Synthesizing the role of epigenetics in the response and adaptation of species to climate change in freshwater ecosystems

Freshwater ecosystems are amongst the most threatened ecosystems on Earth. Currently, climate change is one of the most important drivers of freshwater transformation and its effects include changes in the composition, biodiversity and functioning of freshwater ecosystems. Understanding the capacity of freshwater species to tolerate the environmental fluctuations induced by climate change is critical to the development of effective conservation strategies. In the last few years, epigenetic mechanisms were increasingly put forward in this context because of their pivotal role in gene–environment interactions. In addition, the evolutionary role of epigenetically inherited phenotypes is a relatively recent but promising field. Here, we examine and synthesize the impacts of climate change on freshwater ecosystems, exploring the potential role of epigenetic mechanisms in both short‐ and long‐term adaptation of species. Following this wrapping‐up of current evidence, we particularly focused on bringing together the most promising future research avenues towards a better understanding of the effects of climate change on freshwater biodiversity, specifically highlighting potential molecular targets and the most suitable freshwater species for future epigenetic studies in this context.     

Strategies for the conservation of endangered freshwater pearl mussels (<Emphasis Type="Italic">Margaritifera margaritifera</Emphasis> L.): a synthesis of Conservation Genetics and Ecology

Freshwater pearl mussels (Margartifera margaritifera L.) are among the most critically threatened freshwater bivalves worldwide. The pearl mussel simultaneously fulfils criteria of indicator, flagship, keystone and umbrella species and can thus be considered an ideal target species for the process conservation of aquatic ecosystem functioning. The development of conservation strategies for freshwater pearl mussels and for other bivalve species faces many challenges, including the selection of priority populations for conservation and strategic decisions on habitat restoration and/or captive breeding. This article summarises the current information about the species’ systematics and phylogeny, its distribution and status as well as about its life history strategy and genetic population structure. Based on this information, integrative conservation strategies for freshwater mollusc species which combine genetic and ecological information are discussed. Holistic conservation strategies for pearl mussels require the integration of Conservation Genetics and Conservation Ecology actions at various spatial scales, from the individual and population level to global biodiversity conservation strategies. The availability of high resolution genetic markers for the species and the knowledge of the critical stages in the life cycle, particularly of the most sensitive post-parasitic phase, are important prerequisites for conservation. Effective adaptive conservation management also requires an evaluation of previous actions and management decisions. As with other freshwater bivalves, an integrative conservation approach that identifies and sustains ecological processes and evolutionary lineages is urgently needed to protect and manage freshwater pearl mussel diversity. Such research is important for the conservation of free-living populations, as well as for artificial culturing and breeding techniques, which have recently been or which are currently being established for freshwater pearl mussels in several countries.     

Declining freshwater mussel diversity in the middle and lower reaches of the Xin River Basin: Threat and conservation

Freshwater mussels provide important functions and services for aquatic ecosystems, but populations of many species have been extirpated. Information on biodiversity plays an important role in the conservation and management of freshwater mussels. The Xin River Basin is a biodiversity hotspot for freshwater mussels in China, with more than 43 species known, but populations of which are decreasing. Here, we quantify the diversity of freshwater mussels in the middle and lower reaches of the Xin River Basin and study the correlation of habitat characteristics and freshwater mussel diversity. Compared to the historical period, the number of species, density, and biomass of freshwater mussels decreased 33%, 83%, and 82% in the current period, respectively. Fifty two percent of recorded species were empty shells, and 14 native freshwater mussels were not found in the study area. Four species are currently listed as vulnerable species using IUCN criteria and their global status. The assemblage structure of freshwater mussels exhibits significant spatial differences, and there was a correlation with substrate and physicochemical parameters. The main tributary of the Xin River with higher freshwater mussel diversity should be established as one large protected area because the nestedness component was the main pattern of beta diversity. These results indicated freshwater mussel diversity was declining rapidly, which can help focus conservation effort for freshwater mussel biodiversity.     

