SNIFFER WFD119: Enhancement of the River Invertebrate Classification Tool (RICT)

EXECUTIVE SUMMARY Project funders/partners: Environment Agency (EA), Northern Ireland Environment Agency (NIEA), Scotland & Northern Ireland Forum for Environmental Research (SNIFFER), Scottish Environment Protection Agency (SEPA) Background to research The Regulatory Agencies in the UK (the Environment Agency; Scottish Environment Protection Agency; and the Northern Ireland Environment Agency) now use the River Invertebrate Classification Tool (RICT) to classify the ecological quality of rivers for Water Framework Directive compliance monitoring. RICT incorporates RIVPACS IV predictive models and is a highly capable tool written in a modern software programming language. While RICT classifies waters for general degradation and organic pollution stress, producing assessments of status class and uncertainty, WFD compliance monitoring also requires the UK Agencies to assess the impacts of a wide range of pressures including hydromorphological and acidification stresses. Some of these pressures alter the predictor variables that current RIVPACS models use to derive predicted biotic indices. This project has sought to broaden the scope of RICT by developing one or more RIVPACS model(s) that do not use predictor variables that are affected by these stressors, but instead use alternative GIS based variables that are wholly independent of these pressures. This project has also included a review of the wide range of biotic indices now available in RICT, identifying published sources, examining index performance, and where necessary making recommendations on further needs for index testing and development. Objectives of research •To remove and derive alternative predictive variables that are not affected by stressors, with particular emphasis on hydrological/acidification metric predictors. •To construct one or more new RIVPACS model(s) using stressor independent variables. •Review WFD reporting indices notably AWIC(species), LIFE (species), PSI & WHPT. Key findings and recommendations : Predictor variables and intellectual property rights : An extensive suite of new variables have been derived by GIS for the RIVPACS reference sites that have been shown to act as stressor-independent predictor variables. These include measures of stream order, solid and drift geology, and a range of upstream catchment characteristics (e.g. catchment area, mean altitude of upstream catchment, and catchment aspect). It is recommended that decisions are reached on which of the newly derived model(s) are implemented in RICT so that IPR issues for the relevant datasets can be quickly resolved and the datasets licensed. It is also recommended that licensing is sought for a point and click system (where the dataset cannot be reverse engineered) that is capable of calculating any of the time-invariant RIVPACS environmental predictor variables used by any of the newly derived (and existing) RIVPACS models, and for any potential users. New stressor-independent RIVPACS models : Using the existing predictor variables, together with new ones derived for their properties of stressor-independence, initial step-wise forward selection discriminant models suggested a range of 36 possible models that merited further testing. Following further testing, the following models are recommended for assessing watercourses affected by flow/hydromorphological and/or acidity stress: • For flow/hydromorphological stressors that may have modified width, depth and/or substrate in GB, it is suggested that a new ‘RIVPACS IV – Hydromorphology Independent’ model (Model 24) is used (this does not use the predictor variables width, depth and substratum, but includes a suite of new stressor-independent variables). • For acidity related stressors in GB, it is suggested that a new ‘RIVPACS IV – Alkalinity Independent’ model (Model 35) is used (this does not use the predictor variable alkalinity, but includes new stressor-independent variables). • For flow/hydromorphological stressors and acidity related stressors in GB, it is suggested that a new ‘RIVPACS IV – Hydromorphology & Alkalinity Independent’ model (Model 13) is used (this does not use the predictor variables width, depth, substratum and alkalinity, but includes a suite of new stressor-independent variables). • Reduced availability of appropriate GIS tools at this time has meant that no new models have been developed for Northern Ireland. Discriminant functions and end group means have now been calculated to enable any of these models to be easily implemented in the RICT software. Biotic indices : The RIVPACS models in RICT can now produce expected values for a wide range of biotic indices addressing a variety of stressors. These indices will support the use of RICT as a primary tool for WFD classification and reporting of the quality of UK streams and rivers. There are however a number of outstanding issues with indices that need to be addressed: • There is a need to develop a biotic index for assessing metal pollution. • WFD EQR banding schemes are required for many of the indices to report what is considered an acceptable degree of stress (High-Good) and what is not (Moderate, Poor or Bad). • A comprehensive objective testing process needs to be undertaken on the indices in RICT using UK-wide, large-scale, independent test datasets to quantify their index-stressor relationships and their associated uncertainty, for example following the approach to acidity index testing in Murphy et al., (in review) or organic/general degradation indices in Banks & McFarland (2010). • Following objective testing, the UK Agencies should make efforts to address any index under-performance issues that have been identified, and where necessary new work should be commissioned to modify existing indices, or develop new ones where required so that indices for all stress types meet certain minimum performance criteria. • Testing needs to be done to examine index-stressor relationships with both observed index scores and RIVPACS observed/expected ratios. Work should also be done to compare the existing RIVPACS IV and the new stressor-independent models (developed in this project) as alternative sources of the expected index values for these tests. • Consideration should be given to assessing the extent to which chemical and biological monitoring points co-occur. Site-matched (rather than reach-matched) chemical and biological monitoring points would i) generate the substantial training datasets needed to refine or develop new indices and ii) generate the independent datasets for testing

