Old and new challenges in using species diversity for assessing biodiversity

Although the maintenance of diversity of living systems is critical for ecosystem functioning, the accelerating pace of global change is threatening its preservation. Standardized methods for biodiversity assessment and monitoring are needed. Species diversity is one of the most widely adopted metrics for assessing patterns and processes of biodiversity, at both ecological and biogeographic scales. However, those perspectives differ because of the types of data that can be feasibly collected, resulting in differences in the questions that can be addressed. Despite a theoretical consensus on diversity metrics, standardized methods for its measurement are lacking, especially at the scales needed to monitor biodiversity for conservation and management purposes. We review the conceptual framework for species diversity, examine common metrics, and explore their use for biodiversity conservation and management. Key differences in diversity measures at ecological and biogeographic scales are the completeness of species lists and the ability to include information on species abundances. We analyse the major pitfalls and problems with quantitative measurement of species diversity, look at the use of weighting measures by phylogenetic distance, discuss potential solutions and propose a research agenda to solve the major existing problems.     

Ecological integrity assessment as a metric of biodiversity: are we measuring what we say we are?

As the recognition of the importance of biological diversity in biological conservation grows, an ongoing challenge is to develop metrics that can be used for effective conservation and management. The ecological integrity assessment has been proposed as such a metric. It is held by some to measure species composition, diversity, and habitat quality, as well as ecosystem structure, composition, and function. The methodology relies on proxy variables that include data on landscape characteristics such as patch size, abiotic factors such as hydrology, and some features of vegetation structure and composition. We suggest that the measure is flawed on four levels. First, its putative representation of general ecological form and function, and its lack of specific detail about how it actually represents those attributes, leaves the metric without the focus needed to be useful for measuring ecological features on the ground and testing associated hypotheses and predictions. Second, the proxy variables used to represent biological diversity, such as habitat (vegetation) metrics and vascular plant species diversity, are not empirically correlated with diversity of a range of taxa or of other components of the biota. Third, like other ecological indices that integrate many distinct features, the ecological integrity index is subject to the loss of information in its condensation of multi-dimensional variability into a one-dimensional index, and it may be subject to systematic bias from the conversion of raw data into categorical scores. Fourth, the sampling protocols are at risk of sampling bias, observer bias, and measurement error, any of which can confound the estimation of conservation value. In terms of biological diversity, the methodology produces an unreliable estimate of the number of vascular plant species and their relative percentages of occurrence, and an absence of any protocols for taxa other than plants. For these reasons we believe that ecological integrity assessment is currently of limited value as a measure of site-specific biological diversity and its change over time. A considerable amount of investigation is needed in order to have confidence in the results of an ecological integrity assessment, especially if it is to be used for regulatory purposes. We suggest further refinements and discuss alternative measures of biological diversity that provide reliable metrics for assessing change. A thoughtful choice among measures can help to identify the most appropriate assessment for conservation decisions.     

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.     

Quantifying the multiple facets of isotopic diversity: New metrics for stable isotope ecology

Stable isotope analyses have emerged as an insightful tool for ecologists, with quantitative methods being developed to analyse data at the population, community and food web levels. In parallel, functional ecologists have developed metrics to quantify the multiple facets of functional diversity in a n-dimensional space based on functional traits. Here, we transferred and adapted metrics developed by functional ecologists into a set of four isotopic diversity metrics (isotopic divergence, dispersion, evenness and uniqueness) complementary to the existing metrics. Specifically, these new metrics are mathematically independent of the number of organisms analysed and account for the abundance of organisms. They can also be calculated with more than two stable isotopes. In addition, we also provide a procedure for calculating the levels of isotopic overlap (similarity and turnover) between two groups of organisms. These metrics have been implemented into new functions in R made freely available to users and we illustrated their application using stable isotope values from a freshwater fish community. Transferring the framework developed initially for measuring functional diversity to stable isotope ecology will allow more efficient assessments of changes in the multiple facets of isotopic diversity following anthropogenic disturbances.     

