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.

Fin whale (Balaenoptera physalus) mitogenomics: A cautionary tale of defining sub-species from mitochondrial sequence monophyly.

The advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point was illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013), which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 380 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para- or polyphyly) can lead to erroneous conclusions due to relatively "trivial" aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to the most recent common ancestor and hence the probability that individuals in a sample are monophyletic.

Estimating range to a vocalizing fin whale using the timing and amplitude of multipath arrivals.

A semi-automated method is described to range to vocalizing fin whales using the timing and amplitude of multipath arrivals measured on seafloor receivers. Calls are detected and multipath arrivals identified with a matched filter. Multipath times and relative amplitudes are predicted as a function of range by ray tracing. Because the direct and first water-column multiple arrivals are not always observed, different hypotheses for the observed arrival paths must be considered. For two arrivals, an amplitude threshold is used to determine if the first arrival is the direct path and if not, the call is disregarded as distant. When three or more arrivals are detected, three hypotheses for the paths of arrivals are considered; the solution is the hypothesis and range that minimizes the timing and optionally, amplitude ratio or absolute amplitude residual. The method is tested with data from two ocean bottom seismometers, one on the Juan de Fuca Ridge and the other in the Cascadia Basin. Solutions obtained by minimizing a combined residual from timing and an empirical absolute amplitude model extracted from the data yield reliable ranges up to 5 km at both sites, and are sufficient to estimate call density using point transect distance sampling.

Tracing the spatio-temporal dynamics of endangered fin whales (Balaenoptera physalus) within baleen whale (Mysticeti) lineages: a mitogenomic perspective.

To explore the spatio-temporal dynamics of endangered fin whales (Balaenoptera physalus) within the baleen whale (Mysticeti) lineages, we analyzed 148 published mitochondrial genome sequences of baleen whales. We used a Bayesian coalescent approach as well as Bayesian inferences and maximum likelihood methods. The results showed that the fin whales had a single maternal origin, and that there is a significant correlation between geographic location and evolution of global fin whales. The most recent common female ancestor of this species lived approximately 9.88 million years ago (Mya). Here, North Pacific fin whales first appeared about 7.48 Mya, followed by a subsequent divergence in Southern Hemisphere approximately 6.63 Mya and North Atlantic about 4.42 Mya. Relatively recently, approximately 1.76 and 1.42 Mya, there were two additional occurrences of North Pacific populations; one originated from the Southern Hemisphere and the other from an uncertain location. The evolutionary rate of this species was 1.002 × 10-3 substitutions/site/My. Our Bayesian skyline plot illustrates that the fin whale population has the rapid expansion event since ~ 2.5 Mya, during the Quaternary glaciation stage. Additionally, this study indicates that the fin whale has a sister group relationship with humpback whale (Meganoptera novaeangliae) within the baleen whale lineages. Of the 16 genomic regions, NADH5 showed the most powerful signal for baleen whale phylogenetics. Interestingly, fin whales have 16 species-specific amino acid residues in eight mitochondrial genes: NADH2, COX2, COX3, ATPase6, ATPase8, NADH4, NADH5, and Cytb.

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.

Applying distance sampling to fin whale calls recorded by single seismic instruments in the northeast Atlantic.

Automated methods were developed to detect fin whale calls recorded by an array of ocean bottom seismometers (OBSs) deployed off the Portuguese coast between 2007 and 2008. Using recordings collected on a single day in January 2008, a standard seismological method for estimating earthquake location from single instruments, the three-component analysis, was used to estimate the relative azimuth, incidence angle, and horizontal range between each OBS and detected calls. A validation study using airgun shots, performed prior to the call analysis, indicated that the accuracy of the three-component analysis was satisfactory for this preliminary study. Point transect sampling using cue counts, a form of distance sampling, was then used to estimate the average probability of detecting a call via the array during the chosen day. This is a key step to estimating density or abundance of animals using passive acoustic data. The average probability of detection was estimated to be 0.313 (standard error: 0.033). However, fin whale density could not be estimated due to a lack of an appropriate estimate of cue (i.e., vocalization) rate. This study demonstrates the potential for using a sparse array of widely spaced, independently operating acoustic sensors, such as OBSs, for estimating cetacean density.

Mitogenomic phylogenetics of fin whales (Balaenoptera physalus spp.): genetic evidence for revision of subspecies.

There are three described subspecies of fin whales (Balaenoptera physalus): B. p. physalus Linnaeus, 1758 in the Northern Hemisphere, B. p. quoyi Fischer, 1829 in the Southern Hemisphere, and a recently described pygmy form, B. p. patachonica Burmeister, 1865. The discrete distribution in the North Pacific and North Atlantic raises the question of whether a single Northern Hemisphere subspecies is valid. We assess phylogenetic patterns using ~16 K base pairs of the complete mitogenome for 154 fin whales from the North Pacific, North Atlantic--including the Mediterranean Sea--and Southern Hemisphere. A Bayesian tree of the resulting 136 haplotypes revealed several well-supported clades representing each ocean basin, with no haplotypes shared among ocean basins. The North Atlantic haplotypes (n = 12) form a sister clade to those from the Southern Hemisphere (n = 42). The estimated time to most recent common ancestor (TMRCA) for this Atlantic/Southern Hemisphere clade and 81 of the 97 samples from the North Pacific was approximately 2 Ma. 14 of the remaining North Pacific samples formed a well-supported clade within the Southern Hemisphere. The TMRCA for this node suggests that at least one female from the Southern Hemisphere immigrated to the North Pacific approximately 0.37 Ma. These results provide strong evidence that North Pacific and North Atlantic fin whales should not be considered the same subspecies, and suggest the need for revision of the global taxonomy of the species.