Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics

High‐throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum of phylogenetic lineages. A set of 214 mitochondrial sequences longer than 3000 bp was generated and used to estimate a well‐supported phylogenetic tree of the order Coleoptera. Shorter sequences, including cox1 barcodes, were placed on this mitogenomic tree. Raw Illumina reads were mapped against all available sequences to test for species present in local samples. This approach simultaneously established the species richness, phylogenetic composition and community turnover at species and phylogenetic levels. We find a strong signature of vertical structuring in soil fauna that shows high local community differentiation between deep soil and superficial horizons at phylogenetic levels. Within the two vertical layers, turnover among regions was primarily at the tip (species) level and was stronger in the deep soil than leaf litter communities, pointing to layer‐mediated drivers determining species diversification, spatial structure and evolutionary assembly of soil communities. This integrated phylogenetic framework opens the application of phylogenetic community ecology to the mesofauna of the soil, among the most diverse and least well‐understood ecosystems, and will propel both theoretical and applied soil science.     

生态保护区外斑块对景观连接度的影响评价

快速的城市化过程带来的生境斑块破碎化及损失会影响物种迁移、捕食等生态活动,对生物多样性构成威胁。然而,现有生态保护区可能无法覆盖其内生物的必要活动范围。生态保护区外的生境斑块对于维持生态过程也具有重要作用,因此识别生态保护区外的关键斑块并加以保护非常重要。以北京市延庆区为研究区,划分两种生境斑块,即核心生境斑块和潜在生境斑块,并基于图论构建生境网络。考虑地表覆盖类型、坡度、人类活动等因素构建生境阻力面。结合未来土地利用类型变化的模拟,研究城市化过程对区域生境网络和景观连接度的影响,选用CLUE-S模型模拟土地利用类型变化的格局。结合生境斑块特征和未来城市土地利用变化情况设计了3种未来生境变化情景。利用连接概率指数(PC)和网络连接度变化率(dI)评价不同生境变化情景下生态保护区外潜在生境斑块的景观连接度重要性,判断保护优先顺序,并分析景观格局变化对不同迁移能力物种的影响。结果表明：生态保护区外的全部潜在生境斑块对维持生境整体景观连接度有最大2.15%的影响,单个潜在生境斑块对维持景观连接度有最大0.28%的影响。此外,景观格局及其变化对不同迁移能力物种的影响差异显著,因此需针对保护物种和城市生境特征设计保护方案,研究区需要优先保护大中型斑块和位于关键位置的小型斑块。为了满足对生物多样性保护的需求,建议在区分生境斑块保护优先顺序时考虑生境斑块对景观连接度的贡献和城市化扩展过程的压力。研究为城市生物多样性保护和生境管理提供了方法参考。     

The behavioural ecology and population dynamics of a cryptic ground‐dwelling mammal in an urban Australian landscape

Urbanization results in widespread habitat loss and fragmentation and generally has a negative impact upon native wildlife, in particular ground‐dwelling mammals. The northern brown bandicoot (Isoodon macrourus; Marsupialia: Peramelidae) is one of relatively few native Australian ground‐dwelling mammals that is able to survive within urbanized landscapes. As a consequence of extensive clearing and urban development within the city of Brisbane, bandicoots are now restricted to the mostly small (<10 ha) bushland fragments scattered across the city landscape. Our study examined the behavioural ecology of northern brown bandicoots within habitat fragments located on a major creek‐line, using mark‐recapture population monitoring and radio telemetry. Bandicoots at monitored sites were found to occur at high densities (typically one individual ha^?1), although one‐third of the populations were transient. Radio tracking revealed that bandicoots had relatively small home ranges (mean 1.5 ± 0.2 ha) comprised largely of bushland/grassland with dense, often weed‐infested ground cover. Bandicoots sheltered by day in these densely covered areas and also spent most time foraging there at night, although they occasionally ventured small distances to forage in adjacent maintained parklands and residential lawns. We suggest that introduced tall grasses and other weeds contribute to high habitat quality within riparian habitat fragments and facilitate the persistence of high density populations, comprised of individuals with small home ranges. The generalized dietary and habitat requirements of northern brown bandicoots, as well as a high reproductive output, undoubtedly facilitate the survival of the species in urban habitat fragments. Further research is required on other native mammal species in urbanized landscapes to gain a greater understanding of how best to conserve wildlife in these heavily modified environments.     

