuals, or when trying to detect more distant relationships (e.g., cousins).Methods: Here, we present GRUPS-rs: an update and complete reimplementation of GRUPS (Get Relatedness Using Pedigree Simulations), an ancient DNA kinship estimation software based on the methods originally developed in (Martin et al. 2017). GRUPS-rs both computes an estimate of relatedness from randomly sampled pseudo-haploidized variant calls, and leverages high-definition pedigree simulations to bypass the use of a cohort of individuals.Results: We highlight that GRUPS and GRUPS-rs are especially suitable to perform kinship analysis on a restricted number of ancient samples, and can provide a sufficient statistical significance to estimate genetic relatedness past the second degree, while taking into account user-defined contamination and sequencing error estimates. Importantly, GRUPS-rs offers an estimated 14000-fold speed-up in runtime performance compared to its predecessor — allowing the joint estimation of kinship between dozens of individuals in a matter of minutes — and is now bundled with a user-friendly Shiny interface, in which users can interactively visualize their results.Conclusions: The GRUPS kinship estimation method is now fully operational in its “GRUPS-rs” implementation, whose use is particularly recommended when analyzing a restricted number of low coverage DNA samples

The relationship between distal trunk morphology and object grasping in the African savannah elephant ( Loxodonta africana )

International audienceBackground During reach-to-grasp movements, the human hand is preshaped depending on the properties of the object. Preshaping may result from learning, morphology, or motor control variability and can confer a selective advantage on that individual or species. This preshaping ability is known in several mammals ( i.e., primates, carnivores and rodents). However, apart from the tongue preshaping of lizards and chameleons, little is known about preshaping of other grasping appendages. In particular, the elephant trunk, a muscular hydrostat, has impressive grasping skills and thus is commonly called a hand. Data on elephant trunk grasping strategies are scarce, and nothing is known about whether elephants preshape their trunk tip according to the properties of their food.Methods To determine the influence of food sizes and shapes on the form of the trunk tip, we investigated the morphology of the distal part of the trunk during grasping movements. The influence of food item form on trunk tip shape was quantified in six female African savannah elephants ( Loxodonta africana ). Three food item types were presented to the elephants (elongated, flat, and cubic), as well as three different sizes of cubic items. A total of 107 ± 10 grips per individual were video recorded, and the related trunk tip shapes were recorded with a 2D geometric morphometric approach.Results Half of the individuals adjusted the shape of the distal part of their trunk according to the object type. Of the three elephants that did not preshape their trunk tip, one was blind and another was subadult.Discussion and perspectives We found that elephants preshaped their trunk tip, similar to the preshaping of other species’ hands or paws during reach-to-grasp movements. This preshaping may be influenced by visual feedback and individual learning. To confirm these results, this study could be replicated with a larger sample of elephants

GRUPS-rs, a high-performance ancient DNA genetic relatedness estimation software relying on pedigree simulations

International audienceBackground: The study of fine-grain genetic kinship ties (parents, siblings, cousins, etc.) from ancient remains is now gaining significant interest within the field of paleogenetics, as a means of deciphering the social organization of past societies. However, kinship analyses are in practice often quite difficult to apply within paleogenetic studies, and may carry a high degree of uncertainty in the results they provide, especially when applied on low coverage and/or highly degraded samples, or when studying poorly characterized populations. To overcome these challenges, most of the available kinship estimation methods either refrain from inferring ties beyond the second degree (e.g., half-siblings), and/or rely on the use of a cohort of individuals to obtain a satisfactory statistical significance. Thus, the current state of the art remains intrinsically limited when attempting to estimate kinship on a small number of individuals, or when trying to detect more distant relationships (e.g., cousins).Methods: Here, we present GRUPS-rs: an update and complete reimplementation of GRUPS (Get Relatedness Using Pedigree Simulations), an ancient DNA kinship estimation software based on the methods originally developed in (Martin et al. 2017). GRUPS-rs both computes an estimate of relatedness from randomly sampled pseudo-haploidized variant calls, and leverages high-definition pedigree simulations to bypass the use of a cohort of individuals.Results: We highlight that GRUPS and GRUPS-rs are especially suitable to perform kinship analysis on a restricted number of ancient samples, and can provide a sufficient statistical significance to estimate genetic relatedness past the second degree, while taking into account user-defined contamination and sequencing error estimates. Importantly, GRUPS-rs offers an estimated 14000-fold speed-up in runtime performance compared to its predecessor — allowing the joint estimation of kinship between dozens of individuals in a matter of minutes — and is now bundled with a user-friendly Shiny interface, in which users can interactively visualize their results.Conclusions: The GRUPS kinship estimation method is now fully operational in its “GRUPS-rs” implementation, whose use is particularly recommended when analyzing a restricted number of low coverage DNA samples

Genome-wide analysis of a collective grave from Mentesh Tepe provides insight into the population structure of early neolithic population in the South Caucasus

