Words apart:Standardizing forestry terms and definitions across European biodiversity studies

Forest biodiversity studies conducted across Europe use a multitude of forestry terms,often inconsistently.This hinders the comparability across studies and makes the assessment of the impacts of forest management on biodiversity highly context-dependent.Recent attempts to standardize forestry and stand description terminology mostly used a top-down approach that did not account for the perspectives and approaches of forest biodiversity experts.This work aims to establish common standards for silvicultural and vegetation definitions,creating a shared conceptual framework for a consistent study on the effects of forest management on biodiversity.We have identified both strengths and weaknesses of the silvicultural and vegetation information provided in forest biodiversity studies.While quantitative data on forest biomass and dominant tree species are frequently included,information on silvicultural activities and vegetation composition is often lacking,shallow,or based on broad and heterogeneous classifications.We discuss the existing classifications and their use in European forest biodiversity studies through a novel bottom-up and top-driven review process,and ultimately propose a common framework.This will enhance the comparability of forest biodiversity studies in Europe,and puts the basis for effective implementation and monitoring of sustainable forest management policies.The standards here proposed are potentially adaptable and applicable to other geographical areas and could be extended to other forest interventions.

Tropical forest canopies and their relationships with climate and disturbance： results from a global dataset of consistent field-based measurements

Background： Canopy structure, defined by leaf area index （LAI）, fractional vegetation cover （FCover） and fraction of absorbed photosynthetically active radiation （fAPAR）, regulates a wide range of forest functions and ecosystem services. Spatially consistent field-measurements of canopy structure are however lacking, particularly for the tropics. Methods： Here, we introduce the Global LAI database： a global dataset of field-based canopy structure measurements spanning tropical forests in four continents （Africa, Asia, Australia and the Americas）. We use these measurements to test for climate dependencies within and across continents, and to test for the potential of anthropogenic disturbance and forest protection to modulate those dependences. Results： Using data collected from 887 tropical forest plots, we show that maximum water deficit, defined across the most arid months of the year, is an important predictor of canopy structure, with all three canopy attributes declining significantly with increasing water deficit. Canopy attributes also increase with minimum temperature, and with the protection of forests according to both active （within protected areas） and passive measures （through topography）. Once protection and continent effects are accounted for, other anthropogenic measures （e.g. human population） do not improve the model. Conclusions： We conclude that canopy structure in the tropics is primarily a consequence of forest adaptation to the maximum water deficits historically experienced within a given region. Climate change, and in particular changes in drought regimes may thus affect forest structure and function, but forest protection may offer some resilience against this effect.

Non-breeding movements of the Black-tailed Gull(Larus crassirostris)

With the continued development of tracking technology and increasing interest in animal movement,our understanding of migration behavior has become more comprehensive.However,there are still many species that have not been well studied,particularly sea birds.Here,we present the first year-round Global Positioning System(GPS)tracking data of the Black-tailed Gull(Larus crassirostris)at the population level.We used solar-powered GPS-Global System for Mobile communication(GSM)loggers to successfully track 30 individuals breeding at Xingrentuo Islet,Liaoning Province,China,for 1-3 years.Except for one individual who roamed in the far north of the Yellow Sea during non-breeding period,all others did a directed southward migration.Migration routes and wintering sites differed among migrating gulls and between years for the birds tracked for two or more years.Additionally,during wintering,the migrating gulls were more likely to travel over a large body of water and shift sites,and some trajectories were quite complex,which was probably closely related to what we observed in the field about their boat-chasing behavior.Compared to wintering movements,the post-breeding movements ranged over a smaller area.Specifically,almost all of them had a long post-breeding period near the breeding islet(≥120days,<220 km from the breeding islet),and 80%of the gulls who were tracked more than one year had at least one faithful post-breeding site.Compared to the post-breeding period,only approximately half of the migrating gulls had a pre-breeding period that was shorter(3-20 days)and closer to the breeding islet(≤80 km).Migration distance varied among migrating gulls(range 209-2405 km)and the gulls moved least distance during postbreeding period.Furthermore,we found that the southward movement of the migrating gulls occurred when the temperature near the breeding islet dropped;specifically,the gulls directly migrated southward away from the post-breeding site.Our results suggest that the Black-tailed Gull has a long post-breeding period but a short prebreeding period near the breeding islet and high diversity of their migrating patterns(in especial migration routes and wintering sites).

