DDG P Atlantic Aug 2016

DDG Q Atlantic Aug 2017

CG C Atlantic Aug 2014

CG B HRC Feb 2014

DDG B Atlantic June 2010

CG A HRC Nov 2010

FFG-A Hawaii Range Complex FEB 2010

DDG A Atlantic March 2010

DDG D HRC Feb 2011

DDG C SOCAL July 2010

DDG U Atlantic Sept. 2019

DDG O Atlantic March 2016

DDG S Atlantic June 2018

CG D Atlantic March 2019

DDG M Atlantic April 2015

Introgressive hybridization, in which genetic material from one species persists in the genome of another species following hybridization, can result in gene trees that do not match species trees and seriously mislead phylogenetic studies. This is particularly true in studies based solely on mitochondrial DNA, as introgression of maternally-inherited genomes is predicted to occur far more rapidly and persist longer than introgression of nuclear genomes. Introgressive hybridization has long been suspected as a source of taxonomic confusion in the Delphinidae. We detected mitochondrial introgressive hybridization in bottlenose dolphins (Tursiops truncatus) sampled around the southern islands of the Mariana Archipelago, where five out of 15 animals possess haplotypes characteristic of Fraser's dolphins (Lagenodelphis hosei). We used mitochondrial sequence data and genotypes from 14 nuclear microsatellite loci to further examine introgression of Fraser's dolphin DNA into the Mariana Islands population of bottlenose dolphins. We compared the Mariana Islands samples to bottlenose dolphin samples from elsewhere in the western Pacific and the Hawaiian Archipelago and to Fraser's dolphin samples from throughout the Pacific and Indian Oceans to investigate the extent and origin of hybrid ancestry in Mariana Islands bottlenose dolphins. We estimate that the Mariana Islands animals derive approximately 14% of their nuclear ancestry from Fraser's dolphins. The fact that every Mariana Islands sample showed evidence of nuclear introgression, combined with the fact that those exhibiting mitochondrial introgression all share the same Fraser's dolphin haplotype, suggests that there was a single hybridization event far enough in the past to allow Fraser's dolphin nuclear DNA to permeate the population. The Mariana Islands samples exhibited low genetic diversity compared to other bottlenose dolphin populations, suggesting that they represent a small, genetically isolated population.

As part of the U.S. Navy’s Atlantic Fleet Testing and Training program, we are monitoring the occurrence, distribution and density of cetaceans at three offshore sites along the U.S. Atlantic coast. We are using an identical suite of survey methods (line transect surveys, photo-identification, biopsy sampling and passive acoustic monitoring) at each 500nm2 reference site. Surveys began in Onslow Bay, NC in 2007, Jacksonville, FL in 2009 and Cape Hatteras, NC in 2011. To date we have conducted 48674km, 60687km, and 14213km of aerial surveys with 6883km, 3403km and 2443km of vessel surveys and 1201 days, 1264 days and 28 days of High frequency Acoustic Recording Package (HARP) recordings at Onslow, Jacksonville and Cape Hatteras, respectively. In both Onslow and Jacksonville, the cetacean fauna is dominated by Tursiops truncatus, with densities of 0.034/km2 and 0.025/km2 respectively and Stenella frontalis, with densities of 0.027/km2 and 0.045/km2 respectively. S. frontalis was encountered exclusively over the continental shelf. Grampus griseus and Globicephala macrorhynchus were the most commonly encountered pelagic odontocetes at these two sites. Species richness is much greater at Cape Hatteras than at the two southern sites (with 18 species sighted at Cape Hatteras, 10 at Jacksonville and 9 at Onslow), with the inclusion of several boreal species during colder months and the common occurrence of several deep-diving odontocetes, including Physeter macrocephalus, Ziphius cavirostris and Mesoplodon spp. Mysticetes, including Balaenoptera acutorostrata, B. physalus, Eubalaena glacialis, and Megaptera novaeangliae, were encountered only during winter at all three sites. In addition, we have detected the calls of two species on bottom-mounted HARPS that were not observed during visual surveys, including B. musculus and likely B. borealis. We highlight the particularly high diversity of cetaceans at the Cape Hatteras shelf break and suggest that this is a hotspot of species richness in the North Atlantic.

