Humpback whales (Megaptera novaeangliae) wintering in Hawaiian waters engage in strenuous aggression toward con-specifics. The social context and sex of individuals involved suggest that aggression is the result of male–male competition for sexually mature females, including cows with newborn calves. Characteristic behaviors associated with aggression occur in a roughly hierarchical scaling of intensity and include broadside displays, underwater exhalations, head lunges (in which the throat is inflated and enlarged), physical displacement, and charge–strikes. Humpback whales do not form stable pair bonds during the winter breeding season; females are seen serially and simultaneously with multiple males and males are seen serially with multiple females. Repeated observations of individually identified whales indicate that escorting and singing are interchangeable reproductive roles of mature males. Incidents of aggression show a seasonal increase and decrease that parallel changes in abundance and average pod size. A seasonal peak in the frequency of aggression is probably related to an increase in population density and to changes in the reproductive physiology of mature males and females. It is suggested that singing may function, in part, to synchronize ovulation in females with the peak abundance of mature males on the wintering grounds.

We quantified the relative influence of maternal fidelity to feeding grounds and natal fidelity to breeding grounds on the population structure of humpback whales Megaptera novaeangliae based on an ocean-wide survey of mitochondrial (mt) DNA diversity in the North Pacific. For 2193 biopsy samples collected from whales in 10 feeding regions and 8 breeding regions during the winter and summer of 2004 to 2006, we first used microsatellite genotyping (average, 9.5 loci) to identify replicate samples. From sequences of the mtDNA control region (500 bp) we identified 28 unique haplotypes from 30 variable sites. Haplotype frequencies differed markedly among feeding regions (overall F ST = 0.121, Φ ST = 0.178, p < 0.0001), supporting previous evidence of strong maternal fidelity. Haplotype frequencies also differed markedly among breeding regions (overall F ST = 0.093, Φ ST = 0.106, p < 0.0001), providing evidence of strong natal fidelity. Although sex-biased dispersal was not evident, differentiation of microsatellite allele frequencies was weak compared to differentiation of mtDNA haplotypes, suggesting male-biased gene flow. Feeding and breeding regions showed significant differences in haplotype frequencies, even for regions known to be strongly connected by patterns of individual migration. Thus, the influence of migratory fidelity seems to operate somewhat independently on feeding and breeding grounds over an evolutionary time scale. This results in a complex population structure and the potential to define multiple units to conserve in either seasonal habitat.

Hunting during the last 200 years reduced many populations of mysticete whales to near extinction. To evaluate potential genetic bottlenecks in these exploited populations, we examined mitochondrial DNA control region sequences from 90 individual humpback whales (Megaptera novaeangliae) representing six subpopulations in three ocean basins. Comparisons of relative nucleotide and nucleotype diversity reveal an abundance of genetic variation in all but one of the oceanic subpopulations. Phylogenetic reconstruction of nucleotypes and analysis of maternal gene flow show that current genetic variation is not due to postexploitation migration between oceans but is a relic of past population variability. Calibration of the rate of control region evolution across three families of whales suggests that existing humpback whale lineages are of ancient origin. Preservation of preexploitation variation in humpback whales may be attributed to their long life-span and overlapping generations and to an effective, though perhaps not timely, international prohibition against hunting.Humpback whales (Megaptera novaeangliae) once numbered >125,000 individuals distributed into three oceanic populations: the North Pacific, the North Atlantic, and the southern oceans. Within each population, observations of migratory movement by marked individuals suggest that humpback whales form relatively discrete subpopulations that are not separated by obvious geographic barriers (1). Before protection by international agreement in 1966, the world-wide population of humpback whales had been reduced by hunting to <5000, with some regional subpopulations reduced to <200 individuals (Table 1).To evaluate the possibility that commercial hunting reduced genetic variation in baleen whales, we examined nucleotide sequence variation in the mitochondrial (mt) DNA from 90 humpback whales collected from the three major oceanic basins. We chose humpback whales for this evaluation because their well-described subpopulation divisions and well-documented history of exploitation provide a historical framework within which to evaluate genetic data (Table 1). We chose mtDNA as a genetic marker because of its power in describing the genetic structure of maternal lineages within populations and its sensitivity to demographic changes in populations (20). To allow the use of small skin samples collected by biopsy darting, we applied the polymerase chain reaction (PCR) and direct "solid-phase" sequencing methodology (21) to the mtDNA control region or "D-loop," a noncoding region that is highly variable in most vertebrates (22).The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.We first verified that oceanic populations of humpback whales are independent demographic units by estimating mtDNA gene flow with a cladistic analysis of the control region sequences. We then evaluated mtDNA diversity within each o...

