Long-finned pilot whale population diversity and structure in Atlantic waters assessed through biogeochemical and genetic markers

Acknowledgements. Cetacean samples were collected under the auspices of stranding monitoring programs run by the Sociedade Portuguesa de Vida Selvagem, the Coordinadora para o Estudio dos Mamíferos Mariños (supported by the regional government Xunta de Galicia), the UK Cetacean Strandings Investigation Programme and the Scottish Agriculture College Veterinary Science Division (jointly funded by Defra and the Devolved Governments of Scotland and Wales), the Marine Mammals Research Group of the Institute of Marine Research (Norway), the Museum of Natural History of the Faroe Islands and the International Fund for Animal Welfare Marine Mammal Rescue and Research Program (USA). The authors thank all the members of these institutions and organizations for their assistance with data and sample collection. S.S.M., P.M.F. and M.F. were supported by PhD grants from the Fundação para a Ciência e Tecnologia (POPH/FSE ref SFRH/BD/ 38735/ 2007, SFRH/BD/36766/2007 and SFRH/BD/30240/ 2006, respectively). A.L. was supported by a postdoctoral grant from the Fundação para a Ciência e Tecnologia (ref SFRH/BPD/82407/2011). The work related to strandings and tissue collection in Portugal was partially supported by the SafeSea project EEAGrants PT 0039 (supported by Iceland, Liechtenstein and Norway through the EEA Financial Mechanism), the MarPro project Life09 NAT/PT/000038 (funded by the European Union program LIFE+) and the project CetSenti FCT RECI/AAG-GLO/0470/2012 (FCOMP- 01-0124-FEDER-027472) (funded by the program COMPETE and the Fundação para a Ciência e Tecnologia). G.J.P. thanks the University of Aveiro and Caixa Geral de Depósitos (Portugal) for financial support. The authors acknowledge the assistance of the chemical analysts at Marine Scotland Science with the fatty acid analysis.

Data to Decision in a Dynamic Ocean: Robust Species Distribution Models and Spatial Decision Frameworks

Human use of the oceans is increasingly in conflict with conservation of endangered species. Methods for managing the spatial and temporal placement of industries such as military, fishing, transportation and offshore energy, have historically been post hoc; i.e. the time and place of human activity is often already determined before assessment of environmental impacts. In this dissertation, I build robust species distribution models in two case study areas, US Atlantic (Best et al. 2012) and British Columbia (Best et al. 2015), predicting presence and abundance respectively, from scientific surveys. These models are then applied to novel decision frameworks for preemptively suggesting optimal placement of human activities in space and time to minimize ecological impacts: siting for offshore wind energy development, and routing ships to minimize risk of striking whales. Both decision frameworks relate the tradeoff between conservation risk and industry profit with synchronized variable and map views as online spatial decision support systems.

For siting offshore wind energy development (OWED) in the U.S. Atlantic (chapter 4), bird density maps are combined across species with weights of OWED sensitivity to collision and displacement and 10 km2 sites are compared against OWED profitability based on average annual wind speed at 90m hub heights and distance to transmission grid. A spatial decision support system enables toggling between the map and tradeoff plot views by site. A selected site can be inspected for sensitivity to a cetaceans throughout the year, so as to capture months of the year which minimize episodic impacts of pre-operational activities such as seismic airgun surveying and pile driving.

Routing ships to avoid whale strikes (chapter 5) can be similarly viewed as a tradeoff, but is a different problem spatially. A cumulative cost surface is generated from density surface maps and conservation status of cetaceans, before applying as a resistance surface to calculate least-cost routes between start and end locations, i.e. ports and entrance locations to study areas. Varying a multiplier to the cost surface enables calculation of multiple routes with different costs to conservation of cetaceans versus cost to transportation industry, measured as distance. Similar to the siting chapter, a spatial decisions support system enables toggling between the map and tradeoff plot view of proposed routes. The user can also input arbitrary start and end locations to calculate the tradeoff on the fly.

Essential to the input of these decision frameworks are distributions of the species. The two preceding chapters comprise species distribution models from two case study areas, U.S. Atlantic (chapter 2) and British Columbia (chapter 3), predicting presence and density, respectively. Although density is preferred to estimate potential biological removal, per Marine Mammal Protection Act requirements in the U.S., all the necessary parameters, especially distance and angle of observation, are less readily available across publicly mined datasets.

