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.     

The use of ecological,fishing and environmental indicators in support of decision making in southern Benguela fisheries

Indicators have been recognised as a useful tool aiding the implementation of an ecosystem approach to fisheries in marine ecosystems. Studies, such as the IndiSeas project (www.indiseas.org), use a suite of indicators as a method of assessing the state and trends of several of the world's marine ecosystems. While it is well known that both fishing and climatic variability influence marine fisheries in the southern Benguela ecosystem there are currently few studies in support of fisheries management that make use of environmental indicators in order to include climatic impacts on marine fish populations. Trends in ecological, fishing and environmental indicators can be utilised in a way that allows an overall ecosystem trend to be determined, and can therefore be used to aid decision support within southern Benguela fisheries. In this study trends in indicators were determined using linear regressions across three time periods, Period 1: 1978–1993, Period 2: 1994–2003 and Period 3: 2004–2010. These time periods were selected based on the timing of regime shifts within the southern Benguela, including changes in upwelling, wind stress and temperature. Each ecological indicator received a score based on the direction and significance of the observed trend with respect to fishing. To account for the impacts of fishing and environmental drivers on ecological indicators, scores were adjusted by predetermined factors, depending on the extent and direction of trends in these indicators. Weightings were applied to correlated ecological indicators to account for their redundancy, and lessen their impact on overall ecosystem score. Mean weighted scores were then used to establish an overall ecosystem score for each time period. Ecosystem classification was determined as follows: 1–1.49 = improving, 1.5–2.49 = possibly improving, 2.5–3.49 = no improvement or deterioration, 3.5–4.49 = possible deterioration, 4.5–5 = deteriorating. The ecosystem was observed to neither deteriorate nor improve across Period 1 or 2 (mean weighted scores: 2.75 and 2.56 respectively), however, during Period 3 a possible improvement was observed (mean weighted score: 1.99). This study shows that the sequential analysis of suites of ecological, fishing and environmental indicators can be used in order to determine ecosystem trends, accounting for both the impacts of fishing and the environment on ecosystem components.     

Distribution and conservation status of forest bamboo biodiversity in the Asia-Pacific Region

Although Asian bamboo species constitute a non-timber forest product of major cultural and economic importance, no detailed regional assessment of their distribution patterns has previously been made. To assess the potential of the existing bamboo species distribution data for production of regional mapping tools for planning the conservation of forest-based biodiversity, data on bamboo distribution and forest cover were combined. Over 1000 bamboo species from 60 genera of woody bamboos were incorporated, allowing the mapping of individual species or groups of species and genera, along with potential species richness and biodiversity hotspots. Over 6.3 million km² of Asian forest potentially contains bamboo, with highest densities indicated from northeastern India through Burma to southern China, and through Sumatra to Borneo. The highest figures for potential species richness (144 spp per square km) were recorded in forests of south China, including Hainan Island. Despite substantial inadequacies and inconsistencies in knowledge of the taxonomy and distribution of bamboo species, this approach may provide a valuable tool for planning in situ conservation of forest biodiversity.     

Connectivity,biodiversity conservation and the design of marine reserve networks for coral reefs

Networks of no-take reserves are important for protecting coral reef biodiversity from climate change and other human impacts. Ensuring that reserve populations are connected to each other and non-reserve populations by larval dispersal allows for recovery from disturbance and is a key aspect of resilience. In general, connectivity between reserves should increase as the distance between them decreases. However, enhancing connectivity may often tradeoff against a network’s ability to representatively sample the system’s natural variability. This “representation” objective is typically measured in terms of species richness or diversity of habitats, but has other important elements (e.g., minimizing the risk that multiple reserves will be impacted by catastrophic events). Such representation objectives tend to be better achieved as reserves become more widely spaced. Thus, optimizing the location, size and spacing of reserves requires both an understanding of larval dispersal and explicit consideration of how well the network represents the broader system; indeed the lack of an integrated theory for optimizing tradeoffs between connectivity and representation objectives has inhibited the incorporation of connectivity into reserve selection algorithms. This article addresses these issues by (1) updating general recommendations for the location, size and spacing of reserves based on emerging data on larval dispersal in corals and reef fishes, and on considerations for maintaining genetic diversity; (2) using a spatial analysis of the Great Barrier Reef Marine Park to examine potential tradeoffs between connectivity and representation of biodiversity and (3) describing a framework for incorporating environmental fluctuations into the conceptualization of the tradeoff between connectivity and representation, and that expresses both in a common, demographically meaningful currency, thus making optimization possible.     