FFG B Atlantic July 2019

We conducted aerial-based monitoring of marine mammal behaviors off the Southern California Bight for 7 days during the winter and spring of 2012. We integrated visual methods (visual observations and videography) with passive acoustic methods (sonobuoys) to study behaviors of cetacean groups. We processed data in real-time, and post-survey, using custom-developed software (Difar-Matlab and Mysticetus). We deployed 23 sonobuoys (model AN/SSQ-53F) through a belly chute, with only a 9% (n=2) failure rate. Over 16 hours of acoustic data were recorded and analyzed from 23 inflight hours. We acoustically detected and recorded sounds from focal groups of fin whales, gray whales, humpback whales and bottlenose dolphins, using DIFAR sonobuoys, and from Risso’s dolphins using omni-directional sonobuoys. A possible case of Risso’s dolphin call-matching with sonar (e.g. mimicry) was detected. Fin whales were the most commonly encountered species, as they migrated northward through the study area. We recorded high signal-to-noise acoustic signals and videography from five fin whale focal groups. We plotted bearings to sequential fin whale calls with call sources emanating from different directions, indicating counter-calling. During post-processing, we integrated visually estimated animal locations with acoustically determined bearings and/or localizations. Results indicate that fin whales did not call when at the surface. We greatly improved real-time and post-processing capabilities via integration of hardware and upgrades to software. Additional surveys and improvements to the system are planned to increase our understanding of marine mammal behaviors and the effects of anthropogenic activities. [Work sponsored by NAVFAC Southwest Division]

Passive acoustic data were collected from nine Marine Autonomous Recording Units (MARUs) deployed in a rectangular array 60-150 km off Jacksonville FL, USA. Units were deployed for 26 days during fall 2009, and 37 days in winter 2009-2010. The study area coincides with the U.S. Navy’s planned Undersea Warfare Training Range (USWTR). Data were manually reviewed using the MATLAB program Triton to create long-term spectral averages (LTSAs) and spectrograms, which were used to log marine mammal vocalization events, man-made noise and mid-frequency active sonar. Patterns and probabilities of vocalization events by species or species groups were characterized and related to sonar activities. Seasonal and diel patterns were qualitatively characterized. Vocalizations were detected for minke whales, North Atlantic right whales, sei whales, humpback whales, sperm whales, the blackfish group, and delphinids. Minke whale vocalization events occurred almost continuously during the winter deployment period but absent in fall. Right whale events occurred mostly during winter at shallow-water sites, but unexpectedly, also were detected at deep-water sites. Sperm whale events occurred exclusively near the continental shelf break, and exhibited a strong diel pattern with almost all vocalizations occurring between dusk and dawn. Less obvious patterns were apparent for delphinid events, probably because identification to the species level was not possible. Minke whale events had a strong negative relationship with sonar events when data from all sites were combined. These results provide an initial assessment of marine mammal occurrence and distribution within the U.S. Navy’s planned USWTR and provide important insights on the presence or absence of species-specific vocal responses to sonar events. Ongoing work includes using automated classification methods to identify delphinid whistles to species, and working with researchers at St. Andrews University to develop robust statistical approaches for analyzing the relationship between mid-frequency active sonar and vocal behaviors of marine mammals

Passive acoustic data were collected from nine Marine Autonomous Recording Units (MARUs) deployed 60–150 km in an area that coincides with the U.S. Navy’s planned Undersea Warfare Training Range (USWTR) off Jacksonville FL. MARUs were deployed for 26 days during fall 2009, and 37 days in winter 2009–2010. Data were manually reviewed for marine mammal vocalization events, man-made noise, and mid-frequency active sonar events, which were logged using TRITON software. Seasonal and diel patterns were characterized qualitatively. Patterns and probabilities of vocalization events by species, or species groups, were related to sonar events. Vocalizations were detected for minke whales, North Atlantic right whales, sei whales, humpback whales, sperm whales, the blackfish group, and delphinids. Minke whale pulse-trains occurred almost continuously during the winter deployment but were absent in fall. Right whale events occurred mostly during winter at shallow-water sites but unexpectedly were also detected at deep-water sites. Sperm whale events occurred exclusively near the continental shelf break and exhibited a strong diel pattern. Minke whale events had a strong negative relationship with sonar events. These results provide an initial assessment of marine mammal occurrence within the Navy’s planned USWTR and provide new information on vocalization events in relation to sonar.

