Feasibility of implementing an integrated long-term database to advance ecosystem-based management in the Laurentian Great Lakes basin.

The North American Great Lakes have been experiencing dramatic change during the past half-century, highlighting the need for holistic, ecosystem-based approaches to management. To assess interest in ecosystem-based management (EBM), including the value of a comprehensive public database that could serve as a repository for the numerous physical, chemical, and biological monitoring Great Lakes datasets that exist, a two-day workshop was organized, which was attended by 40+ Great Lakes researchers, managers, and stakeholders. While we learned during the workshop that EBM is not an explicit mission of many of the participating research, monitoring, and management agencies, most have been conducting research or monitoring activities that can support EBM. These contributions have ranged from single-resource (-sector) management to considering the ecosystem holistically in a decision-making framework. Workshop participants also identified impediments to implementing EBM, including: 1) high anticipated costs; 2) a lack of EBM success stories to garner agency buy-in; and 3) difficulty in establishing common objectives among groups with different mandates (e.g., water quality vs. fisheries production). We discussed as a group solutions to overcome these impediments, including construction of a comprehensive, research-ready database, a prototype of which was presented at the workshop. We collectively felt that such a database would offer a cost-effective means to support EBM approaches by facilitating research that could help identify useful ecosystem indicators and management targets and allow for management strategy evaluations that account for risk and uncertainty when contemplating future decision-making.

Detecting sediment recovery below an offshore longline mussel farm: A macrobenthic Biological Trait Analysis (BTA).

Expansion of bivalve aquaculture offshore reports lower environmental impacts compared to inshore farms. Taking a Before-After Control-Impact approach, this study presents the first functional diversity analysis and long-term Biological Trait Analysis (BTA) of infauna functional traits following the development of the United Kingdom's first large-scale, offshore longline mussel farm. Located in an area historically impacted by mobile fishing gear, farm sites had the greatest number of taxa and abundance compared to control sites. Functional diversity varied significantly across treatments (farm, near control, far control); while Functional Diversity, Richness, Divergence and Dispersion increased over time within the farm, Functional Evenness and Redundancy decreased. Bioturbation, body size, diet, feeding mode, life span, motility, sediment position, sensitivity and substrate type were chosen for Community-level Weighted Mean analysis, depicting the most frequently affected biological traits by shellfish farming. Farm sites developed a wider range of traits enhancing ecosystem function and habitat recovery after years of seabed damage. Outcomes support the use of functional diversity and BTA analysis to perform ecosystem assessment, supporting decision-makers implement policy and management.

High vulnerability of coastal wetlands in Chile at multiple scales derived from climate change, urbanization, and exotic forest plantations.

Coastal wetlands are considered one of the most vulnerable ecosystems worldwide; the ecosystem services they provide and the conservation of their biodiversity are threatened. Despite the high ecological and socioenvironmental value of coastal wetlands, regional and national vulnerability assessments are scarce. In this study we aimed to assess the vulnerability of coastal wetlands in Chile from 18°S to 42°S (n = 757) under a multiscale approach that included drivers associated with climate change and land cover change. We assessed multiple drivers of vulnerability at three spatial scales (10 m, 100 m, and 500 m) by analyzing multiple remote sensing data (16 variables) on land cover change, wildfires, climatic variables, vegetation functional properties, water surface and importance for biodiversity. We constructed a multifactorial vulnerability index based on the variables analyzed, which provided a map of coastal wetland vulnerability. Then we explored the main drivers associated with the vulnerability of each coastal wetland by performing a Principal Components Analysis with Agglomerative Hierarchical Clustering, which allowed us to group coastal wetlands according to the drivers analyzed. We found that 42.6 ± 9.2 % of the coastal wetlands evaluated have high or very high vulnerability, with higher vulnerability at the 500 m scale (51.4 %). We identified four groups of coastal wetlands: two located in central Chile, mainly affected by climate change-associated drivers (41.9 ± 2.1 %), and one in central Chile which is affected by land cover change (52.8 ± 6.2 %); the latter has a lower vulnerability level. The most vulnerable coastal wetlands were located in central Chile. Our results present novel findings about the current vulnerability of coastal wetlands, which could be validated by governmental institutions in field campaigns. Finally, we believe that our methodological approach could be useful to generate similar assessments in other world zones.

