The ecological integrity of the Lower Olifants River,Limpopo province,South Africa: 2009–2015 – Part A: Olifants River main stem

The major rivers of the South African ‘Lowveld’ (low-latitude savanna) suffer numerous impacts from upstream economic activities. Whereas monitoring these rivers is required to detect biodiversity losses, record pollution events and devise mitigation strategies, current monitoring programmes are inadequate. In 2009, the South African Earth Observation Network initiated an intensive long-term research programme on the Lowveld reaches of the Olifants River. Physico-chemical parameters, aquatic macroinvertebrates and fish abundances were recorded at four Lowveld sites in the Olifants River. We review six years of this programme. The results suggest deterioration in the ecological condition of the Olifants River with no discernible improvement through protected areas. Trends could not be detected. The parameters measured, sampling methods and/or sampling frequency might be responsible for the limited trends observed, or alternatively the results simply reflect stable conditions despite on-going pollution. Real time monitoring and an expansion in the parameters monitored would add value to the monitoring programme.     

Do SASS5 scores vary with season in the South African highveld? A case study on the Skeerpoort River,North West province,South Africa

Macroinvertebrate assemblages can vary with season as a result of changing environmental conditions and phenology of individual species. The objective of this study was to determine whether results from the South African Scoring System version 5 (SASS5) are affected by season. The standard SASS5 protocol was used to sample three sites on the Skeerpoort River, South Africa, in autumn, winter and spring 2013, and summer 2014. At each site, stream morphology was characterised and physico-chemical variables were measured. Two-way analysis of variance (ANOVA) was used to compare SASS indices in relation to site and season, and a one-way ANOVA was used to test the effect of season using both current and historical data. Macroinvertebrate assemblage similarity of sites was determined using non-metric multidimensional scaling ordination, followed by analysis of similarity. Whilst macroinvertebrate assemblages differed between seasons and sites, there was no seasonal variation in the values of SASS indices, but they did differ between sites. SASS5 appears to be robust to seasonal variation in macroinvertebrate assemblage and seems suitable for use throughout the year in a perennial river draining the South African highveld region.     

Role of DNA barcoding in marine biodiversity assessment and conservation: An update

More than two third area of our planet is covered by oceans and assessment of marine biodiversity is a challenging task. With the increasing global population, there is a tendency to exploit marine resources for food, energy and other requirements. This puts pressure on the fragile marine environment and necessitates sustainable conservation efforts. Marine species identification using traditional taxonomical methods is often burdened with taxonomic controversies. Here we discuss the comparatively new concept of DNA barcoding and its significance in marine perspective. This molecular technique can be useful in the assessment of cryptic species which is widespread in marine environment and linking the different life cycle stages to the adult which is difficult to accomplish in the marine ecosystem. Other advantages of DNA barcoding include authentication and safety assessment of seafood, wildlife forensics, conservation genetics and detection of invasive alien species (IAS). Global DNA barcoding efforts in the marine habitat include MarBOL, CeDAMar, CMarZ, SHARK-BOL, etc. An overview on DNA barcoding of different marine groups ranging from the microbes to mammals is revealed. In conjugation with newer and faster techniques like high-throughput sequencing, DNA barcoding can serve as an effective modern tool in marine biodiversity assessment and conservation.     

Developing products for conservation decision-making: lessons from a spatial biodiversity assessment for South Africa

South Africa's first national assessment of spatial priorities for biodiversity conservation, released in 2005, aimed to identify conservation priority areas for mainstreaming into all sectors at national and provincial scales. This National Spatial Biodiversity Assessment (NSBA) was based on a planning for implementation approach in order to deliver defensible products useful to decision-makers. The NSBA aimed to produce a map of broad-scale priority areas for future finer-scale assessment and conservation action. This map summarized information on species, ecosystems, ecological processes, and the pressures they face from human activities. Owing to the complexity of the priority area map, two additional user-friendly products — maps of ecosystem status and protection levels — were developed. These products represented the habitat loss and protected area coverage of South Africa's ecosystems relative to their conservation targets. A year after release, we reflect on the NSBA process, products and uptake by implementing agencies (with a specific focus on the terrestrial biodiversity assessment) in order to contribute to the growing body of documented best practice in conservation planning. The ecosystem status product has been widely used at national and provincial scales due in large to its clear and compelling message. The protection level and overall priority map have also witnessed uptake, the former in guiding the expansion of protected areas and the latter as an integrated map of national biodiversity status. The strong collaboration of local planners and implementers with in-depth experience of biodiversity assessment, using a systematic approach and focusing on communicating a few high level messages, appears to have contributed to the initial, successful uptake of the NSBA. We conclude with a call to address data and monitoring shortcomings before the next NSBA in 2010.     