Scale‐dependent complementarity of climatic velocity and environmental diversity for identifying priority areas for conservation under climate change

As most regions of the earth transition to altered climatic conditions, new methods are needed to identify refugia and other areas whose conservation would facilitate persistence of biodiversity under climate change. We compared several common approaches to conservation planning focused on climate resilience over a broad range of ecological settings across North America and evaluated how commonalities in the priority areas identified by different methods varied with regional context and spatial scale. Our results indicate that priority areas based on different environmental diversity metrics differed substantially from each other and from priorities based on spatiotemporal metrics such as climatic velocity. Refugia identified by diversity or velocity metrics were not strongly associated with the current protected area system, suggesting the need for additional conservation measures including protection of refugia. Despite the inherent uncertainties in predicting future climate, we found that variation among climatic velocities derived from different general circulation models and emissions pathways was less than the variation among the suite of environmental diversity metrics. To address uncertainty created by this variation, planners can combine priorities identified by alternative metrics at a single resolution and downweight areas of high variation between metrics. Alternately, coarse‐resolution velocity metrics can be combined with fine‐resolution diversity metrics in order to leverage the respective strengths of the two groups of metrics as tools for identification of potential macro‐ and microrefugia that in combination maximize both transient and long‐term resilience to climate change. Planners should compare and integrate approaches that span a range of model complexity and spatial scale to match the range of ecological and physical processes influencing persistence of biodiversity and identify a conservation network resilient to threats operating at multiple scales.     

A Comparison of Body Size,Coat Condition and Endoparasite Diversity of Wild Barbary Macaques Exposed to Different Levels of Tourism

Primate tourism is a rapidly growing industry with the potential to provide considerable conservation benefits. However, assessing the impact of tourists on the animals involved is vital to ensure that the conservation value of primate tourism is maximized. In this study, we compared body size, coat condition, and endoparasite diversity of wild, adult Barbary macaques exposed to different levels of tourism. Study animals belonged to three groups located in the Middle Atlas Mountains, Morocco: “green group” (GG) and “scarlet group” (SG) were exposed to negligible/no tourism, while the “tourist group” (TG) was exposed to very high levels of tourism. We used photogrammetry to quantify body size, scored coat condition from photographs, and quantified endoparasite species number from fecal samples. For both males and females, TG animals had deeper stomachs and wider hips than SG and GG animals. The coat condition of TG males was worse than that of SG and GG males, but no difference between groups was seen for females. Fecal samples from TG males contained a greater mean number of protozoan species than did samples from SG and GG males; for females a similar difference was found between TG and GG, but not between TG and SG. This study provides evidence that tourism has impacts on the body size, coat condition, and endoparasite diversity of Barbary macaques at this site. Further study is required to assess whether such effects are detrimental to the health of these animals.     

Measurements of peripheral and deep body temperature in cattle – A review

Automation of the measurement of the physiological and behavioural parameters of livestock has become an important goal for both scientists and farmers. Accurate data and knowledge about farmed animals, especially in cattle breeding, are needed. Proper early diagnosis of a cow's health status in real time allows for preventing the development of infection, oestrus detection and leads to reduced environmental stress. Thus, it contributes to more effective herd management. Among the physiological parameters, body temperature and its fluctuations are key indicators of health and well-being in animals. Currently, along with the development of technical solutions and their implementation, increasingly more attention is being paid to the continuously measurement of body core and peripheral temperature in animals. Recently there has been an increased number of publications devoted to this subject. However, there is a need to systematise this knowledge as these studies have had different purposes, have been performed in various environmental conditions, and the measurements were taken using different methods and equipment. As such, the results obtained by the different authors often may not be comparable. For this reason, this paper has two main purposes: to present the most widely used continuous methods of peripheral and body core temperature measurement, and to show its references values which characterise the individual locations of the cattle body in thermoneutral ambient. An analysis of the professional publications regarding measurements of peripheral and deep body temperature led to the conclusion that these methods have high research and diagnostic potential. However, it is necessary to standardised research to enable better and more comparable results, including among others; different cattle groups, animal age, health and environmental conditions.     

Quantitative genetics: a promising approach for the assessment of genetic variation in endangered species

The measurement of genetic variation is often an important component of endangered species management programs. Each of several tools available to measure genetic diversity has positive and negative attributes. Quantitative genetic techniques have not received much attention in the conservation field, yet they are likely to reveal variation that is most closely associated with components of fitness. In addition, quantitative genetics may not be as logistically difficult for threatened populations as was once thought. Finally, quantitative genetic models provide a better outlook for conservation programs than single-locus models.     