Impacts of climate change on environmental flows in West Africa's Upper Niger Basin and the Inner Niger Delta

Modified water regimes due to climate change are likely to be a major cause of freshwater ecosystem alteration. General Circulation Model (GCM)-related uncertainty in environmental flows at 12 gauging stations in the Upper Niger Basin and flooding within the Inner Niger Delta is assessed using the Ecological Risk due to the Flow Alteration method and a hydrological model forced with projections from 12 GCM groups for RCP 4.5 in the 2050s and 2080s. Risk varies between GCM groups and stations. It increases into the future and is larger for changes in low flows compared to high flows. For the ensemble mean, a small minority of GCM groups projects no risk for high flows in the 2050s (low risk otherwise). This reverses for the 2080s. For low flows, no risk is limited to three stations in the 2050s and one station in the 2080s, the other experience either low or medium risk. There is greater consistency in the risk of change in flood extent, especially in the dry season (medium risk for all groups and the ensemble mean). Some (low or medium) risk of change in peak annual inundation is projected for most groups. Changing flood patterns have implications for wetland ecology and ecosystem services

Development and application of the Ecological Risk due to Flow Alteration (ERFA) methodology in Cambodia – progress on the TEFRIC project

The hydrological characteristics of a river exert critical controls on aquatic ecosystems. A river’s flow regime (characterised by variability, magnitude, frequency, duration, timing and rate of change of discharge) is central to sustaining aquatic biodiversity and ecosystem integrity. All elements of this regime influence some aspect of riverine ecosystems. Changes in river discharge due to climate change or water resources management have the potential for ecological impacts. The science of environmental flows has developed in order to determine flow regimes necessary to maintain economically, socially and ecologically important ecosystem services

Development of understanding in hydro-climate services in India to inform food and water security

This project aims to improve understanding of hydro-climate services in India in order to inform food and water security. It involves collaboration between UCL and the Centre for Ecology and Hydrology (CEH) in the UK and the National Institute of Hydrology (NIH), Roorkee and Indian Institute of Technology (IIT), Bombay in India. This report is structured around the three main themes of the project: catchment hydrological modelling, assessment of environmental flows under climate change, and a feasibility study to assess the potential of developing guidance for India similar to that of the Flood Estimation Handbook for the UK

Incipient Balancing Selection through Adaptive Loss of Aquaporins in Natural Saccharomyces cerevisiae Populations

A major goal in evolutionary biology is to understand how adaptive evolution has influenced natural variation, but identifying loci subject to positive selection has been a challenge. Here we present the adaptive loss of a pair of paralogous genes in specific Saccharomyces cerevisiae subpopulations. We mapped natural variation in freeze-thaw tolerance to two water transporters, AQY1 and AQY2, previously implicated in freeze-thaw survival. However, whereas freeze-thaw–tolerant strains harbor functional aquaporin genes, the set of sensitive strains lost aquaporin function at least 6 independent times. Several genomic signatures at AQY1 and/or AQY2 reveal low variation surrounding these loci within strains of the same haplotype, but high variation between strain groups. This is consistent with recent adaptive loss of aquaporins in subgroups of strains, leading to incipient balancing selection. We show that, although aquaporins are critical for surviving freeze-thaw stress, loss of both genes provides a major fitness advantage on high-sugar substrates common to many strains' natural niche. Strikingly, strains with non-functional alleles have also lost the ancestral requirement for aquaporins during spore formation. Thus, the antagonistic effect of aquaporin function—providing an advantage in freeze-thaw tolerance but a fitness defect for growth in high-sugar environments—contributes to the maintenance of both functional and nonfunctional alleles in S. cerevisiae. This work also shows that gene loss through multiple missense and nonsense mutations, hallmarks of pseudogenization presumed to emerge after loss of constraint, can arise through positive selection

Understanding the controls on deposited fine sediment in the streams of agricultural catchments

Excessive sediment pressure on aquatic habitats is of global concern. A unique dataset, comprising instantaneous measurements of deposited fine sediment in 230 agricultural streams across England and Wales, was analysed in relation to 20 potential explanatory catchment and channel variables. The most effective explanatory variable for the amount of deposited sediment was found to be stream power, calculated for bankfull flow and used to index the capacity of the stream to transport sediment. Both stream power and velocity category were highly significant (p<<0.001), explaining some 57% variation in total fine sediment mass. Modelled sediment pressure, predominantly from agriculture, was marginally significant (p<0.05) and explained a further 1% variation. The relationship was slightly stronger for erosional zones, providing 62% explanation overall. In the case of the deposited surface drape, stream power was again found to be the most effective explanatory variable (p<0.001) but velocity category, baseflow index and modelled sediment pressure were all significant (p<0.01); each provided an additional 2% explanation to an overall 50%. It is suggested that, in general, the study sites were transport-limited and the majority of stream beds were saturated by fine sediment. For sites below saturation, the upper envelope of measured fine sediment mass increased with modelled sediment pressure. The practical implications of these findings are that (i) targets for fine sediment loads need to take into account the ability of streams to transport/retain fine sediment, and (ii) where agricultural mitigation measures are implemented to reduce delivery of sediment, river management to mobilise/remove fines may also be needed in order to effect an improvement in ecological status in cases where streams are already saturated with fines and unlikely to self-cleanse

