Using Boreholes as Windows into Groundwater Ecosystems

Groundwater ecosystems remain poorly understood yet may provide ecosystem services, make a unique contribution to biodiversity and contain useful bio-indicators of water quality. Little is known about ecosystem variability, the distribution of invertebrates within aquifers, or how representative boreholes are of aquifers. We addressed these issues using borehole imaging and single borehole dilution tests to identify three potential aquifer habitats (fractures, fissures or conduits) intercepted by two Chalk boreholes at different depths beneath the surface (34 to 98 m). These habitats were characterised by sampling the invertebrates, microbiology and hydrochemistry using a packer system to isolate them. Samples were taken with progressively increasing pumped volume to assess differences between borehole and aquifer communities. The study provides a new conceptual framework to infer the origin of water, invertebrates and microbes sampled from boreholes. It demonstrates that pumping 5 m³ at 0.4–1.8 l/sec was sufficient to entrain invertebrates from five to tens of metres into the aquifer during these packer tests. Invertebrates and bacteria were more abundant in the boreholes than in the aquifer, with associated water chemistry variations indicating that boreholes act as sites of enhanced biogeochemical cycling. There was some variability in invertebrate abundance and bacterial community structure between habitats, indicating ecological heterogeneity within the aquifer. However, invertebrates were captured in all aquifer samples, and bacterial abundance, major ion chemistry and dissolved oxygen remained similar. Therefore the study demonstrates that in the Chalk, ecosystems comprising bacteria and invertebrates extend from around the water table to 70 m below it. Hydrogeological techniques provide excellent scope for tackling outstanding questions in groundwater ecology, provided an appropriate conceptual hydrogeological understanding is applied.     

Optimized Spatial Priorities for Biodiversity Conservation in China: A Systematic Conservation Planning Perspective

By addressing several key features overlooked in previous studies, i.e. human disturbance, integration of ecosystem- and species-level conservation features, and principles of complementarity and representativeness, we present the first national-scale systematic conservation planning for China to determine the optimized spatial priorities for biodiversity conservation. We compiled a spatial database on the distributions of ecosystem- and species-level conservation features, and modeled a human disturbance index (HDI) by aggregating information using several socioeconomic proxies. We ran Marxan with two scenarios (HDI-ignored and HDI-considered) to investigate the effects of human disturbance, and explored the geographic patterns of the optimized spatial conservation priorities. Compared to when HDI was ignored, the HDI-considered scenario resulted in (1) a marked reduction (∼9%) in the total HDI score and a slight increase (∼7%) in the total area of the portfolio of priority units, (2) a significant increase (∼43%) in the total irreplaceable area and (3) more irreplaceable units being identified in almost all environmental zones and highly-disturbed provinces. Thus the inclusion of human disturbance is essential for cost-effective priority-setting. Attention should be targeted to the areas that are characterized as moderately-disturbed, <2,000 m in altitude, and/or intermediately- to extremely-rugged in terrain to identify potentially important regions for implementing cost-effective conservation. We delineated 23 primary large-scale priority areas that are significant for conserving China''s biodiversity, but those isolated priority units in disturbed regions are in more urgent need of conservation actions so as to prevent immediate and severe biodiversity loss. This study presents a spatially optimized national-scale portfolio of conservation priorities – effectively representing the overall biodiversity of China while minimizing conflicts with economic development. Our results offer critical insights for current conservation and strategic land-use planning in China. The approach is transferable and easy to implement by end-users, and applicable for national- and local-scale systematic conservation prioritization practices.     