Impact of sand bund removal on seagrass ecosystems: A study of macrobenthic community structure and correlation with macrophytes cover and sediments.

This study investigated the impacts of the removal of sand bund on the macrobenthos community structure, seagrass cover, and sediment particle size in Merambong Shoal, Malaysia. The reclamation project deposited sand bund in the middle of Merambong seagrass shoal, resulting in its division into northern (NS) and southern (SS) halves. Ecosystem changes were monitored over a 31-month period using the transect lines method. Bi-monthly samples were collected for assessment. The results revealed a substantial decline in macrobenthos densities compared to previous studies. However, after the removal of the sand bund, there was a significant increase in macrobenthos density, specifically Polychaeta and Malacostraca, at NS. Seagrass cover at NS was initially lower than SS but showed an increase after the complete removal of the sand blockage. Sediment particle analysis reported a higher silt percentage at NS, indicating greater sedimentation at NS, which was partially sheltered from wave actions.

Uncovering ecological regime shifts in the Sea of Marmara and reconsidering management strategies.

Ecosystem regime shifts can alter ecosystem services, affect human well-being, and trigger policy conflicts due to economic losses and reductions in societal and environmental benefits. Intensive anthropogenic activities make the Sea of Marmara ecosystem suffer from nearly all existing available types of ecosystem pressures such as biological degradation, exposure to hydrological processes, nutrient and organic matter enrichment, plastic pollution, ocean warming, resulting in deterioration of habitats. In this study, using an integrated ecosystem assessment, we investigated for the first time the historical development and ecosystem state of the Sea of Marmara. Multivariate analyses were applied to the most comprehensive and unique long-term data sets of 9 biotic and 15 abiotic variables for ecosystem state and drivers respectively, from 1986 to 2020. Observed changes were confirmed by detecting shifts in the datasets. The Sea of Marmara ecosystem was classified into three regimes: i) an early initial state regime under the top-down control of predatory medium pelagic fish and fisheries exploitation until mid-1990s, ii) a transitional regime between mid-1990s and mid-2010s as from ecosystem restructuring, and iii) an alternate state late regime with prevailing impacts of climate change from mid-2010s until 2020. During the 20 years transitional regime, three different phases were also characterized; i) the 1st phase between mid-1990s and early 2000s with its gradual change in ecosystem state from a decrease in predators and significant shift in physical drivers of the ecosystem, ii) the 2nd phase between 2000 and mid-2000s with a strong shift in ecosystem state, an ongoing increase in climate indices and fishing mortality, and a gradual decrease in water quality; and iii) the 3rd phase between mid-2000s and mid-2010s with the reorganization of the ecosystem dominated by small pelagic fish and ameliorated water quality. During late regime, we observed that most of the biotic variables, mainly fish biomass, and climate variables did not return to their initial state despite the improvement in some abiotic variables such as water quality. We identify these observed changes in the SoM ecosystem as a non-linear regime shift. Finally, we also developed concrete suggestions for improved regional management.

Global insect decline is the result of wilful political failure: A battle plan for entomology.

The Millennium Ecosystem Assessment assessed ecosystem change, human wellbeing and scientific evidence for sustainable use of biological systems. Despite intergovernmental acknowledgement of the problem, global ecological decline has continued, including declines in insect biodiversity, which has received much media attention in recent years. Several roadmaps to averting biological declines have failed due to various economic and political factors, and so biodiversity loss continues, driven by several interacting human pressures. Humans are innately linked with nature but tend to take it for granted. The benefits we gain from the insect world are broad, yet aversion or phobias of invertebrates are common, and stand firmly in the path of their successful conservation. Providing an integrated synthesis for policy teams, conservation NGOs, academic researchers and those interested in public engagement, this article considers: (1) The lack of progress to preserve and protect insects. (2) Examples relating to insect decline and contributions insects make to people worldwide, and consequently what we stand to lose. (3) How to engage the public, governmental organizations and researchers through "insect contributions to people" to better address insect declines. International political will has consistently acknowledged the existence of biodiversity decline, but apart from a few narrow cases of charismatic megafauna, little meaningful change has been achieved. Public values are reflected in political willpower, the progress being made across the world, changing views on insects in the public should initiate a much-needed political sea-change. Taking both existing activity and required future actions, we outline an entomologist's "battle plan" to enormously expand our efforts and become the champions of insect conservation that the natural world needs.

