Integrating phylogenetic and functional biodiversity facets to guide conservation: a case study using anurans in a global biodiversity hotspot

The Cerrado is one of the most threatened biomes in Brazil, with little spatial representation within the Protected Area network. Recently, proposed conservation plans worldwide have advocated for the use of multiple biodiversity facets to protect unique evolutionary and functional processes. Our aim was to identify areas with high biodiversity representativeness applying this multifaceted perspective, and propose conservation plans based on the joint analysis of taxonomic, functional and phylogenetic diversity. We used a database of the Brazilian National Program for Research in Biodiversity, which employs a standard protocol for sampling tadpoles. The Cerrado database includes samples from 165 water bodies spread over 15 localities, covering most of the Central Brazilian Cerrado. We selected four morphological traits to calculate functional diversity and used a dated phylogeny available in the literature to compute phylogenetic diversity. Our approach selected five priority areas for conservation, one of which is already protected. Our results highlighted the importance of four new areas which show high values of diversity, including original lineages and traits, and urgently need conservation prioritization. Furthermore, unlike the current protected network, our approach performs significantly better than random at protecting sites with high phylogenetic and functional diversity. We therefore discuss how the multifaceted indices considered can help protect key ecosystem functions and evolutionary legacy in anuran communities of the Brazilian Cerrado.     

Using floristics,modern systematics and phylogenetics for disentangling biodiversity hotspots across scales: a Mediterranean case study

Abstract

Biodiversity comprises various levels of biological organisation. Global patterns of biodiversity are well established based on species occurrence. However, functional and historical processes underlying biodiversity patterns have been only recently approached. The increasingly active field of phylogenetics has allowed the rise of phylofloristic studies to help in elucidating the historical, evolutionary causes of plant biodiversity in addition to most commonly approached ecological correlates. Here, we review recent phylogeny-based studies disentangling the role of eco-geographic and historical factors on the biodiversity patterns of the Baetic–Rifan range and exemplify the use of barcoding to explore the evolutionary assembly of woody flora in the Spanish Sierra Nevada mountain range super-hotspot. Our species-level DNA barcoding approach resulted in a phylogeny potentially improving refinement of hypotheses in comparison with previous approaches based on phylogenies at genus level, and providing insights into the woody flora of Sierra Nevada subjected to systematic discussion. We show that the roles of elevation and substrate in biodiversity distribution vary according to the biodiversity component considered and also between endemic and non-endemic flora. We aim to illustrate how modern methods can further our understanding of the mechanisms underlying the assemblage of species and, consequently, the conservation of biodiversity.     

Records of a lake's life in time: the sediments

The evidence from analysis of cores from lake sediments is used to identify the influences which, acting through time, have brought about changes in the lakes of the English Lake District. These are: i. climatic changes, recorded mainly in microfossil assemblages ii. soil dynamics on catchments — the natural soil development of an interglacial cycle and its effect on water composition, and iii. perturbations of input resulting from activities of man.The present position of each of 14 lakes in a series of increasing eutrophication is shown to be the result of two processes of modification by man. The first was a significant reduction in volume of the hypolimnion of the shallow lakes, consequent on the accelerated rate of sediment accumulation which followed deforestation and cultivation of catchments in all the lakes — this did not affect the biology of the deep lakes. The second has been the introduction of human and animal wastes into some of the lakes during the last 120 years, which imposed on affected lakes a process of more rapid change which was more intense in the shallow lakes.     

深龋修复的力学模型分析

目的:模拟下颌第一磨牙Ⅰ类洞深龋,计算机分析得到修复体最佳应力分布时基底材料与修复材料厚度比例。方法 采用三维有限元法建立数值模型,利用SAP84(V4.2)程序计算并作力学分析。结果:在能护髓前提下应尽量减少次基厚度(1)银汞修复时,银汞合金厚度应大于基底厚度时应力分布最佳。(2)树脂修复时,树脂厚度与基底厚度相近,应力分布最佳。结论 根据材料弹性模量来决定基底材料与修复材料厚度比例。     

