Evaluating the utility of cox1 for cetacean species identification

The mitochondrial cytochrome c oxidase I (cox1) gene has been promoted as a universal reference gene, or barcode, to identify organisms to the species level. We evaluated whether cox1 would be appropriate to diagnose cetacean species. The 5′ end of cox1 (686 base pairs, bp) was sequenced for 46 of 86 recognized species of cetaceans. In addition, we included 105 sequences from GenBank, increasing our taxonomic coverage to 61 species. Particular focus was placed on sampling two subfamilies that contain closely related taxa: the Delphininae and the Globicephalinae. Species‐specific sequences were observed for all but three taxa (Delphinus delphis, D. capensis, and Stenella coeruleoalba). Although correct assignment was seen for most species, significant overlap between intra‐ and interspecific variation makes cox1 an imperfect barcode for cetaceans. The efficacy of cox1 was compared to the 5′ end of the cytochrome b (cytb) gene, a mitochondrial region routinely used for cetacean species identification. Although cytb performed better than cox1 for some species, this marker could not differentiate other closely related taxa (Eubalaena spp.). Species identification for taxa not reliably identified using cox1 or cytb might be best addressed through use of multiple mitochondrial DNA fragments or other newly developed markers.     

Whale tear glands in the bowhead and the beluga whales: Source and function

Orbital glands are found in many tetrapod vertebrates, and are usually separate structures, consisting of individual glands lying in the eyelids and both canthi of the orbit. In cetaceans, however, the orbital glandular units are less distinct and have been described by numerous authors as a single, periorbital mass. There are few histochemical and immunhistochemical studies to date of these structures. In this study, we examined the orbital glandular region of both the bowhead whale (Balaena mysticetus: Mysticeti) and the beluga whale (Delphinapterus leucas: Odontoceti) using histological, histochemical, and immunohistochemical techniques. Histologically, in the bowhead, three glandular areas were noted (circumorbital, including Harderian and lacrimal poles), palpebral (midway in the lower eyelid), and rim (near the edge of the eyelid). In the beluga, there was only a large, continuous mass within the eyelid itself. Histochemical investigation suggests neither sexual dimorphism nor age-related differences, but both whales had two cell types freely intermingling with each other in all glandular masses. Large cells (cell type 1) were distended by four histochemically distinct intracellular secretory granules. Smaller cells (cell type 2) were not distended (fewer granules) and had two to three histochemically distinct intracellular secretory granules. The beluga orbital glands had additional lipid granules in cell type 1. Counterintuitively, both lipocalin and transferrin were localized to cell type 2 only. This intermingling of cell types is unusual for vertebrates in whom individual orbital glands usually have one cell type with one to two different secretory granules present. The heterogeneity of the orbital fluid produced by cetacean orbital glands implies a complex function, or series of functions, for these orbital glands and their role in producing the tear fluid.     

Mitochondrial DNA diversity of the Southwestern Atlantic humpback whale (Megaptera novaeangliae) breeding area off Brazil, and the potential connections to Antarctic feeding areas

In the Southwestern Atlantic Ocean, humpback whales migrate every winter to the Brazilian coast for breeding and calving in the Abrolhos Bank. This breeding stock represents the remnants of a larger population heavily exploited during the beginning of the 20th century. Despite its relevance to conservation efforts, the degree of current genetic variation and the migratory relationship with Antarctic feeding areas for this population are still largely unknown. To examine these questions, we sequenced ∼400 bp of the mitochondrial DNA control region from samples taken off the Brazilian coast (n = 171) and near the Antarctic Peninsula (n = 77). The genetic variability of the Brazilian humpback whale breeding population was high and similar to that found in other Southern Hemisphere breeding grounds. Phylogenetic analysis suggested the existence of a new mitochondrial clade that exists at low frequency among Southern Hemisphere populations. Direct comparison between the Brazilian and the Colombia breeding populations and the Antarctic Peninsula feeding population showed no genetic differentiation between this feeding region and the Colombian breeding area or between feeding Areas I and II near the Antarctic Peninsula. In contrast, these populations were genetically distinct from the Brazilian population. Two humpback whales sampled off South Georgia Islands, in the Scotia Sea, shared identical haplotypes to whales from Brazil. Our results, supported by photo-identification and satellite telemetry data, suggest that the main feeding area of the Southern Hemisphere humpback whale population is likely to be located near the South Georgia/South Sandwich Islands area and not in the Antarctic Peninsula.     

New Data About Seasonal Distribution and Migrations of Whales and Dolphins in the Sea of Okhotsk

This paper presents new data about the seasonal distribution of whales and dolphins in the Sea of Okhotsk including the ice period. Even under the most severe ice conditions, the migrating species of whales and dolphins may be encountered in the Sea of Okhotsk. In all seasons the density of cetaceans is higher in the eastern part of the sea, which is more abundant in fish.     