Metagenome skimming for phylogenetic community ecology: a new era in biodiversity research

It is now well recognized that considering species evolutionary history is crucial for understanding the processes driving community assembly (Cavender‐Bares et al. 2009 ). Considerable efforts have been made to integrate phylogenetics and community ecology into a single theoretical framework. Yet, assessing phylogenetic structure at the community scale remains a great challenge, in particular for poorly known organisms. While DNA metabarcoding is increasingly used for assessing taxonomic composition of complex communities from environmental samples, biases and limitations of this technique can preclude the retrieval of information on phylogenetic community structure. In this issue of Molecular Ecology, Andújar et al. (2015) demonstrate that shotgun sequencing of bulk samples of soil beetles and subsequent reconstruction of mitochondrial genomes can provide a solid phylogenetic framework to estimate species diversity and gain insights into the mechanisms underlying the spatial turnover of soil mesofaunal assemblages. This work highlights the enormous potential of ‘metagenome skimming’ not only for improving the current standards of DNA‐based biodiversity assessment but also for opening up the application of phylogenetic community ecology to hyperdiverse and poorly known biota, which was heretofore inconceivable.     

城市河流的景观生态学研究:概念框架

城市河流作为城市景观中一种重要的生态廊道,其功能的正常实现与否关系到整个城市的可持续发展。通过分析当前城市河流的研究概况,发现应用景观生态学原理对城市河流展开多尺度、多学科的综合研究是实现“自然-人类-水体”可持续发展的必然趋势。从景观生态学的角度出发,结合城市河流的特点,提出了更为综合的、景观水平上的城市河流研究的概念框架。特别针对景观生态学研究的核心问题,对城市河流的研究尺度、格局分析、干扰程度等重要方面进行了详细论述,以期在景观水平上构建城市河流的可持续发展预案。     

农业景观动态对林地地表节肢动物多样性的影响

以黄河下游典型农区封丘县为研究区,在林地景观中进行地表节肢动物的观测。用物种丰富度和香农多样性指数代表物种多样性,选择代表景观背景的5个竞争模型:生境特性(H1,2012)、基质特性(H2,2012)、生境变化(H3,1984—2012)、基质变化(H4,1984—2012)和土壤-环境条件(H5,2012)从4个空间尺度上(100,250,350和500 m)进行分析,通过运用基于赤池信息量准则(Akaike information criterion,AIC)的多模型推理(Multi-model Inference,MMI)方法,在R软件里用广义线性模型(Generalized Linear Models,GLM)探究了研究区近30年(1984—2012年)景观背景变化对林地地表节肢动物多样性的影响。研究表明,不同景观背景模型对地表节肢动物多样性的影响具有尺度依赖性。在100 m的尺度下,生境特性(H1)最能够解释香农多样性和物种丰富度,但是随着尺度的增加,生境特性变化(H3)在较大(250、350 m和500 m)的尺度对物种丰富度和香农多样性影响最大,而基质特性和土壤-环境条件(H2和H5)的作用不显著。景观背景对地表节肢动物多样性的解释量达到40%。在研究区域,生境特性是表征香农多样性指数和物种丰富度的指标。     

