Results of these 2017 experiments were compared with data collected in 2013 and 2014 using satellite tagging and associated genetics. In that case there was evidence of greater interception of east coast salmon at Armadale and good correspondence between predictions of home river from genetics and observations from satellite tagging, albeit based of a small sample size.

Each salmon sampled in 2017 was assessed for presence of red vent syndrome (RVS) whereby the vent area of the fish was swollen and reddened. The incidence of RVS was 82%, higher than recorded previously. No difference could be detected in the subsequent survival of fish with and without RVS, but the power to detect any effect was very low because there were so few fish without the syndrome.

This report describes surveys carried out in the Sound of Harris and Ayrshire coast, Clyde in late August and early September 2017. A combination of commercial electrofishing rig and towed video rig was deployed at potential razor clam grounds using the fishing vessel ‘Nicola Jane’. Recorded video was analysed for the number and sizes of razor clams forced to the surface by the electrofishing equipment. Data were converted to area densities (numbers of razor clams m-2) based on estimates of the area swept (m2) by the video recording. The aim of this project was to use a combination of electrofishing with towed video to assess the quantities and sizes of razor clams (Ensis sp.) across a number of grounds on the west of Scotland. The results are intended to inform Marine Scotland in the setting of catch limits for potential commercial-scale fisheries on razor clams using the electrofishing technique.

Associated data are presented for download.

• Table 4 was a duplicate of Table 3, this has been updated to show the correct information for Table 4

• Figure and table headings have been revised to accurately account for the correct material

• Table 11 was not originally numbered - correct numeration has been added

For a previous Scottish Government funded project (MMSS/001/11), seal telemetry data were combined with haul-out specific population data to generate usage maps for both grey and harbour seals around the UK at a spatial resolution of 5 x 5 km (Jones et al., 2013). These maps provided estimates of seal abundance (and associated confidence intervals) aggregated between 1988 and 2012, thus taking into account changes in population size through time. For Jones et al. (2015), maps were generated which were scaled to the estimated population size in 2013, resulting in the most up-to-date understanding of current seal usage at that time. The Department of Business and Industrial Strategy (BEIS) funded a large deployment of tags on grey seals in the southern North Sea and subsequently commissioned an updated North Sea usage map reflecting the estimated grey seal population size in 2015 (Jones and Russell, 2016). At the request of Scottish Government, usage maps have been generated for Orkney on a finer spatial resolution (0.6 x 0.6 km; Jones et al., 2016; Jones et al., 2017b). Changes A requirement to update the UK-wide usage maps was identified. As part of this, three updates were proposed: (1) inclusion of additional telemetry data (up to 2016); (2) improvement in how count data are incorporated into the usage map framework (Jones et al., 2016; Jones et al., 2017a) and updating count data resulting in estimates of usage scaled to the estimated population size in 2015; and (3) clustering of haul-out sites to increase the proportion of sites for which there are associated telemetry data (Jones and Russell, 2016). Data are also available, with a DOI of 10.7489/2029-1.

This report describes a research project, the aim of which was to review the use of Population Viability Analysis (PVA) metrics in the context of assessing the effect of offshore renewable developments on seabirds and to test PVA metric sensitivity to mis-specification of input parameters. The most useful metrics in this context are those that are least sensitive to such mis-specification, enabling more robust assessment of offshore renewable effects. Recent work has tested PVA metric sensitivity using a simulation approach. To complement these findings, the objective in this project was to test metric sensitivity using real-world data. This approach is useful where one wishes to understand a specific region where real data are available, or where one wishes to address generic questions with real data. If the same metrics show low sensitivity in models of real world data as in simulation models, then this would provide re-assurance that these metrics are the most appropriate for use in assessments. Five study species were selected: black-legged kittiwake Rissa tridactyla; common guillemot Uria aalge; razorbill Alca torda; herring gull Larus argentatus and European shag Phalacrocorax aristolelis. Of these, the first four were considered in population modelling in the Forth/Tay region in a previous Marine Scotland Science project (Freeman et al. 2014). Similar models have, in the interim, also been fitted for shags in this region so this species was also considered. The SPAs considered in this report were Buchan Ness to Collieston Coast SPA, Fowlsheugh SPA, Forth Islands SPA and St Abb’s Head to Fastcastle SPA.

A small number of phytoplankton species have the ability to produce algal toxins which can accumulate in filter feeding bivalves such as oysters, scallops and mussels. The bioaccumulation of algal toxins can potentially cause serious health issues to shellfish consumers. Countries with a shellfish aquaculture industry (such as Scotland) have set up for their classified production areas a phytoplankton monitoring programme as part of their legal obligations (EC 854/2004 and amendments). This involves the regular collection of water samples to assess the phytoplankton community using light microscopy, with a particular emphasis on the toxin producing species. However, this technique lacks the ability to identify some key phytoplankton to a species level (e.g. Pseudo-nitzschia sp., Alexandrium sp.), which is critical to appropriately assess the potential toxicity of a phytoplankton bloom event. The objective of this project was to evaluate a microarray technique which was developed during the MIDTAL project (Microarrays For The Detection of Toxic Algae: http://www.midtal.com/) to identify phytoplankton to species level. Microarrays are modified glass supports on which are printed RNA probes that are species-specific. Each targeted phytoplankton species is defined by a set of probes that are statistically unique to each one. For the purpose of this project, water samples were collected offshore from Stonehaven (East coast of Scotland) over a two years period (starting in 2015) and processed using the microarray to assess its specificity and sensitivity in relation to the identification and potential semi-quantification of toxic strains of phytoplankton.

This report presents the results of Scottish regional scallop stock assessments carried out by Marine Scotland Science (MSS) based on commercial catch-at-age data up to 2015 and survey data up to and including 2016. Full analytical assessments are presented for the East Coast, North East, North West, Shetland and West of Kintyre scallop stocks, with catch data presented for the Clyde, Irish Sea and Orkney. The report also provides background information on Scottish fisheries for scallops, a description of the current management and regulatory framework. Associated data are presented for download.

The report describes how adult harbour seals and grey seal pups use the water column within the Brims lease site. Data used in the report are presented for download.

This document reports on the outcomes of a workshop held at Marine Scotland Science, Marine Laboratory, Aberdeen in April 2016. The workshop was convened to examine Version 1 of the Groundfish Survey Monitoring and Assessment (GSMA) data product and revue the methods used to derive it. This data product was derived to support assessment of the state of fish species and communities, and the role of fish in the structure and functioning of marine food webs across the entire Northeast Atlantic region, from Norway to Gibraltar. As such, the data product was intended to meet the monitoring programme obligations of European Union Member States bordering the Northeast Atlantic region under the Marine Strategy Framework Directive. The job of the workshop was to ensure that the GSMA data product was fit for this purpose; that it could indeed meet the data needs necessary to calculate all fish species and community related indicators used in the upcoming OSPAR Interim Assessment 2017 (IA2017), as well indicators likely to be needed in future assessment cycles. The workshop concluded that the data product was indeed fit for the purpose intended. Some minor issues in methodology were identified. These have subsequently been addressed, the methodology documentation (Moriarty et al. 2017) updated to reflect these changes, and a Version 2 data product produced. The Version 2 GSMA data product also takes into account any updates made by national data providers to the database held on the DATRAS portal over the intervening period between the download from which Version 1 was derived and up to approximately the end of October 2016 when data were downloaded to derive the Version 2 data product. The main part of this document then proceeds to describe the content of the Version 2 GSMA data product. For each survey’s standard monitoring programme (excludes samples collected before survey protocols became fully established and trawl samples of extreme short and extreme long tow duration: see Moriarty et al. (2017) for further details), a series of diagnostic plots is presented that display the variation in, and relationships between, a range of key parameter values, temporal trends in sampling effort, and sampling frequency distributions for each ICES statistical rectangle covered by the survey. Charts are provided showing the locations of all trawl samples collected by each survey’s standard monitoring programme. Two criteria for the inclusion of ICES statistical rectangles as part of each surveys standard survey area are presented. These include a new criterion not used in Moriarty et al. (2017) aimed at ensuring that, not only are rectangles sampled reasonably frequently, but that they are also sampled regularly throughout the course of each survey’s time series. The consequences of applying these two criteria are explained and resulting standard survey areas for each individual survey data product are illustrated.

Coastal European Union (EU) Member States (MS) operate groundfish surveys that cover almost the entire continental shelf of the Northeast Atlantic off Western Europe. Some survey work is also carried out in deeper shelf-edge waters and on sea mounts and plateaus further west in the wider Atlantic Ocean. These surveys use different vessels and different fishing gears, are undertaken at different times of year following various methodological approaches. The data are recorded and archived in a variety of different formats. The data obtained from many of these surveys are routinely uploaded and stored on an open access data portal on the ICES website: the DATRAS portal. The DATRAS portal allows for the uploading of data collected, recorded and archived in a variety of different forms and formats, but the resulting database structure required to accommodate this is far more complicated, and potentially confusing for users, than is really necessary, with many fields in the database simply explaining how other fields should be interpreted. Furthermore, the data stored on the DATRAS database have long been known to be affected by various data quality issues. These have not been addressed in a single co-ordinated process, rather it has been left to individual data users to make any corrections that they deem necessary, effectively resulting in multiple different versions being in circulation of what is in fact a single DATRAS data set. The MSFD requires formal assessment of the state of marine ecosystems in EU waters. Fish communities constitute a key component in the structure and functioning of marine ecosystems, so formal assessment of the state of the fish component is, therefore, mandatory. To meet their MSFD obligations, EU MS have invariably nominated their groundfish surveys as part of their marine monitoring programmes. However, to meet the obligation for formal assessment at the required regional seas spatial scale, these issues of data standardisation and quality assurance noted in the groundfish survey data stored on DATRAS all need to be resolved. The Groundfish Survey Monitoring and Assessment (GSMA) data product sets out to address these issues; to derive a single set of fully standardised and quality assured data products for all the surveys operating in the Northeast Atlantic.

Monitoring and assessment of fish communities is essential to demonstrating the achievement of GES across the waters of the Northeast Atlantic covered by the MSFD. Coastal MSs bordering the Northeast Atlantic have invariably nominated their groundfish surveys as part of their monitoring programmes to supply the data necessary to derive the indicators that will be used to assess the state of fish communities, both within their national waters and across the whole Northeast Atlantic region. Data obtained by these groundfish surveys are, for the most part, freely available for download from the DATRAS database portal on the ICES website. Data are initially checked by national data centres prior to submission to ICES and a further screening process is applied at ICES before the data are accepted and incorporated into the DATRAS database. However, the DATRAS screening process was implemented in 2009 only for data from 2004 onwards. Some survey time-series extend back to the 1960s and more historic data may not have been subject to the same level of quality control as these more recent data. Data were initially collected to address fisheries management needs, which primarily focused attention on commercial species. Gradual adoption of an ecosystem approach to management has raised the importance of non-target species, in order to facilitate the development and application of ecological indicators for the broader fish community. Thus the type of information collected, the level of detail and resolution in the data, has gradually evolved over time. These historic changes in groundfish survey practices have left a quality assurance legacy in the data that needs to be addressed to ensure that the groundfish survey monitoring programmes are fully fit to meet modern day needs of the MSFD. Historically the surveys operated by different countries have followed their own particular sets of protocols and practices. The procedure for uploading data to DATRAS has tended to preserve these national differences in data format, and this has necessitated the inclusion in DATRAS of numerous additional fields, each informing as to how other fields in the database should be interpreted. Here 19 surveys involving a dozen different countries are examined. In order to derive a single format, quality assured monitoring programme data product covering the entire Northeast Atlantic region, these national, inter-survey, inconsistencies all need resolution. In many instances, particularly in the more historic data, key information is either absent or incorrect, and these missing or erroneous values need replacement by modelled estimates. This document describes the process by which these issues were all resolved to derive 19 separate consistent and fully quality assured survey data products. These data products constitute a unified monitoring programme covering the continental shelf waters of the Northeast Atlantic, from northern Norway to Gibraltar, which can facilitate assessment of the state of fish communities across this whole region. Each survey is first described and a brief history provided. A strict error checking protocol was developed and applied to data in all key fields used in deriving the survey data products. Details of each of these are provided in this document. Detailed descriptions are provided of the two types of file that make up each individual survey data product: “Sampling Information” and “Biological Information”.

This report presents the results of Scottish regional brown crab (Cancer pagurus), velvet crab (Necora puber) and lobster (Homarus gammarus) stock assessments carried out by Marine Scotland Science (MSS) based on length cohort analyses (LCAs) applied to commercial length frequency data for the period 2013-15. Associated data are presented for download.

Both the quantification and modelling of harbour seal movement are required to predict the consequence of environmental change on population distribution and connectivity. Two modelling approaches were considered. The first is an empirical Inter-Haulout Transition Rate (I-HTR) model which estimates the population probability of an individual moving from one haulout site to another. The second is a mechanistic Individual Based Model (IBM) of movement which uses seal physiology in a simulated quasi-realistic environment to predict movement patterns. The scope of the IBM development is to demonstrate its ‘proof of concept’. To become a useful management tool, an IBM of appropriate complexity must be developed and tested, with the best possible estimates of parameters used to construct the model, e.g. from bioenergetic studies of captive seals or realistic estimates of habitat preference. The validation and checking of IBMs in general is an area of active research and for the seal IBM, appropriate checks may include comparison of model predictions in terms of summary properties and emergent properties of observational data, e.g. general patterns of spatial distribution. The prototype IBM has proven the concept and development work should continue to test whether the available data (seal and environmental), statistical selection and fitting techniques can ultimately progress to producing a robust management tool. However, an important future challenge is to sufficiently map and quantify the dynamics of the geographical resources that seals require, such as haulout sites and foraging areas. Approaches could include the use of synoptic physical and biological data to predict those regions that may be preferred for foraging.

Product type:
• This product is the Standard Survey Area - Standard Monitoring Programme this is the recommended product for all analyses.
• This product is the knn/resolved product which is recommended for all analyses.

Acknowledgements
Corina Chaves, Instituto Portugues do Mar e da Atmosfera
Vaishav Soni, ICES Data Centre
Internaitonal Council for the Exploraiton of the Sea (ICES)

Product type:
• This product is the Standard Survey Area - Standard Monitoring Programme this is the recommended product for all analyses.
• This product is the knn/resolved product which is recommended for all analyses.

Acknowledgements
Gary Burt, CEFAS
Vaishav Soni, ICES Data Centre
Internatioanl Council for the Exploration of the Sea (ICES)

Product type:
• This product is the Standard Survey Area - Standard Monitoring Programme this is the recommended product for all analyses.
• This product is the knn/resolved product which is recommended for all analyses.

Acknowledgements
Anne Sell, Thünen Institute of Sea Fisheries
Matthias Kloppmann, Thünen Institute of Sea Fisheries
Vaishav Soni, ICES Data Centre
International Council for Exploration of the Sea (ICES)

Product type:
• This product is the Standard Survey Area - Standard Monitoring Programme this is the recommended product for all analyses.
• This product is the knn/resolved product which is recommended for all analyses.

Acknowledgements
Gary Burt, CEFAS
Vaishav Soni, ICES Data Centre
International Council for Exploration of the Sea (ICES)

Product type:
• This product is the Standard Survey Area - Standard Monitoring Programme this is the recommended product for all analyses.
• This product is the knn/resolved product which is recommended for all analyses.

Acknowledgements
Mathieu Lundy, AfBI
Vaishav Soni, ICES Data Centre
International Council for Exploration of the Sea (ICES)

Product type:
• This product is the Standard Survey Area - Standard Monitoring Programme this is the recommended product for all analyses.
• This product is the knn/resolved product which is recommended for all analyses.

