Foreword to the thematic cluster: the Arctic in Rapid Transition — marine ecosystems

The Arctic is warming and losing sea ice. Happening at a much faster rate than previously expected, these changes are causing multiple ecosystem feedbacks in the Arctic Ocean. The Arctic in Rapid Transition (ART) initiative was developed by early-career scientists as an integrative, international, multidisciplinary, long-term pan-Arctic network to study changes and feedbacks among the physical and biogeochemical components of the Arctic Ocean and their ultimate impacts on biological productivity on different timescales. In 2012, ART jointly organized with the Association of Polar Early Career Scientists their second science workshop—Overcoming Challenges of Observation to Model Integration in Marine Ecosystem Response to Sea Ice Transitions—at the Institute of Oceanology, Polish Academy of Sciences, in Sopot. This workshop aimed to identify linkages and feedbacks between atmosphere–ice–ocean forcing and biogeochemical processes, which are critical for ecosystem function, land–ocean interactions and productive capacity of the Arctic Ocean. This special thematic cluster of Polar Research brings together seven papers that grew out of workgroup discussions. Papers examine the climate change impacts on various ecosystem elements, providing important insights on the marine ecological and biogeochemical processes on various timescales. They also highlight priority areas for future research

Arctic in Rapid Transition (ART) : science plan

The Arctic is undergoing rapid transformations that have brought the Arctic Ocean to the top of international political agendas. Predicting future conditions of the Arctic Ocean system requires scientific knowledge of its present status as well as a process-based understanding of the mechanisms of change. The Arctic in Rapid Transition (ART) initiative is an integrative, international, interdisciplinary pan-Arctic program to study changes and feedbacks among the physical and biogeochemical components of the Arctic Ocean and their ultimate impacts on biological productivity. The goal of ART is to develop priorities for Arctic marine science over the next decade. Three overarching questions form the basis of the ART science plan: (1) How were past transitions in sea ice connected to energy flows, elemental cycling, biological diversity and productivity, and how do these compare to present and projected shifts? (2) How will biogeochemical cycling respond to transitions in terrestrial, gateway and shelf-to-basin fluxes? (3) How do Arctic Ocean organisms and ecosystems respond to environmental transitions including temperature, stratification, ice conditions, and pH? The integrated approach developed to answer the ART key scientific questions comprises: (a) process studies and observations to reveal mechanisms, (b) the establishment of links to existing monitoring programs, (c) the evaluation of geological records to extend time-series, and (d) the improvement of our modeling capabilities of climate-induced transitions. In order to develop an implementation plan for the ART initiative, an international and interdisciplinary workshop is currently planned to take place in Winnipeg, Canada in October 2010

Laryngeal teflonoma identified by Fourier-transform infrared microspectroscopy after forensic autopsy: An interesting tool for foreign material identification in forensic cases

International audienceForensic pathologists are sometimes confronted with microscopic foreign bodies mixed in with soft tissues surrounding wounds and which are thus difficult to identify. This identification, however, could be primordial in investigating a crime and in determining the weapon used. A case of a fatal respiratory distress syndrome due to conjoining suicidal drug intoxication and laryngeal obstruction by a voluminous foreign body giant cell granuloma is presented. The classical histological examination showed exogenous particles in the vocal cord tumor with birefringent qualities. Their analysis with Fourier-Transform infrared (FTIR) spectrometry coupled with infrared microscope allows the determination of their chemical nature as polytetrafluoroethylene and to the diagnosis of teflonoma. This case report put the emphasis on the forensic interest of the FTIR imaging

Homogénéisation périodique d'un matériau élastoplastique compressible anisotrope : application aux structures sandwichs à coeur cellulaire

Grâce à leurs bonnes propriétés mécaniques spécifiques, les matériaux cellulaires architecturés présentent un fort intérêt pour répondre aux problématiques du secteur aéronautique, notamment pour la tenue structurale et la résistance à l'impact. De par leurs architectures, ces matériaux présentent en général trois échelles caractéristiques: l'échelle macroscopique de la structure, l'échelle mésoscopique associée à la cellule élémentaire et l'échelle microscopique liée au matériau constitutif. La modélisation d'architectures de grande dimension est difficile à mettre en oeuvre car couteuse en temps de calcul. Pour contourner ce problème, la mise en place d'une modélisation multi-échelle basée sur l'identification d'une Loi Homogène Equivalente (LHE) est proposée. L'étude du comportement multi-axial du matériau cellulaire à l'échelle de son Volume Elémentaire Représentatif (VER) nous permet, par homogénéisation périodique, d'expliciter le comportement macroscopique et d'identifier une LHE compressible et anisotrope. La structure sandwich est ensuite modélisée en remplaçant le coeur cellulaire par un Milieu Homogène Equivalent (MHE). Pour des cas de chargements quasi-statiques, l'influence des effets de bords sur le comportement macroscopique de la structure en fonction des différents types d'empilement des tubes, de la taille des structures sandwichs et du type de chargement a été analysée. La méthode donne des résultats satisfaisants mais présente des limites quant à la validité de la séparation des échelles, indispensable à l'approche par homogénéisation, il est donc envisagé d'enrichir la méthode par les milieux continus généralisés pour mieux prendre en compte les phénomènes induits par la localisation des déformations. Une confrontation avec des essais mécaniques sera entreprise pour discuter de la validité des modèles proposés, avec une extension progressive à des chargements dynamiques

