A multi-faceted framework of diversity for prioritizing the conservation of fish assemblages

Floodplain waterbodies and their biodiversity are increasingly threatened by human activities. Given the limited resources available to protect them, methods to identify the most valuable areas for biodiversity conservation are urgently needed. In this study, we used freshwater fish assemblages in floodplain waterbodies to propose an innovative method for selecting priority areas based on four aspects of their diversity: taxonomic (i.e. according to species classification), functional (i.e. relationship between species and ecosystem processes), natural heritage (i.e. species threat level), and socio-economic (i.e. species interest to anglers and fishermen) diversity. To quantitatively evaluate those aspects, we selected nine indices derived either from metrics computed at the species level and then combined for each assemblage (species rarity, origin, biodiversity conservation concern, functional uniqueness, functional originality, fishing interest), or from metrics directly computed at the assemblage level (species richness, assemblage rarity, diversity of biological traits). Each of these indices belongs to one of the four aspects of diversity. A synthetic index defined as the sum of the standardized aspects of diversity was used to assess the multi-faceted diversity of fish assemblages. We also investigated whether the two main environmental gradients at the catchment (distance from the sea) and at the floodplain (lateral connectivity of the waterbodies) scales influenced the diversity of fish assemblages, and consequently their potential conservation value. Finally, we propose that the floodplain waterbodies that should be conserved as a priority are those located in the downstream part of the catchment and which have a substantial lateral connectivity with the main channel.     

景观指数之间的相关分析

应用辽宁省1997~1998年的TM 5影像数据,编制了景观类型图,以78个县市区为单位,分割成78个景观,共计算39个景观格局指数,对它们进行了相关分析。总面积是最基本的景观指数,它决定景观总边界长度、斑块数、类型密度等基本指数,同时与多个指数有显著的相关关系(相关系数绝对值大于0.75)。形状指数的独立性强,极少数指数与其它指数有显著的相关关系;多样性指数和蔓延度指数之间信息重复量最多,都表示景观的异质性,但多样性指数以面积百分比表示景观异质性,而蔓延度指数以类型之间相邻边界的百分比表示景观异质性。研究发现,如果两个指数之间存在显著的相关关系,而由它们两个构成的指数与它们之间没有显著的相关关系。如果指数平均值之间存在显著的相关关系,则它们的变异系数之间不存在显著的相关关系。景观指数间的相关系数不仅与景观格局本身有关,还与空间尺度,分类系统、计算公式及其参数、计算单元和生态学意义关系密切。指数之间影响因子的相同之处越多,它们之间存在显著相关关系的概率越大。     

Assessing nutritional diversity of cropping systems in African villages

Background

In Sub-Saharan Africa, 40% of children under five years in age are chronically undernourished. As new investments and attention galvanize action on African agriculture to reduce hunger, there is an urgent need for metrics that monitor agricultural progress beyond calories produced per capita and address nutritional diversity essential for human health. In this study we demonstrate how an ecological tool, functional diversity (FD), has potential to address this need and provide new insights on nutritional diversity of cropping systems in rural Africa.

Methods and Findings

Data on edible plant species diversity, food security and diet diversity were collected for 170 farms in three rural settings in Sub-Saharan Africa. Nutritional FD metrics were calculated based on farm species composition and species nutritional composition. Iron and vitamin A deficiency were determined from blood samples of 90 adult women. Nutritional FD metrics summarized the diversity of nutrients provided by the farm and showed variability between farms and villages. Regression of nutritional FD against species richness and expected FD enabled identification of key species that add nutrient diversity to the system and assessed the degree of redundancy for nutrient traits. Nutritional FD analysis demonstrated that depending on the original composition of species on farm or village, adding or removing individual species can have radically different outcomes for nutritional diversity. While correlations between nutritional FD, food and nutrition indicators were not significant at household level, associations between these variables were observed at village level.

Conclusion

This study provides novel metrics to address nutritional diversity in farming systems and examples of how these metrics can help guide agricultural interventions towards adequate nutrient diversity. New hypotheses on the link between agro-diversity, food security and human nutrition are generated and strategies for future research are suggested calling for integration of agriculture, ecology, nutrition, and socio-economics.     

