Descriptions of Scottish Priority Marine Features (PMFs).

Background The seas around Scotland are rich and diverse – Scotland’s position at the edge of the continental shelf, the long coastline, large area of sea and the mixing of warm and coldwater currents combine to make its waters a special place for marine wildlife and habitats. Scotland has over 18,000 km of coastline and its inshore and offshore areas are among the largest of any EU country, representing 13% of all European seas. Scotland’s seas are of outstanding scenic, historical and cultural value and are part of the national identity at home and abroad. The Marine (Scotland) Act 2010 and the UK Marine and Coastal Access Act 2009 include new powers and duties to ensure that our seas are managed sustainably for future generations, integrating the economic growth of marine industries with the need to protect these assets. Measures to conserve Scotland’s marine natural heritage are based on a three pillar approach, with action at the wider seas level (e.g. marine planning or sectoral controls); specific species conservation measures (e.g. improved protection for seals); and through site protection measures - the identification of new Marine Protected Areas (MPAs). To help target action under each of the three pillars, Scottish Natural Heritage (SNH) and the Joint Nature Conservation Committee (JNCC) have generated a focused list of habitats and species of priority conservation importance - the Priority Marine Features (PMFs). The aim of the current study was to produce a descriptive catalogue of the Scottish PMFs (including component habitats and species where appropriate) to serve as a reference for future nature conservation action. Whilst derived from available existing accounts, the succinct 1-page descriptions are written from a Scottish perspective, refining, but clearly linking to more generic UK, EC or OSPAR (Oslo and Paris Commission) commentary. Available information on the geographic distribution of the features was collated as part of the project and a summary map is provided in each description. Main findings  This project has generated a descriptive catalogue of the 81 PMFs that have been identified in the seas around Scotland (out to the limit of the UK continental shelf). The list comprises 26 broad habitats (e.g. burrowed mud), seven low or limited mobility species (e.g. ocean quahog) and 48 mobile species, including fish (e.g. blue ling) and marine mammals (e.g. minke whale).  Information on the distribution of the PMFs was collated within a Geographic Information System (GIS). This is the first time that data about such a diverse range of Scottish marine nature conservation interests have been compiled within a single repository. These data have and will be used in conjunction with other contextual base-mapping to inform the development of nature conservation advice and commentary (e.g. in the production of the Scotland’s Marine Atlas - Baxter et al., 2011).  The feature distribution mapping used in the production of this report is being made available to view online via the National Marine Plan Interactive web portal (NMPi - http://www.gov.scot/Topics/marine/seamanagement/nmpihome). As new or refined data on Scottish PMFs become available, these will be fed into updates to the project geodatabase and NMPi.

Descriptions of Scottish Priority Marine Features (PMFs).

Background The seas around Scotland are rich and diverse – Scotland’s position at the edge of the continental shelf, the long coastline, large area of sea and the mixing of warm and coldwater currents combine to make its waters a special place for marine wildlife and habitats. Scotland has over 18,000 km of coastline and its inshore and offshore areas are among the largest of any EU country, representing 13% of all European seas. Scotland’s seas are of outstanding scenic, historical and cultural value and are part of the national identity at home and abroad. The Marine (Scotland) Act 2010 and the UK Marine and Coastal Access Act 2009 include new powers and duties to ensure that our seas are managed sustainably for future generations, integrating the economic growth of marine industries with the need to protect these assets. Measures to conserve Scotland’s marine natural heritage are based on a three pillar approach, with action at the wider seas level (e.g. marine planning or sectoral controls); specific species conservation measures (e.g. improved protection for seals); and through site protection measures - the identification of new Marine Protected Areas (MPAs). To help target action under each of the three pillars, Scottish Natural Heritage (SNH) and the Joint Nature Conservation Committee (JNCC) have generated a focused list of habitats and species of priority conservation importance - the Priority Marine Features (PMFs). The aim of the current study was to produce a descriptive catalogue of the Scottish PMFs (including component habitats and species where appropriate) to serve as a reference for future nature conservation action. Whilst derived from available existing accounts, the succinct 1-page descriptions are written from a Scottish perspective, refining, but clearly linking to more generic UK, EC or OSPAR (Oslo and Paris Commission) commentary. Available information on the geographic distribution of the features was collated as part of the project and a summary map is provided in each description. Main findings  This project has generated a descriptive catalogue of the 81 PMFs that have been identified in the seas around Scotland (out to the limit of the UK continental shelf). The list comprises 26 broad habitats (e.g. burrowed mud), seven low or limited mobility species (e.g. ocean quahog) and 48 mobile species, including fish (e.g. blue ling) and marine mammals (e.g. minke whale).  Information on the distribution of the PMFs was collated within a Geographic Information System (GIS). This is the first time that data about such a diverse range of Scottish marine nature conservation interests have been compiled within a single repository. These data have and will be used in conjunction with other contextual base-mapping to inform the development of nature conservation advice and commentary (e.g. in the production of the Scotland’s Marine Atlas - Baxter et al., 2011).  The feature distribution mapping used in the production of this report is being made available to view online via the National Marine Plan Interactive web portal (NMPi - http://www.gov.scot/Topics/marine/seamanagement/nmpihome). As new or refined data on Scottish PMFs become available, these will be fed into updates to the project geodatabase and NMPi.