Tackling rapid radiations with targeted sequencing

In phylogenetic studies across angiosperms, at various taxonomic levels, polytomies have persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large amount of genomic data now available and statistical tools to analyze them provide unprecedented power for phylogenetic inference. Targeted sequencing has emerged as a strong tool for estimating species trees in the face of rapid radiations, lineage sorting, and introgression. Evolutionary relationships in Cyperaceae have been studied mostly using Sanger sequencing until recently. Despite ample taxon sampling, relationships in many genera remain poorly understood, hampered by diversification rates that outpace mutation rates in the loci used. The C4 Cyperus clade of the genus Cyperus has been particularly difficult to resolve. Previous studies based on a limited set of markers resolved relationships among Cyperus species using the C3 photosynthetic pathway, but not among C4 Cyperus clade taxa. We test the ability of two targeted sequencing kits to resolve relationships in the C4 Cyperus clade, the universal Angiosperms-353 kit and a Cyperaceae-specific kit. Sequences of the targeted loci were recovered from data generated with both kits and used to investigate overlap in data between kits and relative efficiency of the general and custom approaches. The power to resolve shallow-level relationships was tested using a summary species tree method and a concatenated maximum likelihood approach. High resolution and support are obtained using both approaches, but high levels of missing data disproportionately impact the latter. Targeted sequencing provides new insights into the evolution of morphology in the C4 Cyperus clade, demonstrating for example that the former segregate genus Alinula is polyphyletic despite its seeming morphological integrity. An unexpected result is that the Cyperus margaritaceus-Cyperus niveus complex comprises a clade separate from and sister to the core C4 Cyperus clade. Our results demonstrate that data generated with a family-specific kit do not necessarily have more power than those obtained with a universal kit, but that data generated with different targeted sequencing kits can often be merged for downstream analyses. Moreover, our study contributes to the growing consensus that targeted sequencing data are a powerful tool in resolving rapid radiations

Targeted sequencing supports morphology and embryo features in resolving the classification of Cyperaceae tribe Fuireneae s.l.

Molecular phylogenetic studies based on Sanger sequences have shown that Cyperaceae tribe Fuireneae s.l. is paraphyletic. However, taxonomic sampling in these studies has been poor, topologies have been inconsistent, and support for the backbone of trees has been weak. Moreover, uncertainty still surrounds the morphological limits of Schoenoplectiella, a genus of mainly small, amphicarpic annuals that was recently segregated from Schoenoplectus. Consequently, despite ample evidence from molecular analyses that Fuireneae s.l. might consist of two to four tribal lineages, no taxonomic changes have yet been made. Here, we use the Angiosperms353 enrichment panel for targeted sequencing in order to: (1) clarify the relationships of Fuireneae s.l. with the related tribes Abildgaardieae, Eleocharideae and Cypereae; (2) define the limits of Fuireneae s.s., and (3) test the monophyly of Fuireneae s.l. genera with emphasis on Schoenoplectus and Schoenoplectiella. Using more than a third of Fuireneae s.l. diversity, our phylogenomic analyses strongly support six genera and four major Fuireneae s.l. clades that we recognise as tribes: Bolboschoeneae stat.nov., Fuireneae s.s., Schoenoplecteae, and Pseudoschoeneae tr.nov. These results are consistent with morphological, micromorphological (nutlet epidermal cell shape), and embryo differences detected for each tribe. At the generic level, most sub‐Saharan African perennials currently treated in Schoenoplectus are transferred to Schoenoplectiella. Our targeted sequencing results show that these species are nested in Schoenoplectiella, and their treatment here is consistent with micromorphological and embryo characters shared by all Schoenoplectiella species. Keys to recognised tribes and genera are provided

