Phylogenomics of Gesneriaceae using targeted capture of nuclear genes.

Gesneriaceae (ca. 3400 species) is a pantropical plant family with a wide range of growth form and floral morphology that are associated with repeated adaptations to different environments and pollinators. Although Gesneriaceae systematics has been largely improved by the use of Sanger sequencing data, our understanding of the evolutionary history of the group is still far from complete due to the limited number of informative characters provided by this type of data. To overcome this limitation, we developed here a Gesneriaceae-specific gene capture kit targeting 830 single-copy loci (776,754 bp in total), including 279 genes from the Universal Angiosperms-353 kit. With an average of 557,600 reads and 87.8% gene recovery, our target capture was successful across the family Gesneriaceae and also in other families of Lamiales. From our bait set, we selected the most informative 418 loci to resolve phylogenetic relationships across the entire Gesneriaceae family using maximum likelihood and coalescent-based methods. Upon testing the phylogenetic performance of our baits on 78 taxa representing 20 out of 24 subtribes within the family, we showed that our data provided high support for the phylogenetic relationships among the major lineages, and were able to provide high resolution within more recent radiations. Overall, the molecular resources we developed here open new perspectives for the study of Gesneriaceae phylogeny at different taxonomical levels and the identification of the factors underlying the diversification of this plant group

Phylogeny and systematic position of Mesoptychia (Lindb.) A. Evans

A phylogenetic analysis of the leafy liverwort genus Mesoptychia (incl. Leiocolea and Hattoriella), using two chloroplast markers, rbcL and rps4, was performed to clarify the circumscription of the genus and to establish its systematic position within the Jungermanniales. Ten species and one variety of Mesoptychia (out of a total of 17 accepted specific names), together with 85 species from 57 genera representing different lineages of Jungermanniales, were sampled. The results support the monophyly of Mesoptychia and its inclusion within the Jungermanniaceae, which itself forms a clade with the Delavayellaceae. Gymnocolea borealis, previously treated under Leiocolea (=Mesoptychia), is nested in the Anastrophyllaceae. The synonymy of Hattoriella with Mesoptychia is phylogenetically confirmed. Four major clades are identified within Mesoptychia and their circumscriptions and distinguishing morphological features are discusse

Quelles dynamiques de l'emploi en milieu rural : peut-on oser l'expression de « vitalité cachée » ?

La controverse joue un rôle essentiel dans les résultats et le progrès des sciences sociales. L'Emploi rural, une vitalité cachée, cette recherche collective et pluraliste sur l'avenir des emplois dans l'espace rural français publiée fin 1995, n'a pas épuisé les divergences d'interprétation sur le sujet et continue, une fois achevée, à opposer même les auteurs entre eux. L'objectif de cette table ronde, qui s'est tenue en décembre 1996, fut d'approfondir ces désaccords par leur discussion. Dans ce débat, chacun cherche, dans une langue vive et polémique, à préciser sa pensée en même temps que ce qui fait contradiction. On aboutit pourtant à un consensus : pour avancer plus loin dans l'analyse de phénomènes sociaux encore incertains, il faut théoriser les désaccords et prolonger la recherche à plusieurs voies.Dynamics of the employment in rural areas : may we speak of a vitality ? This paper relates the debate organized after the publication of L’Emploi rural, une vitalité cachée ?, in order to cross the contradictory points of view of the authors in the face of an outward sociologist reader. Though it was quite hot, the discussion has deepened the analysis and opened up to new approaches and questions