In the case of predicting cetacean presence in the U.S. Atlantic (chapter 2), I extracted datasets from the online OBIS-SEAMAP geo-database, and integrated scientific surveys conducted by ship (n=36) and aircraft (n=16), weighting a Generalized Additive Model by minutes surveyed within space-time grid cells to harmonize effort between the two survey platforms. For each of 16 cetacean species guilds, I predicted the probability of occurrence from static environmental variables (water depth, distance to shore, distance to continental shelf break) and time-varying conditions (monthly sea-surface temperature). To generate maps of presence vs. absence, Receiver Operator Characteristic (ROC) curves were used to define the optimal threshold that minimizes false positive and false negative error rates. I integrated model outputs, including tables (species in guilds, input surveys) and plots (fit of environmental variables, ROC curve), into an online spatial decision support system, allowing for easy navigation of models by taxon, region, season, and data provider.

For predicting cetacean density within the inner waters of British Columbia (chapter 3), I calculated density from systematic, line-transect marine mammal surveys over multiple years and seasons (summer 2004, 2005, 2008, and spring/autumn 2007) conducted by Raincoast Conservation Foundation. Abundance estimates were calculated using two different methods: Conventional Distance Sampling (CDS) and Density Surface Modelling (DSM). CDS generates a single density estimate for each stratum, whereas DSM explicitly models spatial variation and offers potential for greater precision by incorporating environmental predictors. Although DSM yields a more relevant product for the purposes of marine spatial planning, CDS has proven to be useful in cases where there are fewer observations available for seasonal and inter-annual comparison, particularly for the scarcely observed elephant seal. Abundance estimates are provided on a stratum-specific basis. Steller sea lions and harbour seals are further differentiated by ‘hauled out’ and ‘in water’. This analysis updates previous estimates (Williams & Thomas 2007) by including additional years of effort, providing greater spatial precision with the DSM method over CDS, novel reporting for spring and autumn seasons (rather than summer alone), and providing new abundance estimates for Steller sea lion and northern elephant seal. In addition to providing a baseline of marine mammal abundance and distribution, against which future changes can be compared, this information offers the opportunity to assess the risks posed to marine mammals by existing and emerging threats, such as fisheries bycatch, ship strikes, and increased oil spill and ocean noise issues associated with increases of container ship and oil tanker traffic in British Columbia’s continental shelf waters.

Starting with marine animal observations at specific coordinates and times, I combine these data with environmental data, often satellite derived, to produce seascape predictions generalizable in space and time. These habitat-based models enable prediction of encounter rates and, in the case of density surface models, abundance that can then be applied to management scenarios. Specific human activities, OWED and shipping, are then compared within a tradeoff decision support framework, enabling interchangeable map and tradeoff plot views. These products make complex processes transparent for gaming conservation, industry and stakeholders towards optimal marine spatial management, fundamental to the tenets of marine spatial planning, ecosystem-based management and dynamic ocean management.