Acknowledgements
Finlay Burns, Marine Scotland Science
Jens Rasmussen, Marine Scotland Science
Vaishav Soni, ICES Data Centre
International Council for Exploration of the Sea (ICES)

Product type:
• This product is the Standard Survey Area - Standard Monitoring Programme this is the recommended product for all analyses.
• This product is the knn/resolved product which is recommended for all analyses.

Acknowledgements
Mathieu Lundi, AfBI
Vaishav Soni, ICES Data Centre
International Council for Exploration of the Sea (ICES)

Acknowledgments
Franck Coppin, Ifremer
Michele Salaun, Ifremer
Morgane Travers, Ifremer
Vaishav Soni, ICES Data Centre
Yves Verin, Ifremer
International Council for Exploration of the Sea (ICES)

The Interim Population Consequences of Disturbance (iPCoD) framework was developed by SMRU Consulting and the University of St Andrews in 2013 to forecast the potential effects on marine mammal populations in UK waters of any disturbance, hearing damage or collisions that might result from the construction or operation of offshore renewable energy devices.
A detailed description of the approach can be found in Harwood et al. (2013) and King et al. (2015). The iPCoD framework was designed to cope with the current situation, in which there is only limited knowledge about the potential effects of these developments on marine mammals. It should be recognised that it is very much an interim solution to the evaluation of these effects, and that there remains an urgent need for additional scientific research to address the knowledge gaps that were identified by Harwood et al. (2014).
Since its initial release (v1.0) in February 2014 on the Marine Scotland website: http://data.marine.gov.scot/dataset/protocol-implementing-interim-popula..., the tool was updated with amendments to the code and helpfiles in October 2014 (v1.1). Since then, the iPCoD tool has been used for a number of offshore wind developments in Germany, Netherlands, France and the UK (and possibly others) and has been used to explore the potential population level effects of collisions of a range of species with marine renewable energy devices in Scotland and Wales. Also during this time, SMRU Consulting and John Harwood have explored developing the tool further to improve the model framework.
Since the release of v1.1 there have been several internal iterations of the code (leading to a version 2). This release marks a significant material increase in the efficiency and capability of the interim PCoD framework (version 3).
References:
Harwood, J., S. King, R. Schick, C. Donovan & C. Booth 2013. A Protocol for Implementing the Interim Population Consequences of Disturbance (PCoD) Approach: Quantifying and Assessing the Effects of UK Offshore Renewable Energy Developments on Marine Mammal Populations. Scottish Marine and Freshwater Science 5(2). <http://www.gov.scot/Resource/0044/00443360.pdf >

Harwood, J. and King, S.L. (2017). The Sensitivity of UK Marine Mammal Populations to Marine Renewables Developments - Revised Version. Report number SMRUC-MSS-2017-005. (See downloadable resource below).

King, S. L., Schick, R. S., Donovan, C., Booth, C. G., Burgman, M., Thomas, L., et al. (2015). An interim framework for assessing the population consequences of disturbance. Methods in Ecology and Evolution, 6(10), 1150e1158. http://dx.doi.org/10.1111/2041-210X.12411

Acknowledgements
Franck Coppin, Ifremer
Michele Salaun, Ifremer
Morgane Travers, Ifremer
Vaishav Soni, ICES Data Centre
Yves Vérin, Ifremer
International Council for Exploration of the Sea (ICES)

Acknowledgements
Finlay Burns, Marine Scotland Science
Jens Rasmussen, Marine Scotland Science
Vaishav Soni, ICES Data Centre
International Council for Exploration of the Sea (ICES)

Acknowledgements
Finlay Burns, Marine Scotland Science
Jens Rasmussen, Marine Scotland Science
Vaishav Soni, ICES Data Centre
International Council for Exploration of the Sea (ICES)

Acknowledgements
Anne Sell, Thünen Institute of Sea Fisheries
Barbara Bland, Swedish University of Agricultural Sciences
Finlay Burns, Marine Scotland Science
Franck Coppin, Ifremer
Gary Burt, CEFAS
Ingeborg de Boois, Wageningen Marine Research
Jenifer Devine, Institute of Marine Research, Norway
Jens Rasmussen, Marine Scotland Science
Jim Ellis, CEFAS
Kai Ulrich Wieland, DTU Aqua
Michele Salaun, Ifremer
Morgane Travers, Ifremer
Trine Haugen, Institute of Marine Research, Norway
Vaishav Soni, ICES Data Centre
Yves Vérin, Ifremer
International Council for Exploration of the Sea (ICES)

Acknowledgements
David Stokes, Marine Institute, Ireland
Vaishav Soni, ICES Data Centre
International Council for Exploration of the Seas (ICES)
ICES Working groups:

The use of active high frequency echo sounders for commercial activities and marine research has been increasing in recent years. Compared to other anthropogenic noise sources, high frequency echo sounders have received little attention in terms of their potential impacts on marine life. However, while these devices typically operate at centre frequencies outside the hearing range of most marine species, recent work has demonstrated that they may produce unintended energy at lower frequencies. These lower frequencies may extend into the audible range for several species of marine mammals and have the potential to affect their behaviour (Deng et al. 2014). Given the theoretical detectability of these lower frequencies by marine mammals, both signal types have the potential to elicit behavioural responses towards them. This should be considered in environmental impact assessments of activities using these devices and when planning marine mammal monitoring studies alongside ecosystem studies using active acoustic sonar systems.

Acknowledgements
Anne Sell, Thünen Institute of Sea Fisheries
Barbara Bland, Swedish University of Agricultural Sciences
Finlay Burns, Marine Scotland Science
Franck Coppin, Ifremer
Ingeborg de Boois, Wageningen Marine Research
Jenifer Devine, Institute of Marine Research, Norway
Jens Rasmussen, Marine Scotland Science
Kai Ulrich Wieland, DTU Aqua
Michele Salaun, Ifremer
Morgane Travers, Ifremer
Ralf van Hal, Wageningen Marine Research
Trine Haugen, Institute of Marine Research, Norway
Vaishav Soni, ICES Data Centre
Yves Vérin, Ifremer
International Council for Exploration of the Seas (ICES)
ICES Export Groups: IBTSWG, WGBEAM, WGMSFDemo

Acknowledgements:
Ingeborg de Boois, Wageningen Marine Research
Vaishav Soni, ICES Data Centre
Internationa Council for Exploration of the Sea (ICES)
ICES Expert Groups: IBTSWG, WGBEAM, WGMSFDEMO

Diode array detectors (DAD) are widely used for the analysis of complex phytoplankton pigments in marine waters. A spectrum of each peak in the sample is collected, and when compared with that of a reference standard, the presence of a particular pigment can be confirmed or refuted, resulting in an increased confidence in pigment identification over a conventional UV detector. A method was developed and validated using high performance liquid chromatography (HPLC) with a DAD with the aim of replacing the pigment HPLC method using a UV detector. This report describes the development of that method.

This report has been prepared to accompany the UK Climate Projections 2009 (UK CP09) layers added to ‘Marine Scotland MAPS NMPi'. NMPi is Marine Scotland’s on-line portal to provide spatial information and data to support national and regional marine planning and the state of the sea assessments required to support national and regional planning. This report briefly summarises the climate change data layers selected. A variety of time baselines are used in the climate change future projections (although all are generally for about 100 years in the future). Unfortunately the different time periods reflect how the source information was published, and this cannot be rectified in this report. Users can convert changes over the period published here to relative change per year, or per decade, and then estimate the size of changes for any specific year of their interest. When multiple emission scenarios have been used to give a range of future climate variable possibilities, the 50% probability solution has been used. For projections when only one emissions scenario is available, a medium emissions scenario of future societal change has been used in this report, although other emissions scenarios are available in the information sources listed.

The Gear Innovation and Technology Advisory Group (GITAG) funded trials to assess whether the unwanted by-catch of round and flatfish could be reduced in the Nephrops trawl fishery using a modified Nephrops trawl incorporating 200mm bobbins and a 200mm square mesh panel. Catches of Nephrops and monkfish remained consistent with that of a standard commercial Nephrops trawl. There were significant reductions in relative catch rates of cod and larger haddock (>25cm) and whiting (>28cm). There was no significant difference between the two trawls for haddock below 24cm and for whiting below 27cm. There was a significant reduction in the quantities of smaller common dab (<19cm) and long rough dab (<21cm) that were caught when using the modified trawl. However, significantly more larger plaice above 30cm were retained by the modified trawl.

Polycyclic aromatic hydrocarbon (PAHs) were measured in environmental samples (water, fish and sediment) collected in 2014 and 2016 from the Faroe-Shetland Channel and Rosemary Bank Seamount. These data could be used to provide a baseline against which any changes can be assessed in the event of an oil spill and contribute to any environmental impact assessment. Concentrations in all samples were low, often below the detection limits, and were typical of reference sites. Sponges can be used as an alternative indicator species to mussels for monitoring PAHs in the marine environment as they can accumulate PAHs from both the dissolved and particulate phase. PAH concentrations in marine sponges from Scottish waters have not previously been reported. Concentrations were low, but contained a higher proportion of heavier 4- to 6-ring PAHs compared to the fish samples.

This report describes the work of the Scottish Marine Animal Strandings Scheme between 2012 and 2015. Data on marine animal strandings in Scotland are described and analysed within the report.

This paper considers the process of modelling sediment transport and morphological change in the Pentland Firth and Orkney Waters using coastal area models. This region is atypical of regions commonly modelled using such techniques: it is high energy with limited and highly variable regions of mobile sediment. This causes challenges with regards both model capability and availability of data. Computational time restrictions for fully coupled modelling solutions should also be recognised which limits practical duration of simulation. Impacts to modelled bed level change over test periods are noted for both wave and tidal energy extraction scenarios. In both cases the magnitude of difference is equal to the magnitude of the change itself, however, lack of data and poor validation of the morphological modelling for the wave energy test case means confidence is low in these results.

Fisheries for razor clams (Ensis siliqua and Ensis arcuatus) have gone through a series of expansions in Scotland associated with changes in markets and the introduction of new harvesting techniques. Electrofishing has been recently introduced as an efficient method of forcing clams to the surface of the seabed where they can be collected by divers. Although electrofishing is illegal under European legislation the available evidence suggests that the method could be less impacting on the benthic habitat than alternate techniques, such as mechanical and hydraulic dredges. Electrofishing is also much more efficient than forcing the clams to emerge by pouring high concentration brine into the burrows (a technique known as ‘salting’). Concerns over the use of electrofishing therefore relate mainly to its efficiency and the health and safety risks of using the equipment itself (potential H&S risks are not dealt with in this report). Electrofishing therefore, has the potential to lead to over-harvesting and depletion of razor clam beds, especially considering the slow growth rates of razor clams. A further concern is that there have been very limited surveys of the stock status of Ensis beds around Scotland so that the impacts of harvesting would be difficult to assess. Historical stock assessments in Ireland and Scotland have mainly used dredges or salting followed by divers counting the emergent clams within quadrats . As mentioned previously dredges cause damage to the habitat, as well as to the clams themselves, whilst counting using divers is slow, expensive and samples relatively small areas. The present project was designed to evaluate whether combining an electrofishing rig with a towed video-camera array could be used to assess the razor clam resources in a bed in an efficient manner.

The primary aim of this project was to investigate the commercial viability of fishing with demersal fish traps and automated handlines in the Scottish demersal fishery. Establishing a demersal fishery with traps and automated handlines would provide the inshore sector with additional options for undertaking an environmentally friendly fishing method. A similar project was successfully undertaken by NAFC Marine Centre in 2005, investigating the commercial viability of automated handline fishing for demersal species such as pollack (Pollachius pollachius), saithe, cod and ling (Molva molva). In this study, two separate projects ran concurrently in the North Sea and the west coast of Scotland.

Data files for the net fisheries contain effort data. Fixed engine effort is summarised as median number of traps operated within a given district in any month.

Fishery data are provided at the finest geographical (fishery district) and time (month) scales consistently available. Fishery districts correspond either to a single river catchment together with adjacent coast or to groups of neighbouring river catchments and associated coastline. Districts may be further aggregated into regions. (Collecting the Marine Scotland Salmon and Sea Trout Fishery Statistics Topic Sheet #67, http://www.gov.scot/Topics/marine/Publications/TopicSheets/tslist). Districts are characterised by Name, District ID and Report Order. Ordering the data with respect to “Report Order” sorts the Districts spatially. Districts are ordered counter-clockwise starting with the Tweed as Report Order 1.

The categories by which sea trout data have been reported have varied through the time series (Topic Sheet #67.) Finnock catches have been reported since 2004. Finnock are sea trout which have spent less than a year at sea and making their first return to fresh water. They may also be known as whitling or herling.

Catches of farmed salmon and grilse have been reported since 1994.

Data files for the net fisheries contain effort data. Net and coble effort is summarised as median number of crews operated within a given district in any month.

Fishery data are provided at the finest geographical (fishery district) and time (month) scales consistently available. Fishery districts correspond either to a single river catchment together with adjacent coast or to groups of neighbouring river catchments and associated coastline. Districts may be further aggregated into Regions. (Collecting the Marine Scotland Salmon and Sea Trout Fishery Statistics Topic Sheet #67, http://www.gov.scot/Topics/marine/Publications/TopicSheets/tslist). Districts are characterised by Name, District ID and Report Order. Ordering the data with respect to “Report Order” sorts the Districts spatially. Districts are ordered counter-clockwise starting with the Tweed as Report Order 1.

The categories by which sea trout data have been reported have varied through the time series (Topic Sheet #67.) Finnock catches have been reported since 2004.Finnock are sea trout which have spent less than a year at sea and making their first return to fresh water. They may also be known as whitling or herling.

Catches of farmed salmon and grilse have been reported since 1994.

Reported catches are provided at the finest geographical (fishery district) and time (month) scales consistently available. Fishery districts correspond either to a single river catchment together with adjacent coast or to groups of neighbouring river catchments and associated coastline. Districts may be further aggregated into Regions. (Collecting the Marine Scotland [Salmon and Sea Trout Fishery Statistics Topic Sheet #67], http://www.gov.scot/Topics/marine/Publications/TopicSheets/tslist). Districts are characterised by Name, District ID and Report Order. Ordering the data with respect to “Report Order” sorts the Districts spatially. Districts are ordered counter-clockwise starting with the Tweed as Report Order 1.

The categories by which sea trout data have been reported have varied through the time series (Topic Sheet #67.) Finnock catches have been reported since 2004. Finnock are sea trout which have spent less than a year at sea and making their first return to fresh water. They may also be known as whitling or herling.

Catches of farmed salmon and grilse have been reported since 1994.

Reported catches are provided at the finest geographical (fishery district) and time (month) scales consistently available. Fishery districts correspond either to a single river catchment together with adjacent coast or to groups of neighbouring river catchments and associated coastline. Districts may be further aggregated into Regions. (Collecting the Marine Scotland Salmon and Sea Trout Fishery Statistics Topic Sheet #67, http://www.gov.scot/Topics/marine/Publications/TopicSheets/tslist). Districts are characterised by Name, District ID and Report Order. Ordering the data with respect to “Report Order” sorts the Districts spatially. Districts are ordered counter-clockwise starting with the Tweed as Report Order 1.

The categories by which sea trout data have been reported have varied through the time series (Topic Sheet #67.)
Finnock catches have been reported since 2004.Finnock are sea trout which have spent less than a year at sea and making their first return to fresh water. They may also be known as whitling or herling.

Catches of farmed salmon and grilse have been reported since 1994.

There is considerable interest in the use of genetic tools to assess the conservation status of Atlantic salmon. Here we assess the feasibility of using genetic methods to estimate effective population size and number of breeders outlining their merits together with potential drawbacks.