The role of phytoplankton diversity metrics in shallow lake and river quality assessment

Ecological water quality problems are frequently connected to increment of phytoplankton productivity and overdominance of some phytoplankton species. Metrics that show monotonously increasing or decreasing tendencies along stressor gradients is recommended for ecological state assessment. Diversity metrics are influenced by various physical disturbances and show high within-year variability; thus, there is no agreement on the usefulness of these metrics as state indicators.To test the usefulness of phytoplankton diversity in ecological state assessment we investigated the productivity–diversity relationships for lakes and rivers in the Carpathian Basin (Hungary). We demonstrated that the shape of productivity–diversity relationship depends on the investigated water body type. Regarding lakes, hump-shaped relationship was found for all computed metrics. Parallel with the increase in phytoplankton productivity values, diversity metrics showed monotonously increasing tendencies in rhithral and decreasing tendencies in large potamal rivers. We found no systematic relationship in the case of small lowland rivers.Changes of diversity metrics calculated for species and functional groups showed similar tendencies within the types, only the slopes of regression lines differ each other.The use of diversity metrics as ecological state indicators should be restricted to water body types where diversity decreases or increases monotonously with phytoplankton biomass. Regarding the lakes the use of diversity metrics is not recommended for ecological state assessment. In rhithral and large potamal river assessment, application of diversity metrics should be strongly considered. We demonstrated that diversity metrics can be useful components of multimetric indices proposed to use by the Water Framework Directive.     

Contrasting changes in the abundance and diversity of North American bird assemblages from 1971 to 2010

Although it is generally recognized that global biodiversity is declining, few studies have examined long‐term changes in multiple biodiversity dimensions simultaneously. In this study, we quantified and compared temporal changes in the abundance, taxonomic diversity, functional diversity, and phylogenetic diversity of bird assemblages, using roadside monitoring data of the North American Breeding Bird Survey from 1971 to 2010. We calculated 12 abundance and diversity metrics based on 5‐year average abundances of 519 species for each of 768 monitoring routes. We did this for all bird species together as well as for four subgroups based on breeding habitat affinity (grassland, woodland, wetland, and shrubland breeders). The majority of the biodiversity metrics increased or remained constant over the study period, whereas the overall abundance of birds showed a pronounced decrease, primarily driven by declines of the most abundant species. These results highlight how stable or even increasing metrics of taxonomic, functional, or phylogenetic diversity may occur in parallel with substantial losses of individuals. We further found that patterns of change differed among the species subgroups, with both abundance and diversity increasing for woodland birds and decreasing for grassland breeders. The contrasting changes between abundance and diversity and among the breeding habitat groups underscore the relevance of a multifaceted approach to measuring biodiversity change. Our findings further stress the importance of monitoring the overall abundance of individuals in addition to metrics of taxonomic, functional, or phylogenetic diversity, thus confirming the importance of population abundance as an essential biodiversity variable.     

On Permian and Triassic insect faunas in relation to biogeography and the Permian-Triassic crisis

The taxonomic diversity dynamics of pterygote insects in the Permian and Triassic at the family/age level are considered. Different metrics of taxonomic diversity are compared. Biogeographic and taphonomic aspects of changes in the composition of insect faunas in the Permian and about the P-T transition are discussed. Some changes in the Permian insect faunas are of a biogeographic nature and do not indicate global changes in diversity. Insects with aquatic immatures were rather common in the Permian and Early Triassic, but these immatures are well represented in only few localities.     