Genetic sampling for identification of species, subspecies or stock of whales, dolphins and porpoises at sea remains challenging. Most samples have been collected with some form of a biopsy dart requiring a close approach of a vessel while the individual is at the surface. Here we have adopted droplet digital (dd)PCR technology for detection and species identification of cetaceans using environmental (e)DNA collected from seawater. We conducted a series of eDNA sampling experiments during 25 encounters with killer whales, Orcinus orca, in Puget Sound (the Salish Sea). The regular habits of killer whales in these inshore waters allowed us to locate pods and collect seawater, at an initial distance of 200 m and at 15-min intervals, for up to 2 h after the passage of the whales. To optimize detection, we designed a set of oligonucleotide primers and probes to target short fragments of the mitochondrial (mt)DNA control region, with a focus on identification of known killer whale ecotypes. We confirmed the potential to detect eDNA in the wake of the whales for up to 2 h, despite movement of the water mass by several kilometers due to tidal currents. Re-amplification and sequencing of the eDNA barcode confirmed that the ddPCR detection included the "southern resident community" of killer whales, consistent with the calls from hydrophone recordings and visual observations.

We estimated the abundance of humpback whales in the North Pacific by capture‐recapture methods using over 18,000 fluke identification photographs collected in 2004–2006. Our best estimate of abundance was 21,808 (CV = 0.04). We estimated the biases in this value using a simulation model. Births and deaths, which violate the assumption of a closed population, resulted in a bias of +5.2%, exclusion of calves in samples resulted in a bias of −10.5%, failure to achieve random geographic sampling resulted in a bias of −0.4%, and missed matches resulted in a bias of +9.3%. Known sex‐biased sampling favoring males in breeding areas did not add significant bias if both sexes are proportionately sampled in the feeding areas. Our best estimate of abundance was 21,063 after accounting for a net bias of +3.5%. This estimate is likely to be lower than the true abundance due to two additional sources of bias: individual heterogeneity in the probability of being sampled (unquantified) and the likely existence of an unknown and unsampled breeding area (−8.7%). Results confirm that the overall humpback whale population in the North Pacific has continued to increase and is now greater than some prior estimates of prewhaling abundance.

Humpback whales (Megaptera novaeangliae) migrate nearly 10,000 km each year between summer feeding grounds in temperate or near-polar waters and winter breeding grounds in shallow tropical waters. Observations of marked individuals suggest that major oceanic populations of humpback whales are divided into a number of distinct seasonal subpopulations which are not separated by obvious geographic barriers. To test whether these observed patterns of distribution and migration are reflected in the genetic structure of populations, we looked for variation in the mitochondrial DNA of 84 individual humpback whales on different feeding and wintering grounds of the North Pacific and western North Atlantic oceans. On the basis of restriction-fragment analysis, we now report a marked segregation of mitochondrial DNA haplotypes among subpopulations as well as between the two oceans. We interpret this segregation to be the consequence of maternally directed fidelity to migratory destinations.

Few studies have examined systematic relationships of right whales (Eubalaena spp.) since the original species descriptions, even though they are one of the most endangered large whales. Little morphological evidence exists to support the current species designations for Eubalaena glacialis in the northern hemisphere and E. australis in the southern hemisphere. Differences in migratory behaviour or antitropical distribution between right whales in each hemisphere are considered a barrier to gene flow and maintain the current species distinctions and geographical populations. However, these distinctions between populations have remained controversial and no study has included an analysis of all right whales from the three major ocean basins. To address issues of genetic differentiation and relationships among right whales, we have compiled a database of mitochondrial DNA control region sequences from right whales representing populations in all three ocean basins that consist of: western North Atlantic E. glacialis, multiple geographically distributed populations of E. australis and the first molecular analysis of historical and recent samples of E. glacialis from the western and eastern North Pacific Ocean. Diagnostic characters, as well as phylogenetic and phylogeographic analyses, support the possibility that three distinct maternal lineages exist in right whales, with North Pacific E. glacialis being more closely related to E. australis than to North Atlantic E. glacialis. Our genetic results provide unequivocal character support for the two usually recognized species and a third distinct genetic lineage in the North Pacific under the Phylogenetic Species Concept, as well as levels of genetic diversity among right whales world-wide.

DNA sequences from orthologous loci can provide universal characters for taxonomic identification. Molecular taxonomy is of particular value for groups in which distinctive morphological features are difficult to observe or compare. To assist in species identification for the little known family Ziphiidae (beaked whales), we compiled a reference database of mitochondrial DNA (mtDNA) control region (437 bp) and cytochrome b (384 bp) sequences for all 21 described species in this group. This mtDNA database is complemented by a nuclear database of actin intron sequences (925 bp) for 17 of the 21 species. All reference sequences were derived from specimens validated by diagnostic skeletal material or other documentation, and included four holotypes. Phylogenetic analyses of mtDNA sequences confirmed the genetic distinctiveness of all beaked whale species currently recognized. Both mitochondrial loci were well suited for species identification, with reference sequences for all known ziphiids forming robust species-specific clades in phylogenetic reconstructions. The majority of species were also distinguished by nuclear alleles. Phylogenetic comparison of sequence data from "test" specimens to these reference databases resulted in three major taxonomic discoveries involving animals previously misclassified from morphology. Based on our experience with this family and the order Cetacea as a whole, we suggest that a molecular taxonomy should consider the following components: comprehensiveness, validation, locus sensitivity, genetic distinctiveness and exclusivity, concordance, and universal accessibility and curation.