Final Report on HDR Task Order 002/1000300001856

DDG R HRC Feb 2018

DDG E SOCAL April 2011

DDG K HRC Jan 2014

The relative occurrence of the 16 most common cetacean species in the Southern California Bight (SCB) was compared from the 1950s through 2012 by examining at-sea sighting and stranding data. While systematic survey and population abundance/density data have been available since the 1970s, prior data were collected opportunistically. Comparisons were made through a literature review and using recent results from 15 aerial surveys conducted in the SCB from 2008 through 2012. We attempted to address inconsistency in type of effort across studies by ranking the relative sighting frequency of the most common species based on the most representative study for each period. This comparison revealed changes in the relative occurrence of some species across the approximately 60-y reviewed period. Since the 1950s, common dolphins have remained the most common “species” of cetacean in the SCB. Risso’s dolphin and fin, blue, humpback, and Bryde’s whales appear to have increased in relative occurrence. The relative occurrence of the common bottlenose and northern right whale dolphins; Dall’s porpoise; and gray, killer, minke, Cuvier’s beaked, and sperm whales do not appear to have changed notably since the 1950s. There is possible indication of recent decreased relative occurrence of the Pacific white-sided dolphin. The short-finned pilot whale has decreased since the 1950s and has not been recorded in the SCB since the 1990s, concurrent with the observed relative increase in Risso’s dolphins. Overall, recent aerial surveys indicate that the 16 most commonly seen species in the SCB, in descending order of frequency, were common dolphins (two species), Risso’s dolphin, fin whale, common bottlenose dolphin, gray whale, blue whale, Pacific white-sided dolphin, humpback whale, northern right whale dolphin, common minke whale, Dall’s porpoise, killer whale, Bryde’s whale, Cuvier’s beaked whale (the latter three tied in ranking), and sperm whale. Given that the reviewed historical data from the 1950s and 1960s are virtually the only sources of information available to examine trends over the last 50 to 60 y in this area, we believe this comparative ranking approach provides useful information not available from other sources.

Behavioral ecology of pelagic Risso’s and short- and long-beaked common dolphins is poorly known. The comparative approach was used to predict group size and behavior relative to risks/rewards of group living in the same eco-region. Risso’s were predicted to occur in smaller, less-cohesive groups and mill less/rest more during daytime than common dolphins based on distribution of prey and predation risk. Video and scan sampling documented firstobserved group size, behavior state, and individual spacing (in body lengths [BL]) during aerial surveys (72,467 km) off southern California in January-November 2008-2012 for 290 Risso’s and 564 common dolphin groups (commons were combined due to small confirmed D. capensis sample size). Behavior was significantly influenced by species, calf presence, time of day, and water depth. Group size was significantly smaller for Risso’s (18.4) vs. commons (277.1), and higher with calf presence (Risso’s: 25 with calf vs. 15 without) (commons: 485 with calf vs. 205 without). Mean spacing was significantly less for commons (5.1 BL) vs. Risso’s (6.7) and decreased significantly across the day for both. Risso’s were 13 times more likely to rest than commons. Risso’s rest increased significantly across the day and over deep water/steep slopes. Both species associated with deep underwater slopes. Smaller group size, looser group spacing, and more daytime resting of Risso’s are adapted to nocturnal foraging. Larger group size, tighter cohesion, and frequent daytime foraging of commons matches clumped, highdensity daytime distribution of schooling fish and presumed higher predation risk. Larger group size likely benefits calf survival through dilution effects. Results suggest the species have diverged ecologically in the same habitat in response to differences in food resources and 101 predation pressure as predicted by group-living patterns documented for well-studied terrestrial mammal species. Data lend insight into ecological triggers influencing behavior.

