Meta-Fish-Lib: A generalised,dynamic DNA reference library pipeline for metabarcoding of fishes

The accuracy and reliability of DNA metabarcoding analyses depend on the breadth and quality of the reference libraries that underpin them. However, there are limited options available to obtain and curate the huge volumes of sequence data that are available on public repositories such as NCBI and BOLD. Here, we provide a pipeline to download, clean and annotate mitochondrial DNA sequence data for a given list of fish species. Features of this pipeline include (a) support for multiple metabarcode markers; (b) searches on species synonyms and taxonomic name validation; (c) phylogeny assisted quality control for identification and removal of misannotated sequences; (d) automatically generated coverage reports for each new GenBank release update; and (e) citable, versioned DOIs. As an example we provide a ready-to-use curated reference library for the marine and freshwater fishes of the U.K. To augment this reference library for environmental DNA metabarcoding specifically, we generated 241 new MiFish-12S sequences for 88 U.K. marine species, and make available new primer sets useful for sequencing these. This brings the coverage of common U.K. species for the MiFish-12S fragment to 93%, opening new avenues for scaling up fish metabarcoding across wide spatial gradients. The Meta-Fish-Lib reference library and pipeline is hosted at https://github.com/genner-lab/meta-fish-lib .     

Physical enrichment research for captive fish: Time to focus on the DETAILS

Growing research effort has shown that physical enrichment (PE) can improve fish welfare and research validity. However, the inclusion of PE does not always result in positive effects and conflicting findings have highlighted the many nuances involved. Effects are known to depend on species and life stage tested, but effects may also vary with differences in the specific items used as enrichment between and within studies. Reporting fine-scale characteristics of items used as enrichment in studies may help to reveal these factors. We conducted a survey of PE-focused studies published in the last 5 years to examine the current state of methodological reporting. The survey results suggest that some aspects of enrichment are not adequately detailed. For example, the amount and dimensions of objects used as enrichment were frequently omitted. Similarly, the ecological relevance, or other justification, for enrichment items was frequently not made explicit. Focusing on ecologically relevant aspects of PE and increasing the level of detail reported in studies may benefit future work and we propose a framework with the acronym DETAILS ( D imensions, E cological rationale, T iming of enrichment, A mount, I nputs, L ighting and S ocial environment). We outline the potential importance of each of the elements of this framework with the hope it may aid in the level of reporting and standardization across studies, ultimately aiding the search for more beneficial types of PE and the development of our understanding and ability to improve the welfare of captive fish and promote more biologically relevant behaviour.     

陆地生态系统环境控制实验的研究方法及技术体系

生物及生态系统与环境变化间的反馈关系及其过程机制是生态学研究的重要内容。不同类型的生物环境因素控制实验以及大尺度的联网野外控制实验被认为是认识生态系统响应和适应环境变化过程机制、精细定量表达的有效手段及认知过程的加速器。近年来发展了大型野外物理模拟实验装置网络(如ECOTRON)、生态系统分析与实验平台(AnaEE)、国际干旱实验研究网络(Drought Network)、氮沉降联合实验网络(Nutrient Network),以及基于各区域性生态观测实验站的联网控制实验(如USA-ILTER)。发展大陆尺度联网实验研究平台事业正日益受到学术界的重视,将会在认知生态系统环境响应过程机制方面发挥更重要的作用。基于以上背景,本文综述了生态系统环境控制实验的研究方法和实验体系的发展,明确指出各种类型的生物环境控制实验需要形成联合协作体系,共同解决生态系统对环境变化的响应及适应的基本科学问题。目前的控制实验包括: 1) 实验室封闭装置内的生物生理生态学控制实验;2) 野外实验场的半开放部分环境要素控制实验;3) 近自然状态的野外环境控制实验;以及4) 基于野外生态站的联网控制实验。进而,本文还深入讨论了陆地生态系统的环境响应及适应过程机制实验系统设计的发展趋势,分析了基于大尺度自然环境梯度实验及生态站尺度的要素控制实验的优势,提出了整合两种实验技术、发展新一代的野外联网实验体系的科学设想,讨论了基于野外联网控制实验的研究体系,论证了研究生态系统对环境变化短期响应和长期适应的规律和机制、生态系统环境响应定量表达的技术途径。若本文提出的控制实验体系设计方案能够得以实施,必将大大促进我国乃至全球生态系统和环境变化科学的研究水平,对我国应对气候变化和生态环境建设具有重要的科学意义。     