农业景观生物多样性与害虫生态控制

现代农业的一个重要特征就是人类对农田生态系统的干扰强度及频率不断增加,严重影响农业景观的结构及其生物多样性.农业景观结构的变化及其生物多样性的丧失,必然引起生态系统服务功能的弱化,不利于实施以保护自然天敌为主的害虫生态控制.农业的集约化经营导致自然生境破碎化,减少了农业景观的复杂性,使得作物和非作物变成一种相对离散化的生境类型和镶嵌的景观格局;破碎化的生境不仅会减少某些物种的丰度,还会影响物种之间的相互关系及生物群落的多样性和稳定性.非作物生境类型如林地、灌木篱墙、田块边缘区、休耕地和草地等,是一种比较稳定的异质化环境.非作物生境较少受到干扰,可以为寄生性和捕食性节肢动物提供适宜的越冬或避难场所以及替代猎物、花粉和花蜜等资源,因此,非作物生境有利于自然天敌的栖息和繁衍,也有利于它们迁入邻近的作物生境中对害虫起到调节和控制作用.景观的格局-过程-尺度影响农田生物群落物种丰富度、多度、多样性以及害虫与天敌之间的相互作用.从区域农业景观系统的角度出发,运用景观生态学的理论和方法来研究作物、害虫、天敌等组分在不同斑块之间的转移过程和变化规律,揭示害虫在较大尺度和具有异质性的空间范围内的灾变机理,可为利用农业景观生物多样性来保护农田自然天敌,实施害虫的区域性生态控制提供新的研究思路和手段.     

The integration of biodiversity and climate change: A contextual assessment of the carbon farming initiative

Summary The Carbon Farming Initiative (CFI) allows the creation of tradable Australian Carbon Credit Units (ACCUs) derived from across the ecosystem sector via project‐level baseline and credit activities: it is the first national offset scheme in the world to broadly include farming and forestry projects. Because these activities have the potential to produce both biodiversity and climate change benefits, a crucial outcome is for widespread uptake of the policy. However, the design, complexity and cost of the CFI project development process, and low prices as a result of ACCUs trading in the voluntary market, will all likely militate against this. This article shows how international politics and policy surrounding the Kyoto Protocol have influenced the design of the CFI, with its potential to proliferate complex and narrow methodologies and counter‐productive approaches to integrity standards such as permanence. The article shows that despite the pressing need to integrate biodiversity and climate change considerations as equally important challenges, their global integration remains poorly articulated. Biodiversity considerations are also not integrated into the CFI but, rather, are dealt with indirectly through safeguard measures that avoid perverse incentives and unintended harm, and as an optional co‐benefit via the development of an index. This article suggests that we need to move past the shackles of Kyoto towards streamlined and standardized approaches such as risk‐based assessments and the use of regional baselines. Using regionally specific baselines such as for avoided deforestation would allow landholders to opt‐in to regional‐scale mitigation opportunities. Activities that Australia accounts for, such as reforestation and deforestation, should also be able to opt‐in for coverage under the Clean Energy Act (and out of the voluntary carbon market) to obtain a secure price.     

Investigating the distribution of prairie dogs in an urban landscape

Habitat fragmentation is a prevalent threat to biological diversity, and urbanization is a primary agent of fragmentation and a leading cause of species endangerment. Landscape biogeographic and local habitat characteristics can be important determinants of the distribution of species in habitat patches in urban landscapes. However, the specifics of which characteristics are most critical to maintaining biological diversity are not fully known for prairie ecosystems, especially in fragmented urban habitat. This study focuses on black-tailed prairie dogs along an urban gradient in Denver, CO. Prairie dogs have declined precipitously throughout the region and are an essential part of the prairie ecosystem, making them excellent study subjects. We identified a series of habitat fragments along a gradient of urbanization in the fully urbanized areas and south suburbs of Denver, CO, both containing and not containing prairie dogs. Local characteristics, including fragment slope and vegetative cover, and landscape characteristics, including fragment size, age and connectivity, were measured on each fragment. We used likelihood-based methods to explore which variables most accurately predicted prairie dog occurrence within our study area. Multiple factors influenced the distribution of prairie dogs in urban settings, with colony connectivity the strongest predictor of occupancy. Large and recently isolated fragments near other prairie dog colonies, flat areas and those with high graminoid cover were most likely to support prairie dog populations. Our study provides the first attempt to model prairie dog occurrence in highly fragmented urban habitat and has important implications for the management and conservation of prairie dogs.     