Metabarcoding技术在真菌多样性研究中的应用

由于受到气候变化、土地利用变化及环境污染等诸多因素的干扰, 真菌多样性受到不容忽视的威胁, 亟需得到保护。构建物种数据库是实现真菌多样性研究和保护的重要前提。近年来兴起的DNA条形码及metabarcoding技术能够在很大程度上弥补传统鉴定方法的缺陷, 可对真菌物种进行大规模、准确、快速、高效地鉴定。本文梳理了metabarcoding技术在真菌物种多样性评估、真菌多样性影响机制和真菌古生态重建等研究中的应用, 同时强调了metabarcoding技术用于真菌多样性研究尚处于初期阶段, 在构建有效参照数据库、优化实验流程以及升级生物信息学工具等方面仍需要进一步的完善。建议加强真菌分类学家、生态学家以及计算机工具研发工程师之间的合作, 共同解决metabarcoding技术在真菌多样性研究及应用中面临的问题, 为宏观尺度上真菌多样性保护提供更加科学的依据。     

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.     

城市公园和郊区公园生物多样性评估的指标

随着城市化进程的加快,城市的生物多样性不可避免地受到城市化的各种影响,城市及其郊区的生物多样性保护越来越受到人们的重视。城市公园与郊区公园中往往具有高度多样化的生境,并保存着某些自然植被片段和动物物种,那里的生物多样性较高。可见,在城市和郊区的生物多样性保护中,公园生物多样性的保护是一个非常关键的环节,而对其生物多样性的评估又是有效保护的基础。目前,我国生物多样性评估方面的研究工作多集中于物种水平,而对生境的研究较少,但实践证明,保护生境比保护物种更为重要。本文介绍了比利时学者Hermy & Cornelis在比利时西佛兰德省的Loppem市立公园的保护实践中构建的一种对城市公园和郊区公园中的生物多样性进行评估的方法。该方法从两个方面展开：生境多样性和物种多样性。在生境水平上,首先对各种生境单元进行分类,这些单元被分为面状、线状和点状要素。针对每种要素,分别计算了Shannon-Wiener多样性指数和饱和度指数。饱和度指数是实际的多样性指数与最大可能的多样性指数之比。在物种水平上,使用了物种数、Shannon-Wiener多样性指数和饱和度指数来评估公园中的高等植物、蝴蝶、两栖动物和饲养的鸟类等物种。这样,就获得了20个生物多样性指标,根据这些指数就可以对Loppem市立公园内的生物多样性进行评估。结合我国生物多样性评估工作的实际要求,文章最后对上述方法进行了讨论,指出该方法对我国公园的生物多样性评估工作具有借鉴意义,但在运用时各地需要结合本地的实际情况。     

Molecular tools and analytical approaches for the characterization of farm animal genetic diversity

Genetic studies of livestock populations focus on questions of domestication, within- and among-breed diversity, breed history and adaptive variation. In this review, we describe the use of different molecular markers and methods for data analysis used to address these questions. There is a clear trend towards the use of single nucleotide polymorphisms and whole-genome sequence information, the application of Bayesian or Approximate Bayesian analysis and the use of adaptive next to neutral diversity to support decisions on conservation.     

On the comparison of population-level estimates of haplotype and nucleotide diversity: a case study using the gene cox1 in animals

Estimates of genetic diversity represent a valuable resource for biodiversity assessments and are increasingly used to guide conservation and management programs. The most commonly reported estimates of DNA sequence diversity in animal populations are haplotype diversity (h) and nucleotide diversity (π) for the mitochondrial gene cytochrome c oxidase subunit I (cox1). However, several issues relevant to the comparison of h and π within and between studies remain to be assessed. We used population-level cox1 data from peer-reviewed publications to quantify the extent to which data sets can be re-assembled, to provide a standardized summary of h and π estimates, to explore the relationship between these metrics and to assess their sensitivity to under-sampling. Only 19 out of 42 selected publications had archived data that could be unambiguously re-assembled; this comprised 127 population-level data sets (n ≥ 15) from 23 animal species. Estimates of h and π were calculated using a 456-base region of cox1 that was common to all the data sets (median h=0.70130, median π=0.00356). Non-linear regression methods and Bayesian information criterion analysis revealed that the most parsimonious model describing the relationship between the estimates of h and π was π=0.0081 h(2). Deviations from this model can be used to detect outliers due to biological processes or methodological issues. Subsampling analyses indicated that samples of n>5 were sufficient to discriminate extremes of high from low population-level cox1 diversity, but samples of n ≥ 25 are recommended for greater accuracy.     