Twin trawl trials were conducted in the West Coast of Scotland to examine the selectivity of Nephrops (Nephrops norvegicus) with regards to codends of the following mesh size and construction: • 80 mm diamond mesh codend of 4 mm single Brezline polyethylene (PE) twine both with and without a lifting bag (here designated 80 mm and 80 mmL respectively). • 100 mm diamond mesh codend of 5 mm double Brezline (PE) twine both with and without a lifting bag (100 mm and 100 mmL). The results can be summarised as follows: • For Nephrops, increasing the mesh size and removing the lifting bag improves the selective performance of the gear and the analysis suggests that the codends can be ranked from least to most selective as follows; 80 mmL, 100 mmL, 80 mm and 100 mm. We are not able to show this in a statistical sense as the side of the twin trawl on which the test codend was fished influenced the number of Nephrops caught and as a result the subsequent analysis was unable to calculate 95% confidence bands. • For whiting (Merlangius merlangus), selectivity improves with increasing mesh size and removal of the lifting bag. There was no side effect. • For haddock (Melanogrammus aeglefinus) only the presence/absence of a lifting bag proved significant. There was no influence of mesh size, which is probably due to the small sizes of haddock caught, and there was no side effect.

In this manual we describe the different stages of the fish capture process, highlight how different parts of the gear may influence selection and identify possible design changes which can alter the selectivity of the gear. The intention is to make fishermen, net makers and fisheries managers more aware of the possible modifications that can be made to their gears so that they can design and develop gears with a selective performance suitable for their particular fishery. Individual factsheets may be downloaded from the Discardless project website.

The current genetic analysis alludes to finer scale structuring of Atlantic cod stocks in the IVa and VIa stock units than had previously been reported by Heath et al. (2014). Consistent with previous studies of maturation, cod from Viking sampled in 2014 matured at a later age and larger size than other areas, providing a phenotypic population marker. During spawning time there was no indication that the Viking group extended beyond the > 100 m waters of the northern North Sea. Indeed, the new genetic and maturity evidence suggests that Shetland coastal cod (ShIE) appear to extend into waters > 100 m east of Shetland. The possible separation of cod from Scottish inshore waters from those offshore is also reminiscent of the inshore-offshore division seen in the northern North Sea. There is some indication of mixing of populations outside the breeding season in the genetic analysis as well as the observation of large immature cod present in west coast samples. The present study has considerably expanded our understanding of the Viking cod from northern IVa and when combined with the studies by Poulsen et al. (2011) and Heath et al. (2014), provides a good indication of population extent at spawning time and suggests a split around 0030 W.

Salmon fry densities on the river Dee were estimated from juvenile electrofishing data using a capture probability model initially developed in 2015. The resulting density estimates were compared to two potential reference levels that also varied by habitat; (1) a mean National Reference, and (2) a Dee Reference. Despite the limitations of the current approach, it provides useful insights into status of salmon on the River Dee and with future developments will offer a useful assessment to complement those based on adult returns.

This report is comprised of three parts: Part 1- Executive Summary, Part 2 –Description of Scotland’s Coastal Monitoring Sites, Part 3 - Appendices. MSS has been monitoring the physics, chemistry and biology at multiple sites in Scotland’s Coastal Waters since 1997. Parameters measured include temperature, salinity, nutrients, carbonate chemistry, algal toxins and plankton. The data from this monitoring programme provided a thorough description of the seasonality of these parameters and the variation that can occur from year to year. It is also generating the baseline information to allow the Scottish Government to investigate the impacts of anthropogenic drivers such as climate change in coastal environments. Time series of data such as this are very rare and interest is this data set is growing at a national and international level. Requests to MSS to access the data to perform assessments, support project proposals and studentships are increasing. In order place this programme into the context of the global development of coastal observatories, it has been renamed the Scottish Coastal Observatory (SCObs). One of the first tasks of SCObs was to produce a basic description of the seasonality and variability of the main parameters collected; temperature, salinity, nutrients, carbonate chemistry, phytoplankton, chlorophyll, algal toxins and zooplankton. This description comprises a three part report: The Scottish Coastal Observatory 1997-2013 all available to download from the Scottish Government Website. An accompanying data set which contains all the monthly mean values for the 135 environmental parameters and 68 supporting parameters described in Part 2 has been given a doi number 10.7489/1761-1 and can be accessed remotely or by emailing Scobs@gov.scot.

Following a leak from the Clair platform on 2 October 2016, water samples were collected at five depths from ten sites, including a reference site, to assess any environmental impact of the oil leak in the area. All samples were analysed for polycyclic aromatic hydrocarbons (PAHs) and two samples (9.9 m and 29.7 m samples) from each site were analysed for n-alkanes. The total PAH concentrations in the water samples were low, ranging from 1.4 to 16.3 ng l-1 and could be considered to be at background concentrations. The n-alkane profiles showed no evidence of crude oil contamination.

This report presents the results of the 2015 survey of cockle (Cerastoderma edule) stocks in the Scottish Solway Firth. It continues a series of surveys conducted between 1990 and 2009 by Marine Scotland Science (MSS) (previously Fisheries Research Services) and a further survey in 2013, conducted by Marine Ecological Solutions Ltd under contract to Marine Scotland (Stamp et al., 2013). Tables in the report are available to download as .csv files.

Diet composition estimates for pinnipeds are widely conducted using prey hard remains recovered from faeces. To estimate the size and number of prey consumed accurately, digestion correction factors must be applied to measurements and counts of fish otoliths and cephalopod beaks.

This report covers the polycyclic aromatic hydrocarbon (PAHs) and n-alkane analysis of farmed mussels and salmon (liver and muscle) from Loch Roag following the Transocean Winner rig grounding incident, August 2016. Samples were collected from three fish farms and three shellfish farms in Loch Roag on 10/11, 16/17 and 23 August. PAH concentrations were low on all sampling occasions, with a number of PAHs being below the limit of detection. Concentrations were at background levels in both the mussels and in the salmon muscle. n-Alkane profiles showed no evidence of petrogenic contamination. In addition, sensory analyses of the salmon muscle samples were undertaken and no taint was detected in any of the samples.

The objective of this study was to provide seasonal and regional estimates of harbour seal diet composition and regional estimates of prey consumption, and to investigate how harbour seal diet (composition and/or diversity) relates to the different population trajectories observed around Scotland. In this report the work to address the following objectives is described: • Estimate harbour seal diet composition in 2010/11, regionally and seasonally; • Estimate the size of prey consumed by harbour seals, regionally and seasonally; • Examine if there is sex-specific variation in harbour seal diet; • Investigate how harbour seal diet relates to the different population trajectories observed around Scotland; • Estimate harbour seal prey consumption in 2010/11, regionally.

In this report the work to address the following objectives is described: • To compare harbour and grey seal diet composition, regionally and seasonally; • To compare harbour and grey seal diet diversity; with the aim: • To investigate patterns of similarity or difference in harbour and grey seal diet in relation to regional differences in population trajectories of harbour seals around Scotland.

There is currently considerable uncertainty regarding the potential for lethal and injurious interactions between marine mammals and tidal turbines. This uncertainty is particularly concerning for harbour seals in the Orkney and North Coast management unit, where the population has been undergoing a protracted decline. This has led to constraints being placed on tidal developments in this area until more information is available on the real risks presented to this species by tidal turbines. The aim of this research project was to provide improved assessments of the level of mortality to harbour seals potentially caused by tidal turbines in the Pentland Firth and Orkney Waters region, using recently available information from a number of areas of work. These include the consequences of collision for individuals, detailed information on tidal flow, updated tidal turbine parameters and data on temporal and spatial variation of harbour seals within the water column. Specifically, this project was developed to review the assessment process to determine areas where inputs could be refined to improve estimates in the short term; and to use the outputs of these reviews to generate an updated model that is fit for use to estimate the no-avoidance collision rates between seals and tidal turbines. Finally, this updated model was applied to an agreed envelope of consented tidal energy projects in the Orkney and Pentland Firth region. This envelope consisted of two projects: the MeyGen Phase 1a array of four turbines at the Inner Sound in the Pentland Firth, and the multiberth European Marine Energy Centre (EMEC) tidal test site at the Fall of Warness, Orkney.

In late 2014, observations of grey seal (Halichoerus grypus) predation on conspecifics which produced similar wounds provided a plausible alternative explanation of the likely cause of spiral lacerations. At that time there was insufficient evidence to rule out interactions with vessels as a possible cause of some of these mortalities, so the requirement to investigate the temporal and spatial overlap between seals and vessels remained.

Since the last comprehensive assessment of grey seal diet around Britain in 2002, grey seal numbers have continued to rise in the North Sea while harbour seal numbers have declined in Shetland, Orkney and southeast Scotland. Stocks of gadid fish have also declined. In this report on task CSD3.3 of the MMSS/001/11 programme, grey seal diet is reassessed in 2010/11 and compared to previous assessments in 1985 and 2002, and estimates of prey consumed by grey seals are compared with fish stock sizes to estimate percent predation mortality. In this report on task CSD3 of the MMSS/001/11 programme, work to address the following objectives is described: • Estimate grey seal diet composition in 2010/11, regionally and seasonally; • Assess how diet around Britain in 2010/11 has changed compared to 1985 and 2002; • Estimate grey seal prey consumption in 2010/11, regionally; • Assess how consumption by seals as a percentage of estimated stock size of commercially important fish stocks in the North Sea (ICES Subarea IV) and west of Scotland (ICES Division VIa) has changed in 2010/11 compared to 1985 and 2002.

As coastal communities continue to increase in geographical size and population, associated marine economies will have to expand in unison. This relationship gives rise to an increase in user – user and user – environment conflicts, as users of the marine environment proliferate in size, number, and intensity. Such conflicts demand the implementation in marine spatial planning (MSP) in order to effectively manage various users and uses taking place within the marine environment. Furthermore, negative implications arising from global climate change increasingly threaten the integrity of ecosystem services within the marine environment, thereby effecting natural marine ecosystem functions and the economies of coastal communities relying upon such ecosystem services. Such a dilemma has increased political support for the adoption of commercial-scale offshore renewable energy implementation in order to assist in the global energy transition away from a carbon-based economy. These drivers have triggered Scotland to construct and implement the world’s first sectoral marine plan for tidal energy (SMPTE) in an effort to streamline the licensing and permitting processes of tidal current turbines (TCTs), subsequently facilitating the commercial-deployment of TCTs within a structured governance framework.

In this report, we review the use of indicators in the assessment and advisory process and management of data limited stocks, both fish and shellfish, worldwide. For the purposes of the review, we define an ‘indicator’ as quantifiable information that acts as a proxy for, or can be related to the state of the stock (spawning stock biomass, demographic properties or recruitment) and anthropogenic pressure (fishing mortality). Measured (or derived) regularly, indicators are able to show changes in the state of the population or system and can give information on stock status and fishing mortality and support a data-limited stock assessment. Used alone or more often in combination, indicators can provide the means to assess progress towards one or more management objectives. We describe the derivation and theoretical basis of a variety of indicators which can be calculated from commercial fishery data, fishery-independent survey data and biological data, and the ways in which indicators are used in fisheries management. We give details on methods for selecting, evaluating and combining indicators, for developing management strategies, determining reference points and for the testing of harvest control rules (HCRs). We then consider examples of shellfish stocks worldwide for which an indicator-based approach has been applied. Finally, we consider candidate indicators for Scottish shellfish stocks and fisheries and discuss their development in the context of existing and potential future data collection programmes.

The Strategic Environmental Assessments (SEA) for wave and tidal renewable energy generation in Scottish Waters (Faber, Maunsell & Metoc, 2007) identified a need to evaluate the potential interactions between marine renewables and marine wildlife as a matter of priority. In order to study the fine scale movements of animals close to a tidal energy device and potentially monitor collisions, monitoring systems are required with the ability to track animals with a high spatial and temporal resolution and over a range of several tens of metres from the turbine for a period of several months. This report details the progress of Phase 1 of the Scottish Government Demonstration Strategy (SGDS) project: Developing and testing methodologies for measuring fine scale marine mammal movements around tidal energy devices. The approach considered here comprises three sensor systems: Passive Acoustic Monitoring (PAM), Active Acoustics Monitoring (AAM) and Video Surveillance. Whilst each of these systems have been used to study marine animal movements, their combined application in a high tidal energy environment requires development and testing.

The work reported here is the second phase of what is envisaged as a four phase project to develop a facility for the fishing fleet to estimate the size of mackerel using sonar. In the first phase a new sonar system was tested at Woods Hole Oceanographic Institution, analysis software was acquired and adapted, and a fish sizing algorithm was developed. The algorithm was initially tested on model data. In this second phase, the sonar system was deployed at sea during the mackerel fishing season and data was collected to refine the sizing algorithm.

Data on swimming depth of sea trout Salmo trutta (L.) in Icelandic waters was extracted and collated into a suitable format for use in marine renewables risk assessment. The data shows that the fish are close to the surface much of the time, with some time being spent at greater depths.

This report presents summaries of historic and recent landings data and the results of stock assessments for brown crab, velvet crab and lobster, based on data collected between 2009 and 2012. A description of the biology, habitat and life history of these species is provided in Mill et al., 2009.

This project has trialled self-sampling by fishermen as a means of collecting information on discards. In the process a significant quantity of additional information has been collected on the nature and scale of discarding in the Scottish mixed whitefish fishery in the northern North Sea. The results have confirmed species such as hake, saithe and cod as some of the biggest components of whitefish discards. They have also indicated that the vast majority of discard fish in this area are potentially marketable; that is, larger than the minimum landing size (the primary reason given by Shetland fishermen for discarding is lack of quota over the course of the year). The principal exceptions were rays (there is little market demand for small rays) and ling (where most discarded fish are below the minimum landing size). The results have also identified small, but regular, discards of pelagic species such as herring and mackerel in the whitefish fishery. In the absence of observers it was not possible to directly verify the results obtained from the analysis of the samples, but comparison with data from other sources and the internal consistency of the self-sampling data has suggested a reasonable level of confidence in them. An analysis has also been carried out of the potential implications of the discards ban for fishermen in the Scottish mixed whitefish fishery, including an estimation of the potential costs of handling, landing and disposing of unmarketable discards, and an evaluation of the potential impacts of quota limits on individual species.

This report describes carefully controlled laboratory based experiments conducted to consider the potential impact of pile driving noise on Atlantic salmon behaviour and physiology. It is divided into two sections - Part 1: Audiometry, using Auditory Evoked Potentials (AEP) to Determine Hearing Thresholds of a Number of Cohorts of Salmon and Part 2: The Impact of Pile-Driving Playback on the Behaviour and Physiology of Atlantic salmon (Salmo salar).

Report of a three year project carried out by Marine Scotland to investigate the spring component of the River South Esk salmon stock. The following questions were addressed: • In which geographic region of the River South Esk do spring salmon spawn? • How does the status of the juvenile salmon stock vary within the River South Esk and how does this relate to spawning regions used by spring fish? • Is it possible to assess to what extent changes in rod fishing effort have accounted for the declining trend in rod catches of spring salmon? • What proportion of the catch from the coastal net fishery adjacent to the River South Esk was destined to spawn in the River South Esk? The outcome of this investigation is summarised in this report.

Atlantic salmon (Salmo salar) are culturally and economically important to Scotland. Salmon are now the target of large conservation actions due to growing concerns about their population status and the potential impacts of human activities on their productivity. To adequately assess the current and future status of salmon populations, accurate estimates of their population sizes are needed. In Scotland, electronic fish counter technology has been the cornerstone methodology used to accurately assess salmon population sizes. Marine Scotland Science (MSS) seeks to expand the current counter distribution to include new counter sites throughout Scotland. An expanded network will provide valuable information for salmon fisheries management, sustainable marine planning, the development of renewable energy, and the growth of aquaculture. Planning and implementing a counter network requires knowledge of the technical constraints, engineering requirements, operational protocols and economic costs. This report was commissioned by MSS to address a knowledge gap in the technical, logistical and economic understanding in the development of a Scottish salmon counter network. The overall objective of this report was to inform the future development of a fish counter network for Scotland.