Freshwater biodiversity: importance, threats, status and conservation challenges

Freshwater biodiversity is the over‐riding conservation priority during the International Decade for Action ‐‘Water for Life’ ‐ 2005 to 2015. Fresh water makes up only 0.01% of the World's water and approximately 0.8 % of the Earth's surface, yet this tiny fraction of global water supports at least 100 000 species out of approximately 1.8 million ‐ almost 6% of all described species. Inland waters and freshwater biodiversity constitute a valuable natural resource, in economic, cultural, aesthetic, scientific and educational terms. Their conservation and management are critical to the interests of all humans, nations and governments. Yet this precious heritage is in crisis. Fresh waters are experiencing declines in biodiversity far greater than those in the most affected terrestrial ecosystems, and if trends in human demands for water remain unaltered and species losses continue at current rates, the opportunity to conserve much of the remaining biodiversity in fresh water will vanish before the ‘Water for Life’ decade ends in 2015. Why is this so, and what is being done about it? This article explores the special features of freshwater habitats and the biodiversity they support that makes them especially vulnerable to human activities. We document threats to global freshwater biodiversity under five headings: overexploitation; water pollution; flow modification; destruction or degradation of habitat; and invasion by exotic species. Their combined and interacting influences have resulted in population declines and range reduction of freshwater biodiversity worldwide. Conservation of biodiversity is complicated by the landscape position of rivers and wetlands as ‘receivers’ of land‐use effluents, and the problems posed by endemism and thus non‐substitutability. In addition, in many parts of the world, fresh water is subject to severe competition among multiple human stakeholders. Protection of freshwater biodiversity is perhaps the ultimate conservation challenge because it is influenced by the upstream drainage network, the surrounding land, the riparian zone, and ‐ in the case of migrating aquatic fauna ‐ downstream reaches. Such prerequisites are hardly ever met. Immediate action is needed where opportunities exist to set aside intact lake and river ecosystems within large protected areas. For most of the global land surface, trade‐offs between conservation of freshwater biodiversity and human use of ecosystem goods and services are necessary. We advocate continuing attempts to check species loss but, in many situations, urge adoption of a compromise position of management for biodiversity conservation, ecosystem functioning and resilience, and human livelihoods in order to provide a viable long‐term basis for freshwater conservation. Recognition of this need will require adoption of a new paradigm for biodiversity protection and freshwater ecosystem management ‐ one that has been appropriately termed ‘reconciliation ecology’.     

Biodiversity effects on ecosystem functioning: emerging issues and their experimental test in aquatic environments

Recent experiments, mainly in terrestrial environments, have provided evidence of the functional importance of biodiversity to ecosystem processes and properties. Compared to terrestrial systems, aquatic ecosystems are characterised by greater propagule and material exchange, often steeper physical and chemical gradients, more rapid biological processes and, in marine systems, higher metazoan phylogenetic diversity. These characteristics limit the potential to transfer conclusions derived from terrestrial experiments to aquatic ecosystems whilst at the same time provide opportunities for testing the general validity of hypotheses about effects of biodiversity on ecosystem functioning. Here, we focus on a number of unique features of aquatic experimental systems, propose an expansion to the scope of diversity facets to be considered when assessing the functional consequences of changes in biodiversity and outline a hierarchical classification scheme of ecosystem functions and their corresponding response variables. We then briefly highlight some recent controversial and newly emerging issues relating to biodiversity‐ecosystem functioning relationships. Based on lessons learnt from previous experimental and theoretical work, we finally present four novel experimental designs to address largely unresolved questions about biodiversity‐ecosystem functioning relationships. These include (1) investigating the effects of non‐random species loss through the manipulation of the order and magnitude of such loss using dilution experiments; (2) combining factorial manipulation of diversity in interconnected habitat patches to test the additivity of ecosystem functioning between habitats; (3) disentangling the impact of local processes from the effect of ecosystem openness via factorial manipulation of the rate of recruitment and biodiversity within patches and within an available propagule pool; and (4) addressing how non‐random species extinction following sequential exposure to different stressors may affect ecosystem functioning. Implementing these kinds of experimental designs in a variety of systems will, we believe, shift the focus of investigations from a species richness‐centred approach to a broader consideration of the multifarious aspects of biodiversity that may well be critical to understanding effects of biodiversity changes on overall ecosystem functioning and to identifying some of the potential underlying mechanisms involved.     

