A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography.

The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.

Comparative genomic studies on the TGF-ß superfamily in blue whale.

TGF-ß supergene family has a wide range of physiological functions including cell adhesion, motility, proliferation, apoptosis, and differentiation. We systematically analyzed and characterized the TGF-ß gene superfamily from the whole blue whale (Balaenoptera musculus) genome, using comparative genomic and evolutionary analysis. We identified 30 TGF-ß genes and were split into two subgroups, BMP-like and TGF-like. All TGF-ß proteins demonstrating a basic nature, with the exception of BMP1, BMP2, BMP10, GDF2, MSTN, and NODAL modulator, had acidic characteristics. All the blue whale (B. musculus) TGF-ß proteins, excluding BMP1, are thermostable based on aliphatic index. The instability index showed all proteins except the NODAL modulator was unstable. TGF-ß proteins showed a hydrophilic character, with the exception of GDF1 and INHBC. Moreover, all the detected TGF-ß genes showed evolutionary conserved nature. A segmental duplication was indicated by TGF-ß gene family, and the Ka/Ks ratio showed that the duplicated gene pairs were subjected to selection pressure, indicating both purifying and positive selection pressure. Two possible recombination breakpoints were also predicted. This study provides insights into the genetic characterization and evolutionary aspects of the TGF-ß superfamily in blue whales (B. musculus).

Application of a seismic network to baleen whale call detection and localization in the Panama basin-a Bryde's whale example.

Baleen whales use sounds of various characteristics for different tasks and interactions. This study focuses on recordings from the Costa Rica Rift, in the Eastern Tropical Pacific Ocean, made by 25 ocean-bottom seismographs and a vertical array of 12 hydrophones between January and February 2015. The whale calls observed are of two kinds: more commonly, repetitive 4-5 s-long signals separated into two frequency bands centered at ∼20 and ∼36 Hz; less commonly, a series of ∼0.5 to 1.0 s-long, lower amplitude signals with frequencies between 80 and 160 Hz. These characteristics are similar to calls attributed to Bryde's whales which are occasionally sighted in this region. In this study, the repetitive calls are detected using both the short-term average/long-term average approach and a network empirical subspace detector. In total, 188 and 1891 calls are obtained for each method, demonstrating the value of the subspace detector for highly similar signals. These signals are first localized using a non-linear grid search algorithm and then further relocalized using the double-difference technique. The high-resolution localizations reveal the presence of at least seven whales during the recording period, often crossing the instrument network from southwest to northeast.

Effects of duty cycle on passive acoustic monitoring metrics: The case of blue whale songs.

Long-term fixed passive acoustic monitoring of cetacean populations is a logistical and technological challenge, often limited by the battery capacity of the autonomous recorders. Depending on the research scope and target species, temporal subsampling of the data may become necessary to extend the deployment period. This study explores the effects of different duty cycles on metrics that describe patterns of seasonal presence, call type richness richness, and daily call rate of three blue whale acoustics populations in the Southern Indian Ocean. Detections of blue whale calls from continuous acoustic data were subsampled with three different duty cycles of 50%, 33%, and 25% within listening periods ranging from 1 min to 6 h. Results show that reducing the percentage of recording time reduces the accuracy of the observed seasonal patterns as well as the estimation of daily call rate and call call type richness. For a specific duty cycle, short listening periods (5-30 min) are preferred to longer listening periods (1-6 h). The effects of subsampling are greater the lower the species' vocal activity or the shorter their periods of presence. These results emphasize the importance of selecting a subsampling scheme adapted to the target species.

Characteristics and spatiotemporal variation of sei whale (Balaenoptera borealis) downsweeps recorded in Atlantic Canada.