Future experimental programmes in the CROCUS reactor

CROCUS is a teaching and research zero-power reactor operated by the Laboratory for Reactor Physics and Systems Behaviour (LRS) at the Swiss Federal Institute of Technology (EPFL). Three new experimental programmes are scheduled for the forthcoming years. The first programme consists in an experimental investigation of mechanical noise induced by fuel rods vibrations. An in-core device has been designed for allowing the displacement of up to 18 uranium metal fuel rods in the core periphery. The vibration amplitude will be 6 mm in the radial direction (±3 mm around the central position), while the frequency can be tuned between 0.1 and 5 Hz. The experiments will be used to validate computational dynamic tools currently under development, which are based on DORT-TD and CASMO/S3K code systems. The second programme concerns the measurement of in-core neutron noise for axial void profile reconstruction. Simulations performed at Chalmers University have shown how the void fraction and velocity profiles can be reconstructed from noise measurements. The motivation of these experiments is to develop an experimental setup to validate in-core the method in partnership with Chalmers University. The third experimental programme aims at continuing the validation effort on the nuclear data required in the calculation of GEN-III PWR reactors with heavy steel reflectors. This is a collaboration with CEA Cadarache that extends the results of the PERLE experiments carried out in the E reactor at CEA. Scattering cross sections at around 1 MeV will be studied separately by replacing successively the water reflector by sheets of stainless steel alloy and pure metals – iron, nickel, and chromium. Data will be extracted from the measured flux attenuation using foils in the metal reflector and from the criticality effects of these reflectors. In parallel to the three reactor experiments, we develop in-core detectors and measurement systems. Following the last development of a neutron noise measurement station in pulse mode, a second neutron noise station in current mode is being designed. In current mode the reactor can be used at higher power without dead time effects. It allows faster measurement time or lower results uncertainties. Finally, a joint development of a full new detection system based on chemical vapour deposited (sCVD) diamond has been started with the CIVIDEC instrumentation start-up company. A first prototype has been tested in November 2015 in CROCUS. One of the main purposes is to work on the discrimination of gammas, thermal and fast neutrons for demonstrating the interest of this detector type in a mixed neutron-gamma field

Biogeographic history of the pantropical family Gesneriaceae with a focus on the Indian plate and diversification through the Old World

The Gesneriaceae consists of around 150 genera and c. 3750 species with a predominantly tropical and subtropical distribution across all continents. Although previous studies have proposed an American origin of Gesneriaceae, the biogeographic history of this pantropical plant family is still unclear, particularly in the Old World. To address this, we assembled the most comprehensively sampled matrix of Gesneriaceae with 143 Gesneriaceae genera and 355 species, including key samples from Sri Lanka analysed here for the first time. We generated molecular phylogenies based on four plastid gene regions (ndhF, matK, rps16 and trnL-F), obtained fossil-calibrated trees, and reconstructed ancestral areas and dispersal routes using Bayesian methods. Our results confirm the origin for the family in the Early Palaeocene (67. Ma) in the region of present-day Central America & Andean South America, and that diversity in the Old World originated from a long-distance dispersal event from South America around 59 Ma, most likely to the Indian plate, which was an island at the time. This lineage then dispersed to Malesia and later East Asia, which would ultimately become a major centre of diversity and source of many dispersals to other regions. Our results thus highlight the Indian plate as a likely key player in the early diversification of Old World Gesneriaceae, even though it is now more diverse elsewhere, and hence offer novel insights into this plant family’s dispersal routes and areas of diversification in the Old World

Towards specific guidelines for applying LCA in South contexts

The demand for LCA studies on agri-food value chains from South contexts is growing, but the application of LCA in these contexts is challenging. An initiative has been launched to formalize best practices based on the field experience from LCA experts for South contexts. Specificities of the application of LCA in these conditions relate to the diversity and complexity of production conditions and systems, the limited awareness and capacities in LCA as environmental assessment tool by stakeholders, the lack of specific background data, the scarcity and often low-quality of statistic data on studied systems, and the limits imposed to LCA commissioned from abroad. The guidelines in preparation will mainly focus on practical aspects of goal and scope definition, data collection and partnership, inventory and interpretation for key stakeholders

