Options for a new integrated natural resources monitoring framework for Wales. Phase 1 project report

Healthy natural resources underpin significant economic sectors in Wales including agriculture, fisheries, tourism and forestry, they also make a significant contribution across Cabinet policies including the health and well-being agenda. In order to develop policies that build social, economic and environmental resilience and to evaluate policy implementation, a robust natural resources monitoring framework is required. Current monitoring activities are of varying quality, not sufficiently aligned to the new legislative and policy landscape, disjointed and when considered as a whole, potentially not as cost-effective as they could be. This project was tasked with identifying options and developing recommendations for an integrated natural resources monitoring framework for Wales reflecting the ambitions and integrating principles of the Environment Act and Well Being of Future Generations Act. The monitoring community, the Welsh Government and Natural Resources Wales Core Evidence Group, the project team, stakeholders and partners, have agreed on a set of recommendations

The Growth, Yield, and Financial Performance of Isolated Eastern White Pine (Pinus strobus L.) Reserve Trees

The ability of eastern white pine (Pinus strobus L.) to persist as emergent trees makes this species well suited to silvicultural systems in which they are retained as isolated reserves after a regeneration harvest. While such systems are implemented throughout the Acadian spruce-fir region of Maine, little is known about the growth response and financial performance of eastern white pine following complete release from competition. In this study, 77 trees from 8 sites throughout the Acadian spruce-fir region were sampled tree and crown measurements, and increment cores were extracted at breast height, as well as from the top of the valuable first 16 foot log. Volume growth was examined prior to and following release, and overall response to release was favorable. A subsample of 9 trees climbed to measure basal diameter and vertical location of each branch to develop allometric leaf area equations and to examine influence of site productivity and age on growth efficiency. Leaf area-volume increment relationships were modeled with a nonlinear power function with a random effect for site, and employed to forecast future growth. A sawmill simulator was used to estimate postrelease standing tree values and financial analysis was performed to assess performance of completely released trees for an unpruned and a hypothetical pruned scenario. Unpruned trees, on average exhibited peak net present value 52 years post-release. Pruned trees declined in net present value following release, due to high initial values. The net benefit of pruning reached its maximum 30 years after pruning, and stayed positive for 101 years, suggesting that pruning is a viable practice for eastern white pine that will be released and retained as reserve trees. The retention of eastern white pine reserve trees appears to be both biologically and financially sound, but forest managers should be careful to select vigorous younger trees as reserves to maximize financial performance

Imputation, modelling and optimal sampling design for digital camera data in recreational fisheries monitoring

Digital camera monitoring has evolved as an active application-oriented scheme to help address questions in areas such as fisheries, ecology, computer vision, artificial intelligence, and criminology. In recreational fisheries research, digital camera monitoring has become a viable option for probability-based survey methods, and is also used for corroborative and validation purposes. In comparison to onsite surveys (e.g. boat ramp surveys), digital cameras provide a cost-effective method of monitoring boating activity and fishing effort, including night-time fishing activities. However, there are challenges in the use of digital camera monitoring that need to be resolved. Notably, missing data problems and the cost of data interpretation are among the most pertinent. This study provides relevant statistical support to address these challenges of digital camera monitoring of boating effort, to improve its utility to enhance recreational fisheries management in Western Australia and elsewhere, with capacity to extend to other areas of application. Digital cameras can provide continuous recordings of boating and other recreational fishing activities; however, interruptions of camera operations can lead to significant gaps within the data. To fill these gaps, some climatic and other temporal classification variables were considered as predictors of boating effort (defined as number of powerboat launches and retrievals). A generalized linear mixed effect model built on fully-conditional specification multiple imputation framework was considered to fill in the gaps in the camera dataset. Specifically, the zero-inflated Poisson model was found to satisfactorily impute plausible values for missing observations for varied durations of outages in the digital camera monitoring data of recreational boating effort. Additional modelling options were explored to guide both short- and long-term forecasting of boating activity and to support management decisions in monitoring recreational fisheries. Autoregressive conditional Poisson (ACP) and integer-valued autoregressive (INAR) models were identified as useful time series models for predicting short-term behaviour of such data. In Western Australia, digital camera monitoring data that coincide with 12-month state-wide boat-based surveys (now conducted on a triennial basis) have been read but the periods between the surveys have not been read. A Bayesian regression framework was applied to describe the temporal distribution of recreational boating effort using climatic and temporally classified variables to help construct data for such missing periods. This can potentially provide a useful cost-saving alternative of obtaining continuous time series data on boating effort. Finally, data from digital camera monitoring are often manually interpreted and the associated cost can be substantial, especially if multiple sites are involved. Empirical support for low-level monitoring schemes for digital camera has been provided. It was found that manual interpretation of camera footage for 40% of the days within a year can be deemed as an adequate level of sampling effort to obtain unbiased, precise and accurate estimates to meet broad management objectives. A well-balanced low-level monitoring scheme will ultimately reduce the cost of manual interpretation and produce unbiased estimates of recreational fishing indexes from digital camera surveys