Quantitative criteria for choosing targets and indicators for sustainable use of ecosystems

Wide-ranging, indicator-based assessments of large, complex ecosystems are playing an increasing role in guiding environmental policy and management. An example is the EU’s Marine Strategy Framework Directive, which requires Member States to take measures to reach “good environmental status” (GES) in European marine waters. However, formulation of indicator targets consistent with the Directive’s high-level policy goal of sustainable use has proven challenging. We develop a specific, quantitative interpretation of the concepts of GES and sustainable use in terms of indicators and associated targets, by sharply distinguishing between current uses to satisfy current societal needs and preferences, and unknown future uses. We argue that consistent targets to safeguard future uses derive from a requirement that any environmental state indicator should recover within a defined time (e.g. 30 years) to its pressure-free range of variation when all pressures are hypothetically removed. Within these constraints, specific targets for current uses should be set. Routes to implementation of this proposal for indicators of fish-community size structure, population size of selected species, eutrophication, impacts of non-indigenous species, and genetic diversity are discussed. Important policy implications are that (a) indicator target ranges, which may be wider than natural ranges, systematically and rationally derive from our proposal; (b) because relevant state indicators tend to respond slowly, corresponding pressures should also be monitored and assessed; (c) support of current uses and safeguarding of future uses are distinct management goals, they require different types of targets, decision processes, and management philosophies.     

A comparison of some population density sampling techniques for biodiversity, conservation, and environmental impact studies

Twelve terrestrial and marine studies were conducted at various sites in Malaysia, Brazil, and the United States between April 1999 and February 2004. These data were analyzed using five density estimate techniques for stationary (non-motile) organisms including Stratified Random Sampling, Point-Center Quarter, Third Nearest Object, Weinberg, and Strong. The Strong method gave the most accurate density estimates of stationary animals and plants. Stratified Random Sampling ranked second best and the Third Nearest Object the third best. Belt or strip transects may be preferable but can be restrictive in some situations because of logistics and associated time constraints. Straight line measurements on reefs were 3–27% more accurate than reef slack line and reef contour measurements. Most study areas measured with the standardized Morisita index of dispersion were moderately aggregated. Results from the Third Nearest Object and Point-Center Quarter techniques indicate that the addition of more data to establish a density correction factor does not necessarily give more accurate estimates of density.     

Sacred groves of Manipur,northeast India:biodiversity value,status and strategies for their conservation

The people of Manipur, a state in northeast India, follow ancestral worship and animism in the form of deity worship, with the central focus on worship in forest patches. The beliefs and taboos associated with the Sylvan deities (Umanglais) in the forest patches are restricted to any sort of disturbance of flora and fauna. These social boundaries help to conserve the entire organism as a whole, which stand the concept of sacred groves. The pleasing of deities is performed every year by the Meiteis, a dominant community of Manipur, in honour of the deities and to gain their favour. Indigenous cultural and rituals practices of the local people in sacred groves serve as a tool for conserving biodiversity. Sacred groves are distributed over a wide ecosystem and help in conservation of rare and endemic species. Well-preserved sacred groves are store houses of valuable medicinal and other plants having high economic value, and serve as a refuge to threatened species. One hundred and sixty-six sacred groves were inventoried in Manipur valley that comprises Imphal east, Imphal west, Thoubal and Bishnupur districts of the state. Detailed studies were carried out in four selected sacred groves, to know the importance of biodiversity status and vegetation characteristics. A total of 173 plant species representing 145 genera under 70 families were recorded through baseline floristic survey. The species diversity indices were compared among the four studied groves. The vegetation composition and community characteristics were recorded. Ethnobotanical uses of species were examined, which reveal that 96% of the species were used as medicine for the treatment of various ailments. Utilization of herbal medicine by the Meiteis is closely related to the cultural and ritual practices. A few of the medicinal plants which have disappeared from the locality are now confined only to the groves. Socio-cultural aspects were investigated taking into account the attitudes of local people, which indicate social beliefs and taboo are eroding, simultaneously degrading the degree of protection of sacred groves. Therefore, conservation measures of sacred groves need to be formulated considering the factor of degradation and the basic necessities of the local people. Until and unless a viable option is provided to the local people (especially those who habitat nearby the adjoining areas) for sustaining their economic condition, no step for conservation of biodiversity will be successful.     