Please note
An updated version of the GIS data was added to this dataset February 2018. The older GIS resources have been removed, but are available on request.

Please note
An updated version of the GIS data was added to this dataset February 2018. The older GIS resources have been removed, but are available on request.

• To provide detailed information in relation to the Areas of Search identified in the 2012 Scoping Report for Wave Energy Developments in Scottish Waters
• To identify suitable options for inclusion in the sectoral marine planning process.
• To inform key stakeholders and other interested parties of the key regional issues in relation to developing offshore wave energy in Scottish Waters
• To inform the process for determining marine license applications to develop offshore renewable energy in Scottish Waters

Please note
An updated version of the GIS data was added to this dataset February 2018. The older GIS resources have been removed, but are available on request.

Marine Scotland has led the development of a hydrodynamic model (FVCOM) for the Scottish continental shelf waters called the Scottish Shelf Model (SSM). A series of six reports have been produced documenting the development of the hydrodynamic model. This report is Part 6: Wider Domain and Sub-Domains Integration, documenting the development of the integrated model.

Marine Scotland has led the development of a hydrodynamic model (FVCOM) for the Scottish continental shelf waters called the Scottish Shelf Model (SSM). A series of six reports have been produced documenting the development of the hydrodynamic model. This report is Part 5: Wider Loch Linnhe System Sub-Domain, documenting the development of this sub-domain model. A companion volume contains additional details on the model development and lessons learned.

Marine Scotland has led the development of a hydrodynamic model (FVCOM) for the Scottish continental shelf waters called the Scottish Shelf Model (SSM). A series of six reports have been produced documenting the development of the hydrodynamic model. This report is Part 4: East Coast of Lewis and Harris Sub-Domain, documenting the development of this sub-domain model. A companion volume contains additional details on the model development and lessons learned.

Marine Scotland has led the development of a hydrodynamic model (FVCOM) for the Scottish continental shelf waters called the Scottish Shelf Model (SSM). A series of six reports have been produced documenting the development of the hydrodynamic model. This report is Part 3: St Magnus Bay Sub-Domain, documenting the development of this sub-domain model. A companion volume contains additional details on the model development and lessons learned.

Marine Scotland has led the development of a hydrodynamic model (FVCOM) for the Scottish continental shelf waters called the Scottish Shelf Model (SSM). A series of six reports have been produced documenting the development of the hydrodynamic model. This report is Part 2: Pentland Firth and Orkney Waters Sub-Domain, documenting the development of this sub-domain model. A companion volume contains additional details on the model development and lessons learned.

Marine Scotland has led the development of a hydrodynamic model (FVCOM) for the Scottish continental shelf waters called the Scottish Shelf Model (SSM). A series of six reports have been produced documenting the development of the hydrodynamic model. This report is Part 1: Shelf-Wide Domain, documenting the development of the large scale hydrodynamic model covering Scottish Waters. A companion volume contains additional details on the model development and lessons learned.

This report provides the background, the process and the outcomes of an interdisciplinary project entitled “The Cooperative Participatory Evaluation of Renewable Technologies on Ecosystem Services: CORPORATES”, funded by the UK Natural Environment Research Council (NERC). The aims of the project was to exchange knowledge between researchers and a range of public and private sectors stakeholders around the understanding of marine ecosystem services (ES), in the context marine spatial planning (MSP) decisions around marine renewable energy (MRE). The project developed a pilot study located at the Firth of Forth, Scotland, considering current development of a number of large windfarms in an area important to both fishing and nature conservation. The project included the involvement of a wide range of highly experienced stakeholders over the course of two day-long workshops in November 2014 and March 2015. While the process centred on a ‘live’ decision-making case study, the focus of the CORPORATES project was to provide an example of a decision support tool for knowledge exchange around ES rather than influencing decision-making in the Forth. The project design and delivery was highly transdisciplinary, involving experts with backgrounds in ecology, oceanography, marine management, policy, law, environmental psychology, anthropology and ecological economics as well as public and private sector stakeholders.

Historical tagging studies have shown that there was considerable scatter in the recaptures of salmon tagged in various locations around Scotland, with fish being found far from their natal rivers. More recently, satellite tags have enabled at-sea locations of salmon on their return migrations to be collected in Scottish waters. However, a thorough understanding of the tagging information was constrained by a lack of knowledge of where the salmon were headed before their tags detached. Here, genetic assignment techniques are used in order to investigate the origins of salmon satellite-tagged at Armadale on the north coast of Scotland. The marine distribution of tagged fish assigned to different parts of Scotland showed no obvious pattern. As such, results of this analysis confirm those seen with conventional tagging investigations and show that homing fish show considerable spatial mixing around the Scottish coast before finally returning to their natal rivers. It is thus also clear that the deployment of renewable energy devices may not only affect local salmon populations, but also more distant ones.

The objective of the project was to determine spatial turnover rates of scallops at two spatial scales: (i) at the scale of individual fishing patches (tens to hundreds of metres), determining immigration rates following fishing; and (ii) at the local fishery scale (1-10 km and greater), determining potential sources of immigration to fishing patches from more distant areas. This report addresses the first of these spatial scales, using depletion fishing experiments coupled with tagging to estimate size-specific population size and site-fidelity to small experimental areas.

It is widely acknowledged that Atlantic salmon (Salmo salar) sub-stocks exist in Scottish rivers. These sub-stocks are associated with diverse life-histories, relating to different environments and pressures. However, there are significant challenges associated with the analysis of populations at the sub-river scale. This report investigates the potential for assessment of fish populations at a sub-river scale. A sophisticated mathematical model was used to separate salmon from a single river (North Esk, eastern Scotland) into three sub-stocks, based on the number of years the adults have spent at sea (their sea-age) and the month of the year in which the adults return to freshwater to breed (their run-timing).

The report describes the data required, and the methods used, to estimate collision risk. It is accompanied by a worked example and R code (available at http://dx.doi.org/10.7489/1657-1), which enables the collision risk calculations to be performed in a standardised and reproducible way. In the UK, the most frequently used avian collision risk model is commonly known as ‘the Band model’ (Band, Madders & Whitfield 2007) and was originally conceived in 1995. Since then it has undergone several iterations with the most recent associated with the Strategic Ornithological Support Services (SOSS) (Band 2012a; b). The Band model (Band 2012b) provides four different options for calculating collision risk. • Option 1 - Basic model, i.e. assuming that a uniform distribution of flight heights between the lowest and the highest levels of the rotors and using the proportion of birds at risk height as derived from site survey. • Option 2 - Basic model, but using the proportion of birds at risk height as derived from a generic flight height distribution provided. • Option 3 - Extended model and using a generic flight height distribution. • Option 4 - Extended model and using a flight height distribution generated from site survey.

The main aim of this work was to trial the use of Succorfish’s SC2 VMS tracking technology on vessels from the inshore scallop dredge fleet around Shetland and to evaluate its effectiveness as a tool for informing management decisions and protecting the environment.

The seal usage maps are currently being updated with a new version due for publication in spring 2017. Until then, the maps are available at http://www.smru.st-andrews.ac.uk/smrudownloader/uk_seal_usage_of_the_sea

The seal usage maps and report have been produced by SMRU as a deliverable of the Scottish Government Marine Mammal Scientific Support Research Programme (MMSS/001/11 ). The Maps are produced by looking at movement patterns from electronically tagged seals. The resulting patterns of usage are scaled to population levels using data collected in aerial survey counts at haul-out sites, to produce estimates of mean density (seals per 5 x 5 km grid cells).

Little is known about effects of magnetic fields (MFs, 50 Hz, measured in Teslas) associated with high voltage cables on behaviour of European eels. It has previously been shown in a field study that swimming speed of European eels in the Baltic Sea slowed when crossing a 130 kV AC power cable. However, no details of fish behaviour during passage over the cable were recorded in this study, and it is not known whether the observed reduction in swimming speed was due to the MF associated with the cable, or some other factor. The aim of the present study was to observe the response of European eels at the silver eel stage of their life-cycle to an AC MF of approximately 9.6 µT at a fine scale in a controlled laboratory setting. During 28 trials, each lasting 4 hours and using a single eel per trial, 10 eels (termed “swimmers”) made between 1 and 43 passes through coils. There was no evidence of a difference in movement due to the MF nor observations of startle or other obvious behavioural changes associated with the magnetic fields. Level of movement decreased as the experiments progressed and increased with eel size. Eel passage through coils was unaffected by whether or not they were activated. In applying these results it must be kept in mind that the sample size was small, nocturnal behaviour was not tested and the field strengths were lower than might be encountered in the wild in some situations.

Effects of mains frequency (50Hz) magnetic fields (MF) on behaviour of captive Atlantic salmon were examined in a large arena. Fish swam spontaneously within the arena passing from one side to the other through Helmholtz coils (arranged in four pairs) that penetrated a net barrier. When activated, a uniform intensity MF was generated between coils within a pair. Salmon were considered in two size categories: large fish (62-85 cm) and smaller post-smolts (24-41 cm). Large fish were tested in groups of six and considered at the individual level. For each fish, measurements were made of the times to approach, traverse and leave an activated coil pair (intensity = 95 µT) on first encounter across defined distances. These times were compared with previous passage times for the same coil in a deactivated state across similar distances. There were no significant differences in approach, traverse or departure times associated with activation state of the coils. Post-smolts (18 trials of groups of six fish) were exposed to three 30-min periods of MF at 1.3, 11.4 and 95 µT with 30-min controls before each treatment. The sequence in which the different MF levels were presented was varied sequentially. There was no evidence that the numbers of fish passing through the coils depended on the sequence in which the MF intensities were presented (p = 0.18) or on the field intensity itself. Similarly, the numbers of shoals passing through coils did not depend on sequence or field intensity. There were no observations of unusual behaviours in association with MF up to 95 µT.

Descriptor 9 (Contaminants in fish and other seafood for human consumption do not exceed levels established by Community legislation or other relevant standards) is one of eleven Marine Strategy Framework Directive (MSFD) qualitative Descriptors to be used in determining whether Good Environmental Status (GES) has been achieved for European regional seas (Directive EC/2008/56). For monitoring of compliance with GES for Descriptor 9, contaminant concentrations in fish and seafood should be compared against the EC regulatory levels. PCBs were mainly below detection limits in monkfish and haddock, but above detection limits in herring where concentrations for the ICES6 CBs ranged from < LoD (in one sample only) to 17.5 µg kg-1 wet weight. For metals, Cd and Pb were mainly below detection limits, whereas Hg was detected in all samples. Concentrations of Hg were higher in monkfish than in haddock and herring. Although monkfish has a low lipid content, it is at the highest trophic level of the three species. Cd, Hg, Pb and the ICES6 PCB concentrations were below the regulatory levels in all samples. The 95th percentile of the distributions of the trace metal and ICES6 PCBs concentrations were estimated for each species and area and compared against the regulatory limits. All were significantly below the regulatory levels, except for mercury in monkfish from the West coast.

The north-eastern Atlantic stock of spurdog (Squalus acanthias) is assessed as being at a historical low by ICES and others (De Oliveira et al. 2013, ICES 2014). In consequence a zero Total Allowable Catch limit was set throughout EU waters (European Commission 2015). The aims of the present project were to collect new data on the levels of spurdog by-catch, locations of by-catch and to collect biological information in terms of the sizes and sex of the fish caught in order to inform the debate on whether a controlled incidental by-catch (i.e. not targeted) fishery could be considered. The project was funded to run over the winters of 2013/14 and 2014/15. Because not all the available budget for sampling in 2013/2014 was spent, sampling was extended to cover the spring and summer 2014.

The aim of this project was to review the potential issue of "turnover‟ of individual seabirds at sea during the breeding season and to assess how this may lead abundance estimates derived from boat or aerial surveys to underestimate the total number of birds that use an area during the course of the breeding season. Turnover rates in species for which sufficient data were available are estimated.

This project provides relevant information to assist Marine Scotland Science with identifying knowledge gaps that may benefit from further data collection. It will also enable Marine Scotland Licensing Operations Team and Marine Renewables Developers to make more informed assessments of the potential impacts of development projects as part of the required environmental evaluations. The project, therefore, has significant strategic relevance for site characterisation and monitoring in Scotland and beyond. Turnover is clearly only one factor that will need to be considered when assessing the risks to seabird populations from offshore developments. A related task will involve quantifying the fate of birds that lie within the development footprint. Further work is needed in order to understand whether higher levels of turnover lead, all else being equal, to higher or lower estimates of development-related mortality.

Models of juvenile salmonid abundance are required to inform electrofishing based assessment approaches and potentially as an intermediate step in scaling conservation limits from data rich to data poor catchments. This report describes an approach for modelling large-scale spatio-temporal variability in fish densities using GIS derived covariates. The technical challenges, modelling approaches and software developed during the project are described. The utility of the approach was illustrated by fitting models to data on Atlantic salmon fry.

The introduction of hatchery-reared Atlantic salmon smolts to rivers in support of local salmon fisheries (termed ranching) is a controversial subject with little information available to fishery managers on the value of the method in a Scottish context. Here we present recapture data from monitored smolt releases on four Scottish rivers and compare return rates of hatchery and wild-reared salmon smolts originating from a common stock on two of these rivers. Rod recapture rates from stocked hatchery smolts ranged from 0-0.23%. In comparative tests return rates for wild-reared fish were on average ten times greater than those for stocked fish (range 6 to 13-fold where at least one reared fish returned). Given the relatively poor returns and associated production costs any benefit to fisheries of stocking with hatchery-reared smolts is unlikely to be sustainable in the Scottish context. Furthermore, risks of adverse genetic effects should be considered.

A set of trials were conducted in the West Coast to examine the selectivity of Nephrops (Nephrops norvegicus) with regards to codends with the following mesh size and construction: 80 mm diamond mesh codend of 4 mm single Brezline (PE) twine; 100 mm diamond mesh codend of 5 mm double Brezline (PE) twine; 120 mm diamond mesh codend of 5 mm double Brezline (PE) twine. The results can be summarised as follows: For Nephrops the catch rates of the 3 test gears differed significantly from each other. At a carapace length of 35 mm the 80 mm mesh showed 77% retention, the 100 mm codend showed 61% retention and the 120 mm codend showed 43% retention. For whiting (Merlangius merlangus) the catch rates of the 3 test gears differed significantly from each other with increasing selectivity as mesh size increased. For haddock (Melanogrammus aeglefinus) the selectivity increased as mesh size increased however, that of the 80 mm and 100 mm codends did not differ significantly from each other.

The Scottish Government has set ambitious targets for renewable power generation. Marine Renewable Energy, including wind, wave and tidal power are expected to contribute significantly to these targets. Information on the timing of Atlantic salmon smolt migrations is required for planning coastal development and the timing of particular activities. Information on smolt sizes is required to plan acoustic tagging studies aiming to improve understanding of fish movement and behaviour in the coastal zone. This report assessed pre-existing information on smolt migration timing and sizes. The commencement of migration was characterised as the day of the year (DoY) on which 25% of smolts had migrated (S25); the end of the migration period was characterised as the DoY on which 75% of smolts had emigrated (S75). The start and end of the migration period varied with elevation and over time, but not as a predictable function of geographical location (latitude and longitude). Thus, a single coastal migration DoY range (S25 to S75) was estimated for the whole of Scotland. By including uncertainty in the predictions it was possible to identify a “sensitive window” for development, where large numbers of migrating salmon smolts could be expected in the coastal zone. This window covers the period DoY 103-145. This envelope does not consider the time that smolts will spend in the coastal zone, so further work is required to adjust this window appropriately. It was not possible to model the spatiotemporal variability in smolt sizes given available data and resources. However, considerable inter-site and inter-annual variability was observed. The data presented here could be used to inform future acoustic tagging studies at existing sites, although it is suggested that pilot data should be obtained where work is to be carried out at new sites.