The use of remote sensing and GIS for modelling aquaculture site suitability in relation to changing climate

Globally fish production has continued to increase during recent years at a rate exceeding that of human population growth. However the contribution from capture fisheries has remained largely static since the late 1980s with the increase in production being accounted for by dramatic growth in the aquaculture sector. As of 2012 aquaculture accounted for approximately 42% of total fisheries production and 78% of inland fish production. In view of these figures it is unsurprising that for a number of regions aquaculture represents an important source of both food security and income. The use of Geographical Information Systems (GIS) and spatial data have seen substantial developments in recent years with the help of increasingly affordable computing capacity. From an aquaculture perspective the use of GIS has shown significant potential as a means of combining varied data sources, including those acquired via remote sensing, into models to provide decision support in relation to site selection. A common theme amongst site suitability assessments is the incorporation of climate variables relating to temperature and water availability. These factors in turn can have a significant influence on aquaculture in terms of water availability and quality, and temperature modulated growth performance. There is now a strong consensus that during the 20th century, and especially during recent decades, the earth has experienced a significant warming trend. There is also strong agreement that this warming trend is at least partially a consequence of anthropogenic greenhouse gas emissions and that some degree of further warming is inevitable. While global warming is typically discussed in terms of degrees centigrade of average global temperature increase the full effects in terms of climate changes will be varied both in terms of location and season. The current project focuses on site suitability for aquaculture in relation to changing climate conditions. Significant use is made of GIS and a range of spatial data including remotely sensed data and output from a series of climate models. The project consists of a number of key components: 1. Vulnerability of aquaculture related livelihoods to climate change was assessed at the global scale based on the concept of vulnerability to climate related impacts as a function of sensitivity to climate change, exposure to climate change, and adaptive capacity. Use was made of national level statistics along with gridded climate and population data. Climate change scenarios were supplied using the MAGICC/SCENGEN climate modelling tools. Analysis was conducted for aquaculture in freshwater, brackish, and marine environments with outputs represented as a series of raster images. A number of Asian countries (Vietnam, Bangladesh, Laos, and China) were indicated as most vulnerable to impacts on freshwater production. Vietnam, Thailand, Egypt and Ecuador stood out in terms of brackish water production. Norway and Chile were considered most vulnerable to impacts on Marine production while a number of Asian countries (China, Vietnam, and the Philippines) also ranked highly. 2. Site suitability for pond-based aquaculture was modelled at the global scale using a 10 arcsecond grid. Data from an ensemble of 13 climate models was used to model pond temperature and water availability for rain fed ponds under late 20th century conditions and for a 2°C global warming scenario. Two methods are demonstrated for combining data with a focus on the culture of warm water species. Results suggest both positive and negative impacts in relation to the 2°C warming scenario depending on location and season. Some areas are projected to see negative effects from maximum temperatures during the warmest parts of the year while for many regions there are likely to be potential increases in growth performance during colder months with possible expansion into previously unsuitable areas. 3. Methods for detecting surface water using remotely sensed data were investigated for Bangladesh. Use was made of data from the Moderate-resolution Imaging Spectroradiometer (MODIS) and Landsat ETM+ instruments with accuracy assessed against ground truth data collected in the field. A time series was constructed using all available MODIS data (approximately 13 years with an 8 day temporal resolution) to show areas of: surface water, land, and mixed land and water. The time series was then analysed to produce a layer showing the percentage of the total time series where surface water is indicated thus providing a spatial representation of flood prevalence. 4. A land cover data set was produced using 9 Landsat ETM+ scenes to cover the majority of Bangladesh. 10 different classification routines were evaluated including a decision tree approach unique to the current study. Classification results were assessed against two sets of ground control points produced: one based on field collected ground truth data and the other using a stratified random sampling procedure in association with visual analysis of high resolution true colour satellite images and ETM+ composites. The most accurate classifications were provided by the decision tree method developed for the current study and a Multi-Layer Perceptron (MLP) neural network based classifier. 5. Site suitability for pond-based aquaculture within Bangladesh was assessed using a GIS in combination with the ETM+ based land cover data, the MODIS based surface water time series, and components of the global site suitability assessment including modelled pond temperature data. Assessments were made based on late 20th century conditions and a 2°C global warming scenario. The MODIS surface water time series was also used to show the effects of storm surge flooding in relation to cyclone Aila that struck Bangladesh on 25th May 2009. The south and east of the country were considered most suitable for aquaculture due to more favourable cold season temperatures and higher water balance values. The north west of the country was considered least favourable due to higher maximum modelled pond temperatures and lower water balance values. The effect of the 2°C warming scenario was to enhance these trends. To date the potential spatial implications of changing climate for aquaculture has been significantly under researched. In this respect the current study provides a highly useful indication of where aquaculture related livelihoods may be vulnerable. In addition valuable and unique insights are provided into the distribution of areas of both potential increased, as well as decreased, suitability for existing aquaculture and further aquaculture development