The behavioral ecology of offshore delphinids and baleen whales is poorly known. A comparative approach was used to assess group size and behavior versus risks/rewards of group living in the Southern California Bight, U.S.. Scan sampling/photographs/video documented first-observed group size, maximum nearest-neighbor distance (MNND - in body lengths [BL]), and behavior state during 72,467 km of aerial surveys between 2008-2012. Regression modeling analyses involved 566 common, 293 Risso’s and 96 bottlenose dolphin groups and 115 fin, 78 gray and 62 blue whale groups. Species body size, group size, and MNND were correlated. Group size, MNND and behavior state were significantly influenced by species, sub-region, calf presence, time of day/year, water depth, and/or slope/aspect. Group size was significantly larger for common dolphin sp. (combined) (277.1) vs. bottlenose (19.2) and Risso’s (18.4) and with calf presence. MNND was significantly less for commons (5.1 BL) vs. Risso’s (6.7). Group size was larger for grays (2.2) vs. fins (1.6) and blues (1.7). Gray MNND (1.5) was significantly closer than fins (5.1) and blues (12.6). Risso’s groups were observed resting 13 times more often (38%) than commons (3%). Smaller groupsize and more daytime resting of Risso’s match presumed nocturnal foraging patterns of this species.Larger tighter groups and frequent daytime foraging of commons match clumped highdensity schoolingfish distribution. Larger tighter common and gray whale groups match presumed higher predation pressure associated with smaller relative bodysize. Results indicate species ecological diversion in the same habitat in response to differing predation pressure and food resource availability as predicted by terrestrial mammal group-living patterns. Data lend insight into baseline behavior and ecological triggers influencing behavior. This information is needed to differentiate potential impacts of anthropogenic sources. Larger group size benefits include reduced predation pressure and improved prey detection/mate access, at the risk of increased resource competition.

Small aircraft enable a “bird’s eye” view of marine mammal behavior at/near the water surface. During 2008-2013, we flew 87,734 km of line transect and “focal follow” aerial survey effort in the Southern California Bight to systematically collect data on 2,707 sightings of ~222,457 individual cetaceans representing 19 species, funded by the U.S. Navy Pacific Fleet. Focal follows involved circling a cetacean group for 5-60+ minutes and taking high-definition (HD) video and photos to document behavior primarily of blue, fin, gray, humpback, sperm, minke and killer whales; and Risso’s, common bottlenose, short-beaked and long-beaked common, and northern right whale dolphins. HD media allow photoidentification of individuals and species confirmation from altitudes of 1,000-1,500 feet. The “bird’s eye” 71 perspective facilitates descriptive and quantitative analyses of behavior previously little described for typically offshore species: whale calf nursing/back-riding, group cohesion, social affinity/composition, group shape and dimension “envelope”, cues leading to group behavior changes, mixed species interactions, individual whale respiration/dive rates, etc. Behavior differs significantly by species, calf presence, time of day, time of year, subregion, water depth, slope, distance from shore, and presence of other species. For example, Risso’s dolphins were 13 times more likely to rest than common dolphins, and dolphin group size increased significantly with calf presence. As species body size decreases, group size increases and individuals decrease distance between neighbors. We hypothesize that inter-specific differences of spacing and behavior are related to predation pressure, food resources, and communication capabilities/needs that lead to occupation of different niches within the same ecosystem.

Rare mixed-species association between sperm whales, and Risso’s and northern right whale dolphins off the Southern California Bight: Kleptoparasitism and social parasitism?

Marine mammal seasonal density, abundance, behavior and habitat-use patterns were monitored off southern California 2008-2012 during 15 aerial surveys for the U.S. Navy. Line-transect, scan sampling, and focal follows occurred using video/photography. During 65,238 km of effort (99% Beaufort ≤4), ~190,310 individuals were seen in 2,151 groups (19+ species). Behavior differed significantly by species, depth, slope, aspect, survey sub-region (east or west of San Clemente Island (SCI)), time of year/day, and calf presence. Group size and maximum nearest-neighbor distance (in body lengths) generally increased with body size. Group size was significantly larger with calf presence for Risso’s, common, and bottlenose dolphins. Group size increased significantly across the year among Risso’s but decreased for common dolphins. Risso’s were 13x more likely to rest and significantly less likely to fast travel/be surface active than commons. Resource Selection Function analyses showed that fin whales were significantly more likely to be found west vs. east of SCI, and medium-fast travel predominated over basins vs. rest/mill/slow travel over steep slopes. Density was highest for short-beaked common dolphins followed by long-beaked commons, California sea lions, Risso’s, gray whales, bottlenose dolphins, fin, humpback and blue whales and Pacific white-sided dolphins. Calves occurred in 5% of 331 mysticete sightings.

