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The evolution of cetaceans, fromtheir early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, although the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea,we combined sequence capture with Illumina sequencing to generate data for ∼3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from >38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic data set for cetaceans, spanning 6,527,596 aligned base pairs (bp) and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among oceanic dolphins, especially the problematic subfamily Delphinidae. We carried out Bayesian estimation of species divergence times using MCMCTree andcompared ourcomplete data set to a subset of clocklike genes. Analyses using the complete data set consistently showed less variance in divergence times than the reduced data set. In addition, integration of new fossils (e.g., Mystacodon selenensis) indicates that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as theMiddle Miocene.

Cuvier's beaked whales (Ziphius cavirostris) are known as extreme divers, though behavioral data from this difficult-to-study species have been limited. They are also the species most often stranded in association with Mid-Frequency Active (MFA) sonar use, a relationship that remains poorly understood. We used satellite-linked tags to record the diving behavior and locations of eight Ziphius off the Southern California coast for periods up to three months. The effort resulted in 3732 hr of dive data with associated regional movements--the first dataset of its kind for any beaked whale--and included dives to 2992 m depth and lasting 137.5 min, both new mammalian dive records. Deep dives had a group mean depth of 1401 m (s.d. = 137.8, n = 1142) and duration of 67.4 min (s.d. = 6.9). The group mean time between deep dives was 102.3 min (s.d. = 30.8, n = 783). While the previously described stereotypic pattern of deep and shallow dives was apparent, there was considerable inter- and intra-individual variability in most parameters. There was significant diel behavioral variation, including increased time near the surface and decreased shallow diving at night. However, maximum depth and the proportion of time spent on deep dives (presumed foraging), varied little from day to night. Surprisingly, tagged whales were present within an MFA sonar training range for 38% of days locations were received, and though comprehensive records of sonar use during tag deployments were not available, we discuss the effects frequent acoustic disturbance may have had on the observed behaviors. These data better characterize the true behavioral range of this species, and suggest caution should be exercised when drawing conclusions about behavior using short-term datasets.

Historical patterns of species diversity inferred from phylogenies typically contradict the direct evidence found in the fossil record. According to the fossil record, species frequently go extinct, and many clades experience periods of dramatic diversity loss. However, most analyses of molecular phylogenies fail to identify any periods of declining diversity, and they typically infer low levels of extinction. This striking inconsistency between phylogenies and fossils limits our understanding of macroevolution, and it undermines our confidence in phylogenetic inference. Here, we show that realistic extinction rates and diversity trajectories can be inferred from molecular phylogenies. To make this inference, we derive an analytic expression for the likelihood of a phylogeny that accommodates scenarios of declining diversity, time-variable rates, and incomplete sampling; we show that this likelihood expression reliably detects periods of diversity loss using simulation. We then study the cetaceans (whales, dolphins, and porpoises), a group for which standard phylogenetic inferences are strikingly inconsistent with fossil data. When the cetacean phylogeny is considered as a whole, recently radiating clades, such as the Balaneopteridae, Delphinidae, Phocoenidae, and Ziphiidae, mask the signal of extinctions. However, when isolating these groups, we infer diversity dynamics that are consistent with the fossil record. These results reconcile molecular phylogenies with fossil data, and they suggest that most extant cetaceans arose from four recent radiations, with a few additional species arising from clades that have been in decline over the last ∼10 Myr.

Mid-frequency active sonar (MFAS), used for antisubmarine warfare (ASW), has been associated with multiple beaked whale (BW) mass stranding events. Multinational naval ASW exercises have used MFAS offshore of the Mariana Archipelago semi-annually since 2006. We report BW and MFAS acoustic activity near the islands of Saipan and Tinian from March 2010 to November 2014. Signals from Cuvier's ( Ziphius cavirostris) and Blainville's beaked whales ( Mesoplodon densirostris ), and a third unidentified BW species, were detected throughout the recording period. Both recorders documented MFAS on 21 August 2011 before two Cuvier's beaked whales stranded on 22–23 August 2011. We compared the history of known naval operations and BW strandings from the Mariana Archipelago to consider potential threats to BW populations. Eight BW stranding events between June 2006 and January 2019 each included one to three animals. Half of these strandings occurred during or within 6 days after naval activities, and this co-occurrence is highly significant. We highlight strandings of individual BWs can be associated with ASW, and emphasize the value of ongoing passive acoustic monitoring, especially for beaked whales that are difficult to visually detect at sea. We strongly recommend more visual monitoring efforts, at sea and along coastlines, for stranded cetaceans before, during and after naval exercises.