A Catalog of Neutral and Deleterious Polymorphism in Yeast

The abundance and identity of functional variation segregating in natural populations is paramount to dissecting the molecular basis of quantitative traits as well as human genetic diseases. Genome sequencing of multiple organisms of the same species provides an efficient means of cataloging rearrangements, insertion, or deletion polymorphisms (InDels) and single-nucleotide polymorphisms (SNPs). While inbreeding depression and heterosis imply that a substantial amount of polymorphism is deleterious, distinguishing deleterious from neutral polymorphism remains a significant challenge. To identify deleterious and neutral DNA sequence variation within Saccharomyces cerevisiae, we sequenced the genome of a vineyard and oak tree strain and compared them to a reference genome. Among these three strains, 6% of the genome is variable, mostly attributable to variation in genome content that results from large InDels. Out of the 88,000 polymorphisms identified, 93% are SNPs and a small but significant fraction can be attributed to recent interspecific introgression and ectopic gene conversion. In comparison to the reference genome, there is substantial evidence for functional variation in gene content and structure that results from large InDels, frame-shifts, and polymorphic start and stop codons. Comparison of polymorphism to divergence reveals scant evidence for positive selection but an abundance of evidence for deleterious SNPs. We estimate that 12% of coding and 7% of noncoding SNPs are deleterious. Based on divergence among 11 yeast species, we identified 1,666 nonsynonymous SNPs that disrupt conserved amino acids and 1,863 noncoding SNPs that disrupt conserved noncoding motifs. The deleterious coding SNPs include those known to affect quantitative traits, and a subset of the deleterious noncoding SNPs occurs in the promoters of genes that show allele-specific expression, implying that some cis-regulatory SNPs are deleterious. Our results show that the genome sequences of both closely and distantly related species provide a means of identifying deleterious polymorphisms that disrupt functionally conserved coding and noncoding sequences

A high fat diet during adolescence in male rats negatively programs reproductive and metabolic function which is partially ameliorated by exercise

An interaction between obesity, impaired glucose metabolism and sperm function in adults has been observed but it is not known whether exposure to a diet high in fat during the peri-pubertal period can have longstanding programmed effects on reproductive function and gonadal structure. This study examined metabolic and reproductive function in obese rats programmed by exposure to a high fat (HF) diet during adolescence. The effect of physical training (Ex) in ameliorating this phenotype was also assessed. Thirty-day-old male Wistar rats were fed a HF diet (35% lard w/w) for 30 days then subsequently fed a normal fat diet (NF) for a 40-day recovery period. Control animals were fed a NF diet throughout life. At 70 days of life, animals started a low frequency moderate exercise training that lasted 30 days. Control animals remained sedentary (Se). At 100 days of life, biometric, metabolic and reproductive parameters were evaluated. Animals exposed to HF diet showed greater body weight, glucose intolerance, increased fat tissue deposition, reduced VO 2max and reduced energy expenditure. Consumption of the HF diet led to an increase in the number of abnormal seminiferous tubule and a reduction in seminiferous epithelium height and seminiferous tubular diameter, which was reversed by moderate exercise. Compared with the NF-Se group, a high fat diet decreased the number of seminiferous tubules in stages VII-VIII and the NF-Ex group showed an increase in stages XI-XIII. HF-Se and NF-Ex animals showed a decreased number of spermatozoa in the cauda epididymis compared with animals from the NF-Se group. Animals exposed to both treatments (HF and Ex) were similar to all the other groups, thus these alterations induced by HF or Ex alone were partially prevented. Physical training reduced fat pad deposition and restored altered reproductive parameters. HF diet consumption during the peri-pubertal period induces long-term changes on metabolism and the reproductive system, but moderate and low frequency physical training is able to recover adipose tissue deposition and reproductive system alterations induced by high fat diet. This study highlights the importance of a balanced diet and continued physical activity during adolescence, with regard to metabolic and reproductive health

Guidance on how to identify impacts of hydromorphological degradation on riparian ecosystems. Deliverable 3.4 of REFORM (REstoring rivers FOR effective catchment Management), a collaborative project (large-scale integrating project) funded by the European Commission within the 7th Framework Grant Agreement 282656

The aim of this deliverable is to address the impact of hydromorphological degradation on floodplain and riparian ecosystems, with specific focus on vegetation, fish and invertebrate responses and to provide guidance on how to identify those impacts