关于中国淡水生态系统生物多样性监测与管理的探讨

China is one of the countries in the world with therichest species biodiversityinfreshwater ecosystem.How-ever,duetothe rapid economic growthandthe continuingincrease of human disturbances and destructions of aquatichabitats,the biodiversity of freshwater ecosystemsis dras-tically declining.Waterbodies become more and more“deserted”of sensitive species.Water areas are reduced,fragmentized,and changed in their hydrodynamics(i.e.damming),causing changes in sedimentation and otherchanges.Forinstance,the area o...     

Macroinvertebrate conservation in river ecosystems: Challenges,restoration strategies,and integrated management approaches

River ecosystems face growing threats from human-induced stressors, resulting in habitat degradation and biodiversity loss. Crucial to these ecosystems, macroinvertebrates maintain river health and functioning. In this review, we examine the challenges confronting macroinvertebrates, explore restoration strategies and management approaches, and shed light on knowledge gaps and future research directions. Habitat degradation, water pollution, climate change, and invasive species are discussed as key challenges. Various restoration strategies, such as in-stream habitat restoration, flow regime restoration, riparian zone restoration, and connectivity restoration, are evaluated for macroinvertebrate conservation. Integrated catchment management, adaptive management, community-based management, monitoring, and policy integration are highlighted as essential management approaches, and knowledge gaps in long-term monitoring, innovative restoration techniques, climate change resilience, and policy incorporation are identified as areas calling for further research. Ultimately, a proactive, adaptable, and cooperative approach to river management will ensure macroinvertebrate conservation and sustainable river ecosystems.     

Nearctic earthworm fauna in the southern USA: biodiversity and effects on ecosystem processes

An important aspect of biodiversity is the relative importance of species in the functioning of ecosystems; this is particularly so for the soil biota which regulate organic matter and nutrient dynamics in soil. This paper explores some of the relationships between biodiversity and ecosystem processes, using the example of the nearctic earthworm fauna in the glacial refugium of the southern USA. Competitive exclusion of nearctic earthworm species by exotic species has been postulated but there is little direct evidence of it; habitat alteration is the likely cause of native species decline. Reduced earthworm diversity may or may not strongly affect certain ecosystem processes, but more diverse assemblages may more effectively exploit soil resources and influence a wider array of processes. Nearctic species may be better adapted than exotics to local conditions and thus more strongly influence ecosystem processes. Earthworm communities provide a clear case for the union of functional and taxonomic biodiversity studies, because of the recognized ecological strategies of many species. However, some nearctic taxa may deviate from these strategies. Earthworms utilize course woody debris in forests both as a refuge and a resource, while enhancing the decomposition of wood. Management strategies to maintain or increase biodiversity of soil biota should include residual wood on the forest floor. An important task for ecosystem management is to restore biodiversity in degraded ecosystems; introduction programmes and techniques such as periodic burning may increase the abundance and diversity of native earthworm species. Whole ecosystem conservation and management are probably the most practical ways to conserve biodiversity generally and may be the only ways to maintain soil biodiversity.     

Conserving freshwater biodiversity: The value,status and management of high quality ditch systems

Freshwater biodiversity is globally threatened and while most conservation efforts are focussed on natural and larger freshwater systems such as rivers and lakes, in many lowland agricultural landscapes artificial water bodies including ditches may be equally important as habitats for freshwater species. Ditches occur across the agricultural landscape but in particular, those associated with coastal and floodplain grazing marsh, have high conservation value. The importance of this habitat for rare and threatened species afforded priority status under the UK Biodiversity Action Plan is explored. The characteristics of ditches that have high conservation value are described and a set of targets against which such ditches can be assessed are presented. An analysis of the current condition of Sites of Special Scientific Interest (SSSI) for the wider coastal and floodplain grazing marsh habitat demonstrates the range of pressures affecting these sites and highlights that alongside generic freshwater issues such as eutrophication and non-native species, these sites have a unique set of pressures associated with their ongoing management and the vulnerable location of many sites at the coast. Wider conservation strategies for freshwater biodiversity in lowland landscapes across Europe need to factor in the different management requirements of artificial habitats such as ditches alongside more ambitious restoration projects for natural waterbodies. In low lying coastal areas the threat of coastal squeeze for many important grazing marshes will require a strategic approach to allow upstream migration of important biodiversity.     