Soundscape Ecology of Hawaiian Spinner Dolphin Resting Bays

Sound is a key sensory modality for Hawaiian spinner dolphins. Like many other marine animals, these dolphins rely on sound and their acoustic environment for many aspects of their daily lives, making it is essential to understand soundscape in areas that are critical to their survival. Hawaiian spinner dolphins rest during the day in shallow coastal areas and forage offshore at night. In my dissertation I focus on the soundscape of the bays where Hawaiian spinner dolphins rest taking a soundscape ecology approach. I primarily relied on passive acoustic monitoring using four DSG-Ocean acoustic loggers in four Hawaiian spinner dolphin resting bays on the Kona Coast of Hawai‛i Island. 30-second recordings were made every four minutes in each of the bays for 20 to 27 months between January 8, 2011 and March 30, 2013. I also utilized concomitant vessel-based visual surveys in the four bays to provide context for these recordings. In my first chapter I used the contributions of the dolphins to the soundscape to monitor presence in the bays and found the degree of presence varied greatly from less than 40% to nearly 90% of days monitored with dolphins present. Having established these bays as important to the animals, in my second chapter I explored the many components of their resting bay soundscape and evaluated the influence of natural and human events on the soundscape. I characterized the overall soundscape in each of the four bays, used the tsunami event of March 2011 to approximate a natural soundscape and identified all loud daytime outliers. Overall, sound levels were consistently louder at night and quieter during the daytime due to the sounds from snapping shrimp. In fact, peak Hawaiian spinner dolphin resting time co-occurs with the quietest part of the day. However, I also found that humans drastically alter this daytime soundscape with sound from offshore aquaculture, vessel sound and military mid-frequency active sonar. During one recorded mid-frequency active sonar event in August 2011, sound pressure levels in the 3.15 kHz 1/3rd-octave band were as high as 45.8 dB above median ambient noise levels. Human activity both inside (vessels) and outside (sonar and aquaculture) the bays significantly altered the resting bay soundscape. Inside the bays there are high levels of human activity including vessel-based tourism directly targeting the dolphins. The interactions between humans and dolphins in their resting bays are of concern; therefore, my third chapter aimed to assess the acoustic response of the dolphins to human activity. Using days where acoustic recordings overlapped with visual surveys I found the greatest response in a bay with dolphin-centric activities, not in the bay with the most vessel activity, indicating that it is not the magnitude that elicits a response but the focus of the activity. In my fourth chapter I summarize the key results from my first three chapters to illustrate the power of multiple site design to prioritize action to protect Hawaiian spinner dolphins in their resting bays, a chapter I hope will be useful for managers should they take further action to protect the dolphins.

Spatial Relationships among Hydroacoustic, Hydrographic and Top Predator Patterns: Cetacean Distributions in the Mid-Atlantic Bight

Effective conservation and management of top predators requires a comprehensive understanding of their distributions and of the underlying biological and physical processes that affect these distributions. The Mid-Atlantic Bight shelf break system is a dynamic and productive region where at least 32 species of cetaceans have been recorded through various systematic and opportunistic marine mammal surveys from the 1970s through 2012. My dissertation characterizes the spatial distribution and habitat of cetaceans in the Mid-Atlantic Bight shelf break system by utilizing marine mammal line-transect survey data, synoptic multi-frequency active acoustic data, and fine-scale hydrographic data collected during the 2011 summer Atlantic Marine Assessment Program for Protected Species (AMAPPS) survey. Although studies describing cetacean habitat and distributions have been previously conducted in the Mid-Atlantic Bight, my research specifically focuses on the shelf break region to elucidate both the physical and biological processes that influence cetacean distribution patterns within this cetacean hotspot.

In Chapter One I review biologically important areas for cetaceans in the Atlantic waters of the United States. I describe the study area, the shelf break region of the Mid-Atlantic Bight, in terms of the general oceanography, productivity and biodiversity. According to recent habitat-based cetacean density models, the shelf break region is an area of high cetacean abundance and density, yet little research is directed at understanding the mechanisms that establish this region as a cetacean hotspot.

In Chapter Two I present the basic physical principles of sound in water and describe the methodology used to categorize opportunistically collected multi-frequency active acoustic data using frequency responses techniques. Frequency response classification methods are usually employed in conjunction with net-tow data, but the logistics of the 2011 AMAPPS survey did not allow for appropriate net-tow data to be collected. Biologically meaningful information can be extracted from acoustic scattering regions by comparing the frequency response curves of acoustic regions to theoretical curves of known scattering models. Using the five frequencies on the EK60 system (18, 38, 70, 120, and 200 kHz), three categories of scatterers were defined: fish-like (with swim bladder), nekton-like (e.g., euphausiids), and plankton-like (e.g., copepods). I also employed a multi-frequency acoustic categorization method using three frequencies (18, 38, and 120 kHz) that has been used in the Gulf of Maine and Georges Bank which is based the presence or absence of volume backscatter above a threshold. This method is more objective than the comparison of frequency response curves because it uses an established backscatter value for the threshold. By removing all data below the threshold, only strong scattering information is retained.

