Phylogenomics and morphological evolution of the mega-diverse genus Artemisia (Asteraceae: Anthemideae): implications for its circumscription and infrageneric taxonomy

Background and Aims Artemisia is a mega-diverse genus consisting of ~400 species. Despite its medicinal importance and ecological significance, a well-resolved phylogeny for global Artemisia, a natural generic delimitation and infrageneric taxonomy remain missing, owing to the obstructions from limited taxon sampling and insufficient information on DNA markers. Its morphological characters, such as capitulum, life form and leaf, show marked variations and are widely used in its infrageneric taxonomy. However, their evolution within Artemisia is poorly understood. Here, we aimed to reconstruct a well-resolved phylogeny for global Artemisia via a phylogenomic approach, to infer the evolutionary patterns of its key morphological characters and to update its circumscription and infrageneric taxonomy. Methods We sampled 228 species (258 samples) of Artemisia and its allies from both fresh and herbarium collections, covering all the subgenera and its main geographical areas, and conducted a phylogenomic analysis based on nuclear single nucleotide polymorphisms (SNPs) obtained from genome skimming data. Based on the phylogenetic framework, we inferred the possible evolutionary patterns of six key morphological characters widely used in its previous taxonomy. Key Results The genus Kaschgaria was revealed to be nested in Artemisia with strong support. A well-resolved phylogeny of Artemisia consisting of eight highly supported clades was recovered, two of which were identified for the first time. Most of the previously recognized subgenera were not supported as monophyletic. Evolutionary inferences based on the six morphological characters showed that different states of these characters originated independently more than once. Conclusions The circumscription of Artemisia is enlarged to include the genus Kaschgaria. The morphological characters traditionally used for the infrageneric taxonomy of Artemisia do not match the new phylogenetic tree. They experienced a more complex evolutionary history than previously thought. We propose a revised infrageneric taxonomy of the newly circumscribed Artemisia, with eight recognized subgenera to accommodate the new results.This work was supported by the National Natural Science Foundation of China (grant nos. 31870179, 31570204, 31270237 and J1310002), the International Partnership Program (grant no. 151853KYSB20190027), Sino-Africa Joint Research Center (grant no. SAJC201614), Key technology projects of Jiangxi Province's major scientific and technological research and development project (grant no. 20223AAF01007), Survey of Wildlife Resources in Key Areas of Tibet (grant no. ZL202203601) and National Plant Specimen Resource Center (grant no. E0117G1001) of the Chinese Academy of Sciences, Key Project at Central Government Level: The Ability Establishment of Sustainable Use of Valuable Chinese Medicine Resources (grant no. 2060302) and Project of the Central Siberian Botanical Garden of the Siberian Branch of the Russian Academy of Sciences (grant no. AAAA-A21-121011290024-5).Abstract INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION Conclusions SUPPLEMENTARY DATA FUNDING ACKNOWLEDGEMENTS CONFLICT OF INTEREST LITERATURE CITED Supplementary dat

Définition de l'organisation des collections inertes associées au Jardin Botanique de La Gacilly

Dried collections of the Yves Rocher Botanic Garden in La Gacilly (France) include herbarium, dried seed and fruit collections. The formalization of collections organization is necessary to consider their development in the future. Conservation conditions, completion and sanitary protocols were revised and a new methodology was defined, accession number were used to link in a permanent way physical accessions to their corresponding data in the collection management database. Inventory data were exported from the garden database to online databases (GBIF and BGCI), using the DarwinCore biodiversity sharing standard. A collection management policy document was realized, defining the objectives, organization, and procedural rules.Les collections inertes du Jardin Botanique Yves Rocher de La Gacilly sont constituées des herbiers, carpothèque et séminothèque. L’objectif du stage est de formaliser l’organisation des collections dans la perspective de leur développement futur. Ces collections établies au cours de l’activité du jardin botanique représentent des volumes importants. L’analyse de leurs conditions de réalisation, de conservation a été réalisée. Dans un second temps l’organisation des collections a été envisagée par le référencement et l’intégration des accessions dans la base de données de gestion des collections du jardin. Un lien permanent est établi entre les données numériques et l’objet de collection par un identifiant unique, un numéro d’accession pour la gestion interne au jardin. L’export des données d’inventaire en vue de leur partage sur les réseaux du GBIF et du BGCI et adaptées selon le standard DarwinCore a été effectué. Une politique de gestion pour les collections inertes a été réalisée et formalise les objectifs des collections, leur organisation et les règles de fonctionnement en interne et vis-à-vis des personnes extérieures

La vallée de la Choisille (sud du Bassin parisien – France) : le paysage végétal depuis le Tardiglaciaire jusqu’à l’époque actuelle d’après les données paléopalynologiques

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Structure, Bonding, and Stability of Mercury Complexes with Thiolate and Thioether Ligands from High-Resolution XANES Spectroscopy and First-Principles Calculations

