Samantha Jane Hughes

Atlantic island freshwater ecosystems: challenges and considerations following the EU Water Framework Directive

The Water Framework Directive or WFD constitutes a major step forward in the protection of the aquatic environment and associated habitats, since it legislates for the characterization of surface water bodies across defined ecoregions and the development of ecological monitoring systems based upon elements of the aquatic biota. The Macaronesian archipelagos include the Azores, Madeira and the Canary Islands. The peripheral situation of the Macaronesian islands has set them apart from many European initiatives concerning the implementation of the WFD, which is biased towards better known continental systems. As a result, they have been included in the same ecoregion as the Iberian Peninsula and the Balearic Islands for management purposes. However, because of their oceanic situation and volcanic origin, the freshwater systems of the Macaronesian islands differ strongly from continental systems in watershed morphology and the composition of the biotic assemblages, which merits separate identification rather than inclusion within the larger Iberic-Macaronesian ecoregion and special attention concerning regional implementation of programmes of measures under the Directive.

Temporal and spatial distribution patterns of larval trichoptera in Madeiran streams

Temporal and spatial distribution patterns of lotic larval trichopteran assemblages in relation to environmental variables were investigated in Madeiran streams using multivariate analyses. TWINSPAN classification detected distinct faunal assemblages related to spatial factors between non-polluted high altitude sites and lower lying enriched sites where tolerant taxa were predominant but showed strong seasonal shifts in species composition and abundance. The 15 TWINSPAN end groups were grouped into five arbitrary clusters based upon the seasonal and spatial changes in the trichopteran assemblages detected by the analysis. Significant differences between environmental variables (distance from source, altitude, temperature, conductivity, alkalinity and nitrate) and the trichopteran assemblages (using trichopteran based metrics) of these clusters were confirmed by the Kruskal-Wallis test (H) and Dunn’s test. Chemical classification of samples within the clusters revealed a strong association between trichopteran assemblages and water quality. Canonical Correspondence Analysis and Monte Carlo global permutation tests also identified significant associations between the larval assemblages and physicochemical variables such as temperature and conductivity along a strong physical gradient (altitude, slope) and nitrate along a weaker seasonal gradient. Analysis of functional feeding group distribution patterns clearly showed that mid to high altitude indigenous woodland sites were trophically diverse whilst the lower reaches of the islands streams are trophically impoverished with strong seasonal shifts between two feeding groups of enrichment tolerant taxa. Trichopteran shredders are exclusive to indigenous woodland sites, indicating a limited distribution associated with land use, allochthonous input and habitat destruction. The results indicate that several ‘environmental filters’ operate at different levels upon the islands trichopteran fauna, producing temporally and spatially distinct ‘subsets’ of species best able to exploit conditions and resources at a given site or time, confounding the direct comparison of these insular systems with the findings of the River Continuum Concept, traditionally associated with unaffected continental lotic systems.

Evaluating the Response of Biological Assemblages as Potential Indicators for Restoration Measures in an Intermittent Mediterranean River

Bioindicators are essential for detecting environmental degradation and for assessing the success of river restoration initiatives. River restoration projects require the identification of environmental and pressure gradients that affect the river system under study and the selection of suitable indicators to assess habitat quality before, during and after restoration. We assessed the response of benthic macroinvertebrates, fish, bird and macrophyte assemblages to environmental and pressure gradients from sites situated upstream and downstream of a cofferdam on the River Odelouca, an intermittent Mediterranean river in southwest Portugal. The Odelouca will be permanently dammed in 2010. Principal Component Analyses (PCA) of environmental and pressure variables revealed that most variance was explained by environmental factors that clearly separated sites upstream and downstream of the partially built cofferdam. The pressure gradient describing physical impacts to the banks and channel as a result of land use change was less distinct. Redundancy Analysis revealed significant levels of explained variance to species distribution patterns in relation to environmental and pressure variables for all 4 biological assemblages. Partial Redundancy analyses revealed high levels of redundancy for pH between groups and that the avifauna was best associated with pressures acting upon the system. Patterns in invertebrates and fish were associated with descriptors of habitat quality, although fish distribution patterns were affected by reduced connectivity. Procrustean and RELATE (Mantel test) analyses gave broadly similar results and supported these findings. We give suggestions on the suitability of key indicator groups such as benthic macroinvertebrates and endemic fish species to assess in stream habitat quality and appropriate restoration measures, such as the release of peak flow patterns that mimic intermittent Mediterranean systems to combat habitat fragmentation and reduced connectivity.