In 2008-2012, fifteen aerial surveys of systematic line-transects were conducted off Southern California to obtain baseline data on occurrence, distribution, density, abundance and behavior of marine mammals (MM). Site characteristics at MM locations were analyzed by estimating Resource Selection Functions (RSF) to quantify and describe baseline habitat use as a precursor to assessing potential changes in these patterns relative to anthropogenic activities, including U.S. Navy training exercises. For RSF analyses, habitat characteristics at MM locations were contrasted to characteristics at 35,167 randomly selected “available” locations in the study area. RSFs were estimated via the use-availability approach and predicted probability of species occurrence at all locations in the study area as a function of seven covariate habitat variables. Models (n = 60 fin and 40 gray whale groups, 135 Risso’s and 31 bottlenose dolphin groups, 157 California sea lion groups) were fit for three behavior states (mill, rest/slow travel, medium/fast travel) and combined to document behavior/habitat associations. Species differed significantly in habitat use and corresponding habitat associations based on behavior. Medium-fast traveling fin whales were associated with deep water over flat basins/plateaus (p=0.0017). Fin whales also preferred the San Nicolas Basin (p=0.0517). Risso’s dolphins rested/slow traveled more in deep vs. shallow water (p=0.0803). Overall, resulting habitat-use patterns demonstrate fast movement across basins and rest/slow travel over ridges where upwelling is most likely to occur. The RSF approach quantitatively demonstrates the importance of considering behavior and social context in habitat selection and use.

The continental shelf break and slope off Cape Hatteras, NC supports one of the most diverse cetacean faunal assemblages in the western North Atlantic. Ongoing aerial and vessel-based surveys are characterizing the distribution and density of cetaceans in this region, but these surveys are limited by weather, daylight, and cryptic animal behavior. Passive acoustic monitoring (PAM) provides a rich picture of patterns of occurrence, acoustic behavior, and foraging ecology, particularly for deep-diving odontocetes such as sperm whales (Physeter macrocephalus) and beaked whales (Ziphius and Mesoplodonspp.). During March-April 2012, we collected the first PAM recordings from this site using a bottom-mounted High-frequency Acoustic Recording Package (HARP) moored at 950 m depth and sampling at 200 kHz. We analyzed the recordings by visually inspecting long-term spectral averages (LTSAs) and spectrograms. Odontocete clicks, whistles, and burst-pulse sounds occurred every recording day and across 77% of recording hours. Sperm whale clicks were present on 96% of recording days; the occurrence of these clicks did not differ significantly between day and night, in contrast to the diel pattern observed elsewhere along the southeastern U.S. coast. We identified several beaked whale click events; spectral click parameters and inter-click intervals suggest that these clicks were produced by two species, likely Ziphius cavirostris and Mesoplodon europaeus. Each click event was short in duration (4-20 min), but beaked whale clicks were detected on nearly 40% of recording days, underscoring the value of PAM in monitoring the occurrence of these cryptic species. In addition, we detected frequent calls of fin (Balaenoptera physalus) and minke (B. acutorostrata) whales. We are collecting year-round recordings off Cape Hatteras, which will generate baseline data and allow further comparisons of seasonal and diel patterns in the occurrence and acoustic activity of cetacean species at this site.

DDG N HRC Feb 2016

DDG T HRC Feb 2019

DDG J HRC Aug 2013

DDG H SOCAL July 2012

DDG I HRC Feb 2013

DDG F HRC Nov 2011

DDG G HRC Feb 2012

DDG L HRC Feb 2015