Current status and future directions of applied behavioral research for animal welfare and conservation

The papers that follow in this special issue reflect the state of knowledge and theory in the fields of animal welfare and conservation behavior. A particular focus is placed on how enrichment can be used judiciously to improve welfare and to prepare captive animals for release back to the wild. However, my purpose here is not simply to reiterate what the contributors of this special issue have said, but to provide an overview of the major themes, problems, and opportunities in applied animal behavior related to conservation and welfare. I review major issues in three interrelated areas: captive welfare, captive breeding, and conservation behavior research for wild populations. Despite many advancements in welfare science, one of the most significant impediments to a predictive science of welfare is the need to further refine theories advanced to explain environment–welfare relationships. I provide a brief overview of ten theories that have been proposed to explain good or poor welfare and suggest that they need to be made more conceptually distinct so that clear hypotheses can be articulated, and predictions made and tested. Captive breeding programs for ex situ conservation have borrowed and applied many of the concepts involved in welfare science to great advantage. Other keys to successful breeding programs include applying knowledge of social organization and processes to enhance reproduction; for example, finding the right combination of individuals to get animals breeding. However, behaviorists are only recently learning how to manipulate behavioral mechanisms, such as signaling behavior and mate choice, to optimize captive breeding for conservation. The emerging field of conservation behavior has played a role in captive breeding, but also is poised to play a major role in in situ conservation. Applied behavioral research can illuminate a number of issues important to conservation, including behavioral responses to habitat fragmentation and human disturbance (e.g., pollutants, noise, and light), and human–animal conflict (e.g., crop-raiding). Behavioral decisions made when animals are dispersing and selecting habitat for settlement determine the distribution of animals on the landscape and are important to understand for improving reserve and habitat corridor design. Captive–release and translocation programs require detailed behavioral knowledge to predict responses to novel environments and ensure that animals are adequately prepared for environmental change. This review underscores that many of the behavioral processes of interest to welfare science are also important for conservation behavior: perception, stress, assessment and decision-making rules, and other behavioral and physiological mechanisms. If properly understood, these mechanisms can be manipulated in the service of conservation goals, moving the field of conservation behavior from implication to application. A better integration of the disciplines of animal welfare and conservation behavior – together tackling problems at multiple levels of analysis – will further these goals.     

Recovery of mammal diversity in tropical forests: a functional approach to measuring restoration

Ecological restoration is increasingly applied in tropical forests to mitigate biodiversity loss and recover ecosystem functions. In restoration ecology, functional richness, rather than species richness, often determines community assembly, and measures of functional diversity provide a mechanistic link between diversity and ecological functioning of restored habitat. Vertebrate animals are important for ecosystem functioning. Here, we examine the functional diversity of small‐to‐medium sized mammals to evaluate the diversity and functional recovery of tropical rainforest. We assess how mammal species diversity and composition and functional diversity and composition, vary along a restoration chronosequence from degraded pasture to “old‐growth” tropical rainforest in the Wet Tropics of Australia. Species richness, diversity, evenness, and abundance did not vary, but total mammal biomass and mean species body mass increased with restoration age. Species composition in restoration forests converged on the composition of old‐growth rainforest and diverged from pasture with increasing restoration age. Functional metrics provided a clearer pattern of recovery than traditional species metrics, with most functional metrics significantly increasing with restoration age when taxonomic‐based metrics did not. Functional evenness and dispersion increased significantly with restoration age, suggesting that niche complementarity enhances species' abundances in restored sites. The change in community composition represented a functional shift from invasive, herbivorous, terrestrial habitat generalists and open environment specialists in pasture and young restoration sites, to predominantly endemic, folivorous, arboreal, and fossorial forest species in older restoration sites. This shift has positive implications for conservation and demonstrates the potential of tropical forest restoration to recover rainforest‐like, diverse faunal communities.     