Differences between species in seed bank and vegetation helps to hold functional diversity in a floodable Neotropical savanna

种子库和植被物种之间的差异有助于保持新热带稀树草原的功能多样性 本研究的目的是量化种子库和建立的植被对物种组成、功能组成和多样性的贡献,并讨论这些差异对冲积平原植物群落更新和稳定性的影响。我们在巴西潘塔纳尔湿地的一个周期性洪水泛滥的稀树大草原上,在旱季和雨季对分布在5个地点的25个地块(10 m × 1 m)的1.5 m高度的地面覆盖植被和种子库进行了采样。采用出苗法对土壤种子库进行了评价。研究结果表明,种子库物种具有赋予群落更新的特征,而植被则具有稳定性特征。种子库的功能丰富度高于植被,而功能均匀度则低于植被。由于种子库和植被的植物特征不同,使得具有不同功能稳定性和更新特性的物种得以共存,这将有助于维持植物的功能多样性。这可能会让植物种群在应对干旱、火灾和洪水等不同的环境选择时更具有弹性。     

Eco-evolutionary consequences of habitat warming and fragmentation in communities

Eco-evolutionary dynamics can mediate species and community responses to habitat warming and fragmentation, two of the largest threats to biodiversity and ecosystems. The eco-evolutionary consequences of warming and fragmentation are typically studied independently, hindering our understanding of their simultaneous impacts. Here, we provide a new perspective rooted in trade-offs among traits for understanding their eco-evolutionary consequences. On the one hand, temperature influences traits related to metabolism, such as resource acquisition and activity levels. Such traits are also likely to have trade-offs with other energetically costly traits, like antipredator defences or dispersal. On the other hand, fragmentation can influence a variety of traits (e.g. dispersal) through its effects on the spatial environment experienced by individuals, as well as properties of populations, such as genetic structure. The combined effects of warming and fragmentation on communities should thus reflect their collective impact on traits of individuals and populations, as well as trade-offs at multiple trophic levels, leading to unexpected dynamics when effects are not additive and when evolutionary responses modulate them. Here, we provide a road map to navigate this complexity. First, we review single-species responses to warming and fragmentation. Second, we focus on consumer–resource interactions, considering how eco-evolutionary dynamics can arise in response to warming, fragmentation, and their interaction. Third, we illustrate our perspective with several example scenarios in which trait trade-offs could result in significant eco-evolutionary dynamics. Specifically, we consider the possible eco-evolutionary consequences of (i) evolution in thermal performance of a species involved in a consumer–resource interaction, (ii) ecological or evolutionary changes to encounter and attack rates of consumers, and (iii) changes to top consumer body size in tri-trophic food chains. In these scenarios, we present a number of novel, sometimes counter-intuitive, potential outcomes. Some of these expectations contrast with those solely based on ecological dynamics, for example, evolutionary responses in unexpected directions for resource species or unanticipated population declines in top consumers. Finally, we identify several unanswered questions about the conditions most likely to yield strong eco-evolutionary dynamics, how better to incorporate the role of trade-offs among traits, and the role of eco-evolutionary dynamics in governing responses to warming in fragmented communities.     

青藏高原不同高寒草地类型土壤酶活性及其影响因子

土壤酶活性作为生态系统养分循环的关键因素, 是反映土壤质量和生态系统功能的重要指标, 但是关于高寒草地生态系统中不同草地类型间酶活性的差异研究还很少。因此, 该研究在藏北高寒草地选择高寒草甸、高寒草原、高寒草甸草原、高寒荒漠草原和高寒荒漠5种草地类型进行野外原位调查和采样, 测定了涉及碳(C)、氮(N)和磷(P)循环的14种酶的活性, 并建立了高寒草地酶活性与土壤微生物和土壤理化性质等环境因子的关系。结果表明: C循环酶(蔗糖酶、纤维素酶、β-葡萄糖苷酶、多酚氧化酶和过氧化物酶)和P循环酶(碱性磷酸酶)在不同高寒草地类型间活性差异明显, N循环酶中仅芳香氨基酶和亚硝酸盐还原酶两种酶在不同高寒草地类型间活性差异明显。同时, C、N和P循环酶之间存在一定的相关关系, 其中, 蔗糖酶和碱性磷酸酶、纤维素酶和α-乙酰氨基葡萄糖苷酶活性显著正相关, 多酚氧化酶与亚硝酸还原酶和β-乙酰氨基葡萄糖苷酶活性显著负相关。在测定的19个环境指标中, 土壤有机质(SOM)含量、革兰氏阴性菌数量、土壤N和P含量计量比、革兰氏阳性菌数量、细菌数量、放线菌数量、全氮含量、真菌数量是影响土壤酶活性的关键因子, 且SOM含量的影响最大(解释量为11.9%)。综上所述, 不同高寒草地类型间C循环酶、P循环酶和两种N循环酶(芳香氨基酶和亚硝酸还原酶)活性差异显著, SOM含量、微生物数量和N含量等是影响高寒草地生态系统土壤酶活性的关键因子。     