In pursuit of peak animal welfare; the need to prioritize the meaningful over the measurable

Despite the diversity of animal welfare definitions, most recognise the centrality of the feelings of animals which are currently impossible to measure directly. As a result, animal welfare assessment is heavily reliant upon the indirect measurement of factors that either affect what animals feel, or are effected by how they feel. Physiological and health orientated measures have emerged as popular metrics for assessing welfare because they are quantifiable, can effect and be affected by how animals feel and have merits regardless of their relationship to the feelings of animals. However, their popularity in animal welfare assessment has led to them having a disproportionate influence on animal management to the detriment of animal welfare in numerous instances. Here, the case is made that a tension exists between management that prioritizes aspects of care reflecting popular animal welfare metrics such as those relating to physical health, and management that emphasizes psychological wellbeing. By re‐examining the relative merits of physical and psychological priorities in animal management, an alternate animal welfare paradigm emerges less tied to traditional welfare metrics. This paradigm theorizes about the possibility for an optimal animal welfare state to exist where managed animal populations provided essential psychological outlets but protected from key physical stressors routinely experienced in the wild, might experience higher levels of welfare than wild populations would routinely experience. The proposition that optimal animal welfare could theoretically be achieved in well managed and well designed captive environments challenges a widely held ethical perspective that captivity is inherently bad for animal welfare.     

Promoting inclusive metrics of success and impact to dismantle a discriminatory reward system in science

Success and impact metrics in science are based on a system that perpetuates sexist and racist “rewards” by prioritizing citations and impact factors. These metrics are flawed and biased against already marginalized groups and fail to accurately capture the breadth of individuals’ meaningful scientific impacts. We advocate shifting this outdated value system to advance science through principles of justice, equity, diversity, and inclusion. We outline pathways for a paradigm shift in scientific values based on multidimensional mentorship and promoting mentee well-being. These actions will require collective efforts supported by academic leaders and administrators to drive essential systemic change.

This Essay argues that success and impact metrics in science are based on a system that perpetuates sexist and racist ‘rewards’ by prioritizing citations and impact factors; the authors advocate shifting this outdated value system to advance science through principles of justice, equity, diversity, and inclusion.     

Comparing species and evolutionary diversity metrics to inform conservation

Phylogenetic diversity (PD) is an important measure for identifying areas of conservation. Phylogenetic diversity is a robust biodiversity metric because it accounts for the relationships among species, and not just the number of species. For this reason, it is an essential element for conservation planning. Unfortunately, PD metrics are not used by many for conservation planning. In the case of Colombia, which is rich in crop and wild plant biodiversity, lacks information on genetic resources of Crop Wild Relatives (CWR). Due to deforestation and agriculture expansion, the habitat, where these crop wild relatives grow, is being reduced at an alarming rate and could be destroyed altogether. This study focuses on crop wild relatives in Colombia, comparing species diversity versus PD-based metrics to show the advantages of using evolutionary information for conservation planning. We identified new areas with high PD and endemism among CWR diversity which are important to establishing comprehensive conservation strategies.     

How to choose a biodiversity indicator – Redundancy and complementarity of biodiversity metrics in a freshwater ecosystem

A range of biodiversity metrics are available to assess the ecological integrity of aquatic ecosystems. However, performance varies considerably among different types of metrics and provides different information regarding ecosystem conditions, thus making difficult the selection of appropriate metrics for biomonitoring. The present study evaluated the robustness of six biodiversity metrics to assess environmental change and determine their utility as relevant indicators of ecosystem biodiversity and functionality. Traditional metrics such as species richness and Shannon diversity were considered along with alternative metrics such as functional diversity, size diversity and taxonomic distinctness. To that end, invertebrate assemblages in a river floodplain were used as a case study to evaluate the performance of metrics using Generalized Additive Models (GAM). GAM explained between eight and 49% of the variability in biodiversity. The regression models exhibited differences in the response of biodiversity indicators to environmental factors, suggesting that intermediate levels of turbidity and low salinity are conditions favouring increased biodiversity in the study area. Based on correlations among metrics and responses to primary environmental factors, it is concluded that Shannon and functional diversity, and rarefied species richness generated similar information regarding ecosystem conditions (i.e., the metrics were redundant); while size diversity and distinctness provided useful additional data characterizing ecosystem quality (i.e., the metrics were complementary). Functional diversity indicated not only number and dominance of species, but also each species functional role in the community, and was therefore the most informative biodiversity metric. Nevertheless, the use of a combination of metrics, for example functional and size diversity, and variation in taxonomic distinctness, provides complementary data that will serve to achieve a more thorough understanding of ecosystem structure and function, and response to primary environmental influences.     