Predicting trends of invasive plants richness using local socio-economic data: An application in North Portugal

This study assesses the potential of an integrated methodology for predicting local trends in invasive exotic plant species (invasive richness) using indirect, regional information on human disturbance. The distribution of invasive plants was assessed in North Portugal using herbarium collections and local environmental, geophysical and socio-economic characteristics. Invasive richness response to anthropogenic disturbance was predicted using a dynamic model based on a sequential modeling process (stochastic dynamic methodology-StDM). Derived scenarios showed that invasive richness trends were clearly associated with ongoing socio-economic change. Simulations including scenarios of growing urbanization showed an increase in invasive richness while simulations in municipalities with decreasing populations showed stable or decreasing levels of invasive richness. The model simulations demonstrate the interest and feasibility of using this methodology in disturbance ecology.

Habitat variation at different scales and biotic linkages in lotic systems: consequences for monitorization

The Water Framework Directive (WFD) requires the hydromorphological assessment of water bodies, thereby acknowledging the importance of these features in supporting biological quality elements and providing a more complete ecological characterization of surface water bodies. Using a dataset covering mainland Portugal (about 300 sites spread along the different river types) and based on the River Habitat Survey (RHS) field methodology, our aim was to test the spatial variation and the relative role of an array of multi-scale habitat descriptors, in order to: (a) to analyse their geographical variation; (b) to identify the principal variables that express human disturbance; and (c) to assess how three different aquatic communities (invertebrates, fish, and macrophytes) were related to those environmental descriptors. We found that hydromorphological variables described by RHS varied significantly over large geographical scales and were more strongly associated with the principal catchments rather than river type (derived from climatic, geological, and typological factors). RHS-derived descriptors were of greater importance in assessing disturbance and were closely related to land use and vegetation on the banks and along the river corridor, despite the considerable geographical variation. Habitat variables were more clearly associated with macrophytes and fish than with the benthic macroinvertebrates, a facet of sampling design, since the scale of biological survey for the former two biological groups approaches the scale used to characterize the surrounding environment. An array of environmental variables, ranging from instream features to bankside and river corridor land use features, was associated with each community, making it difficult to discern any common underlying pattern. Based upon our findings, we propose that hydraulic variables should be included in hydromorphological assessment to improve both the performance of physical indicators and the correspondence with the demands of the WFD.

Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome.

The study of processes driving diversification requires a fully sampled and well resolved phylogeny, although a lack of phylogenetic markers remains a limitation for many non-model groups. Multilocus approaches to the study of recent diversification provide a powerful means to study the evolutionary process, but their application remains restricted because multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic insect species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. Whole-genome sequencing data from one member of the species complex were used to identify 59 nDNA loci (32,213 base pairs), followed by Sanger sequencing of 29 individuals sampled from 13 islands of three Macaronesian archipelagos. Multispecies coalescent analyses established six putative species. Three island species formed a monophyletic clade, with one species occurring on the Azores, Europe and North America. Ancestral state reconstruction indicated at least two colonization events from the mainland (to the Canaries, respectively Azores) and one within the archipelago (between Madeira and the Canaries). Random subsets of the 59 loci showed a positive linear relationship between number of loci and node support. In contrast, node support in the multispecies coalescent tree was negatively correlated with mean number of phylogenetically informative sites per locus, suggesting a complex relationship between tree resolution and marker variability. Our approach highlights the value of combining genomics, coalescent-based phylogeography, species delimitation, and phylogenetic reconstruction to resolve recent diversification events in an archipelago species complex.