Ecological effects of non‐native species in marine ecosystems relate to co‐occurring anthropogenic pressures

Predictors for the ecological effects of non‐native species are lacking, even though such knowledge is fundamental to manage non‐native species and mitigate their impacts. Current theories suggest that the ecological effects of non‐native species may be related to other concomitant anthropogenic stressors, but this has not been tested at a global scale. We combine an exhaustive meta‐analysis of the ecological effects of marine non‐native species with human footprint proxies to determine whether the ecological changes due to non‐native species are modulated by co‐occurring anthropogenic impacts. We found that non‐native species had greater negative effects on native biodiversity where human population was high and caused reductions in individual performance where cumulative human impacts were large. On this basis we identified several marine ecoregions where non‐native species may have the greatest ecological effects, including areas in the Mediterranean Sea and along the northwest coast of the United States. In conclusion, our global assessment suggests coexisting anthropogenic impacts can intensify the ecological effects of non‐native species.     

An evaluation framework based on sustainability-related indicators for the comparison of conceptual approaches for ecological networks

Ecological networks (EN) are designed to maintain biodiversity and ecological processes by protecting habitats and their linkages. By considering the functional role of the landscape, EN can support the integration of ecological sustainability with human activities. Although all EN share the same general objectives, there are many different approaches for determining the spatial configuration of their components. The choice of an approach for the design of an EN has a major impact on the spatial configuration, ecological value, and ease of implementation of the resulting network. We applied different approaches to construct EN for the Saint-François River watershed (8700 km²) in southern Quebec, Canada. The approaches were based on single-species, multi-species, and landscape modeling categories. All of the resulting EN were evaluated using ecological, economic, and social spatial thematic indicators (TI) relevant to sustainable landscape management. This allowed us to quantitatively assess the impact of each approach and to establish their relative performance within a common framework. Our results showed that the conceptual approach for EN has a direct influence on their spatial configuration and performance. Single-species-, multi-species- and landscape-based categories produced very different EN. These results emphasize the importance of the selection of focal species and/or key environments for the design of EN. Our results also highlight the importance of adequately defining the desired objectives and expected functions of an EN, knowing that the results of the conceptual approach will be modified depending on the environment. Results are discussed in relation to the objectives sought by the implementation of the EN, spatial scale, and land use. Our evaluation framework is a useful tool for mitigating uncertainties associated with EN by facilitating the integration of stakeholders’ priorities and landscape management objectives.     

An approach to analyzing spatial patterns in annual dynamics of planktonic ciliate communities and their environmental drivers in marine ecosystems

The environmental drivers to shape the spatial patterns in annual dynamics of the planktonic ciliate communities were studied based on an annual dataset from a bay, northern Yellow Sea. Samples were biweekly collected at five stations with different environmental condition status during a 1-year period. The second-stage-analysis-based multivariate approaches were used to reveal the internal dynamics in annual patterns of the ciliate assemblages. Results showed that: (a) there was a clear spatial variability in annual dynamics among five stations; (b) the dominant species represented different succession dynamics among four samples stations during the 1-year cycle; and (c) the spatial variations in annual patterns of the ciliates were significantly correlated with nutrients, alone or in combination with salinity and dissolve oxygen (DO). Thus, it is suggested that the nutrients may be the main drivers to shape the spatial patterns in annual dynamics of planktonic ciliate communities in marine ecosystems.     