Rapid biodiversity monitoring of freshwater ponds using environmental DNA : traversing the aquatic-terrestrial boundary in pondscapes

Environmental DNA (eDNA) analysis is transforming biodiversity monitoring in aquatic ecosystems with immense potential to inform their conservation and management. eDNA analysis is rapid, non-invasive, cost-efficient, and often more accurate and sensitive than conventional monitoring tools for single species detection and community survey. Ponds are extremely diverse yet understudied freshwater habitats that require novel tools to enable comprehensive, systematic, long-term monitoring. eDNA monitoring could radically improve assessments of pond biodiversity, but the applications and methodical constraints of this tool in ponds are largely unexplored. In this thesis, eDNA analysis was examined as a tool for monitoring biodiversity associated with ponds, including aquatic, semi-aquatic, and terrestrial taxa. eDNA analysis using metabarcoding was shown to have comparable detection sensitivity for Triturus cristatus to targeted eDNA analysis using quantitative PCR, depending on species detection thresholds applied. Using the community data generated by this method comparison, eDNA metabarcoding was validated as a tool for ecological hypothesis testing, specifically biotic and abiotic determinants of T. cristatus and vertebrate species richness. A novel eDNA assay was designed and validated for targeted survey of the threatened Carassius carassius, a fish species characteristic of ponds. Furthermore, eDNA metabarcoding was compared to established methods of freshwater invertebrate assessment, and all methods used to evaluate the impact of stocking C. carassius for conservation purposes. Finally, eDNA metabarcoding was vindicated as a tool to monitor semi-aquatic and terrestrial mammals associated with ponds, and investigate the spatiotemporal distribution of their eDNA signals in these water bodies as a function of behaviour. These results combined emphasise the biological and scientific importance of ponds, and the prospects of eDNA analysis - targeted and community approaches - for enhanced conservation, management, monitoring, and research of these valuable ecosystems

INVESTIGATING THE EFFECTS OF WINTER DRAWDOWNS ON THE ECOLOGICAL CHARACTER OF LITTORAL ZONES IN MASSACHUSETTS LAKES

Anthropogenic alteration of water levels in lakes is a major stressor to the ecological integrity of littoral zones, which provide critical heterogenous resources that support diverse biological communities. Annual winter drawdowns have been practiced in Massachusetts (MA) for several decades; however, few studies have estimated impacts to littoral zone habitat and biological communities, particularly at relatively mild magnitudes (i.e., m) and in lakes that co-occur with other anthropogenic pressures (e.g., lakeshore development) as seen in MA lakes. My dissertation reviewed the winter drawdown literature and collected empirical data in MA lakes to characterize winter drawdown hydrological regimes and estimate responses of physical habitat (macrophytes, sediment texture, coarse wood), macroinvertebrate assemblages, and mussel assemblages to variable levels of drawdown magnitude. Through a stratified random selection approach, I selected 21 MA lakes (18 drawdown, 3 non-drawdown) based on drawdown information from an email survey to local conservation commissions and lake and pond associations. I continuously monitored water levels for 3–4 years within these lakes that represented a drawdown magnitude gradient. Drawdown regimes displayed considerable inter- and intra-lake variability in the timing and duration of annual drawdown events. The majority of winter drawdown events were incongruous to MA state issued timing guidelines, particularly for April 1st refill dates. In the same set of lakes, I found increased drawdown magnitude was correlated with coarser substrates and reduced silt, reductions in macrophyte biomass and biovolume, and proportional increases of macrophyte taxa with annual longevity strategy and amphibious growth form. During normal water levels, I found markedly lower freshwater mussel densities at drawdown-exposed depths compared to the same depths in non-drawdown lakes. I also found drawdown magnitude significantly structured macroinvertebrate taxonomic and functional composition with evidence that suggests several drawdown-sensitive taxa (e.g., Amnicola) and traits (e.g., semivoltinism). To minimize losses to lake ecological integrity, winter drawdown management should consider the extent of lakebed and littoral zone area exposed during drawdowns, incorporate depth-specific monitoring efforts for susceptible biota (e.g., mussels), and anticipate water level responses to climate change