Macroevolution of the plant–hummingbird pollination system

ABSTRACTPlant–hummingbird interactions are considered a classic example of coevolution, a process in which mutually dependent species influence each other's evolution. Plants depend on hummingbirds for pollination, whereas hummingbirds rely on nectar for food. As a step towards understanding coevolution, this review focuses on the macroevolutionary consequences of plant–hummingbird interactions, a relatively underexplored area in the current literature. We synthesize prior studies, illustrating the origins and dynamics of hummingbird pollination across different angiosperm clades previously pollinated by insects (mostly bees), bats, and passerine birds. In some cases, the crown age of hummingbirds pre‐dates the plants they pollinate. In other cases, plant groups transitioned to hummingbird pollination early in the establishment of this bird group in the Americas, with the build‐up of both diversities coinciding temporally, and hence suggesting co‐diversification. Determining what triggers shifts to and away from hummingbird pollination remains a major open challenge. The impact of hummingbirds on plant diversification is complex, with many tropical plant lineages experiencing increased diversification after acquiring flowers that attract hummingbirds, and others experiencing no change or even a decrease in diversification rates. This mixed evidence suggests that other extrinsic or intrinsic factors, such as local climate and isolation, are important covariables driving the diversification of plants adapted to hummingbird pollination. To guide future studies, we discuss the mechanisms and contexts under which hummingbirds, as a clade and as individual species (e.g. traits, foraging behaviour, degree of specialization), could influence plant evolution. We conclude by commenting on how macroevolutionary signals of the mutualism could relate to coevolution, highlighting the unbalanced focus on the plant side of the interaction, and advocating for the use of species‐level interaction data in macroevolutionary studies

Diatom DNA metabarcoding for ecological assessment: Comparison among bioinformatics pipelines used in six European countries reveals the need for standardization

Ecological assessment of lakes and rivers using benthic diatom assemblages currently requires considerable taxonomic expertise to identify species using light microscopy. This traditional approach is also time-consuming. Diatom metabarcoding is a promising alternative and there is increasing interest in using this approach for routine assessment. However, until now, analysis protocols for diatom metabarcoding have been developed and optimised by research groups working in isolation. The diversity of existing bioinformatics methods highlights the need for an assessment of the performance and comparability of results of different methods. The aim of this study was to test the correspondence of outputs from six bioinformatics pipelines currently in use for diatom metabarcoding in different European countries. Raw sequence data from 29 biofilm samples were treated by each of the bioinformatics pipelines, five of them using the same curated reference database. The outputs of the pipelines were compared in terms of sequence unit assemblages, taxonomic assignment, biotic index score and ecological assessment outcomes. The three last components were also compared to outputs from traditional light microscopy, which is currently accepted for ecological assessment of phytobenthos, as required by the Water Framework Directive. We also tested the performance of the pipelines on the two DNA markers (rbcL and 185-V4) that are currently used by the working groups participating in this study. The sequence unit assemblages produced by different pipelines showed significant differences in terms of assigned and unassigned read numbers and sequence unit numbers. When comparing the taxonomic assignments at genus and species level, correspondence of the taxonomic assemblages between pipelines was weak. Most discrepancies were linked to differential detection or quantification of taxa, despite the use of the same reference database. Subsequent calculation of biotic index scores also showed significant differences between approaches, which were reflected in the final ecological assessment. Use of the rbcL marker always resulted in better correlation among molecular datasets and also in results closer to these generated using traditional microscopy. This study shows that decisions made in pipeline design have implications for the dataset's structure and the taxonomic assemblage, which in turn may affect biotic index calculation and ecological assessment. There is a need to define best-practice bioinformatics parameters in order to ensure the best representation of diatom assemblages. Only the use of similar parameters will ensure the compatibility of data from different working groups. The future of diatom metabarcoding for ecological assessment may also lie in the development of new metrics using, for example, presence/absence instead of relative abundance data. (C) 2020 The Authors. Published by Elsevier B.V

The use of visual and automatized behavioral markers to assess methodologies: a study case on PIT-tagging in the Alpine newt

peer reviewedBiomarkers are now widely used as tools in various research fields to assess individual integrity. The recent advances in quantification methods of behavioral patterns, such as computerized video-tracking procedures, make them valuable biomarkers. However, the corollary of these novelties is that they remain relatively unknown and unused. In this study, we show that such tools can assess the validity of research methods, such as individual recognition. To demonstrate this we employed as a model a marking method (Passive Integrate Transponders: PIT-tagging) widely used in amphibians. Both detailed visual observations and video-tracking methods were complementary in highlighting components at different behavioral scales: locomotion, feeding, and breeding. We illustrate the scientific and ethical adequacy of the targeted marking method but also suggest that more studies should integrate behavioral analyses. Such biomarkers are a powerful tool to assess conservation concerns when other techniques cannot detect detrimental effects