In Chapter Three I analyze the distribution of the categorized acoustic regions of interest during the daytime cross shelf transects. Over all transects, plankton-like acoustic regions of interest were detected most frequently, followed by fish-like acoustic regions and then nekton-like acoustic regions. Plankton-like detections were the only significantly different acoustic detections per kilometer, although nekton-like detections were only slightly not significant. Using the threshold categorization method by Jech and Michaels (2006) provides a more conservative and discrete detection of acoustic scatterers and allows me to retrieve backscatter values along transects in areas that have been categorized. This provides continuous data values that can be integrated at discrete spatial increments for wavelet analysis. Wavelet analysis indicates significant spatial scales of interest for fish-like and nekton-like acoustic backscatter range from one to four kilometers and vary among transects.

In Chapter Four I analyze the fine scale distribution of cetaceans in the shelf break system of the Mid-Atlantic Bight using corrected sightings per trackline region, classification trees, multidimensional scaling, and random forest analysis. I describe habitat for common dolphins, Risso’s dolphins and sperm whales. From the distribution of cetacean sightings, patterns of habitat start to emerge: within the shelf break region of the Mid-Atlantic Bight, common dolphins were sighted more prevalently over the shelf while sperm whales were more frequently found in the deep waters offshore and Risso’s dolphins were most prevalent at the shelf break. Multidimensional scaling presents clear environmental separation among common dolphins and Risso’s dolphins and sperm whales. The sperm whale random forest habitat model had the lowest misclassification error (0.30) and the Risso’s dolphin random forest habitat model had the greatest misclassification error (0.37). Shallow water depth (less than 148 meters) was the primary variable selected in the classification model for common dolphin habitat. Distance to surface density fronts and surface temperature fronts were the primary variables selected in the classification models to describe Risso’s dolphin habitat and sperm whale habitat respectively. When mapped back into geographic space, these three cetacean species occupy different fine-scale habitats within the dynamic Mid-Atlantic Bight shelf break system.

In Chapter Five I present a summary of the previous chapters and present potential analytical steps to address ecological questions pertaining the dynamic shelf break region. Taken together, the results of my dissertation demonstrate the use of opportunistically collected data in ecosystem studies; emphasize the need to incorporate middle trophic level data and oceanographic features into cetacean habitat models; and emphasize the importance of developing more mechanistic understanding of dynamic ecosystems.

Distribution and Conservation of the Antillean Manatee in Hispaniola

Antillean manatees (Trichechus manatus manatus) were heavily hunted in the past throughout the Wider Caribbean Region (WCR), and are currently listed as endangered on the IUCN Red List of Threatened Species. In most WCR countries, including Haiti and the Dominican Republic, remaining manatee populations are believed to be small and declining, but current information is needed on their status, distribution, and local threats to the species.

To assess the past and current distribution and conservation status of the Antillean manatee in Hispaniola, I conducted a systematic review of documentary archives dating from the pre-Columbian era to 2013. I then surveyed more than 670 artisanal fishers from Haiti and the Dominican Republic in 2013-2014 using a standardized questionnaire. Finally, to identify important areas for manatees in the Dominican Republic, I developed a country-wide ensemble model of manatee distribution, and compared modeled hotspots with those identified by fishers.

Manatees were historically abundant in Hispaniola, but were hunted for their meat and became relatively rare by the end of the 19th century. The use of manatee body parts diversified with time to include their oil, skin, and bones. Traditional uses for folk medicine and handcrafts persist today in coastal communities in the Dominican Republic. Most threats to Antillean manatees in Hispaniola are anthropogenic in nature, and most mortality is caused by fisheries. I estimated a minimum island-wide annual mortality of approximately 20 animals. To understand the impact of this level of mortality, and to provide a baseline for measuring the success of future conservation actions, the Dominican Republic and Haiti should work together to obtain a reliable estimate of the current population size of manatees in Hispaniola.

In Haiti, the survey of fishers showed a wider distribution range of the species than suggested by the documentary archive review: fishers reported recent manatee sightings in seven of nine coastal departments, and three manatee hotspot areas were identified in the north, central, and south coasts. Thus, the contracted manatee distribution range suggested by the documentary archive review likely reflects a lack of research in Haiti. Both the review and the interviews agreed that manatees no longer occupy freshwater habitats in the country. In general, more dedicated manatee studies are needed in Haiti, employing aerial, land, or boat surveys.