Dynamic body acceleration (DBA) has been used as a proxy for energy expenditure in logger-equipped animals, with researchers summing the acceleration (overall dynamic body acceleration--ODBA) from the three orthogonal axes of devices. The vector of the dynamic body acceleration (VeDBA) may be a better proxy so this study compared ODBA and VeDBA as proxies for rate of oxygen consumption using humans and 6 other species. Twenty-one humans on a treadmill ran at different speeds while equipped with two loggers, one in a straight orientation and the other skewed, while rate of oxygen consumption (VO2) was recorded. Similar data were obtained from animals but using only one (straight) logger. In humans, both ODBA and VeDBA were good proxies for VO2 with all r(2) values exceeding 0.88, although ODBA accounted for slightly but significantly more of the variation in VO2 than did VeDBA (P<0.03). There were no significant differences between ODBA and VeDBA in terms of the change in VO2 estimated by the acceleration data in a simulated situation of the logger being mounted straight but then becoming skewed (P = 0.744). In the animal study, ODBA and VeDBA were again good proxies for VO2 with all r(2) values exceeding 0.70 although, again, ODBA accounted for slightly, but significantly, more of the variation in VO2 than did VeDBA (P<0.03). The simultaneous contraction of muscles, inserted variously for limb stability, may produce muscle oxygen use that at least partially equates with summing components to derive DBA. Thus, a vectorial summation to derive DBA cannot be assumed to be the more 'correct' calculation. However, although within the limitations of our simple study, ODBA appears a marginally better proxy for VO2. In the unusual situation where researchers are unable to guarantee at least reasonably consistent device orientation, they should use VeDBA as a proxy for VO2.

A combination of machine learning and expert analyst review was used to detect odontocete echolocation clicks, identify dominant click types, and classify clicks in 32 years of acoustic data collected at 11 autonomous monitoring sites in the western North Atlantic between 2016 and 2019. Previously-described click types for eight known odontocete species or genera were identified in this data set: Blainville’s beaked whales ( Mesoplodon densirostris ), Cuvier’s beaked whales ( Ziphius cavirostris ), Gervais’ beaked whales ( Mesoplodon europaeus ), Sowerby’s beaked whales ( Mesoplodon bidens ), and True’s beaked whales ( Mesoplodon mirus ), Kogia spp ., Risso’s dolphin ( Grampus griseus ), and sperm whales ( Physeter macrocephalus ). Six novel delphinid echolocation click types were identified and named according to their median peak frequencies. Consideration of the spatiotemporal distribution of these unidentified click types, and comparison to historical sighting data, enabled assignment of the probable species identity to three of the six types, and group identity to a fourth type. UD36, UD26, and UD28 were attributed to Risso’s dolphin ( G . griseus ), short-finned pilot whale ( G . macrorhynchus ), and short-beaked common dolphin ( D . delphis ), respectively, based on similar regional distributions and seasonal presence patterns. UD19 was attributed to one or more species in the subfamily Globicephalinae based on spectral content and signal timing. UD47 and UD38 represent distinct types for which no clear spatiotemporal match was apparent. This approach leveraged the power of big acoustic and big visual data to add to the catalog of known species-specific acoustic signals and yield new inferences about odontocete spatiotemporal distribution patterns. The tools and call types described here can be used for efficient analysis of other existing and future passive acoustic data sets from this region.

Fear of predation can induce profound changes in the behaviour and physiology of prey species even if predator encounters are infrequent. For echolocating toothed whales, the use of sound to forage exposes them to detection by eavesdropping predators, but while some species exploit social defences or produce cryptic acoustic signals, deep-diving beaked whales, well known for mass-strandings induced by navy sonar, seem enigmatically defenceless against their main predator, killer whales. Here we test the hypothesis that the stereotyped group diving and vocal behaviour of beaked whales has benefits for abatement of predation risk and thus could have been driven by fear of predation over evolutionary time. Biologging data from 14 Blainville's and 12 Cuvier's beaked whales show that group members have an extreme synchronicity, overlapping vocal foraging time by 98% despite hunting individually, thereby reducing group temporal availability for acoustic detection by killer whales to <25%. Groups also perform a coordinated silent ascent in an unpredictable direction, covering a mean of 1 km horizontal distance from their last vocal position. This tactic sacrifices 35% of foraging time but reduces by an order of magnitude the risk of interception by killer whales. These predator abatement behaviours have likely served beaked whales over millions of years, but may become maladaptive by playing a role in mass strandings induced by man-made predator-like sonar sounds.

