Assessing significance for biodiversity conservation on private land in New Zealand

The assessment of ecological significance is a key part of a territorial local authority’s (TLA) responsibility to provide for the protection of areas of significant indigenous vegetation and significant habitats of indigenous fauna as required under Section 6(c) of the Resource Management Act (RMA) 1991. While a number of methods have been used to achieve this, these have been largely unpublished and there is considerable variability in the approach taken by different TLAs. We propose four criteria (rarity and distinctiveness, representativeness, ecological context, and sustainability) for assessing significance of indigenous biodiversity in terms of RMA Section 6(c). These criteria could form the basis for a consistent national approach to significance assessment. These criteria have been developed from early assessment schemes such as the Protected Natural Areas Programme. While there is no one “right” system for conservation assessment, we hope this paper will stimulate discussion amongst the ecological community on the best ways to undertake significance assessment.     

Ecological assessment of groundwater ecosystems – Vision or illusion?

Environmental policy and in particular the European water legislation, in the framework of the EU Groundwater Directive, has started to consider groundwater not only as a resource but as a living ecosystem. A precondition for comprehensive groundwater protection is thus the assessment of the biological and ecological state. The assessment of ecosystems requires consideration of ecological criteria, which so far are not available for groundwater systems. In the framework of a national project, the German Federal Environment Agency (UBA) supports a consortium of scientists and stakeholders from water boards and regional environmental authorities to develop a first concept for an ecological assessment scheme for groundwater ecosystems. The attempts towards an integrative concept include the following steps: (i) selection of appropriate biological and ecological parameters, (ii) typology of groundwater ecosystems, (iii) derivation of a reference status (Leitbild) and natural background values for biological variables, (iv) identification of potential bioindicators and definition of threshold values, and (v) development of an assessment model. These proposed steps are discussed on the basis of a data set from two groundwater landscapes in Southern Germany. Investigations considered three different spatial units, i.e. the habitat unit at the local scale, and the aquifer type unit as well as the landscape unit at the regional scale. Fauna as well as bacterial communities could provide valuable ecological information on the ecosystems status. The paper reviews ‘state of the art’ knowledge and evaluates the near future perspectives for the development and implementation of groundwater ecosystems assessment programmes.     

Cannot see the diversity for all the species: Evaluating inclusion criteria for local species lists when using abundant citizen science data

Abundant citizen science data on species occurrences are becoming increasingly available and enable identifying composition of communities occurring at multiple sites with high temporal resolution. However, for species displaying temporary patterns of local occurrences that are transient to some sites, biodiversity measures are clearly dependent on the criteria used to include species into local species lists. Using abundant opportunistic citizen science data from frequently visited wetlands, we investigated the sensitivity of α‐ and β‐diversity estimates to the use raw versus detection‐corrected data and to the use of inclusion criteria for species presence reflecting alternative site use. We tested seven inclusion criteria (with varying number of days required to be present) on time series of daily occurrence status during a breeding season of 90 days for 77 wetland bird species. We show that even when opportunistic presence‐only observation data are abundant, raw data may not produce reliable local species richness estimates and rank sites very differently in terms of species richness. Furthermore, occupancy model based α‐ and β‐diversity estimates were sensitive to the inclusion criteria used. Total species lists (all species observed at least once during a season) may therefore mask diversity differences among sites in local communities of species, by including vagrant species on potentially breeding communities and change the relative rank order of sites in terms of species richness. Very high sampling effort does not necessarily free opportunistic data from its inherent bias and can produce a pattern in which many species are observed at least once almost everywhere, thus leading to a possible paradox: The large amount of biological information may hinder its usefulness. Therefore, when prioritizing among sites to manage or preserve species diversity estimates need to be carefully related to relevant inclusion criteria depending on the diversity estimate in focus.     

A decision tool for listing species for protection on different geographic scales and administrative levels

An important task in conservation biology is to assess the spatial scale pertinent for species protection since some species may require protection throughout their distribution, others in only part of their range. Once this is done, species can be correctly identified for listing at different administrative levels (e.g. continental, national, and local). Here, we propose an objective method to list taxa at nested administrative levels based on three criteria (responsibility, rarity and vulnerability). We tested the method using quantitative data on the distribution, abundance and decline of orchids in France. The proposed method enables increased protection status in regions where species’ abundance and diversity are higher, gives priority to species for which an individual administrative unit has high responsibility and allows objective integration of species decline at different administrative levels. The method also enables the integration of locally rare species at their distribution limits and avoids repetition of species listing across second-level administrative units. The use of an objective method such as this could contribute to a standardised system of priority setting that integrates the geographic scale of rarity in relation to different administrative levels for protection.     