In the Dominican Republic, the documentary archive review and the survey of fishers showed that manatees still occur throughout the country, and occasionally occupy freshwater habitats. Monte Cristi province in the north coast, and Barahona province in the south coast, were identified as focal areas. Sighting reports of manatees decreased from Monte Cristi eastwards to the adjacent province in the Dominican Republic, and westwards into Haiti. Along the north coast of Haiti, the number of manatee sighting and capture reports decreased with increasing distance to Monte Cristi province. There was good agreement among the modeled manatee hotspots, hotspots identified by fishers, and hotspots identified during previous dedicated manatee studies. The concordance of these results suggests that the distribution and patterns of habitat use of manatees in the Dominican Republic have not changed dramatically in over 30 years, and that the remaining manatees exhibit some degree of site fidelity. The ensemble modeling approach used in the present study produced accurate and detailed maps of manatee distribution with minimum data requirements. This modeling strategy is replicable and readily transferable to other countries in the Caribbean or elsewhere with limited data on a species of interest.

The intrinsic value of manatees was stronger for artisanal fishers in the Dominican Republic than in Haiti, and most Dominican fishers showed a positive attitude towards manatee conservation. The Dominican Republic is an upper middle income country with a high Human Development Index. It possesses a legal framework that specifically protects manatees, and has a greater number of marine protected areas, more dedicated manatee studies, and more manatee education and awareness campaigns than Haiti. The constant presence of manatees in specific coastal segments of the Dominican Republic, the perceived decline in the number of manatee captures, and a more conservation-minded public, offer hope for manatee conservation, as non-consumptive uses of manatees become more popular. I recommend a series of conservation actions in the Dominican Republic, including: reducing risks to manatees from harmful fishing gear and watercraft at confirmed manatee hotspots; providing alternative economic alternatives for displaced fishers, and developing responsible ecotourism ventures for manatee watching; improving law enforcement to reduce fisheries-related manatee deaths, stop the illegal trade in manatee body parts, and better protect manatee habitat; and continuing education and awareness campaigns for coastal communities near manatee hotspots.

In contrast, most fishers in Haiti continue to value manatees as a source of food and income, and showed a generally negative attitude towards manatee conservation. Haiti is a low income country with a low Human Development Index. Only a single dedicated manatee study has been conducted in Haiti, and manatees are not officially protected. Positive initiatives for manatees in Haiti include: protected areas declared in 2013 and 2014 that enclose two of the manatee hotspots identified in the present study; and local organizations that are currently working on coastal and marine environmental issues, including research and education on marine mammals. Future conservation efforts for manatees in Haiti should focus on addressing poverty and providing viable economic alternatives for coastal communities. I recommend a community partnership approach for manatee conservation, paired with education and awareness campaigns to inform coastal communities about the conservation situation of manatees in Haiti, and to help change their perceived value. Haiti should also provide legal protection for manatees and their habitat.

(Table 1) Age, sex, length, girth and blubber thickness and content of ringed seals (Pusa hispida) in Kongsfjorden in 2000

This study of vertical fatty acid profiles, based on analysis of 58 fatty acids sampled at 3-mm intervals throughout the blubber column of a model marine mammal, the ringed seal (Pusa hispida), revealed three chemically distinct layers. The average depths of the outer and inner layers were quite consistent (~1.5 and ~1 cm, respectively). Consequently, the middle layer varied greatly in thickness, from being virtually absent in the thinnest animals to 2.5 cm thick in the fattest. The relative consistencies of the thickness and composition of the layers as well as the nature of the fatty acids making up each layer support the generally assumed function of the various layers: (1) the outer layer is primarily structural and thermoregulatory, (2) the inner layer is metabolically active with a fatty acid composition that is strongly affected by recent/ongoing lipid mobilization/deposition, and (3) the middle layer is a storage site that contracts and expands with food availability/consumption. The remarkable dynamics of the middle layer along with the discrete pattern of stratification found in the vertical fatty acid profiles have important implications for methodological sampling design for studies of foraging ecology and toxicology based on analyses of blubber of marine mammals.