Evolutionary study of a potential selection target region in the pig

Domestication, modern breeding and artificial selection have shaped dramatically the genomic variability of domestic animals. In livestock, the so-called FAT1 quantitative trait locus (QTL) in porcine chromosome 4 was the first QTL uncovered although, to date, its precise molecular nature has remained elusive. Here, we characterize the nucleotide variability of 13 fragments of ∼500 bp equally spaced in a 2 Mb region in the vicinity of the FAT1 region in a wide-diversity panel of 32 pigs. Asian and European animals, including local Mediterranean and international pig breeds, were sequenced. Patterns of genetic variability were very complex and varied largely across loci and populations; they did not reveal overall a clear signal of a selective sweep in any breed, although FABP4 fragment showed a significantly higher diversity. We used an approximate Bayesian computation approach to infer the evolutionary history of this SSC4 region. Notably, we found that European pig populations have a much lower effective size than their Asian counterparts: in the order of hundreds vs hundreds of thousands. We show also an important part of extant European variability is actually due to introgression of Asian germplasm into Europe. This study shows how a potential loss in diversity caused by bottlenecks and possible selective sweeps associated with domestication and artificial selection can be counterbalanced by migration, making it much more difficult the identification of selection footprints based on naive demographic assumptions. Given the small fragment analyzed here, it remains to be studied how these conclusions apply to the rest of the genome.     

Estimating biodiversity: a case study on true bugs in argentinian wetlands

The species richness and relative abundance of faunas in defined areas are the raw materials in biodiversity science. The research methodology to acquire these data is inventory, and inventory quality depends on a number of parameters, for example collecting methods, season, and collector experience. To assess the ability of rapid inventory techniques to estimate local richness seven collectors sampled the fauna of true bugs in the Iberá watershed (Corrientes, Argentina) with seven methods during early spring, summer, and late summer (December, May, September) of 1 year. Twenty-three families, 225 spp. and 4,678 adults were found. We also applied various statistical techniques to correct the observed data for undersampling bias, which suggested the lower bound of annual heteropteran species richness at Pellegrini was about 250–300 species. Among heteropteran families, the particular inventory methodology was especially efficient in sampling Miridae. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Roadless areas and biodiversity: a case study in Alabama,USA

Roadless areas are important for biodiversity maintenance and nature conservation but remain politically controversial due to conflicting interests of conservation and development. In this study, we applied a recently developed index of roadless volume (RV) across 67 counties of Alabama, USA as a case study to examine the relationships between roadless areas and local species richness. Our results indicated that with the increase of RV across counties, both the number of total fish and exotic fish species increased, but the relationship was not significant for endemic fish species. The number of both herpetofaunal and plant species also increased with the increasing RV. For all included species, there was a significant positive correlation between species richness and RV values. The number of endangered species decreased with the increase of RV per-capita. Wildfire occurrences increased with the increase of RV. Preserving roadless areas is an important component of biodiversity conservation.     

Arguing for biodiversity in practice: a case study from the UK

With a web of different local actors, often with different perspectives and interests, turning ideas into practice for biodiversity often involves communicating, negotiating, bargaining and, therefore, argumentation. Within this process arguments are selected by actors, to achieve their goals, with varying levels of effectiveness. We examine the use of arguments in UK national biodiversity policies and at the local level from the perspective of those putting forward and receiving arguments. We assess the positive and negative framings within arguments and the effectiveness of arguments. Using interviews and formal documents as sources of data, we analyse nine argumentative interactions from a case study in the Greater Manchester area in the UK. Our findings highlight differences between arguments in national biodiversity policy and those used at the local level. We also show a link between positive framing and salient arguments that were particularly effective. In more polarised, high conflict situations the credibility of the argument, specifically how well it aligned with policy frameworks, strongly influenced its effectiveness. These findings suggest that selecting arguments that identify common ground at the local level contributes to effective outcomes by highlighting areas of mutual benefit. Where this is not possible, a strong policy framework for the conservation of biodiversity is important. A combination of bottom up and top down approaches is most likely to provide effective arguments for biodiversity.     

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.     

The potential of phytoremediation using hyperaccumulator plants: a case study at a lead-zinc mine site

Contamination with heavy metals is one of the most pressing threats to water and soil resources, as well as human health. Phytoremediation might potentially be used to remediate metal-contaminated sites. A major advance in the development of phytoremediation for heavy metal affected soils was the discovery of heavy metal hyperaccumulation in plants. This study applied several established criteria to identify hyperaccumulator plants. A case study was conducted at a mining area in the Hamedan province in the west central region of Iran. The results indicated that plant metal accumulation differed among species and plant parts. Plant species grown in substrata with elevated metal levels contained significantly higher metal levels. Using the most common criteria, Euphorbia macroclada and Centaurea virgata can be classified as hyperaccumulators of specific heavy metals measured in this study and they might potentially be used for the phytoremediation of contaminated soils.     