Colonization,variability, and the use of substratum-filled trays for biomonitoring benthic communities

Sampling variability and colonization rate of introduced substrates (plastic trays filled with pebble and cobble) in two southwestern Virginia streams are described. Substrates were rapidly colonized by aquatic macroinvertebrates, but colonization rates differed between years, possibly due to annual variability in macroinvertebrate abundance. To examine the applicability of using these substrates for biomonitoring benthic communities, trays were placed at several locations in a river receiving power plant discharges. Only six samples were necessary to detect a 15%reduction in macroinvertebrate density and a 12% reduction in number of taxa at effluent sites. Benthic communities established on rock-filled trays and multiplate samplers collected from the same stations during the same period were compared. Although multiplate samplers were more variable than rock trays and were selective for different taxa, both substrate types showed significant differences in community parameters among locations. Rock trays at all sites were dominated by Cheumatopsyche sp., whereas chironomids were more abundant on multiplate samplers. The relative abundance of mayflies was reduced at the effluent site on both substrate types.     

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.     

Long-term biomonitoring of lichen and bryophyte biodiversity at Burnham Beeches SAC and global environmental change

Long-term monitoring began 20 years ago at Burnham Beeches Site of Special Interest (SSSI), National Nature Reserve (NNR) and European Special Area of Conservation (SAC) lying 40 km west of London as a consequence of the authorization of an application to extract gravel from an adjacent site lying north of Slough Trading Estate. Dust monitoring (sticky pads) and photographic monitoring, recording and image analysis was instigated in 1992 on Parmelion communities to assess changes in lichen growth, health and community composition. Long-term monitoring identifies that the lichen flora on free-standing trees has undergone rapid expansion from a near dominance by the SO₂-tolerant ‘acidophyte’ species Lecanora conizaeoides and Hypogymnia physodes following reductions in SO₂ concentrations. Long-term influences of low levels of eutrophication, gaseous pollutants (particularly globally rising background ozone concentrations) on lichen and bryophyte communities and succession under changing climatic conditions are unknown. Soil–plant relationships, lichen–invertebrate interactions and a pollution legacy must also be considered.     

Woody vegetation structure in conserved versus communal land in a biodiversity hotspot: A case study in Maputaland,South Africa

This study evaluated the effects of humans and herbivores on woody vegetation structure in the woodlands and forests of Maputaland. The woody vegetation structure of plant communities at three sites within a similar environment but under different utilisation regimes since the early 1990s was evaluated by means of a stem diameter and tree height class analysis. The effects of human utilisation were evaluated on the land of the rural Manqakulane community; herbivore utilisation was evaluated in the Tembe Elephant Park; and because of the low levels of utilisation since 1992 the vegetation in the Tshanini Community Conservation Area was used as a benchmark for the comparisons. In both woodlands and sand forests, utilisation regime resulted in changes in stem diameter size class distributions, although the height structure remained unchanged. In communal land human-associated disturbance promoted the presence of small woody plants. In general, conserved land under animal utilisation, had the least small diameter woody plants, but most of the large trees, whereas in the absence of utilisation intermediate densities of small diameter woody plants were found but low densities of large trees. This study presents the first quantification of significant changes in the woody vegetation structure in Maputaland due to human utilisation, herbivore utilisation, or lack of utilisation. It also provides a timeframe within which land use can cause significant changes in vegetation structure.     

