Ultra‐Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera,Chalcidoidea)

Recent technical advances combined with novel computational approaches have promised the acceleration of our understanding of the tree of life. However, when it comes to hyperdiverse and poorly known groups of invertebrates, studies are still scarce. As published phylogenies will be rarely challenged by future taxonomists, careful attention must be paid to potential analytical bias. We present the first molecular phylogenetic hypothesis for the family Chalcididae, a group of parasitoid wasps, with a representative sampling (144 ingroups and seven outgroups) that covers all described subfamilies and tribes, and 82% of the known genera. Analyses of 538 Ultra‐Conserved Elements (UCEs) with supermatrix (RAx ML and IQTREE) and gene tree reconciliation approaches (ASTRAL, ASTRID) resulted in highly supported topologies in overall agreement with morphology but reveal conflicting topologies for some of the deepest nodes. To resolve these conflicts, we explored the phylogenetic tree space with clustering and gene genealogy interrogation methods, analyzed marker and taxon properties that could bias inferences and performed a thorough morphological analysis (130 characters encoded for 40 taxa representative of the diversity). This joint analysis reveals that UCEs enable attainment of resolution between ancestry and convergent/divergent evolution when morphology is not informative enough, but also shows that a systematic exploration of bias with different analytical methods and a careful analysis of morphological features is required to prevent publication of artifactual results. We highlight a GC content bias for maximum‐likelihood approaches, an artifactual mid‐point rooting of the ASTRAL tree and a deleterious effect of high percentage of missing data (>85% missing UCEs) on gene tree reconciliation methods. Based on the results we propose a new classification of the family into eight subfamilies and ten tribes that lay the foundation for future studies on the evolutionary history of Chalcididae.     

Circ-IGF1R plays a significant role in psoriasis via regulation of a miR-194-5p/CDK1 axis

Cytotechnology - Psoriasis is a skin disorder that is classed as an autoimmune disease. It is characterized by excessive proliferation, abnormal migration and differentiation of keratinocytes, as...     

Application of plant metabarcoding to identify diverse honeybee pollen forage along an urban–agricultural gradient

Understanding animal foraging ecology requires large sample sizes spanning broad environmental and temporal gradients. For pollinators, this has been hampered by the laborious nature of morphologically identifying pollen. Identifying pollen from urban environments is particularly difficult due to the presence of diverse ornamental species associated with consumer horticulture. Metagenetic pollen analysis represents a potential solution to this issue. Building upon prior laboratory and bioinformatic methods, we applied quantitative multilocus metabarcoding to characterize the foraging ecology of honeybee colonies situated in urban, suburban, mixed suburban–agricultural and rural agricultural sites in central Ohio, USA. In cross‐validating a subset of our metabarcoding results using microscopic palynology, we find strong concordance between the molecular and microscopic methods. Our results suggest that forage from the agricultural site exhibited decreased taxonomic diversity and temporal turnover relative to the urban and suburban sites, though the generalization of this observation will require replication across additional sites and cities. Our work demonstrates the power of honeybees as environmental samplers of floral community composition at large spatial scales, aiding in the distinction of taxa characteristically associated with urban or agricultural land use from those distributed ubiquitously across the sampled landscapes. Observed patterns of high forage diversity and compositional turnover in our more urban sites are likely reflective of the fine‐grain heterogeneity and high beta diversity of urban floral landscapes at the scale of honeybee foraging. This provides guidance for future studies investigating how relationships between urbanization and measures of pollinator health are mediated by variation in floral resource dynamics across landscapes.     

The Bio3D packages for structural bioinformatics

Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and dynamics. Major functionality includes biomolecular database searching and retrieval, sequence and structure conservation analysis, ensemble normal mode analysis, protein structure and correlation network analysis, principal component, and related multivariate analysis methods. Here, we review recent package developments, including a new underlying segregation into separate packages for distinct analysis, and introduce a new method for structure analysis named ensemble difference distance matrix analysis (eDDM). The eDDM approach calculates and compares atomic distance matrices across large sets of homologous atomic structures to help identify the residue wise determinants underlying specific functional processes. An eDDM workflow is detailed along with an example application to a large protein family. As a new member of the Bio3D family, the Bio3D‐eddm package supports both experimental and theoretical simulation‐generated structures, is integrated with other methods for dissecting sequence‐structure–function relationships, and can be used in a highly automated and reproducible manner. Bio3D is distributed as an integrated set of platform independent open source R packages available from: http://thegrantlab.org/bio3d/ .     