Effects of sitting postures on risks for deep tissue injury in the residuum of a transtibial prosthetic-user: a biomechanical case study

Transtibial amputation prosthetic-users are at risk of developing deep tissue injury (DTI) while donning their prosthesis for prolonged periods; however, no study addresses the mechanical loading of the residuum during sitting with a prosthesis. We combined MRI-based 3D finite element modelling of a residuum with an injury threshold and a muscle damage law to study risks for DTI in one sitting subject in two postures: 30°-knee-flexion vs. 90°-knee-flexion. We recorded skin-socket pressures, used as model boundary conditions. During the 90°-knee-flexion simulations, major internal muscle injuries were predicted (>1000 mm³). In contrast, the 30°-knee-flexion simulations only produced minor injury ( < 14 mm³). Predicted injury rates at 90°-knee-flexion were over one order of magnitude higher than those at 30°-knee-flexion. We concluded that in this particular subject, prolonged 90°-knee-flexion sitting theoretically endangers muscle viability in the residuum. By expanding the studies to large subject groups, this research approach can support development of guidelines for DTI prevention in prosthetic-users.     

On the use of parataxonomy in biodiversity monitoring: a case study on wild flora

Monitoring programs that assess species-richness and turnover are now regarded as essential to document biodiversity loss worldwide. Implementation of such programs is impeded by a general decrease in the number of skilled naturalists. Here we studied how morphotypes, instead of species, might be used by unskilled participants (referred to as “volunteers”) to survey common plant communities. Our main questions were: (1) Can morphotypes be used as a robust estimator of species-richness (α-diversity) and assemblage turnover (β-diversity)? and (2) What is the robustness (reproducibility and repeatability) of such methods? Double inventories were performed on 150 plots in arable field margins, one by a non-expert using morphotypes, the other by a taxonomist using species. To test the robustness of morphotype identification among participants, 20 additional plots were surveyed by eight volunteers using the same protocol. We showed that (1) the number of morphotypes identified by unskilled volunteers in a plot was always strongly correlated with species-richness. (2) Morphotypes were sensitive to differences among habitats but were less accurate than species to detect these differences. (3) Morphotype identification varied significantly within and between volunteers. Due to this lack of repeatability and reproducibility, parataxonomy cannot be considered a good surrogate for taxonomy. Nevertheless, assuming that morphotypes are identified with standardized methods, and that results are used only to evaluate gross species-richness but not species turnover, parataxonomy might be a valuable tool for rapid biodiversity assessment of common wild flora.     

Effects of combined ozone and nitrogen deposition on the in situ properties of eleven key plant species of a subalpine pasture

Tropospheric O₃ and deposition of reactive N threaten the composition and function of natural and semi-natural vegetation even in remote regions. However, little is known about effects of these pollutants individually or in combination on plant species in alpine habitats. We analyzed 11 frequent plant species of a subalpine Geo-Montani-Nardetum pasture exposed at 2,000 m a.s.l. in the Swiss Alps during 3 years using a factorial free-air exposure system with three concentrations of O₃ and five rates of N application. The aim was to detect subtle effects on leaf chlorophyll and N concentrations, leaf weight, specific leaf area (SLA), and δ¹⁸O and δ¹³C as proxies for gas exchange. We expected that the species’ responsiveness to O₃ and N would be related to their functional traits and that N-induced changes in these traits would modify the species’ response to O₃ via increased growth and higher leaf conductance (g _s). Most species reacted to N supply with the accumulation of N and chlorophyll, but with no change in SLA, g _s, and growth, except Carex sempervirens which showed increased water use efficiency and leaf weight. Elevated O₃ reduced g _s in most species, but this was not related to a reduction in leaf weight, which was recorded in half of the species. Contrary to our expectation, the magnitude of the response to both O₃ and N was not related to species-specific traits such as SLA or g _s. No pronounced O₃ × N interactions were observed. In conclusion, since for most species neither N nor gas exchange limited growth, their short-term response to O₃ and N and to their combination was small. O₃ × N interactive effects are expected to be more pronounced in habitats where species are more responsive to N due to favorable growth conditions in terms of nutrient availability and temperature. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