Ranking Mammal Species for Conservation and the Loss of Both Phylogenetic and Trait Diversity

The ''edge of existence'' (EDGE) prioritisation scheme is a new approach to rank species for conservation attention that aims to identify species that are both isolated on the tree of life and at imminent risk of extinction as defined by the World Conservation Union (IUCN). The self-stated benefit of the EDGE system is that it effectively captures unusual ''unique'' species, and doing so will preserve the total evolutionary history of a group into the future. Given the EDGE metric was not designed to capture total evolutionary history, we tested this claim. Our analyses show that the total evolutionary history of mammals preserved is indeed much higher if EDGE species are protected than if at-risk species are chosen randomly. More of the total tree is also protected by EDGE species than if solely threat status or solely evolutionary distinctiveness were used for prioritisation. When considering how much trait diversity is captured by IUCN and EDGE prioritisation rankings, interestingly, preserving the highest-ranked EDGE species, or indeed just the most threatened species, captures more total trait diversity compared to sets of randomly-selected at-risk species. These results suggest that, as advertised, EDGE mammal species contribute evolutionary history to the evolutionary tree of mammals non-randomly, and EDGE-style rankings among endangered species can also capture important trait diversity. If this pattern holds for other groups, the EDGE prioritisation scheme has greater potential to be an efficient method to allocate scarce conservation effort.     

Genotype Imputation Reference Panel Selection Using Maximal Phylogenetic Diversity

The recent dramatic cost reduction of next-generation sequencing technology enables investigators to assess most variants in the human genome to identify risk variants for complex diseases. However, sequencing large samples remains very expensive. For a study sample with existing genotype data, such as array data from genome-wide association studies, a cost-effective approach is to sequence a subset of the study sample and then to impute the rest of the study sample, using the sequenced subset as a reference panel. The use of such an internal reference panel identifies population-specific variants and avoids the problem of a substantial mismatch in ancestry background between the study population and the reference population. To efficiently select an internal panel, we introduce an idea of phylogenetic diversity from mathematical phylogenetics and comparative genomics. We propose the “most diverse reference panel”, defined as the subset with the maximal “phylogenetic diversity”, thereby incorporating individuals that span a diverse range of genotypes within the sample. Using data both from simulations and from the 1000 Genomes Project, we show that the most diverse reference panel can substantially improve the imputation accuracy compared to randomly selected reference panels, especially for the imputation of rare variants. The improvement in imputation accuracy holds across different marker densities, reference panel sizes, and lengths for the imputed segments. We thus propose a novel strategy for planning sequencing studies on samples with existing genotype data.     

Mapping Groundwater Dependent Ecosystems in California

Background

Most groundwater conservation and management efforts focus on protecting groundwater for drinking water and for other human uses with little understanding or focus on the ecosystems that depend on groundwater. However, groundwater plays an integral role in sustaining certain types of aquatic, terrestrial and coastal ecosystems, and their associated landscapes. Our aim was to illuminate the connection between groundwater and surface ecosystems by identifying and mapping the distribution of groundwater dependent ecosystems (GDEs) in California.

Methodology/Principal Findings

To locate where groundwater flow sustains ecosystems we identified and mapped groundwater dependent ecosystems using a GIS. We developed an index of groundwater dependency by analyzing geospatial data for three ecosystem types that depend on groundwater: (1) springs and seeps; (2) wetlands and associated vegetation alliances; and (3) stream discharge from groundwater sources (baseflow index). Each variable was summarized at the scale of a small watershed (Hydrologic Unit Code-12; mean size = 9,570 ha; n = 4,621), and then stratified and summarized to 10 regions of relative homogeneity in terms of hydrologic, ecologic and climatic conditions. We found that groundwater dependent ecosystems are widely, although unevenly, distributed across California. Although different types of GDEs are clustered more densely in certain areas of the state, watersheds with multiple types of GDEs are found in both humid (e.g. coastal) and more arid regions. Springs are most densely concentrated in the North Coast and North Lahontan, whereas groundwater dependent wetlands and associated vegetation alliances are concentrated in the North and South Lahontan and Sacramento River hydrologic regions. The percentage of land area where stream discharge is most dependent on groundwater is found in the North Coast, Sacramento River and Tulare Lake regions. GDE clusters are located at the highest percentage in the North Coast (an area of the highest annual rainfall totals), North Lahontan (an arid, high desert climate with low annual rainfall), and Sacramento River hydrologic regions. That GDEs occur in such distinct climatic and hydrologic settings reveals the widespread distribution of these ecosystems.