Comprehensive DNA barcodes for species identification and discovery of cryptic diversity in mayfly larvae from South Korea: Implications for freshwater ecosystem biomonitoring

DNA barcoding of aquatic macroinvertebrates holds much promise as a tool for taxonomic research and for providing baseline reference for phylogenetic analysis and aquatic ecosystem biomonitoring. We obtained 112 novel sequences of the barcode region of the mitochondrial DNA cytochrome c oxidase subunit I gene representing 11 families, 25 genera, and 43 species of mayfly (Insecta: Ephemeroptera) from South Korea. No species shared barcode sequences and all can be identified with barcodes with a possible exception of some species. Minimum levels of interspecific genetic distances ranged from 6.7 to 32.9% (mean: 23.7%), whereas average levels of intraspecific divergence was 3.7%. The latter value was inflated by the presence of very high divergences within some taxa. In fact, approximately 33.3% (15/45) of the species included two or more haplotype clusters showing greater than 5.0% sequence divergence and some values were as high as 32.9%. Many of the species with high intraspecific divergences are para‐ or polyphyletic and represent the possibility of species complexes. Our study suggests that type or topotype specimens should be sequenced to identify accurate barcoding clusters with morphological species concepts and also to determine the status of currently synonymized species.     

Patterns of chironomid body-size distribution in an effluent-impacted river in the Eastern Cape,South Africa

Body size is an important determinant of assemblage structure in rivers and streams impacted by elevated concentrations of pollutants such as salts and metals. In the present study, because of the larger surface-area-tovolume ratio of small-bodied chironomid species compared with large-bodied species, it was hypothesised that the relative abundance of the small-bodied species would decrease at the impacted sites by elevated concentrations of total dissolved solids compared with that at the less-impacted control site. The aim of this study was to analyse and compare patterns of chironomid final instar body-size classes at impacted sites with those at the control site. Chironomid larvae were sampled seasonally from August 2009 to September 2012 from one control site and three impacted sites (Sites 2, 3 and 4) in the Swartkops River, Eastern Cape. Site 2 was impacted by diffuse pollution sources, whereas Sites 3 and 4 were impacted by wastewater effluent discharges in addition to diffuse pollution sources. Small-bodied species dominated the assemblage at the control site and declined significantly at the impacted sites, suggesting that chironomid body size responds predictably to deteriorating water quality in the Swartkops River.     

DNA barcode assessment of Mediterranean mayflies (Ephemeroptera), benchmark data for a regional reference library for rapid biomonitoring of freshwaters

Accurate identification of aquatic species is fundamental to freshwater research. In this paper, we targeted Ephemeroptera, a key taxonomic insect group for biomonitoring of water bodies and present an overview on the efficacy of the DNA barcoding approach to document species identity in the Mediterranean region. We sequenced the mitochondrial cytochrome c oxidase (COI) in 39 nominal species. Sample discrimination and species identification were investigated by evaluating haplotype identity and similarity, intra-/interspecific genetic distances, optimal identification of barcoding gap thresholds, estimates of species monophyly and comparative species matches on available reference libraries. The resolving power of the obtained data was discussed in the light of statistical tools such as Spider R-package and Poisson Tree Processes. High levels of species identification were achieved with all the used methodologies, and the occurrence of cryptic species was suggested. We conclude that DNA barcoding is a powerful tool for taxonomic research in Mediterranean mayflies, with great promise to ameliorate biodiversity inventories of freshwater ecosystems and to provide the necessary accuracy for water quality assessment programs. Our results further indicated we need to upgrade the current regional mayfly diversity knowledge. The development of a Mediterranean reference library could integrate this new information system.     