Although modern beaked whales (Ziphiidae) are known to be highly specialized toothed whales that predominantly feed at great depths upon benthic and benthopelagic prey, only limited palaeontological data document this major ecological shift. We report on a ziphiid–fish assemblage from the Late Miocene of Peru that we interpret as the first direct evidence of a predator–prey relationship between a ziphiid and epipelagic fish. Preserved in a dolomite concretion, a skeleton of the stem ziphiid Messapicetus gregarius was discovered together with numerous skeletons of a clupeiform fish closely related to the epipelagic extant Pacific sardine (Sardinops sagax). Based on the position of fish individuals along the head and chest regions of the ziphiid, the lack of digestion marks on fish remains and the homogeneous size of individuals, we propose that this assemblage results from the death of the whale (possibly via toxin poisoning) shortly after the capture of prey from a single school. Together with morphological data and the frequent discovery of fossil crown ziphiids in deep-sea deposits, this exceptional record supports the hypothesis that only more derived ziphiids were regular deep divers and that the extinction of epipelagic forms may coincide with the radiation of true dolphins.

Depth distributions were analyzed from a study of 19 Cuvier’s beaked whales Ziphius cavirostris that were tagged with satellite transmitting instruments off southern California, USA. Over 113 000 depth measurements were made over the equivalent of ∼200 sampling days. The mean foraging depth was 1182 m (SD = 305 m), and the mean of the maximum depth of all foraging dives was 1427 m (SD = 298 m). Mean foraging depths increased with seafloor depths up to a maximum of ∼1300 m at a seafloor depth of 1900 m, but decreased slightly to a mean of ∼1200 m at seafloor depths of 2000–4000 m. Near-bottom habitat appears to be important for foraging; whales spent ∼30% of their foraging time within 200 m of the bottom at seafloor depths of 1000–2000 m. However, little foraging time was spent near the bottom at seafloor depths greater than 2000 m. The percentage of time spent at near-surface depths (< 50 m) was more than twice as high at night (25%) than during the day (12%). Lunar light also appears to affect diving, with 28% of dark nights and only 17% of brightly moonlit nights spent at these near-surface depths. The apparent avoidance of surface waters during daytime and on brightly moonlit nights is consistent with avoidance of visual predators. A considerably greater fraction of time was spent foraging at night (24.8%) than during the day (15.7%), possibly due to energetic constraints imposed by predator avoidance during the day.

Detection and identification of species, subspecies or stocks of whales, dolphins and porpoises at sea remain challenging, particularly for cryptic or elusive species like beaked whales (Family: Ziphiidae). Here we investigated the potential for using an acoustically assisted sampling design to collect environmental (e)DNA from beaked whales on the U.S. Navy’s Atlantic Undersea Test and Evaluation Center (AUTEC) in The Bahamas. During 12 days of August 2019, we conducted 9 small-boat surveys and collected 56 samples of seawater (paired subsamples of 1L each, including controls) using both a spatial collection design in the absence of visual confirmation of whales, and a serial collection design in the proximity of whales at the surface. There were 7 sightings of whales, including 11 Blainville’s beaked whales ( Mesoplodon densirostris ). All whales were located initially with the assistance of information from a bottom-mounted acoustic array available on the AUTEC range. Quantification by droplet digital (dd)PCR from the four spatial design collections showed no samples of eDNA above the threshold of detection and none of these 20 samples yielded amplicons for conventional or next-generation sequencing. Quantification of the 31 samples from four serial collections identified 11 likely positive detections. eDNA barcoding by conventional sequencing and eDNA metabarcoding by next-generation sequencing confirmed species identification for 9 samples from three of the four serial collections. We further resolved five intra-specific variants (i.e., haplotypes), two of which showed an exact match to previously published haplotypes and three that have not been reported previously to the international repository, GenBank. A minimum spanning network of the five eDNA haplotypes, with all other published haplotypes of Blainville’s beaked whales, suggested the potential for further resolution of differences between oceanic populations.