The microbial diversity of inland waters

The conservation and sustainable use of freshwater resources is of global importance. Microorganisms are not only the most abundant organisms in natural freshwater systems, but are also key players in ecological processes controlling water quality. Detailed knowledge of the diversity and function of microorganisms dwelling in freshwater habitats is an essential prerequisite for the sustainable management of freshwater resources. Freshwater systems are inhabited by microbial communities that are indigenous to this habitat type and usually do not occur in marine systems, saline inland waters and terrestrial habitats. Despite recent advances in the characterization of the diversity of freshwater microorganisms, knowledge essential for a holistic understanding of their ecological roles is still lacking.     

Whole‐landscape modelling of compositional turnover in aquatic invertebrates informs conservation gap analysis: An example from south‐western Australia

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Protected areas: A focus on Brazilian freshwater biodiversity

Brazil has a variety of aquatic ecosystems and rich freshwater biodiversity, but these components have been constantly damaged by the expansion of unsustainable activities. An array of different conservation strategies is needed, especially the creation of protected areas (PAs, hereafter). However, Brazil's PAs are biased towards terrestrial ecosystems and we argue that current PAs have limited efficacy in the protection of freshwater biodiversity. New PAs should better consider aquatic environments, covering entire basins, rivers and other freshwater habitats. We recommend ways to implement these PAs and provide guidance to avoid social impacts. Freshwater systems in Brazil provide essential goods and services but these ecosystems are being rapidly degraded and will be lost if not adequately protected.     

Putting bryophyte communities in the map: A case study on prioritizing monitoring of human pressure in riverscapes

Freshwater ecosystems support biological communities with high species richness and conservation interest. However, these ecosystems are highly altered by human intervention and threatened worldwide, making them a priority in conservation planning and biodiversity monitoring. Bryophytes, including several conservation-interest taxa, are recognized indicators of ecological status in freshwaters. We aimed to develop a framework for designing monitoring networks to detect trends in aquatic and semi-aquatic bryophyte communities, prioritizing high-conservation interest communities in different contexts of human pressure (specifically, resulting from the intersection of two criteria: (i) protection status and (ii) presence of a potential impact area).The framework consists of three steps: (1) Spatial modelling of biodiversity; (2) Spatial conservation prioritization; and (3) Model-assisted monitoring network design. Community-level modelling was used to model the distribution of the main bryophyte assemblages in the study area. A conservation prioritization software was utilized to identify areas with high conservation value. The monitoring network was designed using stratified random sampling and unequal-probability sampling techniques to target high conservation value sites distributed across different contexts of human pressure.We have identified four distinct community types, each characterized both by a small group of common and dominant species, and by small group of rarer, conservation-interest species. This typification of four species assemblages occurring in the study area, also highlighted those with potentially higher conservation-interest. The most valuable areas for the conservation of aquatic and semi-aquatic bryophyte communities coincide with specific environmental zones: mountainous areas in Lusitania, large watercourses in the Mediterranean North and some locations in the Mediterranean Mountains. Finally, we obtained a potential monitoring network consisting of 64 monitoring points, unequally distributed across different contexts of human pressure, privileging locations with higher conservation value.The framework presented here illustrates the potential of combining biodiversity modelling, spatial conservation prioritization and monitoring design in the development of monitoring networks. Namely, this framework allowed us to counter data deficiencies, to identify high priority areas to monitor and to design a monitoring network considering different scenarios of human pressure at a regional scale.This framework can also be valuable for conservation efforts as an approach to monitoring conservation-interest biodiversity features in anthropogenically modified riverscapes, which present different degrees of human pressure and the cumulative effects of these different impact elements. Moreover, this approach allows for the comprehensive monitoring of biodiversity values important for management at the national and regional levels. In addition, this framework is one of the first efforts in the development of monitoring networks that target aquatic and semi-aquatic bryophyte communities, a long-neglected plant group of high ecological and conservation importance in freshwater ecosystems.     