The call characteristics and vocal behaviour of sei whales (Balaenoptera borealis) off eastern Canada, including potential spatiotemporal variation, is poorly understood. Such information can improve the performance of automated detector-classifiers, enhancing the accuracy and efficiency of identifying sei whales in large acoustic datasets. Ultimately, these data can be used to understand the occurrence, distribution, and population structure of sei whales in Atlantic Canada. We measured sei whale downsweep characteristics recorded from six locations off Nova Scotia (NS) and Newfoundland and Labrador (NFLD), Canada over a two-year period (2015-2017), and examined variation between call subtypes (singlets, doublets, triplets+), and seasons (Spring, Summer, Fall, Winter). We found that downsweeps had a mean duration of 1.58 s, sweeping from 75.66 to 34.22 Hz, with a peak frequency of 43.89 Hz and an intra-call interval of 2.22 s. Most call characteristics did not vary between location, subtype, or season; however, significantly longer downsweeps occurred off NS, within doublet calls, and in fall months. We also found that NFLD had a higher proportion of doublets (70%) than NS (52%). This variation may be evidence of acoustically diverging sei whale populations, as well as useful for improving detector-classifiers of sei whales in the region.

Estimating distances to baleen whales using multipath arrivals recorded by individual seafloor seismometers at full ocean depth.

Ocean bottom seismometer networks can record opportunistic data sets of 20-Hz fin whale calls. Because networks are often too sparse for multi-station tracking, single-station methods are needed to estimate call density. We investigated a method to range to singing fin whales at full ocean depths using the spacing of water column multiples. Calls were detected by cross-correlating a spectrogram with a template call. To enhance multipath signals, we considered 20-min windows and either summed the spectrograms of all calls aligned on the strongest detection before measuring the multipath spacing or measured the spacing directly from the autocorrelation of the cross correlation time series. We evaluated the methods at five sites with contrasting seafloor and subsurface properties, bathymetric relief, and water depths of 4000-6000 m, using fin whale songs at four sites and a sei whale song at the fifth. The autocorrelation method works best, and ranges can be obtained to >15 km. Ranging at sedimented sites requires careful accounting for subsurface reflections. Ranges have considerable uncertainty in regions of bathymetric relief. The method requires that the time between calls is different from that of the multipaths and does not work reliably when more than one whale is singing nearby.

Acoustic recording tags provide insight into the springtime acoustic behavior of sei whales in Massachusetts Bay.

The acoustic ecology of sei whales (Balaenoptera borealis) is poorly understood due to limited direct observation of the behavioral context of sound production and individual behavior. Suction cup-attached acoustic recording tags were deployed on sei whales to unambiguously assign call types and explore the acoustic behavior of this endangered species. Twelve tag deployments resulted in ∼173 h of acoustic data and 1030 calls. Sound types included downsweeps and three previously undescribed call types. Knocks were short duration (<1 s), with an average peak frequency of 330 Hz. Pulse type 1 and pulse type 2 calls, typically produced in sequences, were short in duration (0.08 and 0.28 s) and low in average peak frequency (50 and 26 Hz), with relatively high received levels. Average call rates for all call types combined were three calls per hour, but increased during twilight. Sex differences in call type usage included a higher use of pulses by females and knocks by males. Calls were almost exclusively produced at depths <10 m, although whales rarely dove deeper in this study. These data provide a more comprehensive picture of the acoustic and behavioral ecology of sei whales than previously possible, which can inform future conservation efforts for this endangered species.

A New Acoustical Autonomous Method for Identifying Endangered Whale Calls: A Case Study of Blue Whale and Fin Whale.

In this paper, we study to improve acoustical methods to identify endangered whale calls with emphasis on the blue whale (Balaenoptera musculus) and fin whale (Balaenoptera physalus). A promising method using wavelet scattering transform and deep learning is proposed here to detect/classify the whale calls quite precisely in the increasingly noisy ocean with a small dataset. The performances shown in terms of classification accuracy (>97%) demonstrate the efficiency of the proposed method which outperforms the relevant state-of-the-art methods. In this way, passive acoustic technology can be enhanced to monitor endangered whale calls. Efficient tracking of their numbers, migration paths and habitat become vital to whale conservation by lowering the number of preventable injuries and deaths while making progress in their recovery.