The role of environmental and fisheries multi-controls in white seabream (Diplodus sargus) artisanal fisheries in Portuguese coast

Abstract Evaluating the effects of fishing and environmental factors on fish populations are fundamental tenets of fisheries science. In this study, we assess associations between environmental variables (sea surface temperature; North Atlantic Oscillation index; upwelling; wind magnitude; westerly winds; northerly winds; river discharge) and fishing variables (fishing effort) in Diplodus sagus catch rates accounting for regional analyses (northwest coast; southwest coast and Algarve—Algarve south coast). Different time series models for data fitting (multi-model approach) were used. The models were lagged, according to species fishing recruitment age based on the hypothesis that fisheries catches depend on larvae recruitment and survivorship. D. sargus catch rates across areas were unrelated to fishing effort but correlated to environmental variables, with seasonal events explaining much of the variability in trends. On the northwestern coast, the catch rates were mainly set by sea surface temperature (SST) and wind magnitude; however, southwestern coast catch rates were set by NAO winter. On the south coast, only one statistical model (SST, upwelling and westerly winds) associated spring conditions with D. sargus catch rates. The multi-model approach revealed autumn, winter and spring seasonal effects to be related with northwest, southwest and Algarve coastal catch rates, respectively, indicating a possible coastal longitudinal gradient related with given periods of spawning and larval availability. The metadata analysis yielded different results from the regional analyses. In summary, marine resource management should take regional environment characteristics and variability into account when determining sustainable catch rates in given areas for species with high habitat site fidelity.

A multiple index integrating different levels of organization

Many methods in freshwater biomonitoring tend to be restricted to a few levels of biological organization, limiting the potential spectrum of measurable of cause-effect responses to different anthropogenic impacts. We combined distinct organisational levels, covering biological biomarkers (histopathological and biochemical reactions in liver and fish gills), community based bioindicators (fish guilds, invertebrate metrics/traits and chironomid pupal exuviae) and ecosystem functional indicators (decomposition rates) to assess ecological status at designated Water Framework Directive monitoring sites, covering a gradient of human impact across several rivers in northern Portugal. We used Random Forest to rank the variables that contributed more significantly to successfully predict the different classes of ecological status and also to provide specific cut levels to discriminate each WFD class based on reference condition. A total of 59 Biological Quality Elements and functional indicators were determined using this procedure and subsequently applied to develop the integrated Multiple Ecological Level Index (MELI Index), a potentially powerful bioassessment tool.

A modelling framework to predict bat activity patterns on wind farms: An outline of possible applications on mountain ridges of North Portugal

Worldwide ecological impact assessments of wind farms have gathered relevant information on bat activity patterns. Since conventional bat study methods require intensive field work, the prediction of bat activity might prove useful by anticipating activity patterns and estimating attractiveness concomitant with the wind farm location. A novel framework was developed, based on the stochastic dynamic methodology (StDM) principles, to predict bat activity on mountain ridges with wind farms. We illustrate the framework application using regional data from North Portugal by merging information from several environmental monitoring programmes associated with diverse wind energy facilities that enable integrating the multifactorial influences of meteorological conditions, land cover and geographical variables on bat activity patterns. Output from this innovative methodology can anticipate episodes of exceptional bat activity, which, if correlated with collision probability, can be used to guide wind farm management strategy such as halting wind turbines during hazardous periods. If properly calibrated with regional gradients of environmental variables from mountain ridges with windfarms, the proposed methodology can be used as a complementary tool in environmental impact assessments and ecological monitoring, using predicted bat activity to assist decision making concerning the future location of wind farms and the implementation of effective mitigation measures.

Contemporary and future distribution patterns of fluvial vegetation under different climate change scenarios and implications for integrated water resource management

Knowledge of plant community structure and how it can confer resistance to climate change effects is required for the management of fluvial ecosystems. Findings from such studies can be applied in decision making processes to implement measures to maintain, conserve or improve fluvial quality. Floristic and environmental data from 100 sample stations located in three River Basin Districts in northern Portugal were gathered as part of the 2010 Water Framework Directive monitoring program carried out on mainland Portugal. Three habitat types were characterized based on the flow dynamic level: the wetted channel, the bankfull area and the riparian gallery. Hierarchical cluster analysis of environmental data revealed three distinct environmental groups of sites. Floristic data were organized by these environmental groups characterized by altitudinal, temperature and precipitation data variables. The combination of taxonomic diversity and species frequency reflect functional differences for these habitats, here explained by a resistance and resilience approach. More low-frequency species and higher levels of functional diversity occurred at stations with more variable environmental conditions. Predictive modelling of the future distribution of the three environmental groups under two different climate scenarios supported the relevance of low-frequency traits in conferring resistance to climatic change effects.