Conclusions/Significance

Protection and management of groundwater-dependent ecosystems are hindered by lack of information on their diversity, abundance and location. By developing a methodology that uses existing datasets to locate GDEs, this assessment addresses that knowledge gap. We report here on the application of this method across California, but believe the method can be expanded to regions where spatial data exist.     

Ecological Diversity and Biodiversity as Concepts for Conservation Planning: Comments on Ricotta

Ricotta argues against the existence of a unique measure of biodiversity by pointing out that no known measure of α-diversity satisfies all the adequacy conditions that have traditionally been set for it. While that technical claim is correct, it is not relevant in the context of defining biodiversity which is most usefully measured by β-diversity. The concept of complementarity provides a closely related family of measures of biodiversity which can be used for systematic conservation planning. Moreover, these measures cannot be replaced by summary statistics but must rely on inventories of biodiversity surrogates at candidate sites for conservation.     

系统发育多样性与系统发育结构在岛屿植物群落保护中的意义——以蜈支洲岛为例

为探讨系统发育多样性和系统发育结构在岛屿植物群落保护决策制定中的作用,以海南三亚蜈支洲岛被子植物群系为例,分析物种丰富度和系统发育多样性的相关性。结果表明,蜈支洲岛植被可分为10种群系类型,22个样方的物种丰富度与系统发育多样性呈显著正相关,但系统发育多样性与物种丰富度对植物多样性保护优先顺序的指示有差异。森林群系的物种丰富度和系统发育多样性普遍高于灌木和草本群系,4个森林群系样方表现为系统发育结构发散,3个森林群系样方表现为系统发育结构聚集。灌木群系中露兜树(Pandanus tectorius)灌丛和草海桐(Scaevola sericea)灌丛系统发育多样性较高,草本群系中厚藤(Vitex trifolia)灌草丛系统发育多样性较高,灌木和草本群系大多倾向于系统发育结构聚集。距海或人类活动区较近的群系可能受环境过滤的作用,而远离海和人类活动区的群系主要受竞争排斥作用影响。因此,在岛屿植物多样性保护策略制定中应当综合考虑物种和系统发育维度,以及环境、演替阶段及用岛方式等因素的影响。     

Phylogenetic Composition of Rocky Mountain Endolithic Microbial Ecosystems

The endolithic environment, the pore space in rocks, is a ubiquitous microbial habitat. Photosynthesis-based endolithic communities inhabit the outer few millimeters to centimeters of rocks exposed to the surface. Such endolithic ecosystems have been proposed as simple, tractable models for understanding basic principles in microbial ecology. In order to test previously conceived hypotheses about endolithic ecosystems, we studied selected endolithic communities in the Rocky Mountain region of the United States with culture-independent molecular methods. Community compositions were determined by determining rRNA gene sequence contents, and communities were compared using statistical phylogenetic methods. The results indicate that endolithic ecosystems are seeded from a select, global metacommunity and form true ecological communities that are among the simplest microbial ecosystems known. Statistical analysis showed that biogeographical characteristics that control community composition, such as rock type, are more complex than predicted. Collectively, results of this study support the idea that patterns of microbial diversity found in endolithic communities are governed by principles similar to those observed in macroecological systems.     