Temporal scope influences ecosystem driver-response relationships: A case study of Lake Erie with implications for ecosystem-based management.

Understanding environmental driver-response relationships is critical to the implementation of effective ecosystem-based management. Ecosystems are often influenced by multiple drivers that operate on different timescales and may be nonstationary. In turn, contrasting views of ecosystem state and structure could arise depending on the temporal perspective of analysis. Further, assessment of multiple ecosystem components (e.g., biological indicators) may serve to identify different key drivers and connections. To explore how the timescale of analysis and data richness can influence the identification of driver-response relationships within a large, dynamic ecosystem, this study analyzed long-term (1969-2018) data from Lake Erie (USA-Canada). Data were compiled on multiple biological, physical, chemical, and socioeconomic components of the ecosystem to quantify trends and identify potential key drivers during multiple time intervals (20 to 50 years duration), using zooplankton, bird, and fish community metrics as indicators of ecosystem change. Concurrent temporal shifts of many variables occurred during the 1980s, but asynchronous dynamics were evident among indicator taxa. The strengths and rank orders of predictive drivers shifted among intervals and were sometimes taxon-specific. Drivers related to nutrient loading and lake trophic status were consistently strong predictors of temporal patterns for all indicators; however, within the longer intervals, measures of agricultural land use were the strongest predictors, whereas within shorter intervals, the stronger predictors were measures of tributary or in-lake nutrient concentrations. Physical drivers also tended to increase in predictive ability within shorter intervals. The results highlight how the time interval examined can filter influences of lower-frequency, slower drivers and higher-frequency, faster drivers. Understanding ecosystem change in support of ecosystem-based management requires consideration of both the temporal perspective of analysis and the chosen indicators, as both can influence which drivers are identified as most predictive of ecosystem trends at that timescale.

Evidence of climate-driven regime shifts in the Aegean Sea's demersal resources: A study spanning six decades.

Climate change (CC) can alter the configuration of marine ecosystems; however, ecosystem response and resilience to change are usually case-specific. The effect of CC on the demersal resources of the Aegean Sea (east Mediterranean Sea) was investigated during the past six decades applying a combination of multivariate analysis, non-additive modeling and the Integrated Resilience Assessment (IRA) framework. We focused on the study of: (i) the biological "system" complex, using proxies of biomass (landings per unit of capacity) for 12 demersal taxa, and (ii) the environmental "stressor" complex, described by 12 abiotic variables. Pronounced changes have occurred in both the environmental and biological system over the studied period. The majority of the environmental stressors exhibited strikingly increasing trends (temperature, salinity, primary production indices) with values started exceeding the global historical means during late 1980s-early 1990s. It is suggested that the biological system exhibited a discontinuous response to CC, with two apparently climate-induced regime shifts occurring in the past 25 years. There is evidence for two-fold bifurcations and four tipping points in the system, forming a folded stability landscape with three basins of attraction. The shape of the stability landscape for the Aegean Sea's biological system suggests that while the initial state (1966-1991) was rather resilient to CC, absorbing two environmental step-changes, this was not the case for the two subsequent ones (intermediate: 1992-2002; recent: 2003-2016). Given the current trajectory of environmental change, it is highly unlikely that the biological system will ever return to its pre-1990s state, as it is entering areas of unprecedented climatic conditions and there is some evidence that the system may be even shifting toward a new state. Our approach and findings may be relevant to other marine areas of the Mediterranean and beyond, undergoing climate-driven regime shifts, and can assist to their adaptive management.

Ecological perspectives on water, food, and health security linkages: the Minamata case in Japan.

Extant studies address water, food, and health security issues considerably separately and within narrow disciplinary confines. This study investigates the links among these three issues from an ecological viewpoint with a multidisciplinary approach in a modified Millennium Ecosystem Assessment framework developed by the United Nations. The modified framework includes water, food, and health security considerations as the three constituents of human well-being from an ecological (more specifically, ecosystem services) viewpoint. This study examines the links through published data associated with the Minamata incident, which was a historic and horrific methylmercury-induced water, food, and health poisoning crisis in Japan. The results show that when heavy metal pollution changes one component (marine water) of the provisioning ecosystem services, this change subsequently affects another component (seafood) of the services. This then defines the linkages among water, food, and health security as the three constituents of human well-being within the modified framework. The links can have immediate and far-reaching economic, social, legal, ethical, and justice implications within and across generations. This study provides important evidence for emerging economies that ignore the water-food-health security nexus.

