Genomic analyses reveal an absence of contemporary introgressive admixture between fin whales and blue whales, despite known hybrids.

Fin whales (Balaenoptera physalus) and blue whales (B. musculus) are the two largest species on Earth and are widely distributed across the world's oceans. Hybrids between these species appear to be relatively widespread and have been reported in both the North Atlantic and North Pacific; they are also relatively common, and have been proposed to occur once in every thousand fin whales. However, despite known hybridization, fin and blue whales are not sibling species. Rather, the closest living relative of fin whales are humpback whales (Megaptera novaeangliae). To improve the quality of fin whale data available for analysis, we assembled and annotated a fin whale nuclear genome using in-silico mate pair libraries and previously published short-read data. Using this assembly and genomic data from a humpback, blue, and bowhead whale, we investigated whether signatures of introgression between the fin and blue whale could be found. We find no signatures of contemporary admixture in the fin and blue whale genomes, although our analyses support ancestral gene flow between the species until 2.4-1.3 Ma. We propose the following explanations for our findings; i) fin/blue whale hybridization does not occur in the populations our samples originate from, ii) contemporary hybrids are a recent phenomenon and the genetic consequences have yet to become widespread across populations, or iii) fin/blue whale hybrids are under large negative selection, preventing them from backcrossing and contributing to the parental gene pools.

Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow.

Reconstructing the evolution of baleen whales (Mysticeti) has been problematic because morphological and genetic analyses have produced different scenarios. This might be caused by genomic admixture that may have taken place among some rorquals. We present the genomes of six whales, including the blue whale (Balaenoptera musculus), to reconstruct a species tree of baleen whales and to identify phylogenetic conflicts. Evolutionary multilocus analyses of 34,192 genome fragments reveal a fast radiation of rorquals at 10.5 to 7.5 million years ago coinciding with oceanic circulation shifts. The evolutionarily enigmatic gray whale (Eschrichtius robustus) is placed among rorquals, and the blue whale genome shows a high degree of heterozygosity. The nearly equal frequency of conflicting gene trees suggests that speciation of rorqual evolution occurred under gene flow, which is best depicted by evolutionary networks. Especially in marine environments, sympatric speciation might be common; our results raise questions about how genetic divergence can be established.

Seasonal and Diel Vocalization Patterns of Antarctic Blue Whale (Balaenoptera musculus intermedia) in the Southern Indian Ocean: A Multi-Year and Multi-Site Study.

Passive acoustic monitoring is an efficient way to provide insights on the ecology of large whales. This approach allows for long-term and species-specific monitoring over large areas. In this study, we examined six years (2010 to 2015) of continuous acoustic recordings at up to seven different locations in the Central and Southern Indian Basin to assess the peak periods of presence, seasonality and migration movements of Antarctic blue whales (Balaenoptera musculus intermedia). An automated method is used to detect the Antarctic blue whale stereotyped call, known as Z-call. Detection results are analyzed in terms of distribution, seasonal presence and diel pattern of emission at each site. Z-calls are detected year-round at each site, except for one located in the equatorial Indian Ocean, and display highly seasonal distribution. This seasonality is stable across years for every site, but varies between sites. Z-calls are mainly detected during autumn and spring at the subantarctic locations, suggesting that these sites are on the Antarctic blue whale migration routes, and mostly during winter at the subtropical sites. In addition to these seasonal trends, there is a significant diel pattern in Z-call emission, with more Z-calls in daytime than in nighttime. This diel pattern may be related to the blue whale feeding ecology.

Observations and Bayesian location methodology of transient acoustic signals (likely blue whales) in the Indian Ocean, using a hydrophone triplet.

A notable sequence of calls was encountered, spanning several days in January 2003, in the central part of the Indian Ocean on a hydrophone triplet recording acoustic data at a 250 Hz sampling rate. This paper presents signal processing methods applied to the waveform data to detect, group, extract amplitude and bearing estimates for the recorded signals. An approximate location for the source of the sequence of calls is inferred from extracting the features from the waveform. As the source approaches the hydrophone triplet, the source level (SL) of the calls is estimated at 187 ± 6 dB re: 1 µPa-1 m in the 15-60 Hz frequency range. The calls are attributed to a subgroup of blue whales, Balaenoptera musculus, with a characteristic acoustic signature. A Bayesian location method using probabilistic models for bearing and amplitude is demonstrated on the calls sequence. The method is applied to the case of detection at a single triad of hydrophones and results in a probability distribution map for the origin of the calls. It can be extended to detections at multiple triads and because of the Bayesian formulation, additional modeling complexity can be built-in as needed.

Software for real-time localization of baleen whale calls using directional sonobuoys: A case study on Antarctic blue whales.