环境因子对海南岛野生兰科植物物种组成与分布格局的影响

海南岛是中国兰科植物物种丰富度较高的地区, 了解环境因子对海南岛野生兰科植物物种组成和分布格局的影响, 对于该地区野生兰科植物的保护管理和相关研究具有重要指导意义。基于海南岛野生兰科植物调查分布样方的植被类型、海拔、坡向、坡度、年平均气温、年降水量的数据, 采用典范相关分析探索了环境因子对物种组成的影响, 并计算各个环境因子对物种组成的总效应与净效应, 同时分析了6个环境因子对野生兰科植物分布格局的影响。结果表明, 所选的6个环境因子共解释了海南岛野生兰科植物组成变异的3.7%; 植被类型、海拔、年平均气温、年降水量、坡向、坡度这6个环境因子的总效应与净效应均达显著水平, 但其解释率依次减小。所选的6个环境因子对海南岛野生兰科植物的分布均有影响, 野生兰科植物在海南岛主要分布在中海拔段、5°-35°的坡度范围、阴坡与半阴坡、年平均气温较低且年降水量较高的环境, 并且于原生植被中分布最多。     

Modeling the circular economy in environmentally extended input–output: A web application

Global environmental and resource problems ask for new ways of managing the production and consumption of resources. The implementation of new paradigms, such as the circular economy, requires decision‐makers at multiple levels to make complex decisions. For this, clear analyses and modeling of scenarios are of utmost importance. Meanwhile, as the sophistication of databases and models increases so does the need for user‐friendly tools to use them. The RaMa‐Scene web platform reduces these barriers by allowing users to visualize easily diverse impacts of implementing circular‐economy interventions. This online web platform makes use of the multi‐regional environmentally extended input–output database EXIOBASE version 3 in monetary units, which has been modified to show explicit transactions of raw materials from recycling activities.     

Desiccation limits recruitment in the pleometrotic desert seed‐harvester ant Veromessor pergandei

The desert harvester ant Veromessor pergandei displays geographic variation in colony founding with queens initiating nests singly (haplometrosis) or in groups (pleometrosis). The transition from haplo‐ to pleometrotic founding is associated with lower rainfall. Numerous hypotheses have been proposed to explain the evolution of cooperative founding in this species, but the ultimate explanation remains unanswered. In laboratory experiments, water level was positively associated with survival, condition, and brood production by single queens. Queen survival also was positively influenced by water level and queen number in a two‐factor experiment. Water level also was a significant effect for three measures of queen condition, but queen number was not significant for any measure. Foundress queens excavated after two weeks of desiccating conditions were dehydrated compared to alate queens captured from their natal colony, indicating that desiccation can be a source of queen mortality. Long‐term monitoring in central Arizona, USA, documented that recruitment only occurred in four of 20 years. A discriminant analysis using rainfall as a predictor of recruitment correctly predicted recruitment in 17 of 20 years for total rainfall from January to June (the period for mating flights and establishment) and in 19 of 20 years for early plus late rainfall (January–March and April–June, respectively), often with a posterior probability > 0.90. Moreover, recruitment occurred only in years in which both early and late rainfall exceeded the long‐term mean. This result also was supported by the discriminant analysis predicting no recruitment when long‐term mean early and late rainfall were included as ungrouped periods. These data suggest that pleometrosis in V. pergandei evolved to enhance colony survival in areas with harsh abiotic (desiccating) conditions, facilitating colonization of habitats in which solitary queens could not establish even in wet years. This favorable‐year hypothesis supports enhanced worker production as the primary advantage of pleometrosis.