Restoration of a Temperate Reef:Effects on the Fish Community

The extraction of large boulders from coastal reefs for construction of harbours and coastal protection has led to habitat degradation for local fish populations through the destruction of cavernous reefs and changes in macroalgal cover resulting from a loss of substrate. The temperate reef at L?s? Trindel in Kattegat, Denmark, has now been re-established with the aim of restoring the reef’s historical structure and function. The effects of the restoration on the local fish community are reported here. Fishing surveys using gillnets and fyke nets were conducted before the restoration (2007) and four years after the restoration of the reef (2012). Species of the family Labridae, which have a high affinity for rocky reefs, dominated both before and after the restoration. Commercially important species such as cod Gadus morhua, and saithe Pollachius virens, occurred infrequently in the catches in 2007 but were significantly more abundant in the catches in 2012. Cods were especially attracted to the shallow part of the reef that was restored by adding stones. For some species, such as ballan wrasse Labrus bergylta, and cod, the proportion of larger individuals increased after the restoration. The findings highlight the importance of reef habitats for fish communities and the need for their protection.

The Global Soil Mycobiome consortium dataset for boosting fungal diversity research

Fungi are highly important biotic components of terrestrial ecosystems,but we still have a very limited understanding about their diversity and distribution.This data article releases a global soil fungal dataset of the Global Soil Mycobiome consortium(GSMc)to boost further research in fungal diversity,biogeography and macroecology.The dataset comprises 722,682 fungal operational taxonomic units(OTUs)derived from PacBio sequencing of full-length ITS and 18S-V9 variable regions from 3200 plots in 108 countries on all continents.The plots are supplied with geographical and edaphic metadata.The OTUs are taxonomically and functionally assigned to guilds and other functional groups.The entire dataset has been corrected by excluding chimeras,index-switch artefacts and potential contamination.The dataset is more inclusive in terms of geographical breadth and phylogenetic diversity of fungi than previously published data.The GSMc dataset is available over the PlutoF repository.

批量下载GenBank基因序列数据的新工具--NCBIminer

核苷酸序列是生物体遗传信息的载体,是现代生物学和生态学的基础数据。随着测序技术的进步,大量核苷酸序列被提取并存储在公共数据平台中,其中Gen Bank(http://www.ncbi.nlm.nih.gov/genbank/)是目前最大的核苷酸序列数据平台之一。截至2015年2月,该平台收录核苷酸序列总数已超过1.8亿条、覆盖全球超过30万个物种。但如何从如此海量的数据中准确、快速查找并下载所需数据已成为限制基因数据广泛使用的障碍之一。为此,我们开发了一款可高效、准确下载Gen Bank数据的生物信息学软件NCBIminer。NCBIminer可根据用户提供的核苷酸序列名称、数据类型、一或多条初始化参考序列,查找并下载用户指定的多个物种或类群的特定基因序列数据。该软件下载地址为https://github.com/greengirl/NCBIminer/releases/,可在Windows、Linux和MAC操作系统下免费使用;同时,其操作简单,用户无需生物信息学背景。为方便该软件的使用,本文将介绍该软件的工作流程与算法、安装及使用过程中的参数设置等。

Protecting endemic seed plants on the Tibetan Plateau under future climate change: migration matters

Aims Climate change in the near future may become a major threat to high-altitude endemics by greatly altering their distribution.Our aims are to(i)assess the potential impacts of future climate change on the diversity and distribution of seed plants endemic to the Tibetan Plateau and(ii)evaluate the conservation effectiveness of the current National Nature Reserves(NNRs)in protecting the endemic plants in the face of climate change.Methods We projected range shifts of 993 endemic species to the years 2050 and 2070 under two representative concentration pathway scenarios using an ensemble species distribution modeling framework and evaluated range loss,species-richness change and coverage of the current conservation network considering two dispersal scenarios.Important Findings In a full-dispersal scenario,72–81%of the species would expand their distribution by 2070,but 6–20%of the species would experience>30%range loss.Most species would shift to the west.The projected species net richness would increase across the region on average.In a no-dispersal scenario,15–59%of the species would lose>30%of their current habitat by 2070.Severe species loss may occur in the southeastern and the eastern peripheral plateau.Seventeen percent of species ranges are covered by the NNRs on average and may increase in the future if species disperse freely.We found a significant difference of species redistribution patterns between different dispersal scenarios and highlighted the importance of migration in this region.