In February 2014, the Dynamics and Properties of Marine Systems (DPMS) Theme of the Marine Alliance for Science and Technology for Scotland (MASTS) organised a case study workshop on the Loch Linnhe and Firth of Lorn (LL&FL) system. Loch Linnhe is one of the largest sea lochs on the west coast of Scotland, and the Firth of Lorn provides a connection to the open ocean. During the workshop, a review of the current knowledge of LL&FL was undertaken in three subject areas: the physical environment, the aquatic ecosystem and the management and use. This review also identified a number of knowledge gaps and potential collaborations to address these. This report provides an overview of these discussions. A more comprehensive, scientific review of our knowledge of the LL&FL system will be published in the near future.

This report describes a modelling approach which has been developed to correct the reported catch of Scottish rod fisheries by accounting for recaptures associated with these data. In the absence of direct counting systems, the abundance of Atlantic salmon stocks in Scotland is generally estimated indirectly using reported rod fishery data. The widespread adoption of catch and release in Scottish rod fisheries provides a challenge for such assessment techniques, however, as a proportion of fish released from the rod fishery may be re-caught and hence inflate the catch statistics by appearing in the reported data more than once.

The requirement to display sensitive areas relating to the life history of commercially important fish species in British waters is well recognized. Sensitive areas have previously been described as spawning and nursery grounds. Here we consider only areas where there is evidence of aggregations of 0 group fish and/or larvae of key commercial species. 0 group fish are defined as fish in the first year of their lives. These fish sensitivity maps were originally generated to provide a spatial and temporal description of where physical damage could potentially occur to fish species at sensitive stages in essential habitats of their life cycle. Sources of damage in this context referred to seismic surveying conducted by the offshore Oil and Gas industry during their site investigations. In addition to the acoustic energy that the seismic survey activities generate, we should now add other percussive impact noises from pile-driving seabed foundation pins into the seabed, such as those required for offshore renewable energy sites. The spatial location of these fish life history events and their potential interaction with offshore industries can heavily influence the planning, costs and delivery of these offshore developments. It is imperative that these maps reflect the current extent of these areas.

Marine Scotland requires a detailed understanding of fishing activity in Scottish Territorial Waters to inform marine spatial planning at both the national and regional level, and in relation to marine renewable energy development, marine nature conservation designations and fisheries mnagement. For larger fishing vessels (those over 5 m overall length) which fish mainly in offshore wters, spatially resolved information on the ctivity and the value of fishing can be derived fom Vessel Monitoring Systems (VMS) and landings data. The competition for space is, however, often greatest in inshore waters where most fishing is undertaken by small vessels which are not currently fitted with VMS. To improve knowledge of the distribution of fishing activity and the value of fisheries in inshore waters, Marine Scotland carried out a fisheries mapping study known as ScotMap. ScotMap provides spatial information on the fishing activity of Scottish registered commercial fishing vessels under 15 m in overall length.

The selection of appropriate avoidance rates for use in collision risk models at offshore windfarms is often a key part of the Environmental Impact Assessment process. Ideally, these avoidance rates should reflect the behavioural responses of birds to turbines. However, they are often used as a ‘fudge-factor’ to incorporate aspects of model error. The situation is further complicated by a lack of data for marine birds and offshore windfarms. As a consequence, present guidance is based on values that have been derived for terrestrial species at onshore windfarms. This study reviewed data that have been collected from offshore windfarms and consider how they can be used to derive appropriate avoidance rates for use in the offshore environment. Aims of the study were five-fold: To produce definitions for the types and scales of avoidance; To review current use of avoidance rates; To review and critique existing avoidance behaviour studies and any derived rates; To provide summary avoidance rates and a total avoidance rate for each priority species/species group based on the evidence available at present; To undertake an assessment of the sensitivity of the conclusions reached to inputs and conditions under which they were collected. The study focussed on five priority species – northern gannet, black-legged kittiwake, lesser black-backed gull, herring gull and great black-backed gull – whose behaviour and distribution make them particularly prone to collision with offshore turbines.

Marine Scotland Science conducts annual underwater television surveys to estimate the abundance of Nephrops norvegicus on muddy sediments in seas around Scotland. Underwater footage is recorded to DVD and reviewed by two independent observers. Nephrops burrows are counted and burrow densities over each survey tow are estimated from the average counts and viewed area. Additional data are also collected during the surveys, including sediment samples and observations on sea pen abundance, presence of fish and other benthic species and evidence of anthropogenic activities (trawl marks). All survey data are held in a purpose designed database, the ‘Nephrops survey database’. In 2010, following discussions with Scottish Natural Heritage and the Joint Nature Conservation Committee, it was agreed that data within the Nephrops survey database would be used to assist with the Scottish Marine Protected Area project, specifically the mapping of burrowed mud and offshore deep mud habitats (biotopes). This report documents work carried out, including summaries for each area surveyed and maps based on Geographic Information System layers.

The Scottish Government has set a range of challenging targets for energy and climate change. These recognise the potential to take advantage of the extensive marine energy resources (wind, wave and tidal power) available in Scottish waters and include meeting at least 30% of total energy demand from renewable sources by 2020, incorporating: o 100% of electricity demand from renewables (31% by 2011) o 11% of heat demand from renewables o 10% of transport fuel from renewables In addition, the Climate Change (Scotland) Act 2009 sets statutory targets of at least 42% emissions cuts by 2020, and at least 80% by 2050. To assist in meeting these targets, the Scottish Government has adopted an iterative approach to marine planning for the renewable energy sectors. A Sectoral Marine Plan for Offshore Wind Energy in Scottish Territorial Waters (Blue Seas - Green Energy) sets out the Government's vision for developing offshore wind energy up to 2020 and beyond and has identified short term development sites for offshore wind up to 2020, with a potential to deliver almost five Gigawatts (GW) of electricity generation capacity. A new Scoping Study extends the potential development area out to 200 nm. A sensitivity analysis of the process used to develop the offshore wind Plan concluded that, as additional data and monitoring information and improved data handling procedures become available, these should be incorporated into the emerging iterative marine planning process.

The Scottish Government has set a range of challenging targets for energy and climate change. These recognise the potential to take advantage of the extensive marine energy resources (wind, wave and tidal power) available in Scottish waters and include meeting at least 30% of total energy demand from renewable sources by 2020, incorporating: o 100% of electricity demand from renewables (31% by 2011) o 11% of heat demand from renewables o 10% of transport fuel from renewables In addition, the Climate Change (Scotland) Act 2009 sets statutory targets of at least 42% emissions cuts by 2020, and at least 80% by 2050. To assist in meeting these targets, the Scottish Government has adopted an iterative approach to marine planning for the renewable energy sectors. A Sectoral Marine Plan for Offshore Wind Energy in Scottish Territorial Waters (Blue Seas - Green Energy) sets out the Government's vision for developing offshore wind energy up to 2020 and beyond and has identified short term development sites for offshore wind up to 2020, with a potential to deliver almost five Gigawatts (GW) of electricity generation capacity. A new Scoping Study extends the potential development area out to 200 nm. A sensitivity analysis of the process used to develop the offshore wind Plan concluded that, as additional data and monitoring information and improved data handling procedures become available, these should be incorporated into the emerging iterative marine planning process.

This report presents modelling of the acoustic output of operational off-shore wind turbines and its dependence on the type of foundation structure used. Three foundation types are examined: jacket, monopile and gravity foundation. The acoustic output from each of these foundation types is then compared to curves representing the hearing and behavioural response of marine species likely to come into contact with off-shore wind farms in Scottish Waters. The marine species examined are minke whales, harbour porpoise, grey seals, harbour seals, bottlenose dolphins, European eels, allis shad, sea trout and Atlantic salmon.

Descriptor 8 (contaminants and their effects) is one of the eleven Marine Strategy Framework Directive (MSFD) qualitative descriptors for determining Good Environmental Status (GES) (Directive 2008/56/EC). To monitor compliance with Good Environmental Status (GES) for Descriptor 8, contaminant concentrations and biological effects should be measured in environmental samples and compared to assessment criteria. The contaminant monitoring currently undertaken in Scotland’s seas was reviewed. Monitoring programmes include the UK Clean Seas Environment Monitoring Programme (CSEMP), undertaken by Marine Scotland Science (MSS) and the Scottish Environment Protection Agency (SEPA), and the Water Framework Directive (WFD) monitoring, undertaken mainly by SEPA. The suitability of current monitoring programmes in addressing the requirements of Descriptor 8 was assessed.

Descriptor 9 (contaminants in food) is one of eleven Marine Strategy Framework Directive (MSFD) qualitative Descriptors to be used in determining whether Good Environmental Status (GES) has been achieved for European regional seas (Directive EC/2008/56). For monitoring of compliance with GES for Descriptor 9, contaminant concentrations in fish and seafood should be compared against the EC regulatory levels. The fish and shellfish contaminant monitoring currently undertaken in Scotland was reviewed. Monitoring programmes include the UK Clean Seas Environment Monitoring Programme (CSEMP) undertaken by Marine Scotland Science (MSS) and Scottish Environment Protection Agency (SEPA), and the annual surveys of contaminants in shellfish from commercial harvesting areas undertaken by Food Standards Agency for Scotland (FSAS). The suitability of these activities in addressing the requirements of Descriptor 9 was assessed. CSEMP is the main UK monitoring programme for contaminants in fish and, in Scotland, is undertaken by MSS. However, as most fish data are for liver tissue of small flatfish they are of limited use for assessing progress towards GES under Descriptor 9, as in the UK fish liver is not generally consumed. For CSEMP, trace metals are determined in fish muscle and liver, and PCBs in fish liver only. Regulatory levels are available for metals, dioxins and PCBs in fish muscle. However, only metals are analysed in fish muscle as part of UK CSEMP. PCBs and dioxins are not measured in fish muscle as this is not a requirement of the OSPAR Coordinated Environmental Monitoring Programme (CEMP) for the NE Atlantic. Monitoring of shellfish in Scotland is mainly undertaken by FSAS and SEPA. Mussel samples are collected by SEPA to assess compliance with the Water Framework Directive (WFD; 2000/60/EC) and its daughter Directive on Environmental Quality Standards (EQSD; 2008/105/EC) following the repeal of the Dangerous Substances Directive (DSD; 2006/11/EC) in December 2013; samples are analysed for PCBs, PAHs and trace metals, but not dioxins. FSAS undertake contaminant (includes trace metals, PAHs, PCBs and dioxins) monitoring in shellfish or the Shellfish Hygiene Directive (79/923/EEC). Both SEPA and FSAS shellfish contaminant data could be used for Descriptor 9 assessments, although currently FSAS data is not submitted to the UK Marine Environment Monitoring and Assessment National database (MERMAN).

An outbreak of Viral Haemorrhagic Septicaemia (VHS), as defined by European Community Council Directive 2006/88/EC, was detected during December 2012 in multiple species of wrasse (Labridae) stocked onto six sea-water sites around Shetland Mainland. The wrasse were originally captured from the wild off the west coast of the Scottish mainland and were being used as a biological control of sea-lice (Caligidae) on Atlantic salmon (Salmo salar) farms. Inspection, diagnostic testing, contact tracing, epidemiological enquires and other relevant research were undertaken as part of an outbreak investigation, containment areas were established, and the removal of stocked wrasse was initiated. To date three of the six affected sites have been cleared with a substantial proportion (˜99%) of wrasse removed from the remaining sites. Species other than wrasse were also tested for VHS. Lumpsucker (Cyclopterus lumpus) and Atlantic salmon stocked on VHS positive sites tested VHS negative. Wild poor cod (Trisopterus minutus) from within the pens of a VHS positive site tested VHS positive. Free-ranging wild Norway pout (Trisopterus esmarkii), sprat (Sprattus sprattus), grey gurnard (Eutrigla gurnardus), herring (Clupea harengus), whiting (Merlangius merlangus) and plaice (Pleuronectes platessa) from a locality around Shetland tested VHS positive. A qualitative risk analysis suggests that the chance of this outbreak originating from the marine environment around Shetland is moderate and alternative possibilities are either low or negligible.

A biophysical modelling approach that accounts for regional oceanographic variation and some degree of biological realism was used to estimate larval transport of 18 benthic invertebrates identified as priority marine features for possible nature conservation MPAs. Mean transport distance was mostly related to the duration of the pelagic larval phase (PLD), although season of spawning and distance to shore were also important factors. Larvae of species with a PLD = 30 days that were not solely associated with sea lochs or near-shore regions could be advected from the Celtic Sea to the Greater North Sea OSPAR sub-region. These species include tall sea pen, burrowing anemone, spiny lobster and most bivalve molluscs. Due to the limited distance between possible MPAs, connectivity among protected regions should be possible for many species with PLD = 10 d within OSPAR subregions. Those species at risk of local impacts due to low connectivity were species with a short PLD (burrowing amphipod, northern feather star, pink soft coral and northern sea fan) and/or present only in a small number of MPAs (heart cockle and horse mussel). Possible MPAs that were too close to shore to resolve in this analysis are also likely to be less dispersive environments than open water possible MPA sites. The model estimates of larval transport could be significantly influenced by larval behaviour and hatching times, highlighting the need for better information on these parameters. Information on habitat suitability is also needed to resolve suitable settlement areas. Future high resolution hydrodynamic models should allow us to improve our estimation of connectivity.

For over 100 years Marine Scotland, under various names, has conducted marine research in the waters around Scotland. From the earliest times this included the measurement of physical and chemical parameters at standard sections worked routinely over a number of years, and at ad hoc stations whose timing and location were determined by individual projects. This paper presents summary tables of a selection of these parameters in twenty six sub-areas of Scottish waters selected because of their distinct hydrographic characteristics. Only data from 1960 have been used for a number of reasons. Prior to that time salinity, a vital parameter used when determining the origins and history of particular water masses, was determined chemically. Initially salinity samples were analysed by the Laboratory of the Government Chemist, with varying degrees of accuracy and quality control. In later years the analysis was taken on by staff of Marine Scotland, Marine Laboratory, Aberdeen, where it has stayed through to the present day. Many of the chemical techniques presently used for the determination of nutrient concentrations were standardised in the early 1960s. Therefore, data prior to this are of limited value and must be used with caution. Since the early 1960s, analysis techniques, and to a large extent the analysts themselves, have been fairly consistent within the Marine Laboratory. The effect of this has been a high quality, internally consistent data set. Any collection of environmental data, such as that which exists within the Marine Laboratory, is of most value if it can be readily accessible and in a form useful to potential "customers". Today, this means a computer archived database which may be used in a flexible, userfriendly and problem-oriented manner. Such a database has been constructed from oceanographic data collected by the Marine Laboratory since 1960.

This report provides the results and assessment of a survey carried out by Marine Scotland Science, Marine Laboratory, Aberdeen as part of a rocky shore monitoring programme undertaken by Aquatic Survey and Monitoring Limited, commissioned by the Shetland Oil Terminal Environmental Advisory Group (SOTEAG), and funded by the Sullom Voe Association.