Migration and Residence Patterns of Salmonids in Puget Sound, Washington

Thesis (Ph.D.)--University of Washington, 2016-08

Phocid seal leptin: tertiary structure and hydrophobic receptor binding site preservation during distinct leptin gene evolution

The cytokine hormone leptin is a key signalling molecule in many pathways that control physiological functions. Although leptin demonstrates structural conservation in mammals, there is evidence of positive selection in primates, lagomorphs and chiropterans. We previously reported that the leptin genes of the grey and harbour seals (phocids) have significantly diverged from other mammals. Therefore we further investigated the diversification of leptin in phocids, other marine mammals and terrestrial taxa by sequencing the leptin genes of representative species. Phylogenetic reconstruction revealed that leptin diversification was pronounced within the phocid seals with a high dN/dS ratio of 2.8, indicating positive selection. We found significant evidence of positive selection along the branch leading to the phocids, within the phocid clade, but not over the dataset as a whole. Structural predictions indicate that the individual residues under selection are away from the leptin receptor (LEPR) binding site. Predictions of the surface electrostatic potential indicate that phocid seal leptin is notably different to other mammalian leptins, including the otariids. Cloning the grey seal leptin binding domain of LEPR confirmed that this was structurally conserved. These data, viewed in toto, support a hypothesis that phocid leptin divergence is unlikely to have arisen by random mutation. Based upon these phylogenetic and structural assessments, and considering the comparative physiology and varying life histories among species, we postulate that the unique phocid diving behaviour has produced this selection pressure. The Phocidae includes some of the deepest diving species, yet have the least modified lung structure to cope with pressure and volume changes experienced at depth. Therefore, greater surfactant production is required to facilitate rapid lung re-inflation upon surfacing, while maintaining patent airways. We suggest that this additional surfactant requirement is met by the leptin pulmonary surfactant production pathway which normally appears only to function in the mammalian foetus.

Navigating uncertain waters: a critical review of inferring foraging behaviour from location and dive data in pinnipeds

In the last thirty years, the emergence and progression of biologging technology has led to great advances in marine predator ecology. Large databases of location and dive observations from biologging devices have been compiled for an increasing number of diving predator species (such as pinnipeds, sea turtles, seabirds and cetaceans), enabling complex questions about animal activity budgets and habitat use to be addressed. Central to answering these questions is our ability to correctly identify and quantify the frequency of essential behaviours, such as foraging. Despite technological advances that have increased the quality and resolution of location and dive data, accurately interpreting behaviour from such data remains a challenge, and analytical methods are only beginning to unlock the full potential of existing datasets. This review evaluates both traditional and emerging methods and presents a starting platform of options for future studies of marine predator foraging ecology, particularly from location and two-dimensional (time-depth) dive data. We outline the different devices and data types available, discuss the limitations and advantages of commonly-used analytical techniques, and highlight key areas for future research. We focus our review on pinnipeds - one of the most studied taxa of marine predators - but offer insights that will be applicable to other air-breathing marine predator tracking studies. We highlight that traditionally-used methods for inferring foraging from location and dive data, such as first-passage time and dive shape analysis, have important caveats and limitations depending on the nature of the data and the research question. We suggest that more holistic statistical techniques, such as state-space models, which can synthesise multiple track, dive and environmental metrics whilst simultaneously accounting for measurement error, offer more robust alternatives. Finally, we identify a need for more research to elucidate the role of physical oceanography, device effects, study animal selection, and developmental stages in predator behaviour and data interpretation.

Contribuição para a avaliação da dieta do golfinho-comum (Delphinus delphis) na costa continental portuguesa