Evolution and Phylogenetic Diversity of Yam Species (Dioscorea spp.): Implication for Conservation and Agricultural Practices

Yams (Dioscorea spp.) consist of approximately 600 species. Presently, these species are threatened by genetic erosion due to many factors such as pest attacks and farming practices. In parallel, complex taxonomic boundaries in this genus makes it more challenging to properly address the genetic diversity of yam and manage its germplasm. As a first step toward evaluating and preserving the genetic diversity yam species, we use a phylogenetic diversity (PD) approach that has the advantage to investigate phylogenetic relationships and test hypotheses of species monophyly while alleviating to the problem of ploidy variation within and among species. The Bayesian phylogenetic analysis of 62 accessions from 7 species from three regions of Cameroon showed that most Dioscorea sections were monophyletic, but species within sections were generally non-monophyletic. The wild species D. praehensilis and cultivated D. cayenensis were the species with the highest PD. At the opposite, D. esculenta has a low PD and future studies should focus on this species to properly address its conservation status. We also show that wild species show a stronger genetic structure than cultivated species, which potentially reflects the management of the yam germplasm by farmers. These findings show that phylogenetic diversity is a promising approach for an initial investigation of genetic diversity in a crop consisting of closely related species.     

近 20 年国外系统保护规划研究进展及启示

运用系统保护规划（SCP）的方法建立保护地（protected area）对生物多样性资源及其所提供的生态系统服务价值具有重要保护作用。笔者归纳总结了自 19 世纪 80 年代以来系统保护规划思想产生和发展的历程,随后基于近 20 年来系统保护规划相关文献,梳理得到现阶段影响保护规划最为核心的两大背景—气候变化及生态系统服务,此背景对系统保护规划六步法关键步骤的研究动态产生深刻影响,并推动了新的研究进展的产生,其中涵盖了规划理念更新、保护目标多元化、数据及模型算法拓展、管理框架变更。笔者结合中国的自然保护地规划背景和相关实践,从关键内容、监测评估、实施管理 3 个方面提出未来的研究方向,以期通过借鉴国际上保护规划的方法、工具、经验对完善中国的保护地体系构建的实践提供参考。     

Fast Computations for Measures of Phylogenetic Beta Diversity

For many applications in ecology, it is important to examine the phylogenetic relations between two communities of species. More formally, let ?? be a phylogenetic tree and let A and B be two samples of its tips, representing the examined communities. We want to compute a value that expresses the phylogenetic diversity between A and B in ??. There exist several measures that can do this; these are the so-called phylogenetic beta diversity (β-diversity) measures. Two popular measures of this kind are the Community Distance (CD) and the Common Branch Length (CBL). In most applications, it is not sufficient to compute the value of a beta diversity measure for two communities A and B; we also want to know if this value is relatively large or small compared to all possible pairs of communities in ?? that have the same size. To decide this, the ideal approach is to compute a standardised index that involves the mean and the standard deviation of this measure among all pairs of species samples that have the same number of elements as A and B. However, no method exists for computing exactly and efficiently this index for CD and CBL. We present analytical expressions for computing the expectation and the standard deviation of CD and CBL. Based on these expressions, we describe efficient algorithms for computing the standardised indices of the two measures. Using standard algorithmic analysis, we provide guarantees on the theoretical efficiency of our algorithms. We implemented our algorithms and measured their efficiency in practice. Our implementations compute the standardised indices of CD and CBL in less than twenty seconds for a hundred pairs of samples on trees with 7 ⋅ 10⁴ tips. Our implementations are available through the R package PhyloMeasures.     

Quantifying Phylogenetic Beta Diversity: Distinguishing between 'True' Turnover of Lineages and Phylogenetic Diversity Gradients

