On Mesoscale Population Study cruises during summers 2004 and 2005 aboard the sailboat Summer Breeze, researchers from the Sperm Whale Seismic Study (SWSS) surveyed for sperm whales along the continental slope of the northern Gulf of Mexico. SWSS scientists tracked 35 groups of whales during these two summers, recording locations where they did and did not encounter whales. Whales were encountered during both summers at approximately the same frequency (19 groups in 38 survey days in 2004; 16 groups in 29 survey days in 2005), but fluke photo-identifications indicated that 85% of individuals encountered during summer 2005 had never been previously identified in the Gulf throughout 10 years of cetacean research. Composition and distribution of these groups also varied between summers. Oceanographic conditions at the edge of the continental shelf differed between 2004 and 2005, which may have modified the usual trophic cascade that begins with near-surface primary production to create local aggregations of prey at the depths where sperm whales forage. Sperm whales are apex, mesopelagic predators, but have been shown to associate with surface primary productivity over large spatial scales and time scales of months to years. The purpose of this thesis was to look for relationships between sperm whale presence and surface oceanography on smaller spatial and shorter temporal scales. Surface ocean color from NASA’s Moderate Imaging Spectroradiometer (MODIS) and surface dynamic height from NASA’s Earth orbital altimeters were evaluated to assess habitat occupied by sperm whales. Passive acoustic monitoring along transect lines for sperm whale clicks permitted determination of sperm whale presence and absence. Sperm whale encounters were in general associated with negative sea surface height and enhanced sea surface chlorophyll (SSC), especially in or near areas where local SSC anomaly was produced by cyclone induced upwelling of nutrients or from coastal water advected off-margin. During summer 2004, SSC was generally high all along the upper continental slope whereas summer 2005 saw relatively low SSC along the upper continental slope. Whales encountered in this study were most highly correlated with SSC two weeks after the initial development of locally highest-SSC anomalies.

The Gulf of Mexico is home to two of the world?s ten busiest ports by cargo volume, the Port of New Orleans and the Port of Houston; and in 2008, these ports hosted a combined 14,000 ships, a number which is likely only to increase. Past research shows that this increase in shipping worldwide has historically lead to an increase in ambient noise level of 3-5dB per decade. Sperm whales in the Gulf of Mexico are considered a genetically distinct, resident population. They have a preference for the Louisiana-Mississippi Shelf region which directly overlaps with the entrance to the Mississippi and the Port of New Orleans. Disruptions from vessel noise could influence feeding and breeding patterns essential to the health of the stock. Data used in this analysis were collected continuously over 36 days in the summer of 2001 from bottom moored Navy Environmental Acoustic Recording System (EARS) buoys. Results showed a significant difference (P<0.05) in noise level between hours with ships passing and hours without. Metrics for 56 ship passages were analyzed to compare duration of ship passage with duration of maximum received level (MRL) during ship passage. Results of that analysis showed an average ship passage of 29 minutes with average MRL lasting 23% of the ship passage and an average increase of 40dB. Lastly, click counts were made with the Pamguard. Click counts for ship passages were completed for 35 min and 17.5 min before and after the estimated closest point of approach (CPA) for each ship. Results showed a 36% decrease in the number of detectable clicks as a ship approaches when comparing clicks detected at intervals of both 35 minutes before and 17 minutes before the CPA; additionally, 22% fewer clicks were counted 30 min after the ship than 30 min before (results significant at the P=0.01 level). These results indicate a potential change in sperm whale behavior when exposed to large class size vessel traffic (e.g. tankers and container ships) from major shipping lanes. Recommendations for addressing this issue are discussed.

A hull-mounted 38-kHz phased-array acoustic Doppler current profiler (ADCP) was used to acoustically survey the continental margin of the northern Gulf of Mexico (GOM) during 6 cruises in 2002-2003. This is the first backscatter survey with a 38-kHz ADCP in the Gulf of Mexico. ADCPs have been used as a proxy to measure the volume backscatter return from plankton in the water column, however previous studies were restricted to the upper 200 to 300 meters due to the relatively high frequency of operation (150-300 kHz) of the transducers. In addition to measuring deep water current velocities, the 38-kHz phased-array ADCP can measure Relative Acoustic Backscatter Intensity (RABI) as deep as 1000 meters. The daytime depth of the main deep scattering layer at 400 to 500 meters was resolved, and locally high backscatter intensity can be seen down to 800 meters. The objectives were to determine how to analyze RABI from the instrument to resolve scattering layers, and then to seek secondary deep scattering layers of potential prey species below the main deep scattering layer, from 600 to 800 meters in the feeding range for Gulf of Mexico sperm whales. Based on RABI from the 38-kHz ADCP, secondary DSLs in sperm whale diving range were more commonly recorded over the continental shelf than in the deep basin region of the Gulf of Mexico. The daytime depths of migrating plankton showed variation depending on physical circulation features (cyclone, anticyclone, proximity to Mississippi river, and Loop Current) present. Vertical migrations compared between concurrently running 38 and 153-kHz ADCPs showed an overlap of acoustic scatterers recorded by the two instruments, however the 153-kHz instrument has much finer vertical resolution. Vertical migration rates were calculated and simultaneous net tow samples from one of the cruises was used to compare abundance estimates by the two methods.