Oceanic giants dance to atmospheric rhythms: Ephemeral wind-driven resource tracking by blue whales.

Trophic transfer of energy through marine food webs is strongly influenced by prey aggregation and its exploitation by predators. Rapid aggregation of some marine fish and crustacean forage species during wind-driven coastal upwelling has recently been discovered, motivating the hypothesis that predators of these forage species track the upwelling circulation in which prey aggregation occurs. We examine this hypothesis in the central California Current Ecosystem using integrative observations of upwelling dynamics, forage species' aggregation, and blue whale movement. Directional origins of blue whale calls repeatedly tracked upwelling plume circulation when wind-driven upwelling intensified and aggregation of forage species was heightened. Our findings illustrate a resource tracking strategy by which blue whales may maximize energy gain amid ephemeral foraging opportunities. These findings have implications for the ecology and conservation of diverse predators that are sustained by forage populations whose behaviour is responsive to episodic environmental dynamics.

Blue whales increase feeding rates at fine-scale ocean features.

Marine predators face the challenge of reliably finding prey that is patchily distributed in space and time. Predators make movement decisions at multiple spatial and temporal scales, yet we have a limited understanding of how habitat selection at multiple scales translates into foraging performance. In the ocean, there is mounting evidence that submesoscale (i.e. less than 100 km) processes drive the formation of dense prey patches that should hypothetically provide feeding hot spots and increase predator foraging success. Here, we integrated environmental remote-sensing with high-resolution animal-borne biologging data to evaluate submesoscale surface current features in relation to the habitat selection and foraging performance of blue whales in the California Current System. Our study revealed a consistent functional relationship in which blue whales disproportionately foraged within dynamic aggregative submesoscale features at both the regional and feeding site scales across seasons, regions and years. Moreover, we found that blue whale feeding rates increased in areas with stronger aggregative features, suggesting that these features indicate areas of higher prey density. The use of fine-scale, dynamic features by foraging blue whales underscores the need to take these features into account when designating critical habitat and may help inform strategies to mitigate the impacts of human activities for the species.

An accelerometer-derived ballistocardiogram method for detecting heart rate in free-ranging marine mammals.

Physio-logging methods, which use animal-borne devices to record physiological variables, are entering a new era driven by advances in sensor development. However, existing datasets collected with traditional bio-loggers, such as accelerometers, still contain untapped eco-physiological information. Here, we present a computational method for extracting heart rate from high-resolution accelerometer data using a ballistocardiogram. We validated our method with simultaneous accelerometer-electrocardiogram tag deployments in a controlled setting on a killer whale (Orcinus orca) and demonstrate the predictions correspond with previously observed cardiovascular patterns in a blue whale (Balaenoptera musculus), including the magnitude of apneic bradycardia and increase in heart rate prior to and during ascent. Our ballistocardiogram method may be applied to mine heart rates from previously collected accelerometery data and expand our understanding of comparative cardiovascular physiology.

Mathematical models of long term evolution of blue whale song types' frequencies.

The linear decrease in the frequency of blue whale songs around the world is, to date, an unexplained phenomenon. We show it can be reproduced by a mathematical model considering two antagonistic behavioral trends: first, a bias towards conformity in the song, and second, a tendency to try and sing lower than the other whales. We check the robustness of our model by considering some more complex premises. First, different hierarchical relations between the singers are explored, adapting methods used in the flocking motion studies. Then a population-dependant simulation shows that even considering the gradual addition of new whales, the evolution is still globally linear. Finally, we show that intra-annual variations surging from different causes can be naturally incorporated into the model. We then conclude that, unlike other explanations, a cultural hypothesis seems compatible with the observed linearity of the blue whales's songs frequency shift.

A Preliminary Comparison on Faecal Microbiomes of Free-Ranging Large Baleen (Balaenoptera musculus, B. physalus, B. borealis) and Toothed (Physeter macrocephalus) Whales.