Directional frequency analysis and recording (DIFAR) sonobuoys can allow real-time acoustic localization of baleen whales for underwater tracking and remote sensing, but limited availability of hardware and software has prevented wider usage. These software limitations were addressed by developing a module in the open-source software PAMGuard. A case study is presented demonstrating that this software provides greater efficiency and accessibility than previous methods for detecting, localizing, and tracking Antarctic blue whales in real time. Additionally, this software can easily be extended to track other low and mid frequency sounds including those from other cetaceans, pinnipeds, icebergs, shipping, and seismic airguns.

Discrimination of frequency-modulated Baleen whale downsweep calls with overlapping frequencies.

Automatic classification of fin, sei, and blue whale frequency modulated downsweeps has been a challenging task for bioacousticians. These calls overlap in frequency range and have similar time durations. The traditional spectrogram methodology, the Short Time Fourier Transform, tends to be ineffective because of the large temporal ambiguities needed to achieve the necessary frequency resolution to study the fine time-frequency (TF) structures. Spectrograms generated with the Pseudo Wigner-Ville Distribution (PWVD) provide much higher simultaneous TF resolution compared with the traditional method. The PWVD allows bioacousticians to study the fine TF structures of the sound, such as the instantaneous frequency, instantaneous bandwidth, contour slope, etc. These features set the foundation of identifying sounds that are usually considered difficult to discriminate using the traditional method. Wigner-Ville distribution of the baleen whale downsweeps showed distinguishable characteristics; for example, the TF contour of fin and sei whales exhibited concave and convex shapes, which have never been reported in the literature. A Support Vector Machine classifier was trained and tested based on the parameters extracted from the PWVD.

Blue whale vocalizations recorded around New Zealand: 1964-2013.

Previous underwater recordings made in New Zealand have identified a complex sequence of low frequency sounds that have been attributed to blue whales based on similarity to blue whale songs in other areas. Recordings of sounds with these characteristics were made opportunistically during the Southern Ocean Research Partnership's recent Antarctic Blue Whale Voyage. Detections of these sounds occurred all around the South Island of New Zealand during the voyage transits from Nelson, New Zealand to the Antarctic and return. By following acoustic bearings from directional sonobuoys, blue whales were visually detected and confirmed as the source of these sounds. These recordings, together with the historical recordings made northeast of New Zealand, indicate song types that persist over several decades and are indicative of the year-round presence of a population of blue whales that inhabits the waters around New Zealand. Measurements of the four-part vocalizations reveal that blue whale song in this region has changed slowly, but consistently over the past 50 years. The most intense units of these calls were detected as far south as 53°S, which represents a considerable range extension compared to the limited prior data on the spatial distribution of this population.

Population differentiation of 2 forms of Bryde's whales in the Indian and Pacific Oceans.

Accurate identification of units for conservation is particularly challenging for marine species as obvious barriers to gene flow are generally lacking. Bryde's whales (Balaenoptera spp.) are subject to multiple human-mediated stressors, including fisheries bycatch, ship strikes, and scientific whaling by Japan. For effective management, a clear understanding of how populations of each Bryde's whale species/subspecies are genetically structured across their range is required. We conducted a population-level analysis of mtDNA control region sequences with 56 new samples from Oman, Maldives, and Bangladesh, plus published sequences from off Java and the Northwest Pacific. Nine diagnostic characters in the mitochondrial control region and a maximum parsimony phylogenetic analysis identified 2 genetically recognized subspecies of Bryde's whale: the larger, offshore form, Balaenoptera edeni brydei, and the smaller, coastal form, Balaenoptera edeni edeni. Genetic diversity and differentiation indices, combined with a reconstructed maximum parsimony haplotype network, indicate strong differences in the genetic diversity and population structure within each subspecies. Discrete population units are identified for B. e. brydei in the Maldives, Java, and the Northwest Pacific and for B. e. edeni between the Northern Indian Ocean (Oman and Bangladesh) and the coastal waters of Japan.

Seasonal and geographic variation of southern blue whale subspecies in the Indian Ocean.

Understanding the seasonal movements and distribution patterns of migratory species over ocean basin scales is vital for appropriate conservation and management measures. However, assessing populations over remote regions is challenging, particularly if they are rare. Blue whales (Balaenoptera musculus spp) are an endangered species found in the Southern and Indian Oceans. Here two recognized subspecies of blue whales and, based on passive acoustic monitoring, four "acoustic populations" occur. Three of these are pygmy blue whale (B.m. brevicauda) populations while the fourth is the Antarctic blue whale (B.m. intermedia). Past whaling catches have dramatically reduced their numbers but recent acoustic recordings show that these oceans are still important habitat for blue whales. Presently little is known about the seasonal movements and degree of overlap of these four populations, particularly in the central Indian Ocean. We examined the geographic and seasonal occurrence of different blue whale acoustic populations using one year of passive acoustic recording from three sites located at different latitudes in the Indian Ocean. The vocalizations of the different blue whale subspecies and acoustic populations were recorded seasonally in different regions. For some call types and locations, there was spatial and temporal overlap, particularly between Antarctic and different pygmy blue whale acoustic populations. Except on the southernmost hydrophone, all three pygmy blue whale acoustic populations were found at different sites or during different seasons, which further suggests that these populations are generally geographically distinct. This unusual blue whale diversity in sub-Antarctic and sub-tropical waters indicates the importance of the area for blue whales in these former whaling grounds.