Les cétacés grands plongeurs, cachalots Physeteridae et Kogiidae, et baleines à bec Zipiidae, sont des espèces marines rares. Leur faible densité, aire de distribution étendue et faible disponibilité en surface génèrent de faibles taux d’observations. Cette particularité constitue un défi pour la modélisation d’habitat de ces espèces, préalable à leur conservation. Les modèles doivent gérer l’abondance de zéros qui limitent leur capacité à inférer des résultats écologiquement cohérents. Cette thèse vise donc à trouver une méthodologie adaptée aux jeux de données abondants en zéros, à déterminer comment les variables environnementales influencent la distribution des grands plongeurs et à prédire les zones potentielles qu’ils utilisent. Tester la capacité de prédiction de différents modèles d'habitat confrontés à un nombre décroissant d’observations a permis de souligner la pertinence d’un modèle, même si un minimum de 50 observations est nécessaire pour fournir des prédictions fiables. Des données issues de différentes campagnes visuelles ont été assemblées afin de produire les premières cartes de densités de grands plongeurs à l’échelle de l’océan Atlantique Nord et la mer Méditerranée. Les densités les plus élevées sont prédites dans les eaux entre 1500 et 4000 m de profondeur et près des fronts thermiques, particulièrement le long des pentes continentales et à l'ouest de l'océan Atlantique Nord. Par ailleurs, l’analyse de la transférabilité des modèles a montré une variation des habitats préférentiels en fonction des écosystèmes. Finalement, cette thèse permet de discuter les défis de la modélisation statistique appliquée aux espèces rares et les applications de gestion associées. / Deep-diving cetaceans, sperm- and beaked whales Physeteridae, Kogiidae and Ziphiidae, are rare marine species. Due to their low densities, wide distribution ranges and limited presence at the water surface, visual surveys usually result in low sighting rates. This paucity of data challenges the modelling of their habitat, prerequisite for their conservation. Models have to cope with a great number of zeros that weakens the ability to make sound ecological inferences. Consequently, this thesis aimed at finding a methodology suitable for datasets with a large number of zeros, determining how environmental variables influence deep-diver distributions and predicting areas preferentially used by these species. By testing the predictive performance of various habitat models fitted to decreasing numbers of sightings, I selected the most suitable model and determined that at least 50 sightings were needed to provide reliable predictions. However, individual surveys can rarely provide sufficient deep-diver sightings thus I merged many visual survey datasets to produce the first basin-wide deep-diver density maps in the North Atlantic Ocean and the Mediterranean Sea. Highest densities were predicted in waters from 1500-4000 m deep and close to thermal fronts ; hotspots were predicted along the continental slopes, particularly in the western North Atlantic Ocean. In addition, a model transferability analysis highlighted that habitat drivers selected by the models varied between contrasted large ecosystems. Finally, I discussed challenges related to statistical modelling applied to rare species and the management applications of this thesis.

Species distribution maps can provide important information to focus conservation efforts and enable spatial management of human activities. Two sympatric marine predators, grey seals (Halichoerus grypus) and harbour seals (Phoca vitulina), have overlapping ranges but contrasting population dynamics around the UK; whilst grey seals have generally increased, harbour seals have shown significant regional declines. A robust analytical methodology was developed to produce maps of grey and harbour seal usage estimates with corresponding uncertainty, and scales of spatial partitioning between the species were found. Throughout their range, both grey and harbour seals spend the majority of their time within 50 km of the coast. The scalability of the analytical approach was enhanced and environmental information to enable spatial predictions was included. The resultant maps have been applied to inform consent and licensing of marine renewable developments of wind farms and tidal turbines. For harbour seals around Orkney, northern Scotland, distance from haul out, proportion of sand in seabed sediment, and annual mean power were important predictors of space-use. Utilising seal usage maps, a framework was produced to allow shipping noise, an important marine anthropogenic stressor, to be explicitly incorporated into spatial planning. Potentially sensitive areas were identified through quantifying risk of exposure of shipping traffic to marine species. Individual noise exposure was predicted with associated uncertainty in an area with varying rates of co-occurrence. Across the UK, spatial overlap was highest within 50 km of the coast, close to seal haul outs. Areas identified with high risk of exposure included 11 Special Areas of Conservation (from a possible 25). Risk to harbour seal populations was highest, affecting half of all SACs associated with the species. For 20 of 28 animals in the acoustic exposure study, 95% CI for M-weighted cumulative Sound Exposure Levels had upper bounds above levels known to induce Temporary Threshold Shift. Predictions of broadband received sound pressure levels were underestimated on average by 0.7 dB re 1μPa (± 3.3). An analytical methodology was derived to allow ecological maps to be quantitatively compared. The Structural Similarity (SSIM) index was enhanced to incorporate uncertainty from underlying spatial models, and a software algorithm was developed to correct for internal edge effects so that loss of spatial information from the map comparison was limited. The application of the approach was demonstrated using a case study of sperm whales (Physeter macrocephalus, Linneaus 1758) in the Mediterranean Sea to identify areas where local-scale differences in space-use between groups and singleton whales occurred. SSIM is applicable to a broad range of spatial ecological data, providing a novel tool for map comparison.