Large baleen and toothed whales play crucial ecological roles in oceans; nonetheless, very little is known about their intestinal microbiomes. Based on striking differences in natural history and thus in feeding behaviours, it can be expected that intestinal microbiomes of large baleen whales and toothed whales are different. To test this hypothesis, the phylogenetic composition of faecal microbiomes was investigated by a 16S rRNA gene amplicon sequence-based approach for Bacteria and Archaea. Faecal samples from free-ranging large whales collected off the Azores Archipelago (Portugal) were used, comprising 13 individual baleen whales (one sei, two blue and ten fin whales) and four sperm whales. The phylogenetic composition of the Bacteria faecal microbiomes of baleen and toothed whales showed no significant differences at the phylum level. However, significant differences were detected at the family and genus levels. Most abundant phyla were Firmicutes, Bacteroidetes, Proteobacteria, Tenericutes and Spirochaeta. Few highly abundant bacterial genera were identified as key taxa with a high contribution to differences among baleen and toothed whales microbiomes. Only few archaeal sequences were detected, primarily Methanomassiliicoccales representing potential methanogenic Archaea. This is the first study that directly compares the faecal bacterial and archaeal microbiomes of free-ranging baleen and toothed whales which represent the two parvorders of Cetacea which members are fully aquatic large mammals which were evolutionary split millions of years ago.

Memory and resource tracking drive blue whale migrations.

In terrestrial systems, the green wave hypothesis posits that migrating animals can enhance foraging opportunities by tracking phenological variation in high-quality forage across space (i.e., "resource waves"). To track resource waves, animals may rely on proximate cues and/or memory of long-term average phenologies. Although there is growing evidence of resource tracking in terrestrial migrants, such drivers remain unevaluated in migratory marine megafauna. Here we present a test of the green wave hypothesis in a marine system. We compare 10 years of blue whale movement data with the timing of the spring phytoplankton bloom resulting in increased prey availability in the California Current Ecosystem, allowing us to investigate resource tracking both contemporaneously (response to proximate cues) and based on climatological conditions (memory) during migrations. Blue whales closely tracked the long-term average phenology of the spring bloom, but did not track contemporaneous green-up. In addition, blue whale foraging locations were characterized by low long-term habitat variability and high long-term productivity compared with contemporaneous measurements. Results indicate that memory of long-term average conditions may have a previously underappreciated role in driving migratory movements of long-lived species in marine systems, and suggest that these animals may struggle to respond to rapid deviations from historical mean environmental conditions. Results further highlight that an ecological theory of migration is conserved across marine and terrestrial systems. Understanding the drivers of animal migration is critical for assessing how environmental changes will affect highly mobile fauna at a global scale.

Extreme bradycardia and tachycardia in the world's largest animal.

The biology of the blue whale has long fascinated physiologists because of the animal's extreme size. Despite high energetic demands from a large body, low mass-specific metabolic rates are likely powered by low heart rates. Diving bradycardia should slow blood oxygen depletion and enhance dive time available for foraging at depth. However, blue whales exhibit a high-cost feeding mechanism, lunge feeding, whereby large volumes of prey-laden water are intermittently engulfed and filtered during dives. This paradox of such a large, slowly beating heart and the high cost of lunge feeding represents a unique test of our understanding of cardiac function, hemodynamics, and physiological limits to body size. Here, we used an electrocardiogram (ECG)-depth recorder tag to measure blue whale heart rates during foraging dives as deep as 184 m and as long as 16.5 min. Heart rates during dives were typically 4 to 8 beats min-1 (bpm) and as low as 2 bpm, while after-dive surface heart rates were 25 to 37 bpm, near the estimated maximum heart rate possible. Despite extreme bradycardia, we recorded a 2.5-fold increase above diving heart rate minima during the powered ascent phase of feeding lunges followed by a gradual decrease of heart rate during the prolonged glide as engulfed water is filtered. These heart rate dynamics explain the unique hemodynamic design in rorqual whales consisting of a large-diameter, highly compliant, elastic aortic arch that allows the aorta to accommodate blood ejected by the heart and maintain blood flow during the long and variable pauses between heartbeats.