Biodiversity: towards a unifying theme for river ecology

1. A broadened concept of biodiversity, encompassing spatio‐temporal heterogeneity, functional processes and species diversity, could provide a unifying theme for river ecology. 2. The theoretical foundations of stream ecology often do not reflect fully the crucial roles of spatial complexity and fluvial dynamics in natural river ecosystems, which has hindered conceptual advances and the effectiveness of efforts at conservation and restoration. 3. Inclusion of surface waters (lotic and lentic), subsurface waters (hyporheic and phreatic), riparian systems (in both constrained and floodplain reaches), and the ecotones between them (e.g. springs) as interacting components contributing to total biodiversity, is crucial for developing a holistic framework of rivers as ecosystems. 4. Measures of species diversity, including alpha, beta and gamma diversity, are a result of disturbance history, resource partitioning, habitat fragmentation and successional phenomena across the riverine landscape. A hierarchical approach to diversity in natural and altered river‐floodplain ecosystems will enhance understanding of ecological phenomena operating at different scales along multidimensional environmental gradients. 5. Re‐establishing functional diversity (e.g. hydrologic and successional processes) across the active corridor could serve as the focus of river conservation initiatives. Once functional processes have been reconstituted, habitat heterogeneity will increase, followed by corresponding increases in species diversity of aquatic and riparian biota.     

Strong spatial turnover in cichlid fish assemblages in the upper río Madera (Amazon basin) despite the absence of hydrological barriers

In freshwater ecosystems, spatial turnover in fish assemblages is often attributed to dispersal limitation imposed by fragmentation of water bodies. Other factors like environmental properties or biotic interactions have often been assumed to be minute relative to dispersal limitation when hydrogeological barriers are abundant. This study aims to describe the spatial differentiation of cichlid fish assemblages in the upper río Madera in Bolivia, Brazil and Perú, a large drainage system characterized by the absence of significant hydrogeological barriers. We assessed the relative importance of spatial, climatic and geological predictors in the observed biogeographic structure using an integrative combination of cluster analyses, elements of metacommunity structure analysis, variation partitioning, and network analysis. Our results show that distinct assemblages of cichlid fish species replace each other across the landscape and that this turnover is partially determined by climate and geological gradients. A considerable fraction of the cichlid assembly structure could not be assigned to either space, climate or geology and might be explained by unmeasured parameters such as habitat structure or biotic interactions. Incorporating knowledge on spatial turnover of species assemblages into conservation strategies will be essential for the biodiversity management of the diverse aquatic fauna of the upper río Madera.     

The global decline of freshwater megafauna

Freshwater ecosystems are among the most diverse and dynamic ecosystems on Earth. At the same time, they are among the most threatened ecosystems but remain underrepresented in biodiversity research and conservation efforts. The rate of decline of vertebrate populations is much higher in freshwaters than in terrestrial or marine realms. Freshwater megafauna (i.e., freshwater animals that can reach a body mass ≥30 kg) are intrinsically prone to extinction due to their large body size, complex habitat requirements and slow life‐history strategies such as long life span and late maturity. However, population trends and distribution changes of freshwater megafauna, at continental or global scales, remain unclear. In the present study, we compiled population data of 126 freshwater megafauna species globally from the Living Planet Database and available literature, and distribution data of 44 species inhabiting Europe and the United States from literature and databases of the International Union for Conservation of Nature and NatureServe. We quantified changes in population abundance and distribution range of freshwater megafauna species. Globally, freshwater megafauna populations declined by 88% from 1970 to 2012, with the highest declines in the Indomalaya and Palearctic realms (?99% and ?97%, respectively). Among taxonomic groups, mega‐fishes exhibited the greatest global decline (?94%). In addition, freshwater megafauna experienced major range contractions. For example, distribution ranges of 42% of all freshwater megafauna species in Europe contracted by more than 40% of historical areas. We highlight the various sources of uncertainty in tracking changes in populations and distributions of freshwater megafauna, such as the lack of monitoring data and taxonomic and spatial biases. The detected trends emphasize the critical plight of freshwater megafauna globally and highlight the broader need for concerted, targeted and timely conservation of freshwater biodiversity.     