Phylogenetic diversity and the conservation biogeography of African primates

Aim Phylogenetics has an important role in conservation biogeography. However, there are few data on the phylogenetic diversity of African primates. The phylogenetic diversity (PD) of a species is a measure of its taxonomic distinctness and can be estimated by looking at the phylogenetic relationships among taxa. Species‐specific metrics on PD can then be used to determine conservation priorities at various biogeographical scales. We used PD metrics to rank 55 African primate species according to their conservation priorities at the country level and within six African biogeographical regions. We also addressed the following question: are there differences in conservation rankings between the IUCN Red List and our PD metrics? Location Africa. Methods We created a consensus phylogeny for all African primate clades based on genetic studies. Analyses of species distributions were determined using presence/absence scores at two levels: country and biogeographical region. A node‐based method that standardizes for widespread taxa and endemicity was used to calculate PD indices. Hierarchical cluster analysis was used to convert one of the standardized, phylogenetic indices into three clusters that could be ranked and compared with the main IUCN conservation rankings of endangered, vulnerable, and lower risk. Results At the country and region levels, the top‐priority species in terms of PD are Pan paniscus, Macaca sylvanus, Arctocebus calabarensis, Gorilla beringei, Arctocebus aureus, Allenopithecus nigroviridis, Gorilla gorilla, Procolobus verus, Cercopithecus solatus, Cercocebus galeritus, Colobus angolensis, Theropithecus gelada, Galagoides zanzibaricus, Galagoides granti, and Procolobus (Piliocolobus) badius. Geographic rankings were highest for the Democratic Republic of the Congo (country level) and Central Africa (region level). Although there were no overall differences between IUCN conservation ranks and the PD rankings, there were significant differences between the two systems for vulnerable and endangered primate taxa. Main conclusions There are few ecological and behavioural data on populations of some of the African primates that represent the highest levels of phylogenetic diversity. Studies of primate taxa with high PD rankings should focus on identifying sites suitable for intensive studies of population densities, feeding ecology, and reproductive behaviour. We suggest that PD metrics can serve as an important, complementary data set in the IUCN ranking system for primates.     

A framework for estimating niche metrics using the resemblance between qualitative resources

Despite the central importance of the niche concept for the ecological theory, current methods to quantify the species niche from qualitative resources, such as food or habitat types, remain insufficiently developed. Classically, information theory and diversity measures have formed the toolbox used for calculating resource niche metrics on species preference data for a set of qualitative resources. We provide a comprehensive framework that extends these classical approaches by incorporating the resemblance between resources into the calculation of resource niche metrics. This does not only allow estimation of the niche centre, breadth, overlap and displacement with greater accuracy, but also makes the estimates less influenced by the way the resources are subdivided. In addition, all niche metrics can be calculated while taking into account the variation in resource availability, and confidence intervals can be obtained by bootstrapping. We illustrate the utility of the framework with an analysis of dietary preferences in feral pigeons Columba livia.     

Quantifying light-dependent circadian disruption in humans and animal models

Although circadian disruption is an accepted term, little has been done to develop methods to quantify the degree of disruption or entrainment individual organisms actually exhibit in the field. A variety of behavioral, physiological and hormonal responses vary in amplitude over a 24-h period and the degree to which these circadian rhythms are synchronized to the daily light–dark cycle can be quantified with a technique known as phasor analysis. Several studies have been carried out using phasor analysis in an attempt to measure circadian disruption exhibited by animals and by humans. To perform these studies, species-specific light measurement and light delivery technologies had to be developed based upon a fundamental understanding of circadian phototransduction mechanisms in the different species. When both nocturnal rodents and diurnal humans, experienced different species-specific light–dark shift schedules, they showed, based upon phasor analysis of the light–dark and activity–rest patterns, similar levels of light-dependent circadian disruption. Indeed, both rodents and humans show monotonically increasing and quantitatively similar levels of light-dependent circadian disruption with increasing shift-nights per week. Thus, phasor analysis provides a method for quantifying circadian disruption in the field and in the laboratory as well as a bridge between ecological measurements of circadian entrainment in humans and parametric studies of circadian disruption in animal models, including nocturnal rodents.