Extraction of Energy Characteristics of Blue Whale Vocalizations Based on Empirical Mode Decomposition.

This study extracts the energy characteristic distributions of the intrinsic mode functions (IMFs) and residue functions (RF) for a blue whale sound signal, with empirical mode decomposition (EMD) as the basic theoretical framework. A high-resolution marginal frequency characteristics extraction method, based on EMD with energy density intensity (EDI) parameters for blue B call vocalizations, was proposed. The extraction algorithm included six steps: EMD, energy analysis, marginal frequency (MF) analysis with EDI parameters, feature extraction (FE), classification, and Hilbert spectrum (HS) analysis. The blue whale sound sources were obtained from the website of the Scripps Whale Acoustics Lab of the University of California, San Diego, USA. The source is a type of B call with a time duration of 46.65 s, from which 59 analysis samples with a time duration of 180 ms were taken. The average energy distribution ratios of the IMF1, IMF2, IMF3, IMF4, and RF are 49.06%, 20.58%, 13.51%, 10.94% and 3.84%, respectively. New classification criteria and EDI parameters were proposed to extract the blue whale B call vocalization (BWBCV) characteristics. The analysis results show that the main frequency bands of the signal are distributed at 41-43 Hz in the MF of IMF1 for Class I BWBCV and 11-13 Hz in the MF of IMF2 for Class II BWBCV, respectively.

Searching for putative virulence factors in the genomes of Shewanella indica and Shewanella algae.

Bacterial pathogens are a major threat to both humans and animals worldwide. It is crucial to understand the mechanisms of various disease processes at the molecular level. Shewanella species are widespread in the environment and some are considered as emerging opportunistic human and marine mammal pathogens. In this study, putative virulence factors on the genome of Shewanella indica BW, a bacterium isolated from the Bryde's whale (Balaenoptera edeni), were determined. Additionally, for comparative purposes, putative virulence factors from two other S. indica and ten S. algae strains were also determined using the Pathosystems Resource Integration Center (PATRIC) pipeline. We confirmed the presence of previously reported virulence factors and we are proposing several new candidate virulence factors. Interestingly, the putative virulence factors were very similar between the two species with the exception of microbial collagenase which was present in all S. algae genomes, but absent in all S. indica genomes.

Scaling of oscillatory kinematics and Froude efficiency in baleen whales.

High efficiency lunate-tail swimming with high-aspect-ratio lifting surfaces has evolved in many vertebrate lineages, from fish to cetaceans. Baleen whales (Mysticeti) are the largest swimming animals that exhibit this locomotor strategy, and present an ideal study system to examine how morphology and the kinematics of swimming scale to the largest body sizes. We used data from whale-borne inertial sensors coupled with morphometric measurements from aerial drones to calculate the hydrodynamic performance of oscillatory swimming in six baleen whale species ranging in body length from 5 to 25 m (fin whale, Balaenoptera physalus; Bryde's whale, Balaenoptera edeni; sei whale, Balaenoptera borealis; Antarctic minke whale, Balaenoptera bonaerensis; humpback whale, Megaptera novaeangliae; and blue whale, Balaenoptera musculus). We found that mass-specific thrust increased with both swimming speed and body size. Froude efficiency, defined as the ratio of useful power output to the rate of energy input ( Sloop, 1978), generally increased with swimming speed but decreased on average with increasing body size. This finding is contrary to previous results in smaller animals, where Froude efficiency increased with body size. Although our empirically parameterized estimates for swimming baleen whale drag were higher than those of a simple gliding model, oscillatory locomotion at this scale exhibits generally high Froude efficiency as in other adept swimmers. Our results quantify the fine-scale kinematics and estimate the hydrodynamics of routine and energetically expensive swimming modes at the largest scale.