Ecological impacts of parasitic chytrids,syndiniales and perkinsids on populations of marine photosynthetic dinoflagellates

Parasitism is a widespread interaction that plays significant roles in ecosystem balance and evolution. Historically the biology of zoosporic parasites is often a neglected field when studying aquatic ecological dynamics, especially in marine ecosystems. In the marine environment, dinoflagellates represent a significantly large component of primary production, and may be infected by a variety of fungal and fungus-like parasites including chytrids, syndiniales, and perkinsids as well as other microorganisms. The relationship between these organisms and their dinoflagellate hosts constitutes a highly significant pathosystem given the increasing importance of aquaculture. Because of their small size and lack of morphological characteristics these organisms are difficult to identify. This review compares the taxonomy, life cycle, host range, infection strategies, and ecological roles of species of Parvilucifera, Amoebophrya and Dinomyces which are parasites of dinoflagellates. Most of these species have only been described recently. Implications for environmental management are discussed.     

Spatial and temporal response of multiple trait-based indices to natural- and anthropogenic seafloor disturbance (effluents)

To support ecosystem-based management and achieve the Good Environmental Status (GES) of marine waters it is important to better comprehend the relationships between biodiversity and environmental disturbance (anthropogenic and natural). Biotic indices are widely used in studies to help understanding these relationships and to assess the environmental status of waters. In recent years, trait-based indices rapidly emerged as an alternative ‘functional’ approach to serve this purpose. In this study, we analysed how two indices based upon the mean (community-weighted mean trait value–CWM) and the diversity of multiple traits (Rao’s quadratic entropy–Rao) in a macroinvertebrate community respond to natural- and anthropogenic seafloor disturbance (effluents) and we compared their performance with the widely used AMBI and M-AMBI. Our results demonstrate that CWM and Rao were not effective in indicating anthropogenic disturbance in the Basque coast, Bay of Biscay. The main reason was probably that many traits did not have a strong link with this type of disturbance. Besides, the mechanistic links between certain traits and their response to anthropogenic seafloor disturbance in marine environments is currently not well understood. From a management perspective: the CWM does not provide a single value indicating a quality status, which makes it a difficult tool to use and interpret. This index is probably more useful for scientists who want to explore and understand different aspects of community functioning. On the other hand, Rao and other indices expressing trait diversity do provide a single value of functioning; therefore they could potentially be effectively used for management purposes. However, to improve its performance, detailed and accurate trait data is required, which is currently lacking for many marine species.     

Effects on ecosystem resilience of biodiversity, extinctions, and the structure of regional species pools

Resilience is a general concept that aims to help understand how ecosystems respond to disturbances such as extinctions and invasions. Here, we propose a measure of one aspect of resilience, R _X , which is one minus the expected change in functional diversity (X) caused by a species extinction or addition. We show how two components of biodiversity, species richness and functional diversity, and the structure of regional species pools affect this measure. Variation in species richness and in functional diversity have opposite effects on R _X . Speciose assemblages generally have higher R _X than depauperate ones, whereas functionally diverse assemblages have low R _X relative to functionally depauperate ones. The effect of an extinction on R _X reflects this tradeoff. In our analyses, extinctions usually cause only a small decrease in both functional diversity and R _X . However, extinctions sometimes cause a large reduction in functional diversity and then tend to increase R _X . Regional assemblages containing all rather unique species tend to result in speciose assemblages with relatively low R _X and in low richness assemblages with relatively high R _X . The opposite is true of regional assemblages containing functionally similar species. Information about the processes that structure regional assemblages will therefore increase understanding of ecosystem resilience. Generally, these results suggest that management for biodiversity may not always result in management for resilience.     

Endemic birds of the Atlantic Forest: traits,conservation status,and patterns of biodiversity