To date, OSPAR has largely been responsible for the development of an ecosystem approach to the management of marine natural resources. Ten Ecological Quality Issues have been identified, with the intention of setting Ecological Quality Objectives (EcoQOs) for each issue. Since 2000, this scheme has been developed and piloted in the North Sea. Fish Communities is the fifth in the list of Ecological Quality Issues, and is considered to be one of three community-level issues. In addressing concerns regarding anthropogenically induced change in fish communities therefore, a community-level approach has been widely adopted. This has generally involved the application of univariate metrics to groundfish survey data to quantify change in various aspects of the community’s composition, structure and function. The element of Ecological Quality for the North Sea fish community focuses on “changes in the proportion of large fish and hence the average weight and average maximum length of the fish community”, thus clearly identifying the need for a community size composition metric as the “indicator” on which to base an EcoQO for the “fish community” Ecological Quality Issue. The chosen metric, the Large Fish Indicator (LFI) was eventually defined as “the proportion by weight of fish greater than 40cm in length”, based on ICES first quarter (Q1) International Bottom Trawl Survey (IBTS) data. The LFI was intended to be an indicator of the “general health” of the demersal fish community. However, other aspects of the composition, structure and functioning of fish communities, such as abundance, biomass, productivity, species richness, species diversity and mean life-history trait composition, can also be summarised using univariate metrics. Any one, or all, of these alternative metrics might also be considered to be indicative of the “health” of fish communities. The LFI was chosen ahead of these alternative metrics because it was believed to be particularly sensitive to variation in fishing pressure, and therefore to indicate directly the effect of fishing on the state of the fish community. But this raises the question as to whether one indicator is sufficient to inform on the general health of the demersal fish community, or is a suite of indicators necessary in order to provide information on various different aspects of a community’s composition, structure and function? In this assessment of the state of the demersal community in four OSPAR Regions, fifteen univariate metrics are applied to groundfish survey data to quantify changes in five main aspects of community composition, structure and function: abundance/biomass/productivity; size composition; species richness; species diversity; and life-history trait composition (Table 1). Bottom trawl surveys have been carried out as part of the traditional annual fisheries management process for several decades. These surveys routinely provide point estimates of the abundance at length of each species sampled; therefore providing ideal data sets for the application of univariate community metrics. Many of these surveys have run for two or three decades now, providing appropriate time series with which to evaluate changes in the composition, structure and function of fish communities. Furthermore, most coastal European nations have been involved in survey activity, providing data from most of the continental shelf waters in the OSPAR area. In this assessment, otter trawl survey data is analysed to assess changes in the fish communities present in four OSPAR Regions (Figure 1). To assess the state of the demersal fish community in OSPAR Regions, II, III, IV and V, and make a judgement on the changes observed, it was necessary to decide what constituted “beneficial” and “detrimental” change. Emphasis is generally placed on conserving and restoring biodiversity; implying that declines in species diversity (both richness and evenness) are detrimental. The converse was therefore also assumed to hold. The lifehistory trait composition responses of populations and communities to anthropogenically raised levels of mortality have recently received considerable attention. Declines in population age and length at maturity, decreased community average ultimate body length, and an increase in community average growth rate are all considered to be detrimental Assessment of the “State” of the Demersal Fish Communities in OSPAR Regions 3 consequences. Improved management would therefore be expected to induce the opposite, beneficial trends. Established population dynamics theory predicts that size-related fishing mortality reduces the mean size and proportion of large fish in exploited populations (including non-target species taken as by-catch). This concept underpins development of the LFI as the basis for the OSPAR North Sea Fish Community EcoQO. Reductions in LFI are therefore considered detrimental. Changes in LFI were generally inversely correlated with changes in the abundance, biomass and (growth) productivity of the fish community implying that declining abundance, biomass and productivity are indicative of a fish community returning to a more natural state. The von Bertalanffy growth equation makes it clear that larger fish, closer to their ultimate body length (L8), have lower daily specific growth rates. Large fish exert a strong predation loading on small fish abundance. Since trophic transfer efficiency is around 10%, every kg of production by larger fish requires 10kg of production in their smaller prey fish populations. Specific growth rates among smaller fish are approximately twice that of larger fish, so 5kg of prey fish are required to support every kg of larger fish. Reductions in the abundance of larger fish, with the consequent reduction in predation loading on smaller prey fish, would therefore tend to result in a rapid increase in the abundance and biomass of small fish; a typical trophic cascade effect.

To date, OSPAR has largely been responsible for the development of an ecosystem approach to the management of marine natural resources within the convention area. Ten Ecological Quality Issues have been identified, with the intention of setting Ecological Quality Objectives (EcoQOs) for each issue. Since 2000, this scheme has been developed and piloted in the North Sea. Fish Communities is the fifth in the list of Ecological Quality Issues, and is considered to be one of three community-level issues. In addressing concerns regarding anthropogenically induced change in fish communities therefore, a communitylevel approach has been widely adopted. This has generally involved the application of univariate metrics to groundfish survey data to quantify change in various aspects of the community’s composition, structure and function. The element of Ecological Quality for the North Sea fish community focuses on “changes in the proportion of large fish and hence the average weight and average maximum length of the fish community”, thus clearly identifying the need for a community size composition metric as the “indicator” on which to base an EcoQO for the “fish community” Ecological Quality Issue. The chosen metric, the Large Fish Indicator (LFI) was eventually defined as “the proportion by weight of fish greater than 40cm in length”, based on ICES first quarter (Q1) International Bottom Trawl Survey (IBTS) data. The LFI was intended to be an indicator of the “general health” of the demersal fish community. Indeed DEFRA have adopted the LFI as a means of monitoring change in the trophic structure of demersal fish communities, since in marine systems, ontogenetic change and inter-specific variation in diet is so strongly linked to predator body-size. However, other aspects of the composition, structure and functioning of fish communities, such as abundance, biomass, productivity, species richness, species diversity and mean life-history trait composition, can also be summarised using univariate metrics. Any one, or all, of these alternative metrics might also be considered to be indicative of the “health” of fish communities. The LFI was chosen ahead of these alternative metrics because it was believed to be particularly sensitive to variation in fishing pressure, and therefore to indicate directly the effect of fishing on the state of the fish community. But this raises the question as to whether one indicator is sufficient to inform on the general health of the demersal fish community, or is a suite of indicators necessary in order to provide information on various different aspects of a community’s composition, structure and function? In this assessment of the state of the demersal community in UK waters, fifteen univariate metrics are applied to groundfish survey data to quantify changes in five main aspects of community composition, structure and function: abundance/biomass/productivity; size composition; species richness; species diversity; and life-history trait composition (Table 1). Bottom trawl surveys have been carried out as part of the traditional annual fisheries management process for several decades. These surveys routinely provide point estimates of the abundance at length of each species sampled; therefore providing the ideal data sets for the application univariate community metrics. Many of these surveys have run for two or three decades now, providing appropriate time series with which to evaluate changes in the composition, structure and function of fish communities. Furthermore, most coastal European nations have been involved in survey activity, providing data from most western continental shelf waters. In this assessment, otter trawl survey data is analysed to assess changes in the demersal fish communities present in the sea area that constitutes the UK’s Exclusive Economic Zone (EEZ). The UK EEZ has been divided into nine principal subregions (Figure 1), and assessment of the state of the fish community in each sub-region was required. However, one of the sub-regions, the Scottish Continental Shelf, straddled the boundaries between OSPAR Regions II and III, and between ICES area IV and VI. Consequently, none of the groundfish surveys, which are normally aligned with the ICES designated marine regions, covered the entire Scottish Continental Shelf sub-region. A single assessment for the Scottish Continental Shelf was therefore not possible. The subregion had to be further sub-divided in line with the data available for analysis, and three Assessment of the “State” of the Demersal Fish Communities in UK Waters 2 separate assessments made for the southwestern and northeastern sectors of this large area (Figure 1). To assess the state of the demersal fish community and make a judgement on the changes observed, it was necessary to decide what constituted “beneficial” and “detrimental” change. Emphasis is generally placed on conserving and restoring biodiversity; implying that declines in species diversity (both richness and evenness) are detrimental. The converse was therefore also assumed to hold. The life-history trait composition responses of populations and communities to anthropogenically raised levels of mortality have recently received considerable attention. Declines in population age and length at maturity, decreased community average ultimate body length, and increased in community average growth rate are all considered to be detrimental consequences. Improved management would therefore be expected to induce the opposite, beneficial trends. Established population dynamics theory predicts that size-related fishing mortality reduces the mean size and proportion of large fish in exploited populations (including non-target species taken as by-catch). This concept underpins development of the LFI as the basis for the OSPAR North Sea Fish Community EcoQO. Reductions in LFI are therefore considered detrimental. Changes in LFI were generally inversely correlated with changes in the abundance, biomass and (growth) productivity of the fish community, implying that declining abundance, biomass and productivity are indicative of a fish community returning to a more natural undisturbed state. The von Bertalanffy growth equation makes it clear that larger fish, closer to their ultimate body length (L8), have lower daily specific growth rates. Large fish exert a strong predation loading on small fish abundance. Since trophic transfer efficiency is around 10%, every kg of production by larger fish requires 10kg of production in their smaller prey fish populations. Specific growth rates among smaller fish are approximately twice that of larger fish, so 5kg of prey fish are required to support every kg of larger fish. Reductions in the abundance of larger fish, with the consequent reduction in predation loading on smaller prey fish, would therefore tend to result in a rapid increase in the abundance and biomass of small fish; a typical trophic cascade effect. In assessing the state of the demersal fish community, two questions were addressed. Firstly, how has the state of the community changed over the last decade, from 1999 to 2008; the period of particular interest to the current report. Secondly, how does the state of the community over the period 2004 to 2008 (i.e. now) compare with that prevalent during the eight-year period when data were first available for analysis. Detrimental trends were assigned a “red” colour code and beneficial trends “green” (e.g. Table 2). Where no discernable trend was apparent, an “orange” colour code was applied. Five separate aspects of composition, structure and function of the demersal fish community were considered, and a judgement was made based on the trends observed in the 15 univariate community metrics applied to the groundfish survey data. Linear regression was used to make an assessment of metric trends over the last decade. In comparing the current situation with the earlier “reference period”, mean metric values over the period 2004 to 2008 were determined and the assessment was scored red or green depending on whether the recent mean value differed by more than one standard deviation either side of the mean value determined for the earliest possible “reference period”.

An outbreak of infectious salmon anaemia (ISA) in the Scottish Shetland Islands during 2008/9 is described during which six sites were confirmed ISAV positive. Spread of the virus via movement of fish between marine sites, harvest vessels, movements of smolts and wild fish appear to have been of little or no importance. The spread is associated with hydrodynamic currents, although local intra-company activity may have caused some spread. The application of a statutory control strategy by Marine Scotland, based on the use of its established model (Anon 2000) has apparently limited the occurrence and economic impact of ISA to management area 3a; however spread within this area has been extensive. This localised waterborne spread is in contradiction to a previous outbreak in 1998/9 which was spread over a wide geographic area by transport of fish and harvest vessels. The development of industry codes of practice and good biosecurity procedures, following the 1998/9 outbreak, that limited marine site-to-site movement of live fish and improved disinfection of vessels and processing plant waste, may explain why the 2008/9 spread of infection was localised. Depopulation of confirmed sites is a key element of eradication and this was achieved within 7 weeks of confirmation, although the last confirmed case suggests subclinical infection may persist undetected for months. The potential sources of ISAV infection that were investigated did not determine the origin of the 2008/9 outbreak. Local evolution from an avirulent strain of ISAV; importation of ova; or association with movement of equipment could have caused the outbreak. The virus responsible for the 2008/9 outbreak belongs to a different genogroup (group 1) to the 1998/9 virus (group 3). The intensive cultivation of salmon farming, close proximity of sites and historic absence of synchronous fallowing of management areas is considered to have increased the risk of disease outbreaks and their re-emergence, such as ISA in the Shetland Islands. A policy of synchronous fallowing and stocking of sites within management area 3a is being considered by industry in consultation with Marine Scotland to address this risk. Where movement of fish occurs between sites in 1 different management areas, this represents the greatest risk of regional-scale spread of diseases such as ISA. Controls appear to have been effective in minimising that risk.

Halogenated persistent organic pollutants [chlorobiphenyls (CBs), polybrominated diphenyl ethers (PBDEs) and hexabromocyclododecane (HBCD)], along with total lipid, were measured in the liver and muscle of two species of deep water fish (black scabbard and roundnose grenadier) collected from the Rockall Trough, to the west of Scotland, during 2007. The data was compared with that obtained from a similar survey conducted in 2006, and which has recently been published. CB concentrations (SICES7 CBs) greater than 500 µg kg-1 lipid weight were found in 5 of the 30 deep water fish liver samples and 8 of 30 fish muscle samples collected in 2007. Non-ortho CBs (CB81, 77, 126 and 169) were measured in samples with the highest ortho CB concentrations but were not detected in any of the fish muscle or liver samples collected in 2007. Data was assessed using the assessment criteria adopted by OSPAR for use in the 2008 Coordinated Environmental Monitoring Programme (CEMP) assessment and Quality Status Report 2010 and incorporated into a traffic light system. Concentrations were compared to Background Assessment Concentrations (BACs; blue/green transition) and Environmental Assessment Criteriapassive (EACpassive; green/red transition). Concentrations for the individual ICES7 CBs in fish liver were above OSPAR BACs in both species sampled in 2007. The EACpassive was exceeded for CB118 only. As all other CBs were below the EACpassive, CB concentrations in deep water fish were classed as ‘green’. Measured (calculated for the five mono-ortho CBs) and estimated (calculated using published models) Toxic Equivalent (TEQ) concentrations in the fish muscle indicated that consumption of deep water fish muscle is unlikely to represent a risk to human health. PBDEs were detected in both the liver and muscle of the deep water fish collected in 2007. However, concentrations were low with many congeners being below detection limits. HBCD was not detected in any of the Scottish deep water fish collected in 2007. Halogenated persistent organic pollutants were detected in Scottish deep water fish, confirming that these contaminants are transported to the Scottish deep water environment. However, the CB concentrations found are unlikely to give rise to pollution effects and are not of concern from the perspective of human health. PBDE concentrations could not be assessed, due to the lack of assessment criteria. Furthermore there is only very limited data on PBDEs in deep water fish. However, the concentrations observed in this study were similar to the concentrations recently reported in Mediterranean deep water fish.

By 1997 sandeel abundance on the Wee Bankie was already depressed as a result of fishing activities, and continuation of the fishery up to 1999 caused further declines. As a precautionary measure to safeguard marine top predators, particularly seabirds at internationally important colonies in and around the Firth of Forth, an area off the east coast of Scotland, from Rattray Head to St Abbs, was closed to industrial fishing for sandeels in 2000. High levels of recruitment in 1999 and 2000, combined with a lack of any significant fishing activity in 1999, resulted in an immediate and substantial increase in the biomass of sandeels on the Wee Bankie grounds in 2000; the first year of the sandeel closure. Since 2001, sandeel biomass has steadily declined to levels in 2007 that were similar to those observed in 1997 and 1998 when the sandeel fishery in the area was active. In the absence of sustained recruitment, consumption by marine top predators, along with other causes of natural mortality, have exceeded growth production in the population. Closing the area to fishing has not been sufficient to ensure high abundances of sandeels in the area. Recruitment of young sandeels, at or above long-term average levels, is also necessary, and since this is primarily governed by natural process, this may be beyond the capacity of fisheries management alone to achieve. Variation in the abundance and feeding ecology of gadoid predators in the study area was unrelated to variation in sandeel abundance and so remained unaffected by closure of the fishery. Numbers of guillemots, razorbills, puffins and kittiwakes recorded at sea in the study area all appeared to increase with closure of the fishery, and then subsequently to decline again as local sandeel abundance declined. The increase in auk abundance at sea may well have resulted from an influx of non-breeding birds. Only the breeding performance of kittiwakes at the Isle of May appeared related to variation in local sandeel abundance. Simply closing offshore areas close to top predator colonies may not be sufficient to guarantee the long term prospects of predators at these locations.