Variation in the methods leads to variation in the interpretation of biodiversity-ecosystem multifunctionality relationships

生物多样性常常和生态系统多功能性(生态系统同时提供多个生态系统功能的能力)正相关。然而,生物多样性与生态系统多功能性的关系是否依赖于生态系统功能的数目有诸多争议。其中,生物多样性对生态系统多功能性的影响或许不随生态系统功能数目的变化而变化,或者随生态系统功能数目的增多而增强。我们期望通过研究不同生态系统多功能性指数的统计原理来解决这些争议。我们使用了模型模拟和一系列来自不同空间尺度(从局域到全球)和不同生物群系(温带和高寒草地、森林和干旱地)的经验数据。我们回顾了量化生态系统多功能性的三种方法,包括平均值法、加和法和阈值法。我们发现随着生态系统功能数目的增加,生物多样性与生态系统多功能性的关系要么不变,要么增强。这些结果可由平均和加和的多功能性指数的统计原理来解释。具体来讲,当利用生态系统功能的平均值计算多功能性指数时,由于多样性对多功能性的效应等于多样性对单个生态系统功能效应的平均值,所以不会随生态系统功能数目的变化而变化。同样的道理,当利用单个生态系统的加和值计算多功能性指数时,多样性的效应会随着生态系统功能数目的增加而增强。我们提出了一个改进的多功能性指数,将平均或加和多功能性指数转化为标准化的多功能性指数,以便于对不同研究的结果进行比较。此外,我们提出了基于变量数值范围的标准化方法来解决阈值法的数学假象问题(多样性效应随生态系统功能数目的增加而增强)。我们的研究结果表明,量化多功能性指数的方法不同,结果也不同。因此,有必要加深对不同方法数理基础的理解。而标准化的多功能性指数为比较不同研究中的生物多样性与生态系统多功能性的关系提供了有效的方法。

Aboveground resilience to species loss but belowground resistance to nitrogen addition in a montane plant community

Aims Decades of empirical work have demonstrated how dominant plant species and nitrogen fertilization can influence the structure and function of plant communities.More recent studies have examined the interplay between these factors,but few such studies use an explicit trait-based framework.In this study,we use an explicit trait-based approach to identify potential mechanisms for community-level responses and to test ecological niche theory.Methods We experimentally manipulated plant communities(control,−dom-inant species,−random biomass)and nitrogen(N)inputs(control,+organic N,+inorganic N)in a fully factorial design.We predicted that traits related to plants’ability to take up different forms of soil N would differ between dominant and subordinate species,resulting in interactive effects of dominant species loss and N fertilization on plant community structure and function.The study took place in a montane meadow in the Rocky Mountains,Colorado,USA.Important Findings After four years,the plant community in removal plots converged toward a species composition whose leaf and root functional traits resembled those of the previously removed dominant species.Ecosystem productivity generally increased with N addition:soil carbon efflux was~50%greater when either form of N was added,while inorganic N addition increased aboveground biomass pro-duction by~60%relative to controls.The increase in production was mediated by increased average height,leaf mass:area ratio and leaf dry matter content in plant communities to which we added inorganic N.Contrary to our predictions,there were no interactive effects of N fertilization and dominant species loss on plant com-munity structure or ecosystem function.The plant community com-position in this study exhibited resistance to soil N addition and,given the functional convergence we observed,was resilient to spe-cies loss.Together,our results indicate that the ability of species to compensate functionally for species loss confers resilience and maintains diversity in montane meadow communities.