O golfinho-comum (Delphinus delphis) é uma das espécies de cetáceos mais abundantes e mais amplamente distribuídas em todo o planeta, sendo a espécie mais abundante ao longo da costa continental portuguesa. Algumas das suas principais presas apresentam um elevado interesse comercial estando por isso, muitas vezes, associado a capturas acidentais em artes de pesca. Contudo, estudos mais recentes sobre os hábitos alimentares desta espécie na costa portuguesa são escassos. Assim, este estudo visa contribuir para a avaliação da ecologia alimentar deste cetáceo na costa portuguesa através de índices de importância numérica, ocorrência e do peso estimado, permitindo descrever a dieta não só em termos qualitativos, mas também em termos quantitativos. Foram examinados os conteúdos estomacais de 55 golfinhoscomuns arrojados na costa continental portuguesa (norte e centro) entre 2004 e 2015. De um total de 6699 presas identificadas, 66% pertenciam à classe dos peixes, 32% eram cefalópodes e 3% eram crustáceos. As espécies-presa de peixes mais importantes em termos de importância numérica foram os góbios (Gobiidae) e o carapau (Trachurus sp.). Em relação à ocorrência foram o góbio (Gobiidae) e a sardinha (Sardina pilchardus), seguidas de carapau, as espécies predominantes. Relativamente ao peso, a sardinha foi a espécie-presa predominante, seguida de faneca (Trisopterus luscus) e carapau. Quanto aos cefalópodes, a lula-bicuda (Alloteuthis sp.) foi a espécie mais importante, tanto em termos de importância numérica como em termos de ocorrência. A lula-comum (Loligo sp.) foi a mais importante em termos de peso total estimado. As espécies demersais dominaram a dieta do golfinho-comum, com uma percentagem numérica de 40%. Foram detetadas diferenças entre machos e fêmeas na composição da dieta relativamente à sardinha. Foram detetadas diferenças entre indivíduos maturos e imaturos na composição da dieta relativamente à lula-bicuda. A diversidade de presas observada nos conteúdos estomacais do golfinho-comum sugere um comportamento oportunista, consumindo as presas mais abundantes, localmente. As interações com as artes de pesca podem levar a uma elevada mortalidade destes mamíferos marinhos. Deste modo, a realização de estudos sobre os hábitos alimentares de cetáceos permitem uma melhor compreensão das possíveis interações com a pesca, e a melhoria de estratégias de conservação para evitar a morte destes animais.

First molecular determination of herpesvirus from two mysticete species stranded in the Mediterranean Sea

BACKGROUND Herpesvirus can infect a wide range of animal species: mammals, birds, reptiles, fish, amphibians and bivalves. In marine mammals, several alpha- and gammaherpesvirus have been identified in some cetaceans and pinnipeds species. To date, however, this virus has not been detected in any member of the Balaenoptera genus. CASE PRESENTATION Herpesvirus was determined by molecular methods in tissue samples from a male fin whale juvenile (Balaenoptera physalus) and a female common minke whale calf (Balaenoptera acutorostrata) stranded on the Mediterranean coast of the Region of Valencia (Spain). Samples of skin and penile mucosa from the fin whale and samples of skin, muscle and central nervous system tissue from the common minke whale tested positive for herpesvirus based on sequences of the DNA polymerase gene. Sequences from fin whale were identical and belonged to the Alphaherpesvirinae subfamily. Only members of the Gammaherpesvirinae subfamily were amplified from the common minke whale, and sequences from the muscle and central nervous system were identical. Sequences in GenBank most closely related to these novel sequences were viruses isolated from other cetacean species, consistent with previous observations that herpesviruses show similar phylogenetic branching as their hosts. CONCLUSIONS To our knowledge, this is the first molecular determination of herpesvirus in the Balaenoptera genus. It shows that herpesvirus should be included in virological evaluation of these animals.

Novel adenovirus detected in captive bottlenose dolphins (Tursiops truncatus) suffering from self-limiting gastroenteritis

BACKGROUND Adenoviruses are common pathogens in vertebrates, including humans. In marine mammals, adenovirus has been associated with fatal hepatitis in sea lions. However, only in rare cases have adenoviruses been detected in cetaceans, where no clear correlation was found between presence of the virus and disease status. CASE PRESENTATION A novel adenovirus was identified in four captive bottlenose dolphins with self-limiting gastroenteritis. Viral detection and identification were achieved by: PCR-amplification from fecal samples; sequencing of partial adenovirus polymerase (pol) and hexon genes; producing the virus in HeLa cells, with PCR and immunofluorescence detection, and with sequencing of the amplified pol and hexon gene fragments. A causative role of this adenovirus for gastroenteritis was suggested by: 1) we failed to identify other potential etiological agents; 2) the exclusive detection of this novel adenovirus and of seropositivity for canine adenoviruses 1 and 2 in the four sick dolphins, but not in 10 healthy individuals of the same captive population; and 3) the virus disappeared from feces after clinical signs receded. The partial sequences of the amplified fragments of the pol and hexon genes were closest to those of adenoviruses identified in sea lions with fatal adenoviral hepatitis, and to a Genbank-deposited sequence obtained from a harbour porpoise. CONCLUSION These data suggest that adenovirus can cause self-limiting gastroenteritis in dolphins. This adenoviral infection can be detected by serology and by PCR detection in fecal material. Lack of signs of hepatitis in sick dolphins may reflect restricted tissue tropism or virulence of this adenovirus compared to those of the adenovirus identified in sea lions. Gene sequence-based phylogenetic analysis supports a common origin of adenoviruses that affect sea mammals. Our findings suggest the need for vigilance against adenoviruses in captive and wild dolphin populations.