Molecular cloning and expression of leptin in gray and harbor seal blubber, bone marrow, and lung and its potential role in marine mammal respiratory physiology

Leptin is a multifunctional hormone, produced predominantly in adipocytes. It regulates energy balance through its impact on appetite and fat metabolism, and its concentration indicates the size of body fat reserves. Leptin also plays a vital role in stretch-induced surfactant production during alveolar development in the fetus. The structure, expression pattern, and role of leptin have not previously been explored in marine mammals. Phocid seals undergo cyclical changes in body composition as a result of prolonged fasting and intensive foraging bouts and experience rapid, dramatic, and repeated changes in lung volume during diving. Here, we report the tissue-specific expression pattern of leptin in these animals. This is the first demonstration of leptin expression in the lung tissue of a mature mammal, in addition to its expression in the blubber and bone marrow, in common with other animals. We propose a role for leptin in seal pulmonary surfactant production, in addition to its likely role in long-term energy balance. We identify substitutions in the phocine leptin sequence in regions normally highly conserved between widely distinct vertebrate groups, and, using a purified seal leptin antiserum, we confirm the presence of the leptin protein in gray seal lung and serum fractions. Finally, we report the substantial inadequacies of using heterologous antibodies to measure leptin in unextracted gray seal serum.

Design and implementation of sensor networks for the observation and research of harmful algal blooms in southern California coastal waters

Harmful Algal Blooms (HABs) have become an important environmental concern along the western coast of the United States. Toxic and noxious blooms adversely impact the economies of coastal communities in the region, pose risks to human health, and cause mortality events that have resulted in the deaths of thousands of fish, marine mammals and seabirds. One goal of field-based research efforts on this topic is the development of predictive models of HABs that would enable rapid response, mitigation and ultimately prevention of these events. In turn, these objectives are predicated on understanding the environmental conditions that stimulate these transient phenomena. An embedded sensor network (Fig. 1), under development in the San Pedro Shelf region off the Southern California coast, is providing tools for acquiring chemical, physical and biological data at high temporal and spatial resolution to help document the emergence and persistence of HAB events, supporting the design and testing of predictive models, and providing contextual information for experimental studies designed to reveal the environmental conditions promoting HABs. The sensor platforms contained within this network include pier-based sensor arrays, ocean moorings, HF radar stations, along with mobile sensor nodes in the form of surface and subsurface autonomous vehicles. FreewaveTM radio modems facilitate network communication and form a minimally-intrusive, wireless communication infrastructure throughout the Southern California coastal region, allowing rapid and cost-effective data transfer. An emerging focus of this project is the incorporation of a predictive ocean model that assimilates near-real time, in situ data from deployed Autonomous Underwater Vehicles (AUVs). The model then assimilates the data to increase the skill of both nowcasts and forecasts, thus providing insight into bloom initiation as well as the movement of blooms or other oceanic features of interest (e.g., thermoclines, fronts, river discharge, etc.). From these predictions, deployed mobile sensors can be tasked to track a designated feature. This focus has led to the creation of a technology chain in which algorithms are being implemented for the innovative trajectory design for AUVs. Such intelligent mission planning is required to maneuver a vehicle to precise depths and locations that are the sites of active blooms, or physical/chemical features that might be sources of bloom initiation or persistence. The embedded network yields high-resolution, temporal and spatial measurements of pertinent environmental parameters and resulting biology (see Fig. 1). Supplementing this with ocean current information and remotely sensed imagery and meteorological data, we obtain a comprehensive foundation for developing a fundamental understanding of HAB events. This then directs labor- intensive and costly sampling efforts and analyses. Additionally, we provide coastal municipalities, managers and state agencies with detailed information to aid their efforts in providing responsible environmental stewardship of their coastal waters.