Trawling and tank based trials were conducted to assess whether electrofishing (which is currently prohibited under EU regulations) for razor clams Ensis siliqua and E. arquatus affects survival and behaviour patterns in Ensis spp. and non-target species. Boat trials in a number of areas identified that the main non-target species most likely to be affected by this fishery are starfish species, crab species (predominantly hermit crabs), flatfish and sandeels. No mortalities were recorded as a direct result of the fishing equipment or electric field generated and any induced behavioural responses in non-target species were exhibited for a maximum of 10 minutes following exposure. However, during this time stunned animals may be vulnerable to predation. Tank trials indicated that exposure to an electric field typical of that generated through electrofishing by the vessels involved in this project did not affect short term (5 days) survival in razor clams, surf clams, starfish or hermit crabs. These results suggest that electrofishing for razor clams does not have immediate or short term lethal effects, or prolonged behavioural effects, on vertebrate or invertebrate species exposed to the electric field generated. Further research is required to determine medium and long term effects. However, as electrofishing has a very low short term impact on non-target species and the seabed it warrants consideration as a viable fishing method for the commercial razor clam fishery in Scotland within sustainable limits. This project set out to examine the electrofishing process and the potential localised effects on associated fauna. The study did not address the broader question of long term sustainability of razor clam populations under various levels of commercial fishing activity. This report does not offer any advice on the amount of fishing effort which could be applied in the different areas supporting razor clam populations. The authors recognise the need for such assessments to take place and recommend that the next stage should be quantitative assessments of stock size towards the development of a sustainable fishery scaled to the size of the resource.

The established modelling approach to estimating collision risk employed in environmental assessment of wind farms (the Band model) was developed by Band in 2000, updated in 2007 and has since been updated for use in the marine environment (Band 2012). For seabirds this now includes flight height distributions to further refine collision estimates. For this study, UK seabird and non-seabird species populations potentially at risk from collision with turbines at Scottish offshore wind farm sites were shortlisted, proportions of the populations likely to pass the wind farm sites estimated and collision risk modelling performed. Wind farms out-with Scottish waters are not considered, neither are the impacts of displacement and barrier effects, nor are in-combination effects with ‘wet’ renewables and other activities, nor impacts on populations outside of migration periods. In total, modelling was carried out for 27 species of seabirds and 38 non-seabird species. For seabirds, modelling sensitivity analysis was performed by assuming different migratory corridors and distributions within those corridors and species specific flying height distributions. It was not possible to apply a similar approach for non-seabird species, as their migration routes are typically less well known. A number of assumptions were made in the analyses, including on migratory routes and bird distributions within those routes, flight heights and turbine avoidance rates (98% was used for all species). In addition, where contemporary population estimates were not available the analyses made use of historic population counts. The resulting outputs are sensitive to those assumptions, and for most species improvements in the reliability of the estimates presented will require efforts to improve understanding of migration routes and avoidance rates. Seabird collision mortality estimates were dependent on the proximity of passage routes to shore and the distribution (even or asymmetrical) of birds across the migration corridors. Collision mortality estimates were assessed in relation to an indicative threshold value of 1% of the passage population.Modelling estimates for two seabird species – great black-backed gull and herring gull, had collision mortalities of over 1% of the migrant populations (the latter were derived using the flight height collision model ‘Option 3’). When the Option 1 collision model was applied six species had maximum total collision estimates which exceeded 1% of the passage populations: cormorant; common gull; lesser black backed gull; herring gull; great black-backed gull and common tern (derived using the far offshore coastal strip and uniform flight distribution). It should be noted that the 1% value has been used as an indicative threshold to guide interpretation and does not have a specific biological basis. Notwithstanding the assumptions, risks and caveats outlined above, this report’s primary value will be informing large-scale indicative strategic assessments. Overall, birds on migration through Scottish waters are not considered to be at risk of significant levels of additional mortality, due to collisions with Scottish offshore wind farms. Possible exceptions are large gulls, cormorant and common tern.

By 2020 the percentage of Scotland's energy coming from renewable sources will increase. Studies have identified that there is a need to research how offshore renewable developments affect wildlife populations. The surveys presented here will help to find out how one area of marine development, the west coast of Lewis, is used by waterbirds and marine mammals. Areas close to the Isle of Lewis have already been identified as being important for these groups of animals, through the Special Protection Areas (SPA) network.

A key concern expressed by policy makers, regulators and environmental stakeholders about deployment of marine energy devices in open waters relates to the possibility of negative impacts they may have on marine mammals and diving birds. The potential for direct collision with such devices, or harmful effects caused by their presence, including the potential for displacement of marine wildlife from habitual waters, are issues which need to be addressed. In order to get as accurate a picture as possible about the presence and behaviour of marine wildlife in the vicinity of operating devices, data needs to be collected both underwater and at the sea surface. The current wildlife observation programme underway at the European Marine Energy Centre (EMEC) in Orkney gathers surface-visible wildlife information across EMEC?s grid-connected and nursery test sites, and the data gathered can be used to inform regulatory decisionmaking, as well as in guiding developers? device-specific wildlife monitoring programmes. Activities of the wildlife observation programme underway at EMEC are overseen by the EMEC Monitoring Advisory Group (MAG), whose membership includes representatives from Marine Scotland Science, Marine Scotland Licencing Operations Team, Marine Scotland Compliance, Scottish Natural Heritage, Scottish Government, and the Sea Mammal Research Unit at the University of St Andrews. The Billia Croo wildlife observation project commenced in July 2005, with the Scottish Government funding the current contract. During the period 1 April 2013 to 31 March 2014, a total of 886 hours of observations were completed. Observations at the site for this reporting period have shown seasonal peaks in grey and harbour seal abundances corresponding with pupping seasons, which is mirrored in the data collected to date at the site. During this reporting period the majority of cetacean sightings have been of White-beaked Dolphin, whereas typically the most sighted cetacean is Harbour Porpoise. A typically diverse range of marine birds has also been observed, although for several species, numbers in April and May 2013 fell below the mean. This could be due to the enduring winter of 2012/2013 and resultant late spring experienced in Orkney as was the case for the rest of the UK. Detailed analysis of the data collected is outwith the scope of this project; however a separate project, funded by Marine Scotland and Scottish National Heritage, has been established to carry out an in-depth analysis of the data.

A key concern expressed by policy makers, regulators and environmental stakeholders about deployment of marine energy devices in open waters relates to the possibility of negative impacts they may have on marine mammals and diving birds. The potential for direct collision with such devices, or harmful effects caused by their presence, including the potential for displacement of marine wildlife from habitual waters, are issues which need to be addressed. In order to get as accurate a picture as possible about the presence and behaviour of marine wildlife in the vicinity of operating devices, data needs to be collected both underwater and at the sea surface. The current wildlife observation programme underway at the European Marine Energy Centre (EMEC) in Orkney gathers surface-visible wildlife information across EMEC’s grid-connected and nursery test sites, and the data gathered can be used to inform regulatory decisionmaking, as well as in guiding developers’ device-specific wildlife monitoring programmes. Activities of the wildlife observation programme underway at EMEC are overseen by the EMEC Monitoring Advisory Group (MAG), whose membership includes representatives from Marine Scotland Science, Marine Scotland Licencing Operations Team, Marine Scotland Compliance, Scottish Natural Heritage, Scottish Government, and the Sea Mammal Research Unit at the University of St Andrews. The Fall of Warness wildlife observation project commenced in July 2005, with Scottish Government funding current contract. During the period 1 April 2013 to 31 March 2014 a total of 909 hours of observations were completed. Observations at the site for this reporting period have shown seasonal peaks at the site in grey and harbour seal abundances corresponding with pupping seasons, which is mirrored in the data collected to date at the site. The majority of cetacean sightings during this reporting period have been white-beaked dolphins, whereas typically the most sighted cetacean is harbour porpoise. A typically diverse range of marine birds has also been observed, although for several species numbers in April and May 2013 fell below the mean. This could be due to the enduring winter of 2012/2013 and resultant late spring experienced in Orkney as was the case for the rest of the UK. Detailed analysis of the data collected is outwith the scope of this project; however a separate data analysis project, funded by Marine Scotland and Scottish Natural Heritage, has been established to carry out an in-depth analysis of the data.

This project was undertaken in the context of the National Research and Monitoring Strategy for Diadromous Fish (NRMSD) to investigate the potentialfor interactions between diadromous fish and wind, wave and tidal renewable energy developments. By canvassing Scotland’s geographical area, the SFCC believe that the absolute spatial coverage of smolt monitoring locations has been identified. Datasets identified from 13 organisations at 31 locations were requested, resulting in the provision of these datasets. During the project, the fish species scope was expanded to include trout after initially being focused on Atlantic salmon. A total of 126,368 individual fish length measurements and a further separate dataset featuring 292,427 smolt counts were provided. While the majority of smolt trapping was found to occur using rotary screw trap methods, a range of alternative strategies are deployed. Data recording procedures and resolutions were found to vary significantly between organisations and in some cases within organisations. Temporal coverage is also variable with information becoming increasingly limited before 2006. The largest dataset spans 37 years, that of Spey Dam currently operated by Spey Foundation. Out of 31 sites 16 featured individual fish length (1mm) measurements and 2 featured 5mm and 10mm categorical fish length measurements. The remaining 13 datasets were provided as total fish count level observations. 18 of 31 smolt monitoring sites are operated on river main stems, with the remainder on 2nd order tributary rivers. While data are provided in a standard format, considerations relating to crosscompatibility remain specifically around the means by which recordings are made where; fishing did not occur, fishing did occur without the trap being checked, and fishing did occur with the trap being checked resulting in a catch of 0. Strategies for recording the beginning and end of the trapping season also exhibited varied approaches, a caveat which should be considered during further analysis. Further work is recommended to fully quantify the availability of data collected on other fish species captured (while smolt monitoring) and that of river flow and water temperature. Pending analysis by Marine Scotland Science, this collaborative approach may have provided data collected at a local catchment scale, which is also capable of informing research of a national-scale. With 6 organisations reporting the installation of new smolt traps in 2014, the spatial coverage of this dataset will further increase.

This report examines utility of assigning fish to river in Scotland using Single Nucleotide Polymorphic (SNP) markers. The analysis has shown that, depending on baseline coverage, it is possible using SNP markers to be able to assign fish to both region, and where baseline coverage is sufficient, river with high accuracy in most, but not all, situations investigated. Exclusion techniques have also been examined as to their effectiveness in screening out fish from reporting regions not represented in the baseline. The procedures developed and outlined here show a multi-stage process can be employed to assign fish to origin. Firstly fish are assigned to a regional reporting unit. Fish from rivers not represented in the baseline within regional reporting units of interest are then excluded from the analysis, before finally fish are assigned to their river of origin. It has been shown that this can be achieved in most cases analysed with high accuracy (i.e. from 90 to 100 %), although there are situations where differentiating between rivers is problematic (Spey/Dee and rivers within the Kyle of Sutherland). The study has also identified areas where further SNP baseline coverage is required associated with both regional and river level SNPs. Regional coverage of particularly the north and west requires enhancing as do rivers of particular interest on the East coast.

Marine Scotland Science (MSS) prepared a scoping report of the research requirements for Atlantic salmon, sea trout and European eel in the context of offshore renewables (Malcolm et al, 2013). This report was intended to inform the development of a National Research and Monitoring Strategy for Diadromous Fish (hereafter NRMSD) to investigate the potential for interactions between diadromous fish and wind, wave and tidal renewable energy developments. To ensure that the NRMSD had broad sectorial support, meetings were convened to identify and discuss priority areas. There was general agreement on information requirements between the stakeholder groups. The following areas were considered priorities: Fish Distribution, Population Status, Response to noise, Effects of electromagnetic fields Risk of collision. Future engagement events will be convened at suitable stages in the development of the National Research and Monitoring Strategy for Diadromous Fish.

The workshop on “The Science Of Deepwater Oil Spills – Modelling” held in Aberdeen in September 2013 included more than 50 experts drawn from academia, government, consultants and industry to discuss aspects of the science needed to respond in an effective way to a deepwater oil spill west of Shetland. Experts in oceanography, circulation modelling, oil dispersion modelling, oil spill response and deepwater ecology were present. Throughout the four sessions of the workshop, certain themes and ideas were repeated by the participants. These have led to a series of recommendations being made, which are discussed in the report.

Our understanding of the effects of underwater noise and other disturbing activities on marine mammals, and of how to assess and quantify potential impacts, is rapidly evolving. The Steering Group for the Interim PCoD work emphasise that this framework is very much an interim measure, that is, the Interim PCoD approach has been developed to help developers, regulators and advisers working on offshore renewable energy projects now. It is expected that the framework will be further refined and built upon over time as more evidence becomes available. The Interim PCoD approach should be regarded as another tool among others already available for assessing potential impacts of disturbance on marine mammal populations. How appropriate it will be for use with particular projects and situations should be decided on a case by case basis. It is important that developers considering using the Interim PCoD approach seek advice from the SNCBs and/or regulators at an early stage.

Please note that the model code has been updated since this release. See http://dx.doi.org/10.7489/1995-1

The purpose of the Saltire Prize is to stimulate innovation that will lead to delivery of commercial scale wave or tidal stream energy technology. Competitors for the Saltire Prize, of £10 million, must demonstrate commercially viable wave and/or tidal energy technology in Scottish waters that achieve a minimum electrical output of 100 Giga-Watt hours (GWh) over a continuous 2 year period, ending no later than 30 June 2017 (the Prize Competition Period). An earlier study identified the Pentland Firth and Orkney Waters as a prime location for wave and tidal renewable energy development. The Crown Estate subsequently held a leasing round in this area, and on 16th March 2010 announced that companies had been awarded agreement for lease for 1200 MW of projects. This announcement opens up the possibility of further areas being made available for lease for wave and tidal energy projects and is primarily aimed at potential Saltire Prize competitors. The Scottish Government and The Crown Estate have been working in partnership to identify these further areas. This document, by Marine Scotland (part of the Scottish Government), summarises how these proposed areas were identified, as the basis for inviting comments on the suitability and attractiveness of the areas for wave and tidal energy project development and achievement of the Saltire Prize. Following discussion on the proposed areas, the Scottish Government and The Crown Estate intend to finalise areas for lease in a further Scottish leasing round for wave and tidal energy projects.

The OSPAR ICES Study Group on Ocean Acidification (SGOA) and the Global Ocean Acidification Observing Network (GOA-ON) have both identified the need for a commitment to long-term monitoring at sites in coastal and inshore waters to distinguish long-term anthropogenic signals from short-term spatial and temporal variability. 2. Limited monitoring of the changes in ocean acidification is undertaken in coastal waters around the UK. A short UK Integrated Marine Observing Network (UK-IMON) demonstration study was commissioned to monitor coastal waters for the first half of 2013 for the carbonate chemistry parameters, Total Alkalinity (TA) and Dissolved inorganic carbon (DIC). 3. The project was divided into two distinct parts, namely a preliminary feasibility study, to examine the use of moored water samplers to collect water samples for the analysis of dissolved inorganic carbon (DIC), and discrete sampling at various locations around the UK for Total Alkalinty (TA) and DIC analysis. 4. Automated water samplers deployed on existing instrumented moorings may provide a cost effective means of collecting water samples for monitoring ocean acidification in coastal waters and a preliminary assessment of the utility of an automated water sampler for monitoring DIC was undertaken. A small but statistically significant difference was found between the concentrations of DIC measured in water samples collected simultaneously using an automated water sampler and rosette samples. At the present time it is not possible to determine whether this difference is due to the way samples are collected by the automated sampler or small differences in the way the two sets of samples were processed. 5. The authors recommend that a further, more detailed comparison should be undertaken to include a moored sampler with sample preservation. The introduction of a procedure to minimise aeration of samples during processing and filtration, together with any effect of long-term (weeks) storage of samples (during automated sampler deployment) on sample integrity should also be investigated.