基于C-Plan规划软件的生物多样性就地保护优先区规划——以中国东北地区为例

以中国东北地区为研究区域,根据生物多样性属性特征,选择研究区域内具有代表性的濒危物种作为指示物种,利用系统保护规划方法(Systematic Conservation Planning,SCP)和保护规划软件(C-Plan),对该区域进行了优先保护规划研究。通过计算规划单元的不可替代性值(Irreplaceability,IR),找出区域生物多样性热点地区和保护空缺地区,然后利用C-Plan规划软件对该地区进行保护优先等级划分,确定必须保护(Mandatory Reserved,MR)、协商保护(Negotiated Reserved,NR)和部分保护(PartiallyReserved,PR)3个等级保护区域的具体位置和面积,并针对保护现状提出保护规划建议。结果显示,必须保护区域的总面积占区域总面积的8.17%,主要分布于长白山核心地区和大兴安岭北部原始林区;协商保护区域占总面积的7.51%,主要分布于大兴安岭东南部和松嫩平原湿地;部分保护区域占总面积的9%。保护空缺分析结果显示,现有国家级自然保护区对生物多样性的保护存在3个明显的保护空缺,即长白山林区的龙岗山地区、老爷岭北部和张广才岭南部;大兴安岭北部原始林区、呼玛河—黑龙江流域的平原湿地和伊勒呼里山东南部山区;大兴安岭南部森林草原过渡区的东南部森林地区。结合区域内已建立的国家级自然保护区情况,利用C-Plan规划软件对不同时期建立的保护区实现保护目标的贡献率做了分析。截止2000年,已建保护区可实现预期保护目标的17.5%,通过对贡献率大小的比较确定了不同时期保护的有效程度。研究打破了传统的对称几何形状的单元划分方法,根据植被类型和自然地形地貌,采用自然多边形进行单元划分,提高了物种分布范围准确度。研究通过C-Plan规划软件的实际应用,丰富了系统保护规划研究的方法,从理论上为区域保护规划提供了科学依据,并可指导我国自然保护区管理政策的制定和中长期规划的编制。     

Diatoms as water quality indicators in the upper reaches of the Great Fish River,Eastern Cape,South Africa

This study focused on the spring-fed upper reaches of the economically important Great Fish River with the aim of determining if diatoms could be used for biomonitoring in semi-arid conditions in southern Africa. Five sites were monitored monthly from 2010 to 2012. Of the 269 diatom taxa belonging to 51 genera identified, the dominant taxa were mostly those considered to be pollution-tolerant: Amphora pediculus, Craticula buderi, Fragilaria biceps, Nitzschia frustulum, Nitzschia paleacea, Planothidium lanceolatum and Rhopalodia gibba. A number of diatom-based numerical indices were used to infer water quality, including the generic diatom index, the specific pollution sensitivity index, the biological diatom index, and percentage pollution-tolerant valves, which forms part of the UK trophic diatom index. All index scores showed the Great Fish River to be impacted, and showed significant correlations of diatom species abundance with pH, NO₃-N, electrical conductivity, NH4-N and CaCO_3. Analysis revealed EC and NO3-N as the main environmental drivers affecting diatom community composition, followed by pH and PO4-P. The percentage of diatom deformities at all sites was high, at 3.5%. Diatom indices showed the river to be impacted by decades of agricultural activity, which was confirmed by chemical water analysis. Thus diatom indices can be used for biomonitoring in semi-arid areas.     

Managing ski resorts to improve biodiversity conservation: Australian reptiles as a case study

Alpine/subalpine environments are diverse systems that support many endemic species. Worldwide, these ecosystems are under threat from ski resort disturbances – even in areas broadly designated for biodiversity conservation. The effects of ski resorts on reptiles are largely unknown, making it difficult to implement effective conservation actions. Many ski resorts do not currently address the needs of reptiles, even those listed as threatened, in their management plans. If reptiles are to continue inhabiting ski resorts in Australia, strategies must be implemented that target their conservation. To begin to address this problem, we summarise current research investigating the effects of ski resorts on reptiles. Based on this information, we recommend strategies that will enhance the conservation of reptiles in areas affected by ski‐related disturbances. Suggested strategies include (i) restricting intensive disturbances to already highly modified areas of Australian ski resorts, (ii) avoiding disturbance of remaining native vegetation and structural complexity in ski resorts and (iii) re‐establishing structural complexity at highly modified sites through revegetation programmes, or through the cessation of mowing during peak reptile activity periods. While these strategies are designed to facilitate the persistence of reptiles in ski resorts, their long‐term success can only be evaluated by monitoring their effectiveness.     