基于MODIS-EVI的西南地区植被覆盖时空变化及驱动因素研究

基于MODIS-EVI和气象数据,利用最大值合成法、像元二分模型、趋势分析和相关分析等方法,探讨了西南地区2001-2015年植被覆盖时空变化特征及其对气候因子的响应,并分析了温度和降水对植被覆盖时空变化的驱动作用。结果表明：（1）2001-2015年,西南地区植被EVI以0.1%/a的变化率呈波动增加趋势,但空间异质性显著,呈现出从东南向西北逐渐递减的趋势;（2）西南地区以高和极高植被覆盖度为主,极低植被覆盖度区域约占研究区总面积的8.6%,植被覆盖度增加的区域集中分布在广西省北海-钦州、贵州省邵通-毕节-遵义、四川省广元-广安以及西藏那曲等地区,植被覆盖度呈减少趋势区域主要集中在西藏拉萨-阿里地区和四川成都-阿坝州-甘孜州等地区;（3）植被EVI与同期温度和降水相关性较好,均以正相关为主。在0.05显著水平下,受降水驱动的区域呈斑块状分布在西藏自治区和青海省交界处,以及云南和广西部分地区,约占研究区总面积的3.4%;受温度驱动的区域零星分布在各省、自治区,约占研究区总面积的1.6%;受温度和降水共同驱动的区域约占研究区总面积的7.2%,主要分布在西藏自治区的阿里地区北部,青海省的三江源地区以及四川和贵州两省交界处的小部分地区;西南地区大部分区域的植被EVI指数变化表现为非气候因素驱动。     

中国天然林资源保护工程综合评价指标体系与评估方法

天然林资源是国家重要的战略资源与生态资源,在维护国土生态安全、应对气候变化、保护生物多样性等方面发挥着不可替代的重要作用。作为覆盖范围最广、投资规模最大的天然林资源保护工程（简称天保工程）自2000年正式启动以来,对长江上游、黄河上中游地区以及东北、内蒙古、新疆、海南等重点国有林区的森林资源保护修复、区域生态环境改善及经济社会可持续发展等多方面都产生了巨大、深远影响。天保工程二期于2020年结束,全面定量评估天保工程的生态、经济和社会综合效益和国内外的巨大影响,可为全面推进我国天然林资源保护修复提供科技支撑,为后续政策修订提供决策依据。本文基于空间信息技术、样地调查、生态站观测、比较分析等手段,构建了适用于天保工程的综合评价指标体系与评估方法,涵盖森林资源、生态效益、社会经济效益、生态修复措施和政策设计5个方面,对全面贯彻落实国家生态文明战略和《天然林保护修复制度方案》具有重要的现实意义和深远历史意义,为开展全国性的重大生态工程评估提供借鉴和参考。     

闽南渔场游泳动物优势种种群聚集特性

基于2016年4月和10月闽南渔场渔业资源的专项调查数据,运用相对性重要指数、平均拥挤度指数、聚块指数、Cassie指标、Mrisita指数等方法分析闽南渔场游泳动物优势种组成及其种群聚集特性,比较不同的季节、类群和种类及其相互间的聚集状态,探究种群聚集驱动因子,旨在发现闽南渔场游泳动物优势种种群聚集的特征、内在规律和形成机制。结果表明,闽南渔场游泳动物优势种共17种,其中鱼类6种、虾类3种、蟹类4种、头足类4种;鱼类中六指马鲅（Polydactylus se-xfilis）聚集强度最强,头足类中火枪乌贼（Loligo beka）聚集强度最强;虾类和蟹类中春季以哈氏仿对虾（Parapenaeopsis hardwickii）和拥剑梭子蟹（Portunus gladiator）的聚集强度最强,而秋季以鹰爪虾（Trachypenaeus curvirostris）和日本蟳（Charybdis japonica）的聚集强度最强;鱼类、虾类、蟹类和头足类中春季分别以二长棘犁齿鲷（Evynnis cardinali）、鹰爪虾、三疣梭子蟹（P. trituberculatus）和火枪乌贼的平均拥挤度最高,而秋季分别以带鱼（Trichiurus lepturus）、鹰爪虾、拥剑梭子蟹和杜氏枪乌贼（Loligo duvaucelii）的平均拥挤度最高;闽南渔场游泳动物优势种的平均拥挤度呈现出秋季高于春季,虾类、蟹类种群聚集强度大于鱼类、头足类的特点。