The marine environment acts as a sink for many hazardous substances, including persistent organic pollutants (POPs) and trace metals. Many of these compounds are toxic, persistent, bioaccumulative and can be prone to long range transport. Their sources and pathways into the marine environment are diverse with most hazardous substances being produced by anthropogenic activities. Some are, or have been, produced intentionally (such as brominated flame retardants, BFRs) whilst others are by-products of industrial processes (such as polycyclic aromatic hydrocarbons (PAHs) and dioxins). Direct or indirect release to rivers, from industrial discharges and from sewage works discharges, are a major source of a range of hazardous substances. Historically the biggest sources of hazardous substances to the Scottish environment were from heavy industry (steelworks, mining and gasworks), however, increased regulation and closure of some of these industries has reduced contaminant inputs from these sources. Run-off from urban areas and atmospheric deposition continue to be diffuse sources of hazardous substances to the marine environment. Due to the persistent nature of many hazardous substances, high concentrations can still be found in the sediments of industrialised and urbanised estuaries as a result of historical inputs. A number of POPs and trace metals have been highlighted as a cause for concern and have been the subject of extensive study and international regulation. Some contaminants have been monitored for many years and are often called legacy contaminants. Legacy contaminants include trace metals, polycyclic aromatic hydrocarbons (PAHs) and chlorobiphenyls (PCBs) but are still of concern, despite reductions in inputs, as they persist in the marine environment for many years. Others have only recently been highlighted as cause for concern and added to monitoring programmes and are often referred to as emerging contaminants. Examples of emerging contaminants are short chain chlorinated parrafins (SCCPs) and perfluorinated compounds (PFCs). Attempts have been made to create emission inventories for a number of hazardous substances. Breivik et al.1 created a global emission inventory for PCB congeners and Prevedouros et al.2 estimated a European consumption and atmospheric emissions inventory for pentabromo diphenyl ethers. This review is an update of the review undertaken in 20043 by Marine Scotland to identify the hazardous substances monitoring requirements, what hazardous substance data is currently held for the Scottish marine environment and identify any gaps in information that may require further monitoring or method development.

Identification of decapod crustacean larvae can be a difficult task. These taxa present complex life cycles with the presence of several morphologically different phases. In addition, the different phases will each pass through several morphological stages, although these differ little from each other compared with the differences between phases. Complete larval descriptions are not available for some species (e.g. some species belonging to family Paguridae) or in other cases, the information available is not enough to provide an accurate identification of the specimen; such is the case for Liocarcinus species and other polybiinae larvae. Another source of difficulty is that some bibliographic references necessary to identify decapod larvae are dispersed and sometimes restricted to specific areas or species groups. In addition to this, some species have been ascribed in the past to other species or genera, making it more difficult to compile all the references available for the species of interest.

1. High Performance Liquid Chromatography (HPLC) is an alternative method to light microscopy and fluorescence for characterising phytoplankton. The HPLC data provides valuable information about the contribution of different functional groups to the biomass of the phytoplankton community. The HPLC data should be supported by microscopic verification as many algal classes share the same pigments.

2. A quantative HPLC method was developed to quantify chlorophyll a and chlorophyll b. However, due to a lack of commercially available standards at suitable concentrations, only area % data is given for 19 hexanoyloxyfucoxanthin, alloxanthin, alpha-carotene, antheraxanthin, beta-carotene, chlorophyll c2, chlorophyll c3, diadinoxanthin, diatoxanthin, fucoxanthin, gyroxanthin-diester, lutein, neoxanthin, peridinin, prasinoxanthin, violaxanthin and zeaxanthin.

3. Ammonium acetate buffer (0.5 mol l-1) is added to the standards and samples immediately before injection, in order to increase the affinity of the pigments for the column during the loading step. This reaction is temperature dependant and must be carried out at ambient temperature to ensure adequate mixing.

4. The stability of the pigments, in the autosampler at ambient temperature, whilst awaiting injection for a typical analytical run, was investigated. All pigments were found to be stable in the autosampler for 18 hours. A typical analytical batch takes 15 hours of analytical time.

5. Replicate analysis for high standards and samples and low standards and samples on different days gave %CV of <11% for both chlorophyll a concentration and chlorophyll b concentration. This meets the limits for reproducibility given in the UK Clean Seas Environmental Monitoring Programme (CSEMP) Green Book. 2

6. The limit of detection (LOD) was calculated to be 0.1 µg l-1 for chlorophyll a and 0.02 µg l-1 for chlorophyll b. This meets the limits for LOD given in CSEMP Green Book.

7. Recovery for chlorophyll a was calculated to be 105%, and 110% for chlorophyll b, which meets the limits set by the United Kingdom National Marine Chemistry Advisory Group (NMCAG).

The Scottish Government has ambitious targets for renewable energy production, to which offshore renewables could make a substantial contribution. However, the new marine energy industries must develop on a sustainable basis, ensuring that environmental impacts are assessed, and if necessary, minimised through appropriate mitigation. The likelihood of any impacts on Atlantic salmon, sea trout or European eels will depend on interactions between (1) migratory routes and behaviour (2) the distribution of offshore developments (3) the technologies deployed and (4) the dynamics of the relevant fish populations. This report summarises available information on the migratory routes and behaviour of salmon, sea trout and eels in a Scottish context.

Broad scale patterns of migration are identified for adult Atlantic salmon, although the resolution of available data is unlikely to be sufficient to inform site specific risk assessment. Less extensive information is available on juvenile migratory routes and no information is available on juvenile migration from important east coast rivers. The limited information available on sea trout migration suggests predominantly inshore and local use of the marine environment, although wider ranging migrations have been observed from some rivers. No specific migratory routes can be discerned for either juvenile or adult sea trout. European eels in Scotland are part of a single European population for which there is considerable uncertainty regarding migratory routes. The limited evidence which is available suggests that eels from a number of European countries may migrate through Scottish waters. For all the species considered, there is only very limited information on behaviour and swimming depths. Most of this information has been generated outwith Scotland and it is uncertain whether it can be reliably transferred to the Scottish context given differences in the life stages observed and local geography.

Significant knowledge gaps remain for all three species considered in this review. These knowledge gaps should be considered as part of an overall assessment of research needs in relation to offshore renewable developments and diadromous fish.

Many planktonic algae produce biotoxins that can affect grazer feeding, mortality and recruitment rates, or alter swimming behaviour and therefore predation risk. This report reviews the literature on the effects of algal biotoxins (excluding cyanobacteria) on pelagic copepod biology, focussing on copepod species that are important in Scottish waters.

Marine Scotland Science currently holds more than 10 years inshore coastal monitoring data on the occurrence of toxic phytoplankton and corresponding zooplankton species from the Stonehaven and Loch Ewe monitoring sites, and these data are summarised.

The relevant biotoxins that could influence copepod population dynamics in Scottish waters are identified as poly-unsaturated aldehydes from diatoms, and toxins associated with paralytic shellfish poisoning (Alexandrium spp.), diarrhetic shellfish poisoning (Dinophysis spp.) and amnesic shellfish poisoning (Pseudo-nitzschia spp.). There is potential for these Scottish field data and further experimental studies to provide insights into the way that interspecies relationships and energy flow in food webs can be affected by the production, transfer and effects of algal biotoxins.

There are concerns about the environmental impact of aquaculture to the seabed close to fish farm cages, including potential effects from persistent organic pollutants and trace metals. Samples of sediments from aquaculture areas in the Western Isles (3 sea lochs), the north-west coast of Scotland (3 sea lochs) and from the Shetland Isles (3 sea lochs or voes) were collected in 2005 and 2006 and concentrations of persistent organic pollutants (polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs)) and trace metals (copper and zinc) were determined.

The results indicate that any impact on the environment from organic pollutants or trace metals is of a local nature. Concentrations of PCBs are below the EAC (environmental assessment criteria) for all bar one congener in one sample, and below the BAC (background assessment concentration) for most. Although slightly elevated Cu and Zn concentrations were measured in sediments from <330 m from some farms, concentrations in sediments outwith the 25 m AZE (allowable zone of effect) were below those that cause benthic effects. Only the farms in Loch Shell, Loch Greshornish and Loch Kishorn had concentrations for Cu and Zn which might cause adverse affects in the environment, and all of these samples were from within 25 m of the cages.

Of the individual lochs, sediments from Loch Shell, Loch Kishorn and Swinister Voe had Total Organic Carbon (TOC) inversely proportional to particle size (% <63 µm fraction) with the TOC highest at the cage edge, suggesting a measure of organic enrichment below these cages. TOC was proportional to particle size (% <63 µm fraction) for the other fish farms in the study, suggesting that there was no organic enrichment at these fish farms. BACs were exceeded for two thirds of the sites, though not for all congeners.

BACs were not exceeded for any congeners in any sites in Collafirth Voe. Concentrations were below the EAC for all except one site, at the head of Loch Ewe, where CB52 was above the EAC. Therefore, the PCB concentrations in these sea lochs would be considered to be unlikely to give rise to unacceptable biological effects.

There was no correlation between the PBDE concentrations and distance from the fish farm cage. The PBDE concentrations (sum of 9 congeners, excluding BDE209) were comparable to those of a New Brunswick, Canada, fish farm. There are as yet no assessment criteria for PBDEs therefore the significance of the concentrations could not be assessed. Only trace amounts of PBDEs were found in Collafirth Voe, Sandsound Voe, Swinister Voe and Loch Ewe (north) and for all other sea lochs in the study the concentrations are comparable with those found at remote sites around Scotland and comparable with the lower end of concentrations found in the more industrialised Firth of Clyde. Concentrations are significantly less than the concentrations from the former sewage sludge dump site at Garroch Head.

Concentrations of Cu and Zn were highest closest to fish farms and decreased with increasing distance from the fish farm. Concentrations between the lower and upper sediment quality criteria (SQC) for sites within the allowable zone of effect (AZE) indicate benthic effects which are potentially problematic. Only samples from within the AZE of Loch Greshornish and of Loch Shell had concentrations within the potentially problematic region for Zn and in Loch Shell, Loch Kishorn and Swinister Voe for Cu.

Concentrations of hazardous substances, including polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), polybrominated dipheyl ethers (PBDEs) and the metals cadmium (Cd), mercury (Hg) and lead (Pb), were determined in sediment and biota from around Scotland. The concentrations were investigated using assessment criteria developed by OSPAR and ICES.

PAH and PCB concentrations in sediment and biota in all Scottish regions, except the Clyde, are unlikely to give rise to pollution effects.

Lead concentrations in the Clyde and Moray Firth sediment are of concern and may give rise to pollution effects. Concentrations of Cd in deep water fish liver from Rockall were above the EC maximum level and, therefore, may be of concern from the perspective of human health.

Concentrations of PBDEs observed in Scottish sediments were low with all congeners below the limit of detection (LoD; 0.03 µg kg-1 dry weight) in 140 out of a total of 307 samples analysed. Higher concentrations were found in fish liver, although concentrations were low in all regions except the Clyde. The environmental significance of these concentrations could not be assessed due to the lack of suitable assessment criteria.

Organic contaminant concentrations (PAHs, PCBs and PBDEs) in sediment, and also fish liver for PCBs and PBDEs, were significantly higher in the Clyde compared to all other regions. Within the Clyde highest PCB and PAH concentrations were associated with known point sources such as the former sewage sludge dump site at Garroch Head, the dredge spoil dump site at Cloch Point and the former naval base at Holy Loch.

Modelled Toxic Equivalent (TEQ) concentrations indicated that in all Scottish regions, including the Clyde, PCB concentrations in fish liver are unlikely to result in any risk to human health.

Few trends were detected in contaminant concentrations in biota or sediment at any Scottish site with more than five years data, but where a trend was detected, this was downwards. Most downward trends were for PAHs in Clyde sediment.

Concentrations of contaminants in the Clyde were generally at levels such that there is an unacceptable risk of chronic effects occurring in marine species. This is mainly due to historic industrial inputs. However, downward trends were detected for Pb and PAHs in Clyde sediment indicating that the implementation of relevant regulations is beginning to have a positive environmental impact.

For all other regions the status of contaminants is generally acceptable in that concentrations are at levels where it can be assumed that little or no risks are posed to the environment and its living resources at the population or community level. There were some exceptions. These were Pb in Moray Firth sediments, PCBs in East Scotland sediments and Cd in fish from Hebrides, Rockall and Bailey. However, the overall status of the various regions, with respect to the assessed hazardous substances, can be considered to be acceptable (at least green). Thus Scotland has made substantial progress towards delivering a vision that includes clean seas

The Saltire prize of £10 million, announced on the 23 March 2010, will be awarded by
Scottish Government to the team that can demonstrate a commercially viable wave or tidal
stream energy technology that achieves the greatest volume of electrical output of at least
100 GWh over a continuous 2 year period before 2017. All wave and tidal stream energy
developments, including those in The Crown Estate's (TCE) first leasing round in the
Pentland Firth and Orkney waters, will be eligible to compete for the prize, under the
condition that they are in a site in Scottish waters leased by TCE.
In the spirit of encouraging rapid development of wave and tidal energy, and to give
opportunities for other projects to compete for the Saltire Prize, TCE and the Scottish
Government are working in partnership to prepare plans for a further Scottish leasing round
for wave and tidal projects. This leasing round is entirely separate and in addition to the
leasing in the Pentland Firth and Orkney waters. A scoping paper on the proposed
geographic areas to be leased for the Further Scottish Leasing Round was published and
interested parties were invited to comment.
Subsequently and partly in response to comments received on the Scoping Study, Marine
Scotland has undertaken further analysis of the proposed areas. The results of this work are
described in this report and collectively known as Regional Locational Guidance (RLG). The
RLG is provided primarily to assist developers interested in competing for the Saltire Prize to
identify and develop projects rapidly, but may also be of interest to planners and regulators.
The RLG collates and presents a range of information relevant to the development process
and based on this, Marine Scotland’s appreciation of the physical characteristics and
the relative degree of constraints in these areas. Developers are strongly encouraged to
take the information in the RLG into account when selecting and pursuing site
developments, since it may be material to the consents process. However, it is recognised
that developers will also undertake their own site suitability and environmental impact
assessment work.

High levels of suspended sediment caused by anthropogenic activity can be detrimental to the healthy functioning of the marine ecosystem. However, before a proper evaluation can be made, such elevated levels of suspended sediment should be set against the natural pattern of sedimentation in the marine environment. To understand the pattern of natural sedimentation in a hydrographically dynamic environment, this study measured suspended sediment concentrations, settled sediment levels, near-bed current speeds and wind speeds in the Firth of Lorn special area of conservation between December 2008 and March 2009. Background sediment concentrations were found to vary within the 2 – 13 μl l-1 range, with sediment concentrations rapidly increasing above 17 μl l-1 during strong gales from the south. Maximum concentrations of suspended sediment reach 60 μl l-1, with minimum levels typically 1 μl l-1. The study suggests that a prerequisite for high concentrations in suspended load are high levels of settled sediments. Northeast residual currents correspond with periods of high particle suspension with a possible explanation of this being that such flow patterns transport sediment to the site. Tidal currents in the Firth of Lorn caused regular 5 μl l-1 and 1 μl l-1 fluctuations in suspended sand (particle size 50 – 500 μm) and suspended silt (particle size 4 – 58 μm) respectively. Overall, the study suggests that tide and wind driven currents can explain much of the patterns observed in sedimentation, but features specific to the site, such as the islands and sand banks in close proximity, also influence the suspended load.