An Integrated Traits Resilience Assessment of Mediterranean fisheries landings.

An increasing number of studies have been examining the functional configuration of biological communities or ecosystems using biological traits. Here, we investigated the temporal dynamics and resilience of the traits composition in Mediterranean fisheries landings over 31 years (1985-2015). We transcribed the FAO Mediterranean landings dataset for 101 marine species into a dataset of 23 traits related to the life cycle, distribution, ecology and behaviour. Mediterranean mean Sea Surface Temperature (SST) was evaluated as a potential driver of the traits composition. Trait dynamics were evaluated both individually and holistically by developing an Integrated Traits Resilience Assessment (ITRA). ITRA is a variation of the Integrated Resilience Assessment (IRA), a method to infer resilience dynamics and build stability landscapes of complex natural systems. Changes in landings trait dynamics were documented both for individual traits and for the entire traits 'system', and a relevant regime shift was detected in the second half of the 1990s. The traits system switched to higher optimal temperature, more summer spawning, shorter life span, smaller maximum size, shallower optimal depth and planktivorous diet. This shift was found to be a lagged discontinuous response to sea warming, which gradually eroded the resilience of the original state of the traits system, leading it into a new basin of attraction. The inclusion of ecological/response traits (related to environmental preferences) in our analyses indicates potential mechanisms that explain the observed shift, while changes in functional/effect traits indicate potential impacts on ecosystem functioning. Our findings suggest that changes in the Mediterranean ecosystems are evidently larger than previously thought, with profound implications for the management of this highly impacted sea. ​.

An approach for assessing ecosystem-based adaptation in coral reefs at relatively high latitudes to climate change and human pressure.

Relatively high-latitude waters are supposed as a refuge for corals under ocean warming. A systematic assessment of the Weizhou Island reef in the northern South China Sea, a relatively high-latitude region, shows that the ecosystem restoration index decreased from 0.96 to 0.62 during the period between 1990 and 2015. Although the biotic community, supporting services, and regulating services remained at good or very good states, the provisioning services, cultural services, and especially habitat structure deteriorated to very poor or moderate states. Gray relational analysis showed that these ecological declines exhibited a strong relationship with human pressures from tourism activities and the petrochemical industry. The recoveries of the biotic community and supporting services that benefited from wintertime warming appeared to be partly offset by intensive human pressures. The long-term effects on ecosystem structure and functions suggest that anthropogenic disturbances have impaired the possibility of this area serving as a potential thermal refuge for reef-building corals in the South China Sea. This study thus provides an integrated approach for assessing the adaptive responses of coral reef ecosystems to climate change and local human activities.

Coupled reservoir-river systems: Lessons from an integrated aquatic ecosystem assessment.

Sustainable reservoir-river management requires balancing complex trade-offs and decision-making to support both human water demands and ecological function. Current numerical simulation and optimization algorithms can guide reservoir-river operations for optimal hydropower production, irrigation, nutrient management, and municipal consumption, yet much less is known about optimization of associated ecosystems. This ten-year study demonstrates an ecosystem assessment approach that links the environmental processes to an ecosystem response in order to evaluate the impact of climatic forcing and reservoir operations on the aquatic ecosystems of a coupled headwater reservoir-river system. The approach uses a series of numerical, statistical, and empirical models to explore reservoir operational flexibility aimed at improving the environmental processes that support aquatic ecosystem function. The results illustrate that understanding the seasonal biogeochemical changes in reservoirs is critical for determining environmental flow releases and the ecological trajectory of both the reservoir and river systems. The coupled models show that reservoir management can improve the ecological function of complex aquatic ecosystems under certain climatic conditions. During dry hydrologic years, the high post-irrigation release can increase the downstream primary and macroinvertebrate production by 99% and 45% respectively. However, this flow release would reduce total fish biomass in the reservoir by 16%, providing management tradeoffs to the different ecosystems. Additionally, low post-irrigation flows during the winter season supports water temperature that can maintain ice cover in the downstream river for improved ecosystem function. The ecosystem assessment approach provides operational flexibility for large infrastructure, supports transparent decision-making by management agencies, and facilitates framing of environmental legislation.