Of dogs, fish, birds and turds : the social construction of sewage pollution by recreational boaters

Animals are often used as ‘evidence’ of marine pollution. Take for instance the ubiquitous images of miserable oil-soaked marine birds following high profile oil spills such as the Exxon Valdez, Pacific Adventurer and Deepwater Horizon incidents or the images of bloated floating fish carcasses which are used to signal the presence of toxic pollutants. In recent years waste discharges from vessels have come under increased public and regulatory scrutiny both in Australia and around the world. International, regional, national and local restrictions are becoming more stringent for high profile marine pollutants such as oil as well as previously overlooked vessel-sourced pollutants such as sewage. Drawing upon media reports and recreational boater responses to government attempts to regulate the discharge of sewage from recreational vessels, this paper considers the important role played by animals in constructions of marine pollution by sewage and attributions of blame for this pollution. Specifically, this study found that recreational boat owners disputed claims their sewage management practices posed an environmental threat arguing that the sewage discharged was readily and eagerly consumed by fish in the receiving environment. Boat owners also argued that increased levels of bacteria which indicate the presence of faeces within the marine environment could be directly attributed to the excrement of marine mammals and birds or were the result of dog faeces being washed through municipal storm water systems rather than the result of vessel discharges. By contrast the contamination of oysters was provided as evidence of sewage pollution by other stakeholders.

A convolutional neural network for automatic analysis of aerial imagery

This paper introduces a new method to automate the detection of marine species in aerial imagery using a Machine Learning approach. Our proposed system has at its core, a convolutional neural network. We compare this trainable classifier to a handcrafted classifier based on color features, entropy and shape analysis. Experiments demonstrate that the convolutional neural network outperforms the handcrafted solution. We also introduce a negative training example-selection method for situations where the original training set consists of a collection of labeled images in which the objects of interest (positive examples) have been marked by a bounding box. We show that picking random rectangles from the background is not necessarily the best way to generate useful negative examples with respect to learning.

Levels and trends of PBDEs and HBCDs in the global environment : status at the end of 2012

In this paper, we have compiled and reviewed the most recent literature, published from January2010 to December 2012, relating to the human exposure, environmental distribution, behaviour, fate and concentration time trends of polybrominated diphenyl ether (PBDE) and hexabromocyclododecane (HBCD) flame retardants, in order to establish their current trends and priorities for future study. Due to the large volume of literature included, we have provided full detail of the reviewed studies as Electronic Supplementary Information and here summarise the most relevant findings. Decreasing time trends for penta-mix PBDE congeners were seen for soils in northern Europe, sewage sludge in Sweden and the USA, carp from a US river, trout from three of the Great Lakes and in Arctic and UK marine mammals and many birds, but increasing time trends continue in Arctic polar bears and some birds at high trophic levels in northern Europe. This is a result of the time delay inherent in long-range atmospheric transport processes. In general, concentrations of BDE209 (the major component of the deca-mix PBDE product) are continuing to increase. Of major concern is the possible/likely debromination of the large reservoir of BDE209 in soils and sediments worldwide, to yield lower brominated congeners which are both more mobile and more toxic, and we have compiled the most recent evidence for the occurrence of this degradation process. Numerous studies reported here reinforce the importance o f this future concern. Time trends for HBCDs are mixed, with both increases and decreases evident in different matrices and locations and, notably, with increasing occurrence in birds of prey.

Sexing Sirenians: Validation of Visual and Molecular Sex Determination in Both Wild Dugongs (Dugong dugon) and Florida Manatees (Trichechus manatus latirostris)

Sexing wild marine mammals that show little to no sexual dimorphism is challenging. For sirenians that are difficult to catch or approach closely, molecular sexing from tissue biopsies offers an alternative method to visual discrimination. This paper reports the results of a field study to validate the use of two sexing methods: (1) visual discrimination of sex vs (2) molecular sexing based on a multiplex PCR assay which amplifies the male-specific SRY gene and differentiates ZFX and ZFY gametologues. Skin samples from 628 dugongs (Dugong dugon) and 100 Florida manatees (Trichechus manatus latirostris) were analysed and assigned as male or female based on molecular sex. These individuals were also assigned a sex based on either direct observation of the genitalia and/or the association of the individual with a calf. Individuals of both species showed 93 to 96% congruence between visual and molecular sexing. For the remaining 4 to 7%, the discrepancies could be explained by human error. To mitigate this error rate, we recommend using both of these robust techniques, with routine inclusion of sex primers into microsatellite panels employed for identity, along with trained field observers and stringent sample handling.