Understanding microbial community diversity metrics derived from metagenomes: performance evaluation using simulated data sets

Metagenomics holds the promise of greatly advancing the study of diversity in natural communities, but novel theoretical and methodological approaches must first be developed and adjusted for these data sets. We evaluated widely used macroecological metrics of taxonomic diversity on a simulated set of metagenomic samples, using phylogenetically meaningful protein-coding genes as ecological proxies. To our knowledge, this is the first approach of this kind to evaluate taxonomic diversity metrics derived from metagenomic data sets. We demonstrate that abundance matrices derived from protein-coding marker genes reproduce more faithfully the structure of the original community than those derived from SSU-rRNA gene. We also found that the most commonly used diversity metrics are biased estimators of community structure and differ significantly from their corresponding real parameters and that these biases are most likely caused by insufficient sampling and differences in community phylogenetic composition. Our results suggest that the ranking of samples using multidimensional metrics makes a good qualitative alternative for contrasting community structure and that these comparisons can be greatly improved with the incorporation of metrics for both community structure and phylogenetic diversity. These findings will help to achieve a standardized framework for community diversity comparisons derived from metagenomic data sets.     

A national approach for mapping and quantifying habitat-based biodiversity metrics across multiple spatial scales

Ecosystem services, i.e., services provided to humans from ecological systems have become a key issue of this century in resource management, conservation planning, and environmental decision analysis. Mapping and quantifying ecosystem services have become strategic national interests for integrating ecology with economics to help understand the effects of human policies and actions and their subsequent impacts on both ecosystem function and human well-being. Some aspects of biodiversity are valued by humans in varied ways, and thus are important to include in any assessment that seeks to identify and quantify the benefits of ecosystems to humans. Some biodiversity metrics clearly reflect ecosystem services (e.g., abundance and diversity of harvestable species), whereas others may reflect indirect and difficult to quantify relationships to services (e.g., relevance of species diversity to ecosystem resilience, cultural value of native species). Wildlife habitat has been modeled at broad spatial scales and can be used to map a number of biodiversity metrics. In the present study, we present an approach that (1) identifies mappable biodiversity metrics that are related to ecosystem services or other stakeholder concerns, (2) maps these metrics throughout a large multi-state region, and (3) compares the metric values obtained for selected watersheds within the regional context. The broader focus is to design a flexible approach for mapping metrics to produce a national-scale product. We map 20 biodiversity metrics reflecting ecosystem services or other aspects of biodiversity for all vertebrate species except fish. Metrics include species richness for all vertebrates, specific taxon groups, harvestable species (i.e., upland game, waterfowl, furbearers, small game, and big game), threatened and endangered species, and state-designated species of greatest conservation need, and also a metric for ecosystem (i.e., land cover) diversity. The project is being conducted at multiple scales in a phased approach, starting with place-based studies, then multi-state regional areas, culminating into a national-level atlas. As an example of this incremental approach, we provide results for the southwestern United States (i.e., states of Arizona, New Mexico, Nevada, Utah, and Colorado) and portions of two watersheds within this region: the San Pedro River (Arizona) and Rio Grande River (New Mexico). Geographic patterns differed considerably among metrics across the southwestern study area, but metric values for the two watershed study areas were generally greater than those for the southwestern region as a whole.     

From compositional to functional biodiversity metrics in bioassessment: A case study using stream macroinvertebrate communities

While compositional diversity is a common metric for assessing human impacts on aquatic communities, functional diversity is scarcely employed, though highly desirable from the perspective of the European Water Framework Directive. Using abundance data from 99 minimally disturbed sites (i.e., no or very weak anthropogenic impact) from a national survey, we studied the spatial variability of compositional and functional biodiversity metrics across a predefined ecoregional classification. Metrics of compositional diversity comprised taxonomic and EPT richness and Simpson diversity. Functional diversity metrics were based on Rao's Quadratic Entropy (RQE), which described the differences among benthic invertebrate genera in eleven biological traits (e.g., size, life cycle, reproduction types, feeding habits). Using generalized linear models we show that taxonomic richness may vary greatly across ecoregions, contrasting with Simpson diversity and functional metrics that varied weakly in response to natural environmental variability. Functional diversity metrics, because of their stability in response to natural environmental variability, may be useful tools for assessing human impairment to ecosystem function. We further tested the response of functional diversity metrics to a specific human impact (sewage) and demonstrated significant modifications of functional diversity downstream of sewage pollution. Further investigations are required to test the ability of functional diversity metrics to precisely and accurately indicate different types of human impacts.     