Fire management in Tasmania’s Wilderness World Heritage Area: Ecosystem restoration using Indigenous‐style fire regimes?

Summary In many natural areas, changes in fire regimes since European settlement have resulted in adverse impacts on elements of biological diversity that survived millennia of land management by Indigenous people. Some of the rainforest and alpine elements that depend on south‐west Tasmania’s World Heritage Area have been in decline since European settlement of Tasmania due to an increase in the incidence of landscape‐scale fires in the period 1850–1940. Some of the buttongrass moorland elements that also depend on the region are in decline or impending decline because of a decreased incidence and/or size of burns since 1940. Will an Indigenous‐style fire regime serve the interests of biological diversity? We examine this question in the context of the fire ecology and fire history of south‐west Tasmania. From this assessment we argue that a return to Indigenous‐ style burning, modified to address contemporary issues such as the prevention of unplanned ignition, suppression of wildfires and burning to favour rare and threatened species may help to reverse trends towards ecosystem degradation in this region.     

Site prioritisation for the protection of rare subterranean species – the cases of two ostracods from south-western France

1. Delineation of protected areas for rare subterranean species is a key problem for groundwater biodiversity conservation, because of practical difficulties in implementation. Criteria for site selection are presented that are derived from studies on two remarkable Ostracoda, Dolekiella europaea Gidó, Artheau, Colin, Danielopol & Marmonier (Limnocytheridae) and Vestalenula carveli Artheau (Darwinulidae) discovered in south-western France.
2. Arguments for natural heritage value and protection of subterranean species are proposed and illustrated by using information on these two ostracod species. The proposed criteria are: (i) local and/or regional endemism; (ii) known occurrence of the species at a few localities only; (iii) representativeness for ancient phylogenetic lineages with wider geographical distributions in the past; and (iv) suitability for scientific study because of unique morphological or biological traits.
3. It is also proposed to prioritise the protection of subsurface sites using the following criteria: (i) type locality for newly described species; (ii) presence of other rare stygobiotic taxa; and (iii) high population densities of the primary target species.
4. Development and implementation of protection strategies at local scale are likely to benefit from collaboration between scientists, policy makers and stakeholders. The measures taken should complement existing national and/or international attempts at large-scale protection of groundwater biodiversity.     

钱塘江中游水生昆虫群落功能多样性对土地利用变化的响应

基于11个反映水生昆虫生活史、对外界抵抗力和生理特征的生物学性状,应用目前国际上通用的fourth-corner统计方法,系统研究了浙江省钱塘江中游流域水生昆虫功能多样性对土地利用变化的响应.结果表明： 部分生物学性状对土地利用变化敏感,且其随人类干扰强度的变化所发生的改变与预期吻合,其最大个体长度逐渐下降,呼吸方式从以鳃呼吸为主转变为以表皮呼吸为主,掘穴者数量显著增加.参照点的功能多样性指数(Rao值)显著高于干扰点(P<0.001).说明人类活动引起的土地利用变化导致溪流水质和栖境质量下降,引起群落的变异和对生物性状组成的筛选,最终导致水生昆虫群落功能多样性改变.生物性状及功能多样性是未来评价生态健康的潜在指标.     

Uncertainty associated with river health assessment in a varying environment: The case of a predictive fish-based index in France

Sensitive biological measures of river ecosystem quality are needed to assess, maintain or restore ecological conditions of water bodies. Since our understanding of these complex systems is imperfect, decision-making requires recognizing uncertainty. In this study, a new predictive multi-metric index based on fish functional traits was developed to assess French rivers. Information on fish assemblage structure, local environment and human-induced disturbances of 1654 French river sites was compiled. A Bayesian framework was used to predict theoretical metric values in absence of human pressure and to estimate the uncertainty associated with these predictions. The uncertainty associated with the index score gives the confidence associated with the evaluation of site ecological conditions.Among the 228 potential metrics tested, only 11 were retained for the index computation. The final index is independent from natural variability and sensitive to human-induced disturbances. In particular, it is affected by the accumulation of different degradations and specific degradations including hydrological perturbations. Predictive uncertainty is globally lower for IPR+ than for underlying metrics.This new methodology seems appropriate to develop bio-indication tools accounting for uncertainty related to reference condition definition and could be extended to other biological groups and areas. Our results support the use of multi-metric indexes to assess rivers and strengthen the idea that examination of uncertainty could contribute greatly to the improvement of the assessment power of bio-indicators.     