Gear selectivity of large-mesh nets and drumlines used to catch sharks in the Queensland Shark Control Program.

Catches of sharks and bycatch in large-mesh nets and baited drumlines used by the Queensland Shark Control Program were examined to determine the efficacy of both gear types and assess fishing strategies that minimise their impacts. There were few significant differences in the size of both sharks and bycatch in the two gear types, apart from significantly smaller (p < 0.05) tiger sharks Galeocerdo cuvier being taken on drumlines and smaller green turtles Chelonia mydas in nets. Catch per unit effort showed orders of magnitude differences among species, even within the same family. Hammerhead sharks and rays were particularly vulnerable to net capture, whereas higher catch rates of tiger sharks were observed for drumlines. Nets caught more marine mammals, teleost fish and rays, whereas drumlines exhibited higher catch rates of the threatened loggerhead turtle Caretta caretta. Survival of most taxa (particularly obligate ram ventilators) was lower in nets than drumlines. Bycatch species (turtles and marine mammals) were able to swim to the surface to breathe when they were hooked on drumlines, enhancing their survival potential. Fishing strategies that recognise the different selectivity patterns of the gear can be developed to suit local biotic and abiotic conditions, although it is recognised that quantification of both ecological risk and risk to bathers is not a simple task.

Bacterial Community Structure in the Hindgut of Wild and Captive Dugongs (Dugong dugon)

Dugongs (Dugong dugon) are marine mammals that obtain nutrients through hindgut fermentation of seagrass, however, the microbes responsible have not been identified. This study used denaturing gradient gel electrophoresis (DGGE) and 454-pyrosequencing to profile hindgut bacterial communities in wild dugongs. Faecal samples obtained from 32 wild dugongs representing four size/maturity classes, and two captive dugongs fed on cos lettuce were screened using DGGE. Partial 16S rRNA gene profiles of hindgut bacteria from wild dugong calves and juveniles were grouped together and were different to those in subadults and adults. Marked differences between hindgut bacterial communities of wild and captive dugongs were also observed, except for a single captive whose profile resembled wild adults following an unsuccessful reintroduction to the wild. Pyrosequencing of hindgut communities in two wild dugongs confirmed the stability of bacterial populations, and Firmicutes (average 75.6% of Operational Taxonomic Units [OTUs]) and Bacteroidetes (19.9% of OTUs) dominated. Dominant genera were Roseburia, Clostridium, and Bacteroides. Hindgut microbial composition and diversity in wild dugongs is affected by ontogeny and probably diet. In captive dugongs, the absence of the dominant bacterial DNA bands identified in wild dugongs is probably dependent upon prevailing diet and other captive conditions such as the use of antibiotics. This study represents a first step in the characterisation of a novel microbial ecosystem-the marine hindgut of Sirenia.

Molecular and serological studies on the recent seal virus epizootics in Europe and Siberia

The virus epizootics which occurred in seals in both Europe and Siberia during 1987/1988 were caused by two different morbillivirus, referred to as phocid distemper virus (PDV) 1 and 2, respectively. Molecular and serological studies have shown that the European virus is quite distinct from canine distemper virus (CDV), its closest relative in the morbillivirus group. Analysis of tissues obtained from infected seals from a wide geographical distrubution over Northern Europe showed that the infectious agent (PDV 1) was identical in all cases. Nucleotide sequence analysis of one of the virus genes suggested that this virus has evolved away from CDV over a long time period and is most probably an enzootic virus of marine mammals. In contrast, the virus (PDV 2) which caused the deaths of many Siberian seals was indistinguishable, both serologically and at the molecular level, from CDV and must have originated from a land source.