Discovery of a sensory organ that coordinates lunge feeding in rorqual whales.

Top ocean predators have evolved multiple solutions to the challenges of feeding in the water. At the largest scale, rorqual whales (Balaenopteridae) engulf and filter prey-laden water by lunge feeding, a strategy that is unique among vertebrates. Lunge feeding is facilitated by several morphological specializations, including bilaterally separate jaws that loosely articulate with the skull, hyper-expandable throat pleats, or ventral groove blubber, and a rigid y-shaped fibrocartilage structure branching from the chin into the ventral groove blubber. The linkages and functional coordination among these features, however, remain poorly understood. Here we report the discovery of a sensory organ embedded within the fibrous symphysis between the unfused jaws that is present in several rorqual species, at both fetal and adult stages. Vascular and nervous tissue derived from the ancestral, anterior-most tooth socket insert into this organ, which contains connective tissue and papillae suspended in a gel-like matrix. These papillae show the hallmarks of a mechanoreceptor, containing nerves and encapsulated nerve termini. Histological, anatomical and kinematic evidence indicate that this sensory organ responds to both the dynamic rotation of the jaws during mouth opening and closure, and ventral groove blubber expansion through direct mechanical linkage with the y-shaped fibrocartilage structure. Along with vibrissae on the chin, providing tactile prey sensation, this organ provides the necessary input to the brain for coordinating the initiation, modulation and end stages of engulfment, a paradigm that is consistent with unsteady hydrodynamic models and tag data from lunge-feeding rorquals. Despite the antiquity of unfused jaws in baleen whales since the late Oligocene (∼23-28 million years ago), this organ represents an evolutionary novelty for rorquals, based on its absence in all other lineages of extant baleen whales. This innovation has a fundamental role in one of the most extreme feeding methods in aquatic vertebrates, which facilitated the evolution of the largest vertebrates ever.

Circumpolar diversity and geographic differentiation of mtDNA in the critically endangered Antarctic blue whale (Balaenoptera musculus intermedia).

The Antarctic blue whale (Balaenoptera musculus intermedia) was hunted to near extinction between 1904 and 1972, declining from an estimated initial abundance of more than 250,000 to fewer than 400. Here, we describe mtDNA control region diversity and geographic differentiation in the surviving population of the Antarctic blue whale, using 218 biopsy samples collected under the auspices of the International Whaling Commission (IWC) during research cruises from 1990-2009. Microsatellite genotypes and mtDNA sequences identified 166 individuals among the 218 samples and documented movement of a small number of individuals, including a female that traveled at least 6,650 km or 131° longitude over four years. mtDNA sequences from the 166 individuals were aligned with published sequences from 17 additional individuals, resolving 52 unique haplotypes from a consensus length of 410 bp. From this minimum census, a rarefaction analysis predicted that only 72 haplotypes (95% CL, 64, 86) have survived in the contemporary population of Antarctic blue whales. However, haplotype diversity was relatively high (0.968±0.004), perhaps as a result of the longevity of blue whales and the relatively recent timing of the bottleneck. Despite the potential for circumpolar dispersal, we found significant differentiation in mtDNA diversity (F(ST) = 0.032, p<0.005) and microsatellite alleles (F(ST) = 0.005, p<0.05) among the six Antarctic Areas historically used by the IWC for management of blue whales.

Balaenoptera omurai is a newly discovered baleen whale that represents an ancient evolutionary lineage.

Balaenoptera omurai, formerly classified as a small form of Bryde's whale, was recently reclassified as a new baleen whale species of the family Balaenopteridae. Although researchers have investigated the evolutionary history of Balaenopteridae and their relatives using molecular phylogenetic methods, the taxonomy of the ordinary Bryde's whale (Balaenoptera brydei) and small-form Bryde's whales (Balaenoptera edeni and B. omurai) remains unclear. We have used complete mtDNA sequences and short interspersed repetitive element (SINE) insertion patterns to construct the evolutionary history of both B. omurai and the taxonomically redefined species, B. edeni. The combined results demonstrate that B. omurai forms a monophyletic lineage with B. musculus, B. brydei, B. edeni and B. borealis and that B. omurai and B. musculus successively diverged from their common ancestor. In addition, we also showed that B. edeni constitutes a sister taxon to B. brydei. Our data suggest that B. omurai evolved as an ancient independent lineage that diverged much earlier than B. borealis, B. brydei and B. edeni, which were previously believed to be closely related to B. omurai.