Post-fire succession in the northern jarrah forest of Western Australia

Post-fire species changes were documented over a portion of the northern section of the jarrah forest of Western Australia from a series of sites of known age since last fire. Species richness and species diversity were observed to increase following fire for several years, followed by a gradual decline. Dominance-diversity curves indicated that maximum diversity occurred from 3 to 5 years following fire. The species composition of sites of different regions was more similar than sites of similar time since burn. The significance of the results to the programme of controlled burns is discussed.     

Structural analysis, identification, and design of calcium-binding sites in proteins

Assigning proteins with functions based on the 3-D structure requires high-speed techniques to make a systematic survey of protein structures. Calcium regulates many biological systems by binding numerous proteins in different biological environments. Despite the great diversity in the composition of ligand residues and bond angles and lengths of calcium-binding sites, our structural analysis of 11 calcium-binding sites in different classes of proteins has shown that common local structural parameters can be used to identify and design calcium-binding proteins. Natural calcium-binding sites in both EF-hand proteins and non-EF-hand proteins can be described with the smallest deviation from the geometry of an ideal pentagonal bipyramid. Further, two different magnesium-binding sites in parvalbumin and calbindin(D9K) can also be identified using an octahedral geometry. Using the established method, we have designed de novo calcium-binding sites into the scaffold of non-calcium-binding proteins CD2 and Rop. Our results suggest that it is possible to identify calcium- and magnesium-binding sites in proteins and design de novo metal-binding sites.     

Impact of protection on nest take and nesting success of parrots in Africa, Asia and Australasia

Wild parrots represent one of the greatest commercial interests in the legal trade in wild birds. Although it is difficult to quantify, there is a considerable illegal trade in wild parrots. Thirty-six per cent of the world's parrot species are listed by the International Union for the Conservation of Nature as threatened or near threatened, and 55% of these are threatened to some degree by trade. In this paper, we investigate the impact of protection on the number of nests that failed because of nestlings being taken by humans (hereafter nest take) and on nesting success in parrots. We collate data on parrot nest take from published and unpublished studies from Africa, Asia and Australasia, including countries and sites with and without national and local parrot protection measures in place. Nest take was insignificant in Australia, where all studies were from areas with both local and national protection. For less developed countries, levels of nest take were variable between studies, spanning the whole range from 0 to 100%. Protection significantly reduced nest take and correspondingly increased nesting success. Our results corroborate those for the Neotropics; thus, the advantages of protection appear to be independent of geographical location or political and economic conditions. We analysed data on legal trade in wild-caught parrots before and after implementation of the 1992 Wild Bird Conservation Act (which practically eliminated import of parrots to the USA) and found that there was no apparent shift in parrot imports to other global regions from the Neotropics. We suggest that conservation of parrots globally would benefit from similar legislation introduced in other regions, such as the EU (15), which is responsible for more than 60% of global imports of wild parrots.     

Outcome prediction based on microarray analysis: a critical perspective on methods

Background  

Information extraction from microarrays has not yet been widely used in diagnostic or prognostic decision-support systems, due to the diversity of results produced by the available techniques, their instability on different data sets and the inability to relate statistical significance with biological relevance. Thus, there is an urgent need to address the statistical framework of microarray analysis and identify its drawbacks and limitations, which will enable us to thoroughly compare methodologies under the same experimental set-up and associate results with confidence intervals meaningful to clinicians. In this study we consider gene-selection algorithms with the aim to reveal inefficiencies in performance evaluation and address aspects that can reduce uncertainty in algorithmic validation.     