Survival of duck nests, distribution of duck broods, and habitat conservation targeting in the Prairie Pothole Region

Thesis (Ph.D.) University of Alaska Fairbanks, 2011The Prairie Pothole Region (PPR) is an important breeding region for populations of upland-nesting ducks (Anas spp.). I studied survival of duck nests, distribution of duck broods, and conservation easement targeting in the PPR of North and South Dakota, USA. Nest survival of common duck species varied from 0.02 (ŜE = 0.01) to 0.23 (ŜE = 0.02) among study sites and years and was positively related to current pond density and primary productivity and negatively related to recent pond density and primary productivity. This result was consistent with the hypothesis that nest predators and thus nest survival were responding to changes in productivity induced by relatively short-term (1yr-2yr) precipitation cycles. Distribution of broods was positively related to wetland area and proportion of perennial grass cover on the study site. Estimated probability of wetland occupancy for a brood of a representative species, gadwall (Anas strepera), increased from 0.08 (90% Credible Interval: 0.07, 0.10) to 0.28 (0.24, 0.33) as wetland area increased from 0.19 ha to 2.12 ha. As proportion of perennial grass cover on a study site increased from 0.03 to 0.99, estimated probability of wetland occupancy by a gadwall brood increased from 0.12 (0.09, 0.16) to 0.20 (0.16, 0.25). These relationships identified wetland basins and landscapes with a higher probability of occupancy. The extensive repeat-visit brood survey was therefore a useful way to learn about the distribution of duck broods across a large geographic extent. I also investigated need and opportunity to refine current habitat protection strategies in the PPR. Area of habitat protected declined annually during 2000-2009 while cost of protection increased 248% from $210/ha to$730/ha and cropland rental rates increased 40%. Estimated area protected in 2009 was 210 km² (95% Confidence Interval: 133 km² to 287 km²), and 2,792 km² was protected during 2000-2009. Refocusing easement acquisition efforts on the 3,189 km² that was located in landscapes of highest priority based on pair density and was at relatively high risk of conversion, but was below the 25th percentile of cost provided a 24% reduction in per/hectare cost of protection and a 20% increase in area protected.General Introduction -- 1. Duck nest survival in the Prairie Pothole Region relative to time-lagged spatial and temporal variation in environmental conditions -- 2. Occupancy of wetlands by duck broods relative to habitat characteristics in the Prairie Pothole Region -- 3. Integrated targeting of conservation easement acquisition for waterfowl increases conservation benefits in the Prairie Pothole Region -- General conclusions -- Literature cited

Trojan horses in the marine realm: characterizing protistan parasite ecology in coastal waters

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2022.Protists are taxonomically and metabolically diverse drivers of energy and nutrient flow in the marine environment, with recent research suggesting significant roles in global carbon cycling throughout the water column. Top-down controls on planktonic protists include grazing and parasitism, processes that both contribute to nutrient transfer and biogeochemical cycling in the global ocean. Recent global surveys of eukaryotic small subunit ribosomal RNA molecular signatures have highlighted the fact that parasites belonging to the marine alveolate order Syndiniales are both abundant and ubiquitous in coastal and open ocean environments, suggesting a major role for this taxon in marine food webs. Two coastal sites, Saanich Inlet (Vancouver Island, BC) and Salt Pond (Falmouth, MA, USA) were selected as model ecosystems to examine the impacts of Syndinian parasitism on protist communities. Data presented in this thesis combines high-resolution sampling, water chemistry (including nutrients) analyses, molecular marker gene analyses, fluorescence in situ hybridization, and modeling to address key knowledge gaps regarding syndinian ecology. Information is presented on previously undescribed putative host taxa, the prevalence of syndinian parasites and infections on different hosts in coastal waters, and a framework for modeling host-parasite interactions based on field observations.Research was supported by the WHOI Ocean Venture Fund, the National Science Foundation Biological Oceanography OCE-1851012, and the National Science Foundation Graduate Research Fellowship under Grant No. 1745302