Ichthyofaunal assemblages in estuaries: A South African case study

This review places the life-history styles of fishes associated with South African estuaries in a global context and presents a classification system incorporating all the major life-history categories for estuary-associated fish species around the world. In addition, it documents the early life histories of the major fish groups in South African estuaries, with particular emphasis on the differing modes of estuarine utilization by marine, estuarine and freshwater taxa.This review details factors influencing the ichthyofaunal community structure in South African estuaries. The availability of fish for recruitment into an estuary depends primarily upon the distributional range of euryhaline marine and estuarine species, with tropical and temperate taxa showing marked abundance trends. Within a particular biogeographic region, however, estuarine type and prevailing salinity regime have a major influence on the detailed ichthyofaunal structure that develops. There is an increasing preponderance of marine fish taxa when moving from a freshwater-dominated towards a seawater-dominated type of system, and a decline in species diversity between subtropical estuaries in the north-east and cool temperate systems in the south-west. Similar declines in fish species diversity between tropical and temperate estuaries in other parts of the world are highlighted.Fish assemblages in estuaries adjust constantly in response to changing seasons, salinities, turbidities, etc. Despite persistent fluctuations in both the biotic and abiotic environment, the basic ichthyofaunal structure appears to have an underlying stability and to be predictable in terms of the response of individual species to specific conditions. This stability seems to be governed by factors such as the dominance of eurytopic taxa within estuarine assemblages and the robust nature of food webs within these systems. The predictability arises from factors such as the seasonality associated with estuarine spawning cycles and juvenile fish recruitment patterns. These patterns, together with a well-documented resilience to a wide range of physico-chemical and biotic perturbations, appear to be an underlying feature of fish assemblages in estuaries around the world.In contrast to marine fish species, estuary-associated taxa have received little conservation attention. Apart from the designation of protected areas, the main direct means of conserving estuary-associated fish stocks include habitat conservation and controls over fishing methods, effort, efficiency and seasonality. Of these, the conservation of fish habitats, the most important, because healthy aquatic environments invariably support healthy fish populations. The use of estuarine sanctuaries for fish conservation is briefly reviewed, as well as the legislation governing the USA National Estuarine Research Reserve System (NERRS) and the Australian Marine and Estuarine Protected Area (MEPA) system. It is concluded that South Africa requires an expansion of the existing Estuarine Protected Area (EPA) network, as well as the upgrading of selected 'estuarine reserves' where fishing is permitted, into 'estuarine sanctuaries' where no exploitation of biological resources is allowed.     

Rural change and nature conservation in Africa: A case study from Swaziland

High population growth and deteriorating economic conditions imperil Africa's natural environment. Conservationists are trying to cope with the threat by working in rural communities. Yet it is unclear whether they can be effective when social and economic change in rural areas is so rapid. Northeast Swaziland provides a case study. The landscape has been transformed since the 1950s, and conservationists are the only people now giving nature conservation a high priority. Land uses incompatible with local nature reserves are supported because they provide jobs. Thus, conservationists find themselves facing a world where wildlife is increasingly devalued as the forces of change accelerate. This paper concludes: (1) conservationists must expand their influence into rural communities, (2) an integrated development and conservation plan is required for northeastern Swaziland, and (3) only the alleviation of poverty will secure the future of nature conservation in Swaziland as well as the rest of Africa.     

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.     

Informing and influencing the interface between biodiversity science and biodiversity policy in South Africa

South Africa, as a megadiverse country (±21 700 vascular plants, 4800 vertebrates and 68 900 invertebrates described), is presently engaged with an extended, modified Global Strategy for Plant Conservation (GSPC). The country is fortunate in having a strong tradition of systematics research and, inter alia, houses several million preserved plant specimens (±1 million databased and georeferenced), allowing taxonomists and conservationists to track both the occurrence and distribution of indigenous and naturalized plant species. These rich local resources have been extensively drawn upon to deliver, with varying degrees of success, the 16 outcome-oriented GSPC 2010 Targets. The National Environmental Management: Biodiversity Act (NEMBA, 2004), the National Biodiversity Strategy and Action Plan (NBSAP) and the National Biodiversity Framework (NBF) have provided a robust legislative, enabling and policy framework for making operational and advancing GSPC-related efforts. However, within an emerging economy, the conservation of biodiversity has competed for government resources with housing, sanitation, primary education, basic health care and crime prevention, delivery of which translates to the currency of politicians: votes. A key challenge identified by local (and global) biodiversity scientists for the current GSPC phase is broad-scale advocacy, communicating the changing state of nature, and the inter-relatedness of biodiversity and human well-being. The nature of meeting this challenge is explored.