Advances in terrestrial and ocean dynamics studies in India.

The land, oceans, and atmosphere are tightly linked and form the most dynamic component of the climate system. Studies on terrestrial and ocean science enhance the understanding on the impacts of climate change. Across India and the world over, human-driven land use and climate changes are altering the structure, function, and extent of natural terrestrial ecosystems and in turn regional biogeochemical feedbacks. In this special issue, we present 29 manuscripts; those discuss wide-ranging aspects of terrestrial and oceanic characterization and dynamics. These contributions are based on selected presentations made at the 2nd International Workshop on Biodiversity and Climate Change (BDCC-2018) held on 24-27 February 2018 at the Indian Institute of Technology Kharagpur, India. The manuscripts are arranged in five sections such as Ecological Assessment, Plant Invasion, Carbon Dynamics, Ecosystem Characterization, and Ocean Dynamics. We realized that the utility of satellite remote sensing data has been emerging as a dominant trend in environmental monitoring and assessment studies in India.

A systematic review of biodiversity and demographic change: A misinterpreted relationship?

Demographic change is supposed to be the most important indirect driver for changing biodiversity. In this article, a systematic review of 148 studies was conducted to examine the scientific evidence for this relationship and to identify potential gaps in research. We explored the spatial distribution of studies, the categories addressed with respect to biodiversity and demographic change, and the ways in which their relationships were conceptualised (spatially and temporally) and valued. The majority of studies were carried out in Africa, Europe and North America. Our analysis confirms the trend that demographic phenomena were mostly found to negatively influence biodiversity. However, a considerable number of studies also point towards impacts that were context dependent, either positive or negative under certain circumstances. In addition to that we identified significant gaps in research. In particular, there is a lack of addressing (1) other demographic aspects such as population decline, age structure or gender differences, (2) spatial variability of, e.g. human population growth, (3) long-term effects of demographic processes, and (4) the context dependency (e.g. regulations/law enforcement, type of human activities, and choice of scale or proxy). We conclude there is evidence that the relationship between biodiversity and demographic change is much more complex than expected and so far represented in research. Thus, we call for a social-ecological biodiversity research that particularly focusses on the functional relation between biodiversity and human activities, namely the different types, context, and interdependent dynamics (spatial and temporal) of this complex relation.

Assessing the impacts of phosphate mining on coral reef communities and reef development.

Phosphate mining activities on Christmas Island began in the late 1800's providing a unique, long-term case study in which to assess the impacts of mining on coral reef development. Watershed modelling was used to identify potential "hotspots" of mining runoff on to adjacent reefs. Pollution hotspots were also confirmed by analysis of reef sediment. Phosphate rich mining runoff flowed from local watersheds onto nearshore coral reefs with levels of up to 54,000 mg/kg of total phosphate recorded in reef sediment at the Dryers reef site adjacent to the main phosphate storage facility. Using this combination of watershed modelling and in-situ sediment contamination data we identified six coral reef sites along an environmental impact gradient. In-situ benthic transects were paired with a new rubble-encruster method enabling the analysis to combine large scale transect information alongside fine-scale data on epibenthic and encruster assemblages. Results demonstrate that phosphate rich sediment loading negatively impacted coral reef building communities, in particular, branching corals and calcareous encrusting organisms, critical to the future survival of coral reef ecosystems. These findings highlight the importance of curtailing runoff and pollution from catchment based mining activities and protecting reefs for the future.

Estimating intraspecific genetic diversity from community DNA metabarcoding data.