A guide to phylogenetic metrics for conservation,community ecology and macroecology

The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub‐disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub‐disciplines hampers potential meta‐analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo‐diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo‐diversity metrics based on their mathematical form within these three dimensions and identify ‘anchor’ representatives: for α‐diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices.     

不同干扰背景下景观指数与物种多样性的多尺度效应——以巩义市为例

以黄河中下游山地丘陵区的巩义市为研究区,采用典型样地法对灌草丛、人工林和农田边缘3种不同干扰背景下的自然、半自然生境内的植物进行调查。基于景观生态学原理,在地理信息系统技术支持下,借助于Fragstatta3.3软件,以调查样地为中心,计算了150、250、500、750、1000、1250、1500m不同半径缓冲区内表征景观形状(Edge and patch shape)、边缘对照(Edge contrast)、相似度和邻近度(Proximity and similarity)、景观多样性(Diversity)、基质(Texture)、斑块大小和密度(Patch size and patch density)共6类52个指数,运用冗余分析(RDA)筛选出不同尺度下对该区农业景观中植物多样性有显著影响的景观指数。结果表明:不同尺度,景观指数对物种多样性的影响变化显著。灌草丛生境,在500—750m范围内,SHAPE_AM指数和PARA_AM指数能够很好的解释物种多样性,解释量为33.6%;人工林生境,SHAPE_AM指数、AREA_CV指数、SIMI指数和PAFRAC指数在1000—1250m范围内对物种多样性的解释量达到48.1%;农田边缘生境,GYRATE_CV指数、ENN_CV指数、PARA_MN指数和FRAC_AM指数在750—1250m范围内对物种多样性影响显著,解释量为32%。其中,辛普森多样性指数(SIDI)与灌草丛物种多样性在750—1250m范围内作用显著,ENN_CV指数仅对农田边缘物种多样性影响较大。景观指数对物种多样性的影响具有尺度依赖性,未来应全面综合探讨这些指数的尺度效应及在景观生态学中的应用。     

Phylogenetic community structure metrics and null models: a review with new methods and software

Competitive exclusion and habitat filtering influence community assembly, but ecologists and evolutionary biologists have not reached consensus on how to quantify patterns that would reveal the action of these processes. Currently, at least 22 α‐diversity and 10 β‐diversity metrics of community phylogenetic structure can be combined with nine null models (eight for β‐diversity metrics), providing 278 potentially distinct approaches to test for phylogenetic clustering and overdispersion. Selecting the appropriate approach for a study is daunting. First, we describe similarities among metrics and null models across variance in phylogeny size and shape, species abundance, and species richness. Second, we develop spatially explicit, individual‐based simulations of neutral, competitive exclusion, or habitat filtering community assembly, and quantify the performance (type I and II error rates) of all 278 metric and null model combinations against each assembly process. Many α‐diversity metrics and null models are at least functionally equivalent, reducing the number of truly unique metrics to 12 and the number of unique metric + null model combinations to 72. An even smaller subset of metric and null model combinations showed robust statistical performance. For α‐diversity metrics, phylogenetic diversity and mean nearest taxon distance were best able to detect habitat filtering, while mean pairwise phylogenetic distance‐based metrics were best able to detect competitive exclusion. Overall, β‐diversity metrics tended to have greater power to detect habitat filtering and competitive exclusion than α‐diversity metrics, but had higher type 1 error in some cases. Across both α‐ and β‐diversity metrics, null model selection affected type I error rates more than metric selection. A null model that maintained species richness, and approximately maintained species occurrence frequency and abundance across sites, exhibited low type I and II error rates. This regional null model simulates neutral dispersal of individuals into local communities by sampling from a regional species pool. We introduce a flexible new R package, metricTester, to facilitate robust analyses of method performance.     