河口细菌群落多样性及其控制因素:以切萨皮克湾为例

咸淡水的混合和重要营养盐与有机物的再循环,使得河口成为地球上生产力较高而动态变化明显的水生生态系统.一个典型的河口区断面中,细菌群落包含了一些从淡水到海洋的过渡类型:例如α-变形菌(Alphaproteobacteria)、p-变形菌(Betaproteobacteria)、γ-变形菌(Gammaproteobacteria)、蓝细菌(Cyanobactenia)[聚球藻(Synechococcus)]、拟杆菌(Bacteroidetes)、放线细菌(Actinobacteria)和疣微菌(Verrucomicrobia)等.此外,河口也包含其独特的细菌群落:SAR11组、玫瑰杆菌属(Roseobacter)、SAR86和放线细菌(Actinobacteria)的一些进化亚枝(subclades),表明海湾或者大型温带河口区细菌类群具有区域生态适应性.以研究较多的美国切萨皮克湾(Chesapeake Bay)为例,其细菌群落呈现出显著的季节性变化和周期性的年际变化特征;这些变化除了受水的滞留时间和细菌生长速度影响外,还可能受其他许多环境因子的影响.其中叶绿素a和水温变化的影响最大,其他环境因子如溶解氧、铵态氮、亚硝酸盐和硝酸盐以及病毒的丰度也有影响.近年来,基于群落水平的基因组学(genomics)和后基因组学(postgenomics)(转录组学和蛋白质组学)技术应用于研究自然条件下微生物群落错综复杂的基因多样性和表达,提供了揭示水环境中微生物群落组成和新功能基因的途径.     

Key elements in achieving a successful recovery programme: A discussion illustrated by the Gould's Petrel case study

Summary   Surprisingly few faunal taxa worldwide have experienced an improvement in conservation status through direct conservation action. One of the few is Gould's Petrel ( Pterodroma leucoptera leucoptera ) – a threatened species that breeds only in New South Wales. In the early 1990s, the breeding population of this subspecies was small (<250 pairs) and declining. Each year, adult mortality at the breeding grounds exceeded the number of young produced. A recovery programme, focused on reducing adult mortality, commenced in 1993. As a result of the recovery actions undertaken, the Gould's Petrel is now increasing in numbers. Also, the rainforest where this seabird breeds is now regenerating after being degraded for almost a century by the introduced European Rabbit ( Oryctolagus cuniculus ). The creation of artificial nesting habitat and the development of effective translocation procedures have led to the establishment of a second breeding colony of Gould's Petrel, further reducing the risk of extinction.
In this paper, we explore the key elements we believe to be responsible for the success of this particular recovery programme: (i) a strong underpinning of robust ecological research; (ii) adaptive management; (iii) monitoring and reporting; (iv) a multidisciplinary approach; and (v) a willingness to accept risk. We conclude with some suggestions to improve the current recovery planning process.     

Incorporating livelihoods in biodiversity conservation: a case study of cacao agroforestry systems in Talamanca,Costa Rica

Over the past two decades, various organizations have promoted cacao agroforestry systems as a tool for biodiversity conservation in the Bribri-Cabécar indigenous territories of Talamanca, Costa Rica. Despite these efforts, cacao production is declining and is being replaced by less diverse systems that have lower biodiversity value. Understanding the factors that influence household land use is essential in order to promote cacao agroforestry systems as a viable livelihood strategy. We incorporate elements of livelihoods analyses and socioeconomic data to examine cacao agroforestry systems as a livelihood strategy compared with other crops in Talamanca. Several factors help to explain the abandonment of cacao agroforestry systems and their conversion to other land uses. These factors include shocks and trends beyond the control of households such as crop disease and population growth and concentration, as well as structures and processes such as the shift from a subsistence to a cash-based economy, relative prices of cacao and other cash crops, and the availability of market and government support for agriculture. We argue that a livelihoods approach provides a useful framework to examine the decline of cacao agroforestry systems and generates insights on how to stem the rate of their conversion to less diverse land uses.