BACKGROUND: DNA metabarcoding is used to generate species composition data for entire communities. However, sequencing errors in high-throughput sequencing instruments are fairly common, usually requiring reads to be clustered into operational taxonomic units (OTUs), losing information on intraspecific diversity in the process. While Cytochrome c oxidase subunit I (COI) haplotype information is limited in resolving intraspecific diversity it is nevertheless often useful e.g. in a phylogeographic context, helping to formulate hypotheses on taxon distribution and dispersal. METHODS: This study combines sequence denoising strategies, normally applied in microbial research, with additional abundance-based filtering to extract haplotype information from freshwater macroinvertebrate metabarcoding datasets. This novel approach was added to the R package "JAMP" and can be applied to COI amplicon datasets. We tested our haplotyping method by sequencing (i) a single-species mock community composed of 31 individuals with 15 different haplotypes spanning three orders of magnitude in biomass and (ii) 18 monitoring samples each amplified with four different primer sets and two PCR replicates. RESULTS: We detected all 15 haplotypes of the single specimens in the mock community with relaxed filtering and denoising settings. However, up to 480 additional unexpected haplotypes remained in both replicates. Rigorous filtering removes most unexpected haplotypes, but also can discard expected haplotypes mainly from the small specimens. In the monitoring samples, the different primer sets detected 177-200 OTUs, each containing an average of 2.40-3.30 haplotypes per OTU. The derived intraspecific diversity data showed population structures that were consistent between replicates and similar between primer pairs but resolution depended on the primer length. A closer look at abundant taxa in the dataset revealed various population genetic patterns, e.g. the stonefly Taeniopteryx nebulosa and the caddisfly Hydropsyche pellucidula showed a distinct north-south cline with respect to haplotype distribution, while the beetle Oulimnius tuberculatus and the isopod Asellus aquaticus displayed no clear population pattern but differed in genetic diversity. DISCUSSION: We developed a strategy to infer intraspecific genetic diversity from bulk invertebrate metabarcoding data. It needs to be stressed that at this point this metabarcoding-informed haplotyping is not capable of capturing the full diversity present in such samples, due to variation in specimen size, primer bias and loss of sequence variants with low abundance. Nevertheless, for a high number of species intraspecific diversity was recovered, identifying potentially isolated populations and taxa for further more detailed phylogeographic investigation. While we are currently lacking large-scale metabarcoding datasets to fully take advantage of our new approach, metabarcoding-informed haplotyping holds great promise for biomonitoring efforts that not only seek information about species diversity but also underlying genetic diversity.

Sorting things out: Assessing effects of unequal specimen biomass on DNA metabarcoding.

Environmental bulk samples often contain many different taxa that vary several orders of magnitude in biomass. This can be problematic in DNA metabarcoding and metagenomic high-throughput sequencing approaches, as large specimens contribute disproportionately high amounts of DNA template. Thus, a few specimens of high biomass will dominate the dataset, potentially leading to smaller specimens remaining undetected. Sorting of samples by specimen size (as a proxy for biomass) and balancing the amounts of tissue used per size fraction should improve detection rates, but this approach has not been systematically tested. Here, we explored the effects of size sorting on taxa detection using two freshwater macroinvertebrate bulk samples, collected from a low-mountain stream in Germany. Specimens were morphologically identified and sorted into three size classes (body size < 2.5 × 5, 5 × 10, and up to 10 × 20 mm). Tissue powder from each size category was extracted individually and pooled based on tissue weight to simulate samples that were not sorted by biomass ("Unsorted"). Additionally, size fractions were pooled so that each specimen contributed approximately equal amounts of biomass ("Sorted"). Mock samples were amplified using four different DNA metabarcoding primer sets targeting the Cytochrome c oxidase I (COI) gene. Sorting taxa by size and pooling them proportionately according to their abundance lead to a more equal amplification of taxa compared to the processing of complete samples without sorting. The sorted samples recovered 30% more taxa than the unsorted samples at the same sequencing depth. Our results imply that sequencing depth can be decreased approximately fivefold when sorting the samples into three size classes and pooling by specimen abundance. Even coarse size sorting can substantially improve taxa detection using DNA metabarcoding. While high-throughput sequencing will become more accessible and cheaper within the next years, sorting bulk samples by specimen biomass or size is a simple yet efficient method to reduce current sequencing costs.

Architecture of collapse: regime shift and recovery in an hierarchically structured marine ecosystem.