International audienceWe present results obtained from high energy-resolution L3-edge XANES spectroscopy and first-principles calculations for the structure, bonding, and stability of mercury-(II) complexes with thiolate and thioether ligands in crystalline compounds, aqueous solution, and macromolecular naturalorganic matter (NOM). Core-to-valence XANES features that vary in intensity differentiate with unprecedented sensitivity the number and identity of Hg ligands and the geometry of the ligand environment. Post-Hartree−Fock XANES calculations, coupled with natural population analysis, performed on MP2-optimized Hg[(SR)2···(RSR)n] complexes show that the shape, position, and number of electronic transitions observed at high energy-resolution are directly correlated to the Hg and S (l,m)-projected empty densities of states and occupations of the hybridized Hg 6s and 5d valence orbitals. Linear two-coordination, the most common coordination geometry in mercury chemistry, yields a sharp 2p to 6s + 5d electronic transition. This transition varies in intensity for Hg bonded to thiol groups in macromolecular NOM. The intensity variation is explained by contributions from next-nearest, low-charge, thioether-type RSR ligands at 3.0−3.3 Å from Hg. Thus, Hg in NOM has two strong bonds to thiol S and k additional weak Hg···S contacts, or 2 + k coordination. The calculated stabilization energy is −5 kcal/mol per RSR ligand. Detection of distant ligands beyond the firstcoordination shell requires precise measurement of, and comparison to, spectra of reference compounds as well as accuratecalculation of spectra for representative molecular models. The combined experimental and theoretical approaches describedhere for Hg can be applied to other closed-shell atoms, such as AgI and AuI. To facilitate further calculation of XANES spectra,experimental data, a new crystallographic structure of a key mercury thioether complex, Cartesian coordinates of the computedmodels, and examples of input files are provided as Supporting Information

Human impact variability on soil erosion during the Holocene based on valley floor sediments study in a Parisian basin fluvial catchment (France): crossing sedimentological, archaeological and palynological proxies

International audienceThis work is part of the French CNRS ECLIPSE program « Impact anthropique sur l'érosion des sols et la sédimentation dans les zones humides associées durant l'Holocène ». It aims to reconstitute the evolution of human impact on soil erosion at various periods via the study of Holocene sedimentary archives. In this framework the Choisille catchment (288 km²; elevation: 50 - 200 m), tributary of the River Loire near Tours (France), has been the subject of an interdisciplinary study (sedimentology, geophysics, archaeology, palynology). 3 areas are investigated: a downstream stretch, a silicated sub-catchment area and a carbonated sub-catchment area. In the downstream stretch, located near ancient populated areas, drillings were performed along cross sections through valley floor alluviums. They show that a more or less organic clayey silty sedimentation started at the beginning of the Holocene. The sedimentation rates strongly increased at the beginning of the Subbatlantic (Bronze Age), simultaneously with the anthropogenic pressure advent (on set of agriculture), as shown by archaeological and palynological evidences (agricultural settlements, massive loggings on slopes, stockbreeding on valley-floor grasslands). In the silicated sub-catchment area, located upstream, drillings have shown that clayey silty sedimentation began at the end of the Roman Period, continued during the Early Middle Ages and increased during the High Middle Ages. Spatial archaeological prospecting has revealed a faint anthropogenic presence at the Roman Period, then a decline of population until the High Middle Ages, characterised by an agricultural revival. Palynological analyses have shown that, in this area, grasslands were dominant since the Early Middle Ages, with an increase in cereal cultures at the beginning of the High Middle Ages. In the carbonated sub-catchment area, drillings have shown that the more or less organic clayey silty sedimentation has begun during the Bronze Age. Sedimentation rates have increased during the Modern era and the Contemporary history. The high fine sediment storage appeared and evolved differently, depending on the considered period and catchment valley area, due to variation of soil erosion. The difference between a fine, early and regularly increasing sedimentation in the downstream site and the later, intense and non-univocal sedimentation in the sub-catchments doesn't seem to be strictly resulting from natural factors. This idea and the palaeoenvironnemental dataset show that the fine sedimentation basically results from an anthropogenic impact, notably in the sub-catchments. Therefore soil exploitation by humans seems to be the main sedimentary production factor. This work mainly shows that anthropogenic impact (age of appearance, intensity) highly varies spatially, even into a little catchment. This variability would be led by the agricultural potential of the considered catchment valley area

Spatial variability of anthropogenic impact on Holocene fluvial sedimentation. A case study: the Choisille catchment (Parisian basin, France)

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Impact de la dynamique d’occupation du sol sur les flux de matière à l’Holocène : l’exemple de la vallée de la Choisille (France)

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Human interactions with bats and bat coronaviruses in rural Côte d'Ivoire

Bats are presumed reservoirs of diverse α- and β- coronaviruses (CoVs) and understanding the diversity of bat-CoVs and the role bats play in CoV transmission is highly relevant in the context of the current COVID pandemic. We sampled bats in Côte d'Ivoire (2016–2018) living at ecotones between anthropogenic and wild habitats in the Marahoué National Park, a recently encroached protected area, to detect and characterize the CoVs circulating in bats and humans. A total of 314 bats were captured, mostly during the rainy season (78%), and CoV RNA was detected in three of the bats (0.96%). A CoV RNA sequence similar to Chaerephon bat coronavirus/Kenya/KY22/2006 (BtKY22) was found in a Chaerephon cf. pumilus and a Mops sp. fecal swab, while a CoV RNA sequence similar to the two almost identical Kenya bat coronaviruses BtKY55 and BtKY56 (BtKY55/56) was detected in an Epomops buettikoferi oral swab. Phylogenetic analyses indicated differences in the degree of evolutionary host-virus co-speciation for BtKY22 and BtKY55/56. To assess potential for human exposure to these viruses, we conducted human syndromic and community-based surveillance in clinics and high-risk communities. We collected data on participant characteristics, livelihoods, animal contact, and high-risk behaviors that may be associated with exposure to zoonotic diseases. We then collected biological samples for viral testing from 401 people. PCR testing of these biological samples revealed no evidence of CoV infection among the enrolled individuals. We identified higher levels of exposure to bats in people working in crop production and in hunting, trapping and fishing. Finally, we used the ‘Spillover’ risk-ranking tool to assess the potential for viral spillover and concluded that, while there is no evidence to suggest imminent risk of spillover for these CoVs, their host range and other traits suggest caution and vigilance are warranted in people with high exposure risk