The evolutionary dissimilarity between communities (phylogenetic beta diversity PBD) has been increasingly explored by ecologists and biogeographers to assess the relative roles of ecological and evolutionary processes in structuring natural communities. Among PBD measures, the PhyloSor and UniFrac indices have been widely used to assess the level of turnover of lineages over geographical and environmental gradients. However, these indices can be considered as 'broad-sense' measures of phylogenetic turnover as they incorporate different aspects of differences in evolutionary history between communities that may be attributable to phylogenetic diversity gradients. In the present study, we extend an additive partitioning framework proposed for compositional beta diversity to PBD. Specifically, we decomposed the PhyloSor and UniFrac indices into two separate components accounting for 'true' phylogenetic turnover and phylogenetic diversity gradients, respectively. We illustrated the relevance of this framework using simple theoretical and archetypal examples, as well as an empirical study based on coral reef fish communities. Overall, our results suggest that using PhyloSor and UniFrac may greatly over-estimate the level of spatial turnover of lineages if the two compared communities show contrasting levels of phylogenetic diversity. We therefore recommend that future studies use the 'true' phylogenetic turnover component of these indices when the studied communities encompass a large phylogenetic diversity gradient.     

农田生态系统种群结构多样性与系统微环境的关系——对几种多样性农田生态系统的分析评价

农田生物与其环境因素之间关系问题是农业生态系统研究的一个重点问题 ,生物与其所处环境因素之间关系的好坏 ,对生物的生长发育起着重要作用 ,进而影响着农田生态系统的功能发挥。单一生物与其环境因素之间的关系 ,通常是农田生态系统研究的重点。由多种生物组成的生物群落与其环境因素之间的关系 ,由于对农田生态系统的良好发育更起着关键制约作用 ,因而 ,也越来越多地受到研究人员的关注。对农田生态系统生物种群多样性 ,与多种生态环境因子之间关系的研究 ,也由于人们对多样化系统关注程度的提高而显得尤为重要。本文在对已有研究资料系…     

Using Phylogenetic,Functional and Trait Diversity to Understand Patterns of Plant Community Productivity

Background

Two decades of research showing that increasing plant diversity results in greater community productivity has been predicated on greater functional diversity allowing access to more of the total available resources. Thus, understanding phenotypic attributes that allow species to partition resources is fundamentally important to explaining diversity-productivity relationships.

Methodology/Principal Findings

Here we use data from a long-term experiment (Cedar Creek, MN) and compare the extent to which productivity is explained by seven types of community metrics of functional variation: 1) species richness, 2) variation in 10 individual traits, 3) functional group richness, 4) a distance-based measure of functional diversity, 5) a hierarchical multivariate clustering method, 6) a nonmetric multidimensional scaling approach, and 7) a phylogenetic diversity measure, summing phylogenetic branch lengths connecting community members together and may be a surrogate for ecological differences. Although most of these diversity measures provided significant explanations of variation in productivity, the presence of a nitrogen fixer and phylogenetic diversity were the two best explanatory variables. Further, a statistical model that included the presence of a nitrogen fixer, seed weight and phylogenetic diversity was a better explanation of community productivity than other models.

Conclusions

Evolutionary relationships among species appear to explain patterns of grassland productivity. Further, these results reveal that functional differences among species involve a complex suite of traits and that perhaps phylogenetic relationships provide a better measure of the diversity among species that contributes to productivity than individual or small groups of traits.     

Phylogenetic Resolution and Quantifying the Phylogenetic Diversity and Dispersion of Communities

Conservation biologists and community ecologists have increasingly begun to quantify the phylogenetic diversity and phylogenetic dispersion in species assemblages. In some instances, the phylogenetic trees used for such analyses are fully bifurcating, but in many cases the phylogenies being used contain unresolved nodes (i.e. polytomies). The lack of phylogenetic resolution in such studies, while certainly not preferred, is likely to continue particularly for those analyzing diverse communities and datasets with hundreds to thousands of taxa. Thus it is imperative that we quantify potential biases and losses of statistical power in studies that use phylogenetic trees that are not completely resolved. The present study is designed to meet both of these goals by quantifying the phylogenetic diversity and dispersion of simulated communities using resolved and gradually ‘unresolved’ phylogenies. The results show that: (i) measures of community phylogenetic diversity and dispersion are generally more sensitive to loss of resolution basally in the phylogeny and less sensitive to loss of resolution terminally; and (ii) the loss of phylogenetic resolution generally causes false negative results rather than false positives.