Abstract Despite the localisation of the southern Caucasus at the outskirt of the Fertile Crescent, the Neolithisation process started there only at the beginning of the sixth millennium with the Shomutepe-Shulaveri culture of yet unclear origins. We present here genomic data for three new individuals from Mentesh Tepe in Azerbaijan, dating back to the beginnings of the Shomutepe-Shulaveri culture. We evidence that two juveniles, buried embracing each other, were brothers. We show that the Mentesh Tepe Neolithic population is the product of a recent gene flow between the Anatolian farmer-related population and the Caucasus/Iranian population, demonstrating that population admixture was at the core of the development of agriculture in the South Caucasus. By comparing Bronze Age individuals from the South Caucasus with Neolithic individuals from the same region, including Mentesh Tepe, we evidence that gene flows between Pontic Steppe populations and Mentesh Tepe-related groups contributed to the makeup of the Late Bronze Age and modern Caucasian populations. Our results show that the high cultural diversity during the Neolithic period of the South Caucasus deserves close genetic analysis

Effect of nanoparticles on spontaneous Ouzo emulsification

International audienceParticles stabilize fluid interfaces. In particular, oil/water Pickering emulsions undergo limited coalescence, yielding droplets of smaller size as the amount of particles is increased. Herein, we studied the effect of hydrophobic nanoparticles (<10 nm, alkyl-coated) on submicronic droplets (ca 100 nm) formed in an Ouzo system. We investigated thoroughly the water/tetrahydrofuran (THF)/butylated hydroxytoluene (BHT) reference diagram, in the absence and in the presence of nanoparticles, using the Nanoparticle Tracking Analysis (NTA) technique. This allowed us to characterize the size distributions in a much finer way than what is usually obtained using conventional Dynamic Light Scattering (DLS). Both a Surfactant-Free Microemulsion (SFME, thermodynamically stable) and an Ouzo (metastable spontaneous emulsion) domains were identified and the transition from one to the other could be characterized by specific features of the droplet size distributions. We found that the presence of the nanoparticles limits coalescence in the metastable domain. We also show that the alkyl-coated nanoparticles are irreversibly attached to the liquid-liquid interface

Ecotoxicité des produits de transformation des pesticides dans les milieux aquatiques

International audienceUne fois appliquées sur les cultures, les substances actives de pesticides sont soumises à divers processus biotiques et abiotiques qui gouvernent leur devenir et leur transfert dans les différents compartiments de l’environnement. Les produits de transformation (TP) issus de ces processus sont potentiellement très nombreux, présents à faibles teneurs dans les milieux aquatiques. Leur détection et leur occurrence sont amenées à évoluer compte tenu du développement des stratégies analytiques et de la modification des conditions climatiques. L’écotoxicité des TP est encore peu étudiée, mais diverses études indiquent une écotoxicité potentiellement différente de la substance active mère. Dans ce contexte, le projet TAPIOCA, financé dans le cadre de l’APR Ecophyto II+ « Santé écosystèmes », poursuit trois objectifs : i) mettre au point des méthodes analytiques sensibles pour l’identification de TP de pesticides dans les eaux ; ii) améliorer les connaissances sur les effets d’une sélection de pesticides et de TP associés, sur les communautés microbiennes et les macroinvertébrés aquatiques ; et iii) tester l’apport d’outils de prédiction des propriétés de dissipation et de transferts de TP de pesticides pour mieux cerner leur potentiel de présence dans l’environnement.Ici, nous présentons quelques résultats marquants en lien avec la caractérisation de l’écotoxicité chronique à 3 pesticides (le fongicide tébuconazole, l’insecticide fénoxycarbe et l’herbicide terbuthylazine) et leurs TP. Des expérimentations en microcosmes avec des organismes aquatiques (périphyton, communautés microbiennes d’hyphomycètes ou gammares) ont permis d’évaluer les effets de plusieurs scénarios d’exposition aux pesticides et à des TP associés (produits commercialement disponibles ou obtenus par photodégradation contrôlée de pesticides dits « vieillis ») sur différents descripteurs biologiques. Les premiers résultats montrent globalement une toxicité moindre des TP comparativement aux trois molécules mères sur les organismes étudiés. Néanmoins, la terbuthylazine et son TP terbuthylazine-desethyl présentent une toxicité inattendue pour les fonctions de reproduction des gammares, organismes non-cibles de cet herbicide

Development of sensitive and robust multiplex digital PCR assays for the detection of ESR1 mutations in the plasma of metastatic breast cancer patients

International audienceBACKGROUND: Early detection of ESR1 mutations is a key element for better personalization of the management of patients with HR+/HER2- Metastatic Breast Cancer (MBC). Analysis of circulating tumor DNA from liquid biopsies is a particularly well-suited strategy for longitudinal monitoring of such patients. MATERIALS AND METHODS: Using the naica® three-color digital PCR platform, we developed a screening assay allowing the detection of 11 ESR1 mutations and designed a sequential strategy for precise mutation identification. We then applied this strategy in the analysis of plasma circulating cell-free DNA from 109 HR+/HER2- MBC patients and performed a double-blind comparison study on a subset of patients with the multiplex assay used at the Institut Curie (IC) for the PADA-1 study. RESULTS: Thirty-one patients (28.4%) harboured at least one ESR1 mutation, with the following frequencies: D538G (41.03%), Y537S (25.64%), E380Q (10.26%), Y537N (10.26%), "(536-540)" (7.69%), Y537C (2.56%), and L536R (2.56%). The presence of ESR1 mutation(s) was significantly associated with liver metastases (p = 0.0091). A very good agreement (91%) was observed with the IC assay. CONCLUSION: Our assays have proven to be robust and highly sensitive and are very well-suited for monitoring ESR1 mutations in the plasma of MBC patients