Hummingbird diversity, food niche characters, and assemblage composition along a latitudinal precipitation gradient in the Bolivian lowlands

As for many other taxa, hummingbird diversity declines away from the equator, but the causes for this decline are still disputed and might involve, among others, climatic factors or the availability of food resources. Because hummingbirds are one of the classical examples for plant–animal coevolution, it has been proposed that the diversity of hummingbird assemblages might depend on the diversity of food plants available. We tested this hypothesis by studying the hummingbird assemblages and their food plants for 1 year at six sites along a 660-km-long transect in Bolivian lowland forests extending from the southernmost Amazonian rain forests to dry Chaco forests. Hummingbird diversity was higher in the northern three sites as compared to the southern ones, with an abrupt decline in species numbers and a corresponding change in taxonomic composition at the boundary from evergreen to drought deciduous forests. Hummingbird diversity and abundance were only weakly correlated to climatic factors or to the diversity of humming-visited flowers, but strongly to the seasonal abundance of flowers. The overlap in nectar diet between hummingbird species depended on the number of plant species: when numerous species were available, the hummingbirds segregated by feeding preferences, but when few flowers were available, all hummingbirds fed on the same plants. We conclude that the local diversity of hummingbird species is not primarily determined by the diversity of food plants, but rather by the abundance of flowers available at any given point in time.     

Translocations,conservation, and climate change: use of restoration sites as protorefuges and protorefugia

High levels of human activity have affected the quality and usability of the natural landscape, leading to habitat degradation, loss of connectivity between sites, and reduced chances of long‐term survival for individual species. In line with conservation policy, ecological restoration practitioners try to improve degraded sites by means of reestablishing species lost from these sites, thereby returning ecological functionality and maintaining biological diversity. It may appear difficult to integrate the long‐term potential impacts of climate change within restoration strategies. However, more refined climate projections and species distribution models provide us with better understanding of likely scenarios, enabling us to consider future proofing as an integral part of the design of restoration sites, aiding plant conservation. We believe that it is possible to go one step further with a closer integration of restoration and conservation objectives. We introduce the novel concepts of “protorefuges” and “protorefugia”—restoration sites that threatened species can be translocated to, where the restoration design can be specifically adapted to help reduce the decline of threatened species at the leading and trailing edges (respectively) of bioclimatic envelope shifts. This is particularly relevant for nuclear decommissioning sites, which may be free from human activity for decades to centuries.     

Assessing protection for imperiled species of nevada, U.S.A.: are species slipping through the cracks of existing protections?

To assess whether imperiled species are covered by existing protections in the biologically-rich state of Nevada, U.S.A., we compared the distribution of reserves with known imperiled species occurrences. For species poorly represented in reserves, we determined whether they were receiving alternate protection under the U.S. Endangered Species Act or voluntary conservation plans. A majority (212, 55%) of Nevada’s 384 imperiled species had fewer than 25% of occurrences in reserves and most (282, 68%) had fewer than 50% of occurrences in reserves. Of imperiled species with less than 25% or fewer than two occurrences in reserves, only 9% are currently receiving alternate protection from the Endangered Species Act or voluntary plans. These results suggest that providing protection for imperiled species in Nevada will require both an expansion of the existing reserve system, which currently covers 14% of the state, and protection of more species under the Endangered Species Act or other programs. By dividing Nevada into equal-sized hexagons and scoring each of these hexagons based on a rarity-weighted richness index of imperiled species occurrences, we identified 19 imperiled species hot spots in Nevada. No imperiled species occurrences were protected in seven (37%) and less than half were protected in 11 (58%) of these hot spots. Protecting these areas could provide important additional protection for imperiled species in Nevada. Evaluations of protective measures for biological diversity should include the full suite of protections, including both reserves and laws and regulations.     