The bird fauna of the Brazilian Atlantic Forest is exceptionally diverse and threatened, with high levels of endemism. Available lists of the endemic birds of the Atlantic Forest were generated before recent taxonomic revisions lumped or split species and before the recent increase in species occurrence records. Our objective, therefore, was to compile a new list of the endemic birds of the Atlantic Forest, characterize these species in terms of conservation status and natural history traits, and map remaining vegetation and protected areas. We combined GIS analysis with a literature search to compile a list of endemic species and, based on the phylogeny and distribution of these species, characterized areas in terms of species richness, phylogenetic diversity, and endemism. We identified 223 species of birds endemic to the Atlantic Forest, including 12 species not included in previous lists. In addition, 14 species included in previous lists were not considered endemic, either because they occur outside the Atlantic Forest biome or because they are not considered valid species. The typical Atlantic Forest endemic bird is a small forest‐dependent invertivore. Of the species on our list, 31% are considered threatened or extinct. Only ~ 34% of the spatial analysis units had > 10% forest cover, and protected area coverage was consistently low (< 1%). In addition, we found spatial incongruity among the different measures of biodiversity (species richness, relative phylogenetic diversity, restricted‐range species, and irreplaceability). Each of these measures provides information concerning different aspects of biological diversity. However, regardless of which aspect(s) of biodiversity might be considered most important, preservation of the remaining areas of remnant vegetation and further expansion of protected areas are essential if we are to conserve the many endemic species of birds in the Atlantic Forest.     

The adequacy of alfalfa crops as an agri-environmental scheme: A review of agronomic benefits and effects on biodiversity

The agriculture intensification required to provide enough food commodities for humans has negative impacts on the environment. To reduce these drawbacks Agri-Environmental Schemes (AES) have been implemented in Europe since the last decade of the twentieth century. One of the measures included in these schemes was the introduction of alfalfas in crop rotation systems. In order to evaluate their suitability as an AES, we synthesize knowledge on the agronomical benefits of alfalfa cultivations, as well as on the relationships of alfalfa crops with biodiversity at three taxonomic levels: vascular plants, arthropods, and vertebrates. Based on the articles reviewed, alfalfas can help restoring native grassland communities due to the nutrient enrichment they provide. Moreover, this legume crop usually ensures food resources not only for invertebrates, but also for vertebrates. Alfalfas tend to harbour a stable arthropod community that benefits surrounding crops by improving ecological processes (pollination, pest predation) and reducing the need to use agrochemicals. At the same time, arthropod abundance attracts vertebrates, especially birds, which supports the role of alfalfa as a conservation tool to favour endangered farmland birds. Additionally, alfalfa crops may function as a reservoir habitat for voles, which are a preferred food resource for farmland-foraging raptors, many of them endangered. On the other hand, birds nesting in alfalfa crops may suffer higher nest destruction rates due to frequent cuts, and voles using alfalfa crops may also create agricultural damage in surrounding crops in certain cases. The review also highlights that negative ecological relationships of alfalfa crops with biodiversity can be minimized, and positive effects may also be maximized under the appropriate management of this crop. Examples of such management actions include cut delays or higher cuts to avoid nest destruction, the use of grazing cattle to reduce the impacts of rodent pests, reduced frequency of cutting or maintaining unharvested strips in the field to maximize positive effects on predatory arthropods and vole availability to raptors. We conclude that alfalfa crops can be considered globally beneficial for farmland biodiversity and a useful management tool for conservation in agricultural landscapes, for example as an AES, but that management should be adapted to particular taxonomical or functional groups.     

Perspectives on the link between ecosystem services and biodiversity: The assessment of the nursery function

The relationship between biodiversity and each ecosystem service or bundle of ecosystem services (e.g. win−win, win−lose or win−neutral) is an active field of research that requires structured and consistent information. The application of that research for conservation and decision-making can be hampered by the ambiguity found in the definition of the nursery function under the ecosystem service perspective. In this paper, we review how the role of nursery habitats is included in the ecosystem services literature, covering conceptual, biophysical and economic reflections. The role of ecosystems as nurseries is mostly analyzed in coastal environments. The main observation is that there is no consensus on the consideration of the nursery function as a service (e.g. which species or habitats) or on how to assess it (e.g. which indicators or valuation methods). After that review, we analyze three different interpretations given to the nursery function, namely the ecological, conservationist and economic point of view; and we distinguish between different types of assessment that may consider the nursery function.We conclude that the nursery function can be considered an ecosystem service on its own right when it is linked to a concrete human benefit and not when it is represented with indicators of general biodiversity or ecosystem condition. Thus, the analysis of the delivery of ecosystem services should be differentiated from the analysis of ecological integrity. Only with this distinction science may be able to quantify the link between biodiversity and ecosystem services and policy may be effective in halting biodiversity loss. Similar considerations could apply for other biodiversity constituents that may be treated as ecosystem services.