Proceedings of the PICES/CoML/IPRC Workshop on Impact of Climate Variability on Observation and Prediction of Ecosystem and Biodiversity Changes in the North Pacific

Table of Contents [pdf, 0.09 Mb] Section I - Presentations and Discussions at Plenary Sessions Introduction and Overview of Workshop Objectives [pdf, 0.07 Mb] Plenary Session Presentations [pdf, 2.23 Mb] Reports of the Breakout Group Discussions [pdf, 0.43 Mb] Closing Plenary Discussion and Recommendations [pdf, 0.11 Mb] Section II - Extended Abstracts of Individual Presentations at Breakout Group Sessions Breakout Group 1: Physical/Chemical Oceanography and Climate [pdf, 6.14 Mb] Breakout Group 2: Phytoplankton, Zooplankton, Micronekton and Benthos [pdf, 28.14 Mb] Breakout Group 3: Fish, Squid, Crabs and Shrimps [pdf, 4.30 Mb] Breakout Group 4: Highly Migratory Fishes, Seabirds and Marine Mammals [pdf, 6.27 Mb] Appendix 1. Workshop agenda [pdf, 0.15 Mb] Appendix 2. List of participants [pdf, 0.13 Mb] (Document pdf contains 216 pages)

Whales and Sonar: Environmental Exemptions for the Navy’s Mid-Frequency Active Sonar Training

Mid-frequency active (MFA) sonar emits pulses of sound from an underwater transmitter to help determine the size, distance, and speed of objects. The sound waves bounce off objects and reflect back to underwater acoustic receivers as an echo. MFA sonar has been used since World War II, and the Navy indicates it is the only reliable way to track submarines, especially more recently designed submarines that operate more quietly, making them more difficult to detect. Scientists have asserted that sonar may harm certain marine mammals under certain conditions, especially beaked whales. Depending on the exposure, they believe that sonar may damage the ears of the mammals, causing hemorrhaging and/or disorientation. The Navy agrees that the sonar may harm some marine mammals, but says it has taken protective measures so that animals are not harmed. MFA training must comply with a variety of environmental laws, unless an exemption is granted by the appropriate authority. Marine mammals are protected under the Marine Mammal Protection Act (MMPA) and some under the Endangered Species Act (ESA). The training program must also comply with the National Environmental Policy Act (NEPA), and in some cases the Coastal Zone Management Act (CZMA). Each of these laws provides some exemption for certain federal actions. The Navy has invoked all of the exemptions to continue its sonar training exercises. Litigation challenging the MFA training off the coast of Southern California ended with a November 2008 U.S. Supreme Court decision. The Supreme Court said that the lower court had improperly favored the possibility of injuring marine animals over the importance of military readiness. The Supreme Court’s ruling allowed the training to continue without the limitations imposed on it by other courts. (pdf contains 20pp.)

A method for age determination of dolphins.

The use of growth layers in teeth as an indicator of age in odnotocetes and pinnipeds was suggested by Laws (1954) and since then the method has been used extensively in both marine and non-marine mammals. Dentinal growth layers are groups (growth layer groups) of repetitive alternating bands which in cross-section are similar to growth rings in trees. The most commonly used methods for counting growth layer groups (GLGs) are by undecalcified longitudinal thin sections (150 um) or decalcified and stained thin sections (10-30 um). In longitudinal sections viewed with light microscopy, GLGs appear as opaque and translucent cones nestled one inside another, with the oldest dentine Iying adjacent to the enamel, and the newest layer borderinq the pulp cavity.

Age determination and age related factors in the teeth of Western North Atlantic bottlenose dolphins.

Teeth were taken from 120 bottlenose dolphins, Tursiops truncatus, which had stranded on the mid-Atlantic coast of the United States. The number of annual growth layer groups (GLGs) for each animal was used to construct a growth curve. The growth rate of coastal North Atlantic Ocean Tursiops is similar to other cetaceans in having a high initial rate of growth, with no differences in growth between females and males. In females, the first dentinal GLG is thickest and is followed by GLGs which become progressively narrower. In males, the second GLG is thicker than the first; GLGs beyond number two become progressively smaller but at a slower rate than in females. In males and females, the translucent layer makes up proportionally larger parts of the GLG as the animal ages, but in males the percent translucent layer remains constant at about 50% while in females it continues to increase up to about 70% of the GLG. These two factors, GLGs width and translucent layer width, indicate that the sex and age of the animal influence the deposition of GLGs. Incremental layers are also present, averaging 12 per GLG, and seem similar to incremental layers described in other marine mammals. A plot of the relationship of percent growth of the last GLG to time of death suggests that the deposition of GLGs is relatively constant, at least during the first half of the year, and that North Atlantic Ocean Tursiops give birth in the fall as well as in the spring. (PDF contains 31 pages.)