基于DPSEEA模型构建生物安全评价体系：以深圳市为例

由于生物安全内涵外延和基本要素的模糊性、评价指标及评价方法的多元性等因素的限制, 我国至今尚未形成全面有效的生物安全评价指标体系。为构建生物安全评价体系, 研判生物安全现状, 本文首先运用规范分析法剖析《生物安全法》中有关“生物安全”定义的特点及不足, 从国家安全角度认为生物安全是指国家有效防范和应对危险生物因子及相关因素的威胁, 维护和保障自身安全与利益的能力和状态。明晰了生物安全的外延, 即只有对国家安全利益、民众健康、生态环境保护产生威胁的生物风险, 才是生物安全所规制的对象。其次, 生物安全基本要素包括自然生物安全和社会经济生物安全。自然生物安全主要指民众健康和生态环境保护方面, 包括生物个体安全和生物多样性安全。社会经济生物安全的关注点在国家安全利益, 即社会稳定和国家经济利益, 包括生物技术安全、生物实验室安全。第三, 以生物安全基本要素为管理对象的尺度, 将国家安全利益、民众健康和生态环境保护作为评价主体, 以生物法治为理念, 运用模型构建法, 将定性指标和定量指标相结合, 基于驱动力‒压力‒状态‒接触‒影响‒行动模型(driving force-pressure-state-exposure-effect-action, DPSEEA)构建了一套具有生物法治特色的生物安全评价指标体系, 包括生物安全法律法规体系健全水平、生物安全所涉违法犯罪行为的打击力度、生物安全各部门机构协调机制的建立和完善程度、符合规定标准的生物实验室数量和百分比、生物安全人才数量及密度、对生物产业和基本卫生部门的官方援助及其他途径投资总额、疫苗覆盖的目标人群比例、生物安全的宣传教育普及率8项评价指标在内共32项生物安全评价指标。最后, 基于实地调研及数据统计分析, 以2019年和2020年深圳生物安全工作为例对评价体系进行验证。结果显示, 深圳生物安全工作在农业生物安全、动植物防疫、防范外来物种入侵方面成果显著; 但仍在法律法规体系、生物安全人才培养和资金投入、生物安全普及率方面存在不足。针对上述问题提出完善生物安全法律法规体系并注重法律协调衔接、“一个健康”实现多元协同生物治理、加强人才培养和资金投入、加强生物安全宣传教育等建议。     

High variability in patterns of population decline: the importance of local processes in species extinctions

A fundamental goal of conservation science is to improve conservation practice. Understanding species extinction patterns has been a central approach towards this objective. However, uncertainty remains about the extent to which species-level patterns reliably indicate population phenomena at the scale of local sites, where conservation ultimately takes place. Here, we explore the importance of both species- and site-specific components of variation in local population declines following habitat disturbance, and test a suite of hypotheses about their intrinsic and extrinsic drivers. To achieve these goals, we analyse an unusually detailed global dataset for species responses to habitat disturbance, namely primates in timber extraction systems, using cross-classified generalized linear mixed models. We show that while there are consistent differences in the severity of local population decline between species, an equal amount of variation also occurs between sites. The tests of our hypotheses further indicate that a combination of biological traits at the species level, and environmental factors at the site level, can help to explain these patterns. Specifically, primate populations show a more marked decline when the species is characterized by slow reproduction, high ecological requirements, low ecological flexibility and small body size; and when the local environment has had less time for recovery following disturbance. Our results demonstrate that individual species show a highly heterogeneous, yet explicable, pattern of decline. The increased recognition and elucidation of local-scale processes in species declines will improve our ability to conserve biodiversity in the future.     

Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment

Generalized dissimilarity modelling (GDM) is a statistical technique for analysing and predicting spatial patterns of turnover in community composition (beta diversity) across large regions. The approach is an extension of matrix regression, designed specifically to accommodate two types of nonlinearity commonly encountered in large-scaled ecological data sets: (1) the curvilinear relationship between increasing ecological distance, and observed compositional dissimilarity, between sites; and (2) the variation in the rate of compositional turnover at different positions along environmental gradients. GDM can be further adapted to accommodate special types of biological and environmental data including, for example, information on phylogenetic relationships between species and information on barriers to dispersal between geographical locations. The approach can be applied to a wide range of assessment activities including visualization of spatial patterns in community composition, constrained environmental classification, distributional modelling of species or community types, survey gap analysis, conservation assessment, and climate-change impact assessment.     

Assessing significance under the RMA ? moving forwards: a reply to Walker et al. (2008)

Walker et al. (2008) are critical of the methods used by ecologists and others with ?vested interests? to identify significant biodiversity values and provide for their protection under the Resource Management Act (1991) (RMA), particularly the use of the draft criteria proposed in Norton & Roper-Lindsay (2004). However, we believe that their criticism is flawed because of their failure to fully understand the context of the Norton?Roper-Lindsay criteria; unjustified presumptions they make about the roles of ecologists in assisting those applying for resource consents and administering the RMA; and a failure to take into account the current realities of native biodiversity conservation for those parts of New Zealand covered by the RMA. In this reply we address these issues and outline a way to move forwards in this debate.