Diversification in a biodiversity hot spot: landscape correlates of phylogeographic patterns in the African spotted reed frog

The Eastern Afromontane Biodiversity Hotspot is known for microendemism and exceptional population genetic structure. The region's landscape heterogeneity is thought to limit gene flow between fragmented populations and create opportunities for regional adaptation, but the processes involved are poorly understood. Using a combination of phylogeographic analyses and circuit theory, I investigate how characteristics of landscape heterogeneity including regional distributions of slope, rivers and streams, habitat and hydrological basins (drainages) impact genetic distance among populations of the endemic spotted reed frog (Hyperolius substriatus), identifying corridors of connectivity as well as barriers to dispersal. Results show that genetic distance among populations is most strongly correlated to regional and local hydrologic structure and the distribution of suitable habitat corridors, not isolation by distance. Contrary to expectations, phylogeographic structure is not coincident with the two montane systems, but instead corresponds to the split between the region's two major hydrological basins (Zambezi and East Central Coastal). This results in a paraphyletic relationship for the Malawian Highlands populations with respect to the Eastern Arc Mountains and implies that the northern Malawian Highlands are the diversity centre for H. substriatus. Although the Malawian Highlands collectively hold the greatest genetic diversity, individual populations have lower diversity than their Eastern Arc counterparts, with an overall pattern of decreasing population diversity from north to south. Through the study of intraspecific differentiation across a mosaic of ecosystem and geographic heterogeneity, we gain insight into the processes of diversification and a broader understanding of the role of landscape in evolution.     

An estimate of potential threats levels to soil biodiversity in EU

Life within the soil is vital for maintaining life on Earth due to the numerous ecosystem services that it provides. However, there is evidence that pressures on the soil biota are increasing which may undermine some of these ecosystem services. Current levels of belowground biodiversity are relatively poorly known, and so no benchmark exists by which to measure possible future losses of biodiversity. Furthermore, the relative risk that each type of anthropogenic pressures places on the soil biota remains unclear. Potential threats to soil biodiversity were calculated through the use of a composite score produced from data collected from 20 international experts using the budget allocation methodology. This allowed relative weightings to be given to each of the identified pressures for which data were available in the European Soil Data Centre (ESDC). A total of seven different indicators were used for calculating the composite scores. These data were applied through a model using ArcGIS to produce a spatial analysis of composite pressures on soil biodiversity at the European scale. The model highlights the variation in the composite result of the potential threats to soil biodiversity. A sensitivity analysis demonstrated that the intensity of land exploitation, both in terms of agriculture and use intensity, as well as in terms of land‐use dynamics, were the main factors applying pressure on soil biodiversity. It is important to note that the model should not be viewed as an estimate of the current level of soil biodiversity in Europe, but as an estimate of pressures that are currently being exerted. The results obtained should be seen as a starting point for further investigation on this relatively unknown issue and demonstrate the utility of this type of model which may be applied to other regions and scales.     

The effect of terrain and female density on survival of neonatal white‐tailed deer and mule deer fawns

Juvenile survival is a highly variable life‐history trait that is critical to population growth. Antipredator tactics, including an animal's use of its physical and social environment, are critical to juvenile survival. Here, we tested the hypothesis that habitat and social characteristics influence coyote (Canis latrans) predation on white‐tailed deer (Odocoileus virginianus) and mule deer (O. hemionus) fawns in similar ways during the neonatal period. This would contrast to winter when the habitat and social characteristics that provide the most safety for each species differ. We monitored seven cohorts of white‐tailed deer and mule deer fawns at a grassland study site in Alberta, Canada. We used logistic regression and a model selection procedure to determine how habitat characteristics, climatic conditions, and female density influenced fawn survival during the first 8 weeks of life. Fawn survival improved after springs with productive vegetation (high integrated Normalized Difference Vegetation Index values). Fawns that used steeper terrain were more likely to survive. Fawns of both species had improved survival in years with higher densities of mule deer females, but not with higher densities of white‐tailed deer females, as predicted if they benefit from protection by mule deer. Our results suggest that topographical variation is a critical resource for neonates of many ungulate species, even species like white‐tailed deer that use more gentle terrain when older. Further, our results raise the possibility that neonatal white‐tailed fawns may benefit from associating with mule deer females, which may contribute to the expansion of white‐tailed deer into areas occupied by mule deer.     