Unusual striped dolphin mass mortality episode related to cetacean morbillivirus in the Spanish Mediterranean sea

BACKGROUND In the last 20 years, Cetacean Morbillivirus (CeMV) has been responsible for many die-offs in marine mammals worldwide, as clearly exemplified by the two dolphin morbillivirus (DMV) epizootics of 1990-1992 and 2006-2008, which affected Mediterranean striped dolphins (Stenella coeruleoalba). Between March and April 2011, the number of strandings on the Valencian Community coast (E Spain) increased. CASE PRESENTATION Necropsy and sample collection were performed in all stranded animals, with good state of conservation. Subsequently, histopathology, immunohistochemistry, conventional reverse transcription polymerase chain reaction (RT-PCR) and Universal Probe Library (UPL) RT-PCR assays were performed to identify Morbillivirus. Gross and microscopic findings compatible with CeMV were found in the majority of analyzed animals. Immunopositivity in the brain and UPL RT-PCR positivity in seven of the nine analyzed animals in at least two tissues confirmed CeMV systemic infection. Phylogenetic analysis, based on sequencing part of the phosphoprotein gene, showed that this isolate is a closely related dolphin morbillivirus (DMV) to that responsible for the 2006-2008 epizootics. CONCLUSION The combination of gross and histopathologic findings compatible with DMV with immunopositivity and molecular detection of DMV suggests that this DMV strain could cause this die-off event.

Flipper strokes can predict energy expenditure and locomotion costs in free-ranging northern and Antarctic fur seals

Flipper strokes have been proposed as proxies to estimate the energy expended by marine vertebrates while foraging at sea, but this has never been validated on free-ranging otariids (fur seals and sea lions). Our goal was to investigate how well flipper strokes correlate with energy expenditure in 33 foraging northern and Antarctic fur seals equipped with accelerometers, GPS, and time-depth recorders. We concomitantly measured field metabolic rates with the doubly-labelled water method and derived activity-specific energy expenditures using fine-scale time-activity budgets for each seal. Flipper strokes were detected while diving or surface transiting using dynamic acceleration. Despite some inter-species differences in flipper stroke dynamics or frequencies, both species of fur seals spent 3.79 ± 0.39 J/kg per stroke and had a cost of transport of ~1.6-1.9 J/kg/m while diving. Also, flipper stroke counts were good predictors of energy spent while diving (R(2) = 0.76) and to a lesser extent while transiting (R(2) = 0.63). However, flipper stroke count was a poor predictor overall of total energy spent during a full foraging trip (R(2) = 0.50). Amplitude of flipper strokes (i.e., acceleration amplitude × number of strokes) predicted total energy expenditure (R(2) = 0.63) better than flipper stroke counts, but was not as accurate as other acceleration-based proxies, i.e. Overall Dynamic Body Acceleration.

A Biogeographic Assessment off North/Central California: To Support the Joint Management Plan Review for Cordell Bank, Gulf of the Farallones, and Monterey Bay National Marine Sanctuaries: Phase I - Marine Fishes, Birds and Mammals.

In the spring of 2001, NOAA’s National Marine Sanctuary Program (NMSP) and National Centers for Coastal Ocean Science (NCCOS), in consultation with the National Marine Fisheries Service (NMFS), launched a 24-month effort to define and assess biogeographic patterns of selected marine species found within and adjacent to the boundaries of three west coast National Marine Sanctuaries. These sanctuaries, Monterey Bay, Gulf of the Farallones, and Cordell Bank are conducting a joint review process to update sanctuary management plans. The management plans for these sanctuaries have not been updated for over ten years and the status of the natural resources and their management issues in and around the sanctuaries may have changed. In addition, significant accomplishments in research and resource assessments have been made within the region. Thus, it is important to incorporate new and expanding knowledge into the revised management plans for these Sanctuaries.