A roadmap for global synthesis of the plant tree of life

Providing science and society with an integrated, up-to-date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience are often not straightforward due to numerous informatics barriers. While big synthetic plant phylogenies are being built, they remain static and become quickly outdated as new data are published and tree-building methods improve. Moreover, the body of existing phylogenetic evidence is hard to navigate and access for non-experts. We propose that our community of botanists, tree builders, and informaticians should converge on a modular framework for data integration and phylogenetic analysis, allowing easy collaboration, updating, data sourcing and flexible analyses. With support from major institutions, this pipeline should be re-run at regular intervals, storing trees and their metadata long-term. Providing the trees to a diverse global audience through user-friendly front ends and application development interfaces should also be a priority. Interactive interfaces could be used to solicit user feedback and thus improve data quality and to coordinate the generation of new data. We conclude by outlining a number of steps that we suggest the scientific community should take to achieve global phylogenetic synthesis

Toward unifying global hotspots of wild and domesticated biodiversity

Global biodiversity hotspots are areas containing high levels of species richness, endemism and threat. Similarly, regions of agriculturally relevant diversity have been identified where many domesticated plants and animals originated, and co-occurred with their wild ancestors and relatives. The agro-biodiversity in these regions has, likewise, often been considered threatened. Biodiversity and agro-biodiversity hotspots partly overlap, but their geographic intricacies have rarely been investigated together. Here we review the history of these two concepts and explore their geographic relationship by analysing global distribution and human use data for all plants, and for major crops and associated wild relatives.We highlight a geographic continuum between agro-biodiversity hotspots that contain high richness in species that are intensively used and well known by humanity (i.e., major crops and most viewed species onWikipedia) and biodiversity hotspots encompassing species that are less heavily used and documented (i.e., crop wild relatives and species lacking information on Wikipedia). Our contribution highlights the key considerations needed for further developing a unifying concept of agro-biodiversity hotspots that encompasses multiple facets of diversity (including genetic and phylogenetic) and the linkage with overall biodiversity. This integration will ultimately enhance our understanding of the geography of human-plant interactions and help guide the preservation of nature and its contributions to people

A new classification of Cyperaceae (Poales) supported by phylogenomic data

Cyperaceae (sedges) are the third largest monocot family and are of considerable economic and ecological importance. Sedges represent an ideal model family to study evolutionary biology because of their species richness, global distribution, large discrepancies in lineage diversity, broad range of ecological preferences, and adaptations including multiple origins of C4 photosynthesis and holocentric chromosomes. Goetghebeur’s seminal work on Cyperaceae published in 1998 provided the most recent complete classification at tribal and generic level, based on a morphological study of Cyperaceae inflorescence, spikelet, flower and embryo characters plus anatomical and other information. Since then, several family‐level molecular phylogenetic studies using Sanger sequence data have been published. Here, more than 20 years after the last comprehensive classification of the family, we present the first family‐wide phylogenomic study of Cyperaceae based on targeted sequencing using the Angiosperms353 probe kit sampling 311 accessions. Additionally, 62 accessions available from GenBank were mined for overlapping reads and included in the phylogenomic analyses. Informed by this backbone phylogeny, a new classification for the family at the tribal, subtribal and generic levels is proposed. The majority of previously recognized suprageneric groups are supported, and for the first time we establish support for tribe Cryptangieae as a clade including the genus Koyamaea. We provide a taxonomic treatment including identification keys and diagnoses for the 2 subfamilies, 24 tribes and 10 subtribes and basic information on the 95 genera. The classification includes five new subtribes in tribe Schoeneae: Anthelepidinae, Caustiinae, Gymnoschoeninae, Lepidospermatinae and Oreobolinae. This article is protected by copyright. All rights reserved

Target sequence data shed new light on the infrafamilial classification of Araceae

Premise: Recent phylogenetic studies of the Araceae have confirmed the position of the duckweeds nested within the aroids, and the monophyly of a clade containing all the unisexual flowered aroids plus the bisexual‐flowered Calla palustris. The main objective of the present study was to better resolve the deep phylogenetic relationships among the main lineages within the family, particularly the relationships between the eight currently recognized subfamilies. We also aimed to confirm the phylogenetic position of the enigmatic genus Calla in relation to the long‐debated evolutionary transition between bisexual and unisexual flowers in the family. Methods: Nuclear DNA sequence data were generated for 128 species across 111 genera (78%) of Araceae using target sequence capture and the Angiosperms 353 universal probe set. Results: The phylogenomic data confirmed the monophyly of the eight Araceae subfamilies, but the phylogenetic position of subfamily Lasioideae remains uncertain. The genus Calla is included in subfamily Aroideae, which has also been expanded to include Zamioculcadoideae. The tribe Aglaonemateae is newly defined to include the genera Aglaonema and Boycea. Conclusions: Our results strongly suggest that new research on African genera (Callopsis, Nephthytis, and Anubias) and Calla will be important for understanding the early evolution of the Aroideae. Also of particular interest are the phylogenetic positions of the isolated genera Montrichardia, Zantedeschia, and Anchomanes, which remain only moderately supported here