A spatial genomic approach identifies time lags and historical barriers to gene flow in a rapidly fragmenting Appalachian landscape

The resolution offered by genomic data sets coupled with recently developed spatially informed analyses are allowing researchers to quantify population structure at increasingly fine temporal and spatial scales. However, both empirical research and conservation measures have been limited by questions regarding the impacts of data set size, data quality thresholds and the timescale at which barriers to gene flow become detectable. Here, we used restriction site associated DNA sequencing to generate a 2,140 single nucleotide polymorphism (SNP) data set for the copperhead snake (Agkistrodon contortrix) and address the population genomic impacts of recent and widespread landscape modification across an ~1,000‐km² region of eastern Kentucky, USA. Nonspatial population‐based assignment and clustering methods supported little to no population structure. However, using individual‐based spatial autocorrelation approaches we found evidence for genetic structuring which closely follows the path of a historically important highway which experienced high traffic volumes from c. 1920 to 1970 before losing most traffic to a newly constructed alternative route. We found no similar spatial genomic signatures associated with more recently constructed highways or surface mining activity, although a time lag effect may be responsible for the lack of any emergent spatial genetic patterns. Subsampling of our SNP data set suggested that similar results could be obtained with as few as 250 SNPs, and a range of thresholds for missing data exhibited limited impacts on the spatial patterns we detected. While we were not able to estimate relative effects of land uses or precise time lags, our findings highlight the importance of temporal factors in landscape genetics approaches, and suggest the potential advantages of genomic data sets and fine‐scale, spatially informed approaches for quantifying subtle genetic patterns in temporally complex landscapes.     

Climate and geochemistry as drivers of eucalypt diversification in Australia

Eucalypts cover most of Australia. Here, we investigate the relative contribution of climate and geochemistry to the distribution and diversity of eucalypts. Using geostatistics, we estimate major element concentrations, pH, and electrical conductivity at sites where eucalypts have been recorded. We compare the median predicted geochemistry and reported substrate for individual species that appear associated with extreme conditions; this provides a partial evaluation of the predictions. We generate a site‐by‐species matrix by aggregating observations to the centroids of 100‐km‐wide grid cells, calculate diversity indices, and use numerical ecology methods (ordination, variation partitioning) to investigate the ecology of eucalypts and their response to climatic and geochemical gradients. We find that β‐diversity coincides with variations in climatic and geochemical patterns. Climate and geochemistry together account for less than half of the variation in eucalypt species assemblages across Australia but for greater than 80% in areas of high species richness. Climate is more important than geochemistry in explaining eucalypts species distribution and change in assemblages across Australia as a whole but there are correlations between the two sets of environmental variables. Many individual eucalypt species and entire taxonomic sections (Aromatica, Longistylus of subgenus Eucalyptus, Dumaria, and Liberivalvae of subgenus Symphyomyrtus) have distributions affected strongly by geochemistry. We conclude that eucalypt diversity is driven by steep geochemical gradients that have arisen as climate patterns have fluctuated over Australia over the Cenozoic, generally aridifying since the Miocene. The diversification of eucalypts across Australia is thus an excellent example of co‐evolution of landscapes and biota in space and time and challenges accepted notions of macroecology.     

Warming experiments elucidate the drivers of observed directional changes in tundra vegetation

Few studies have clearly linked long‐term monitoring with in situ experiments to clarify potential drivers of observed change at a given site. This is especially necessary when findings from a site are applied to a much broader geographic area. Here, we document vegetation change at Barrow and Atqasuk, Alaska, occurring naturally and due to experimental warming over nearly two decades. An examination of plant cover, canopy height, and community indices showed more significant differences between years than due to experimental warming. However, changes with warming were more consistent than changes between years and were cumulative in many cases. Most cases of directional change observed in the control plots over time corresponded with a directional change in response to experimental warming. These included increases in canopy height and decreases in lichen cover. Experimental warming resulted in additional increases in evergreen shrub cover and decreases in diversity and bryophyte cover. This study suggests that the directional changes occurring at the sites are primarily due to warming and indicates that further changes are likely in the next two decades if the regional warming trend continues. These findings provide an example of the utility of coupling in situ experiments with long‐term monitoring to accurately document vegetation change in response to global change and to identify the underlying mechanisms driving observed changes.