Blubber endocrine profiles provide insights into reproductive biology in blue whales from the eastern North Pacific Ocean.

The goal of the present study was to complement existing data of testosterone and progesterone in blue whale (Balaenoptera musculus) blubber from the eastern North Pacific Ocean to evaluate effects of seasonality and location on these hormones and to better assess reproductive status of individuals. Physiological parameters regarding reproduction are fundamental for describing population dynamics, and hormones can be a valid tool to estimate those for wildlife populations. In this study, blubber tissue was validated for testosterone and progesterone assays. Hormone concentrations were measured in 69 (35 males and 34 females) blubber samples from live (n = 66) and stranded (n = 3) animals collected between 2002 and 2016 from a known winter reproductive ground in the Gulf of California (GoC) and summer feeding areas along the United States West Coast (USWC), specifically off the states of California and Oregon. Results were combined with sighting histories as a tool to determine reproductive status of individual whales. Testosterone concentrations in adult male blue whales were significantly higher (p < 0.05) in blubber biopsies sampled off the USWC between the months of June and November compared to those sampled in the GoC between February and April. Elevated testosterone concentrations likely indicate physiological preparation for reproductive activity while the animals were present off the USWC. Progesterone concentrations were significantly elevated in pregnant females, confirming progesterone as an indicator of pregnancy in blue whales. Probabilities of being pregnant were estimated for adult females with unknown sighting histories based on progesterone concentrations. Testosterone in females was detected and measured only in pregnant whales suggesting its biosynthesis or metabolism is altered during gestation. These results provide updated and new information on the reproductive cycle of blue whales in the eastern North Pacific, posing new milestones to better estimate the timing of the mating season for this endangered population.

Investigation of keratinase digestion to improve steroid hormone extraction from diverse keratinous tissues.

Monitoring the physiology of wild populations presents many technical challenges. Blood samples, long the gold standard of wildlife endocrinology studies, cannot always be obtained. The validation and use of non-plasma samples to obtain hormone data have greatly improved access to more integrated information about an organism's physiological state. Keratinous tissues like skin, hair, nails, feathers, or baleen store steroid hormones in physiologically relevant concentrations, are stable across decades, and can be used to retrospectively infer physiological state at prior points in time. Most protocols for steroid extraction employ physical pulverization or cutting of the sample, followed by mixing with a solvent. Such methods do produce repeatable and useful data, but low hormone yield and detectability issues can complicate research on small or rare samples. We investigated the use of keratinase, an enzyme that breaks down keratin, to improve the extraction and yield of corticosterone from vertebrate keratin tissues. Corticosterone content of keratinase-digested extracts were compared to non-keratinase extracts for baleen from three species of whale (blue, Balaenoptera musculus; bowhead, Balaena mysticetus; southern right, SRW; Eubalaena australis), shed skin from two reptiles (tegu lizard, Salvator merianae; narrow-headed garter snake, Thamnophis rufipunctatus), hair from arctic ground squirrel (AGS; Urocitellus parryii), feathers from Purple Martins (PUMA; Progne subis), and spines from the short-beaked echidna (Tachyglossus aculeatus). We tested four starting masses (10, 25, 50, 100 mg) for each sample; digestion was most complete in the 10 and 25 mg samples. A corticosterone enzyme immunoassay (EIA) was validated for all keratinase-digested extracts. In all sample types except shed skin from reptiles, keratinase digestion improved hormone yield, with PUMA feathers and blue whale baleen having the greatest increase in apparent corticosterone content (100% and 66% more hormone, respectively). The reptilian shed skin samples did not benefit from keratinase digestion, actually yielding less hormone than controls. With further optimization and refinement, keratinase digestion could greatly improve yield of steroid hormones from various wildlife epidermal tissue types, allowing more efficient use of samples and ultimately improving understanding of the endocrine physiology of wild populations.