Stream order-dependent diversity metrics of epilithic diatom assemblages

Diatoms are considered as an appropriate indicator group for ecological status assessment of surface waters. These organisms can be indicative not only of the waterchemical but also of the hydro-morphological characteristics (e.g., stream size, physical habitat diversity) of running waters. In this study, diatom diversity metrics (species number, Shannon diversity, and evenness) from 506 sites in Pannon ecoregion (Hungary) were compared to the Strahler stream order system established with ArcView GIS 3.2. SOM analyses were performed to exclude the effect of nutrients on diversity metrics along the stream orders. Mixed-effects linear models and Tukey’s post hoc test revealed a linear relationships between species number, diversity and stream orders on ecoregion level from first- to eighth-order streams. The species number increases with an average of 8%, and the diversity by 10% per unit increase of the stream order. However, we could not find relationships with evenness. Autotrophic diversity metrics based on diatom species data appear to increase parallel with the stream order while those of heterotrophic metrics (published in the literature) maximize at medium stream orders. We argue that stream order is a relevant typological parameter which can basically determine the diatom diversity metrics, and it is well applicable in biomonitoring.     

Impacts of multiple anthropogenic stressors on stream macroinvertebrate community composition and functional diversity

Ensuring the provision of essential ecosystem services in systems affected by multiple stressors is a key challenge for theoretical and applied ecology. Trait‐based approaches have increasingly been used in multiple‐stressor research in freshwaters because they potentially provide a powerful method to explore the mechanisms underlying changes in populations and communities. Individual benthic macroinvertebrate traits associated with mobility, life history, morphology, and feeding habits are often used to determine how environmental drivers structure stream communities. However, to date multiple‐stressor research on stream invertebrates has focused more on taxonomic than on functional metrics. We conducted a fully crossed, 4‐factor experiment in 64 stream mesocosms fed by a pristine montane stream (21 days of colonization, 21 days of manipulations) and investigated the effects of nutrient enrichment, flow velocity reduction and sedimentation on invertebrate community, taxon, functional diversity and trait variables after 2 and 3 weeks of stressor exposure. 89% of the community structure metrics, 59% of the common taxa, 50% of functional diversity metrics, and 79% of functional traits responded to at least one stressor each. Deposited fine sediment and flow velocity reduction had the strongest impacts, affecting invertebrate abundances and diversity, and their effects translated into a reduction of functional redundancy. Stressor effects often varied between sampling occasions, further complicating the prediction of multiple‐stressor effects on communities. Overall, our study suggests that future research combining community, trait, and functional diversity assessments can improve our understanding of multiple‐stressor effects and their interactions in running waters.     

Structural type diversity: measuring structuredness of communities by type diversity

Recently, the notion of diversity, which is directed towards (effective) numbers of types (states of a trait such as species and genotypes), is increasingly used as an umbrella term akin to “variation”, thus including classical metrics of dispersion among others. This is probably due to the growing interest in functional aspects of variation which involve variable differences between types. Though the traditional notion of diversity does not cover these aspects, it shows up in many interpretations. To overcome this ambiguity, the traditional notion of diversity is extended in this paper to include variable differences with emphasis on their general significance as structuring features. For this purpose, structure is conceived to be captured by the representation of types via variable differences and abundances. Structural diversity then results from application of traditional measures of diversity to the relative structural representations of types in addition to their relative abundances. Since diversity as effective number of types alone provides no information about their mutual distinctness and the range covered by them, connections to measures of dispersion are indispensable. This is considered via two approaches that rely on dispersion characteristics and one approach that allows for an assessment of structural diversity for controlled levels of type distinctness. Effects of structure on dispersion and diversity are analyzed. The use of the approaches for discovering rarely considered characteristics of phylogenetic structure is demonstrated.