PREDICTING NUCLEAR GENE COALESCENCE FROM MITOCHONDRIAL DATA: THE THREE-TIMES RULE

Abstract.— Coalescence theory predicts when genetic drift at nuclear loci will result in fixation of sequence differences to produce monophyletic gene trees. However, the theory is difficult to apply to particular taxa because it hinges on genetically effective population size, which is generally unknown. Neutral theory also predicts that evolution of monophyly will be four times slower in nuclear than in mitochondrial genes primarily because genetic drift is slower at nuclear loci. Variation in mitochondrial DNA (mtDNA) within and between species has been studied extensively, but can these mtDNA data be used to predict coalescence in nuclear loci? Comparison of neutral theories of coalescence of mitochondrial and nuclear loci suggests a simple rule of thumb. The “three‐times rule” states that, on average, most nuclear loci will be monophyletic when the branch length leading to the mtDNA sequences of a species is three times longer than the average mtDNA sequence diversity observed within that species. A test using mitochondrial and nuclear intron data from seven species of whales and dolphins suggests general agreement with predictions of the three‐times rule. We define the coalescence ratio as the mitochondrial branch length for a species divided by intraspecific mtDNA diversity. We show that species with high coalescence ratios show nuclear monophyly, whereas species with low ratios have polyphyletic nuclear gene trees. As expected, species with intermediate coalescence ratios show a variety of patterns. Especially at very high or low coalescence ratios, the three‐times rule predicts nuclear gene patterns that can help detect the action of selection. The three‐times rule may be useful as an empirical benchmark for evaluating evolutionary processes occurring at multiple loci.     

Detection of baleen whale species using kernel dynamic mode decomposition-based feature extraction with a hidden Markov model

The negative effects of human activities within the ecological space of whales remains an issue of concern to marine ecologists. The accurate detection and subsequent classification of whale species are vital in mitigating these negative effects. Automatic detection techniques have come in handy for the efficient detection of the various whale species without human error. Hidden Markov model (HMM) remains one the most efficient detectors of whale species. However, its performance efficiency is greatly influenced by the feature vectors adapted with it. In this work, we propose the use of the kernel dynamic mode decomposition (kDMD) algorithm as a tool to extract features of baleen whale species, which are then adapted with HMM for their detection. Dynamic mode decomposition (DMD) is an eigendecomposition-based algorithm that is capable of extracting latent underlying features of non-linear signals such as those vocalised by whales. However, the underlying cost of DMD is the singular value decomposition (SVD), which adds significant complexity to the modes derivation steps. Thus, this work is introducing the kernel method into the DMD, in order to find a more efficient way of computing DMD without explicitly using the SVD algorithm. Furthermore, the feature formation steps in the original DMD was modified (mDMD) in this work, to make it more generic for datasets with sparse whale sound samples. The performance of the detectors was tested on datasets containing sounds of southern right whales (SRWs) and humpback whales. The results obtained show a high true positive rate (TPR), high precision (PREC) and low error rate (ERR) for both species. The performance of the three DMD-based feature-extraction methods were compared. The kDMD-HMM generally performed better than the mDMD-HMM and DMD-HMM detectors. The methods proposed here can be tailored for the automatic detection and classification of other vocalising animal species through their sounds.     

False killer whales and fisheries interactions in Hawaiian waters: Evidence for sex bias and variation among populations and social groups

We assessed scarring patterns as evidence of fisheries interactions for three populations of false killer whales in Hawai‘i. Bycatch of the pelagic population in the tuna longline fishery exceeds their Potential Biological Removal level. Scarring was assessed by seven evaluators as consistent, possibly consistent, or not consistent with fisheries interactions, and average scores computed. Scores were highest for scarred main Hawaiian Island (MHI) false killer whales, followed by pelagic and Northwestern Hawaiian Island (NWHI) individuals. Considering only whales for which the majority of evaluators scored scarring as consistent revealed significant differences among populations in the percentage of individuals scarred; MHI: 7.5%, pelagic: 0%, NWHI: 0%. Assessment by social cluster for the MHI population showed that 4.2% of Cluster 1, 7.1% of Cluster 2, and 12.8% of Cluster 3 individuals had such scarring, although differences between clusters were not statistically significant. There was a significant sex bias; all sexed individuals (n = 7) with injuries consistent with fisheries interactions were female. The higher proportion of MHI individuals with fisheries‐related scarring suggests that fisheries interactions are occurring at a higher rate in this population. The bias towards females suggests that fisheries‐related mortality has a disproportionate impact on population dynamics.     

Whale killers: Prevalence and ecological implications of killer whale predation on humpback whale calves off Western Australia

Reports of killer whales (Orcinus orca) preying on large whales have been relatively rare, and the ecological significance of these attacks is controversial. Here we report on numerous observations of killer whales preying on neonate humpback whales (Megaptera novaeangliae) off Western Australia (WA) based on reports we compiled and our own observations. Attacking killer whales included at least 19 individuals from three stable social groupings in a highly connected local population; 22 separate attacks with known outcomes resulted in at least 14 (64%) kills of humpback calves. We satellite‐tagged an adult female killer whale and followed her group on the water for 20.3 h over six separate days. During that time, they attacked eight humpback calves, and from the seven known outcomes, at least three calves (43%) were killed. Overall, our observations suggest that humpback calves are a predictable, plentiful, and readily taken prey source for killer whales and scavenging sharks off WA for at least 5 mo/yr. Humpback “escorts” vigorously assisted mothers in protecting their calves from attacking killer whales (and a white shark, Carcharodon carcharias). This expands the purported role of escorts in humpback whale social interactions, although it is not clear how this behavior is adaptive for the escorts.