Evolutionary adaptations by fish to ecotonal complexity in spatially variable landscapes — a perspective

In most types of freshwater ecosystems fish diversity depends greatly on land/inland water ecotones. So, to maintain biodiversity of fish communities in inland waters, management and restoration of aquatic terrestrial ecotones will be an important tool. However, to provide a scientific background for such conservation activities, it will be desirable to test the importance of different types of ecotones in structuring and maintaining the genetic diversity of fish populations. The relevance of population genetics data to ecotone studies can only be understood in an ecological context as evolution is a function of environment. We suggest that as ecotone complexity increases opportunities for survival of individuals, improving trophic conditions and spatial habitat heterogeneity, so the population size and variation increase with increased genetic diversity and vulnerability to environment changes decreases.     

Seasonal and spatial variability of zooplankton diversity in the Poyang Lake Basin using DNA metabarcoding

Freshwater ecosystems face multiple threats to their stability globally. Poyang Lake is the largest lake in China, but its habitat has been seriously degraded because of human activities and natural factors (e.g. climate change), resulting in a decline in freshwater biodiversity. Zooplankton are useful indicators of environmental stressors because they are sensitive to external perturbations. DNA metabarcoding is an approach that has gained significant traction by aiding ecosystem conservation and management. Here, the seasonal and spatial variability in the zooplankton diversity were analyzed in the Poyang Lake Basin using DNA metabarcoding. The results showed that the community structure of zooplankton exhibited significant seasonal and spatial variability using DNA metabarcoding, where the community structure was correlated with turbidity, water temperature, pH, total phosphorus, and chlorophyll‐a. These results indicated habitat variations affected by human activities and seasonal change could be the main driving factors for the variations of zooplankton community. This study also provides an important reference for the management of aquatic ecosystem health and conservation of aquatic biodiversity.     

Habitat loss in the restricted range of the endemic Ghanaian cichlid Limbochromis robertsi

Remote sensing has become an integral and invaluable tool to inform biodiversity conservation and monitoring of habitat degradation and restoration over time. Despite the disproportionately high levels of biodiversity loss in freshwater ecosystems worldwide, ichthyofauna are commonly overlooked in favor of other keystone species. Freshwater fish, as indicators of overall aquatic ecosystem health, can also be indicators of larger scale problems within an ecosystem. As a case study with multi-temporal, multi-resolution satellite imagery, we examined deforestation and forest fragmentation around the Atewa Forest Reserve, Ghana. Within small creeks, Limbochromis robertsi, a unique freshwater cichlid with an extremely limited distribution range, can be found. Historically, the land cover in the area has undergone substantial deforestation for agriculture and artisanal small-scale mining. In the 1389-km² study area, we found deforestation accelerated along with increased forest fragmentation in the 2014–2017 period (167.4 km² of deforestation) with the majority of the forest loss along the river and creek banks due to small-scale mining operations and increased agriculture. Field visits indicated a decrease in the total L. robertsi population by approximately 90% from the early 1990s to 2018. Its distribution has been reduced to higher elevations by anthropogenic habitat barriers at low elevations and the presence of predatory species. Loss of riparian forest through land use and cover change to mining and agriculture contributes to the habitat degradation for this endemic species. Fine spatial- and temporal-scale studies are required to assess habitat characteristics are not captured by global- or continental-scale datasets.     

Maintaining and restoring hydrologic habitat connectivity in mediterranean streams: an integrated modeling framework

Hydrologic alterations designed to provide a stable water supply and to prevent flooding are commonly used in mediterranean-climate river (med-rivers) basins, and these alterations have led to habitat loss and significant declines in aquatic biodiversity. Often the health of freshwater ecosystems depends on maintaining and recovering hydrologic habitat connectivity, which includes structural components related to the physical landscape, functionality of flow dynamics, and an understanding of species habitat requirements for movement, reproduction, and survival. To advance our understanding of hydrologic habitat connectivity and benefits of habitat restoration alternatives we provide: (1) a review of recent perspectives on hydrologic connectivity, including quantitative methods; and (2) a modeling framework to quantify the effects of restoration on hydrologic habitat connectivity. We then illustrate this approach through a case study on lateral hydrologic habitat connectivity that results from channel restoration scenarios using scenarios with different historic and climate-change flows to restore fish floodplain habitat in a med-river, the San Joaquin River, California. Case study results show that in addition to the channel alterations, higher flows are required to recover significant flooded habitat area, especially given reductions in flows expected under climate change. These types of studies will help the planning for restoration of hydrologic habitat connectivity in med-rivers, a critical step for mediterranean species recovery.