By the late 20th century, a series of events or 'natural experiments', for example the depletion of apex predators, extreme eutrophication and blooms of invasive species, had suggested that the Black Sea could be considered as a large ecosystem 'laboratory'. The events resulted in regime shifts cascading through all trophic levels, disturbing ecosystem functioning and damaging the water environment. Causal pathways by which the external (hydroclimate, overfishing) and internal (food web interactions) drivers provoke regime shifts are investigated. Statistical data analyses supported by an interpretative framework based on hierarchical ecosystem theory revealed mechanisms of hierarchical incorporation of environmental factors into the ecosystem. Evidence links Atlantic teleconnections to Black Sea hydroclimate, which together with fishing shapes variability in fish stocks. The hydroclimatic signal is conveyed through the food web via changes in productivity at all levels, to planktivorous fish. Fluctuating fish abundance is believed to induce a lagged change in competitor jelly plankton that cascades down to phytoplankton and influences water quality. Deprived of the stabilising role of apex predators, the Black Sea's hierarchical ecosystem organisation is susceptible to both environmental and anthropogenic stresses, and increased fishing makes fish stock collapses highly probable. When declining stocks are confronted with burgeoning fishing effort associated with the inability of fishery managers and decision-makers to adapt rapidly to changes in fish abundance, there is overfishing and stock collapse. Management procedures are ineffective at handling complex phenomena such as ecosystem regime shifts because of the shortage of suitable explanatory models. The proposed concepts and models reported here relate the hydroclimate, overfishing and invasive species to shifts in ecosystem functioning and water quality, unravelling issues such as the causality of ecosystem interactions and mechanisms and offering potential for finding ways to reverse regime shifts. We advocate a management approach aiming at restoring ecosystem hierarchy that might mitigate the costly consequences of regime shifts.

Community assessment techniques and the implications for rarefaction and extrapolation with Hill numbers.

Diversity estimates play a key role in ecological assessments. Species richness and abundance are commonly used to generate complex diversity indices that are dependent on the quality of these estimates. As such, there is a long-standing interest in the development of monitoring techniques, their ability to adequately assess species diversity, and the implications for generated indices. To determine the ability of substratum community assessment methods to capture species diversity, we evaluated four methods: photo quadrat, point intercept, random subsampling, and full quadrat assessments. Species density, abundance, richness, Shannon diversity, and Simpson diversity were then calculated for each method. We then conducted a method validation at a subset of locations to serve as an indication for how well each method captured the totality of the diversity present. Density, richness, Shannon diversity, and Simpson diversity estimates varied between methods, despite assessments occurring at the same locations, with photo quadrats detecting the lowest estimates and full quadrat assessments the highest. Abundance estimates were consistent among methods. Sample-based rarefaction and extrapolation curves indicated that differences between Hill numbers (richness, Shannon diversity, and Simpson diversity) were significant in the majority of cases, and coverage-based rarefaction and extrapolation curves confirmed that these dissimilarities were due to differences between the methods, not the sample completeness. Method validation highlighted the inability of the tested methods to capture the totality of the diversity present, while further supporting the notion of extrapolating abundances. Our results highlight the need for consistency across research methods, the advantages of utilizing multiple diversity indices, and potential concerns and considerations when comparing data from multiple sources.

A framework for inferring biological communities from environmental DNA.

Environmental DNA (eDNA), genetic material recovered from an environmental medium such as soil, water, or feces, reflects the membership of the ecological community present in the sampled environment. As such, eDNA is a potentially rich source of data for basic ecology, conservation, and management, because it offers the prospect of quantitatively reconstructing whole ecological communities from easily obtained samples. However, like all sampling methods, eDNA sequencing is subject to methodological limitations that can generate biased descriptions of ecological communities. Here, we demonstrate parallels between eDNA sampling and traditional sampling techniques, and use these parallels to offer a statistical structure for framing the challenges faced by eDNA and for illuminating the gaps in our current knowledge. Although the current state of knowledge on some of these steps precludes a full estimate of biomass for each taxon in a sampled eDNA community, we provide a map that illustrates potential methods for bridging these gaps. Additionally, we use an original data set to estimate the relative abundances of taxon-specific template DNA prior to PCR, given the abundance of DNA sequences recovered post-PCR-and-sequencing, a critical step in the chain of eDNA inference. While we focus on the use of eDNA samples to determine the relative abundance of taxa within a community, our approach also applies to single-taxon applications (including applications using qPCR), studies of diversity, and studies focused on occurrence. By grounding inferences about eDNA community composition in a rigorous statistical framework, and by making these inferences explicit, we hope to improve the inferential potential for the emerging field of community-level eDNA analysis.