Pre-whaling genetic diversity and population ecology in eastern Pacific gray whales: insights from ancient DNA and stable isotopes

Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of particular interest is the possibility of a large population decline prior to whaling, as such a decline could explain the ~5-fold difference between genetic estimates of prior abundance and estimates based on historical records. We analyzed genetic (mitochondrial control region) and isotopic information from modern and prehistoric gray whales using serial coalescent simulations and Bayesian skyline analyses to test for a pre-whaling decline and to examine prehistoric genetic diversity, population dynamics and ecology. Simulations demonstrate that significant genetic differences observed between ancient and modern samples could be caused by a large, recent population bottleneck, roughly concurrent with commercial whaling. Stable isotopes show minimal differences between modern and ancient gray whale foraging ecology. Using rejection-based Approximate Bayesian Computation, we estimate the size of the population bottleneck at its minimum abundance and the pre-bottleneck abundance. Our results agree with previous genetic studies suggesting the historical size of the eastern gray whale population was roughly three to five times its current size.     

MIGRATION AND POPULATION STRUCTURE OF NORTHEASTERN PACIFIC WHALES OFF COASTAL BRITISH COLUMBIA: AN ANALYSIS OF COMMERCIAL WHALING RECORDS FROM 1908-1967

Data recorded from 24,862 whales killed by British Columbia coastal whaling stations between 1908 and 1967 revealed trends in the abundance, sex ratios, age structure, and distribution of sperm ( Physeter macrocephalus ), fin ( Balaenoptera physalus ), sei ( Balaenoptera borealis ), humpback ( Megaptera novaeangliae ), and blue ( Balaenoptera musculus ) whales. The catch data were analyzed using annual and monthly mean values. Monthly and annual variation in whaling effort was deduced from accounts of the history of British Columbia coastal whaling, and biases arising from changes in effort were considered in the interpretation of the results. During the later years of whaling (1948-1967), the mean lengths of captured whales declined significantly and pregnancy rates dropped to near zero in fin, sei, and blue whales. Monthly patterns in numbers killed revealed a summer migration of sei and blue whales past Vancouver Island, and confirms anecdotal suggestions that local populations of fin and humpback whales once spent extended periods in the coastal waters of British Columbia. Furthermore, the data strongly suggest that sperm whales mated (April-May) and calved (July-August) in British Columbia's offshore waters. The historic whaling records reveal much about the migratory behavior and distribution of the large whales species as they once were, and may continue to be, in the northeastern Pacific. Verifying the persistence of these trends in the remnant populations is a necessary and logical next step.     

Species identification and likely catch time period of whale bones from South Georgia

Skeletal remains of baleen whales killed during the onset of 20th century commercial whaling lie scattered across the shores and abandoned whaling stations of the subantarctic island of South Georgia. Here we report on genetic species identification of whale bones collected from South Georgia using standard historical DNA protocols. We amplified and sequenced short fragments of the mitochondrial DNA (mtDNA) control region from 281 available bone samples. Of these, 231 provided mtDNA sequences of sufficient quality and length (174–194 bp) for species identification: 158 bones were identified as humpback whale (Megaptera novaeangliae), 51 bones were identified as fin whale (Balaenoptera physalus), 18 bones were identified as blue whale (B. musculus), two bones were identified as sei whale (B. borealis), one bone was identified as a southern right whale (Eubalaena australis), and one bone was identified as a southern elephant seal (Mirounga leonina). The prominence of humpback, fin, and blue whale bones in the sample collection corresponds to the catch record of the early years of whaling on the island of South Georgia (pre‐1915), prior to the depletion of these populations.     

Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100

Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range.     

Hierarchical structure of mitochondrial DNA gene flow among humpback whales Megaptera novaeangliae, world-wide

The genetic structure of humpback whale populations and subpopulation divisions is described by restriction fragment length analysis of the mitochondrial (mt) DNA from samples of 230 whales collected by biopsy darting in 11 seasonal habitats representing six subpopulations, or 'stocks', world-wide. The hierarchical structure of mtDNA haplotype diversity among population subdivisions is described using the analysis of molecular variance (AMOVA) procedure, the analysis of gene identity, and the genealogical relationship of haplotypes as constructed by parsimony analysis and distance clustering. These analyses revealed: (i) significant partitioning of world-wide genetic variation among oceanic populations, among subpopulations or 'stocks' within oceanic populations and among seasonal habitats within stocks; (ii) fixed categorical segregation of haplotypes on the south-eastern Alaska and central California feeding grounds of the North Pacific; (iii) support for the division of the North Pacific population into a central stock which feeds in Alaska and winters in Hawaii, and an eastern or 'American' stock which feeds along the coast of California and winters near Mexico; (iv) evidence of genetic heterogeneity within the Gulf of Maine feeding grounds and among the sampled feeding and breeding grounds of the western North Atlantic; and (v) support for the historical division between the Group IV (Western Australia) and Group V (eastern Australia, New Zealand and Tonga) stocks in the Southern Oceans. Overall, our results demonstrate a striking degree of genetic structure both within and between oceanic populations of humpback whales, despite the nearly unlimited migratory potential of this species. We suggest that the humpback whale is a suitable demographic and genetic model for the management of less tractable species of baleen whales and for the general study of gene flow among long-lived, mobile vertebrates in the marine ecosystem.     

Status of the world's baleen whales

No global synthesis of the status of baleen whales has been published since the 2008 IUCN Red List assessments. Many populations remain at low numbers from historical commercial whaling, which had ceased for all but a few by 1989. Fishing gear entanglement and ship strikes are the most severe current threats. The acute and long‐term effects of anthropogenic noise and the cumulative effects of multiple stressors are of concern but poorly understood. The looming consequences of climate change and ocean acidification remain difficult to characterize. North Atlantic and North Pacific right whales are among the species listed as Endangered. Southern right, bowhead, and gray whales have been assessed as Least Concern but some subpopulations of these species ‐ western North Pacific gray whales, Chile‐Peru right whales, and Svalbard/Barents Sea and Sea of Okhotsk bowhead whales ‐ remain at low levels and are either Endangered or Critically Endangered. Eastern North Pacific blue whales have reportedly recovered, but Antarctic blue whales remain at about 1% of pre‐exploitation levels. Small isolated subspecies or subpopulations, such as northern Indian Ocean blue whales, Arabian Sea humpback whales, and Mediterranean Sea fin whales are threatened while most subpopulations of sei, Bryde's, and Omura's whales are inadequately monitored and difficult to assess.     

Mitochondrial and nuclear genetic variation across calving lagoons in Eastern North Pacific gray whales (Eschrichtius robustus)

Accurate knowledge of population structure in cetaceans is critical for preserving and managing breeding habitat, particularly when habitat is not uniformly protected. Most eastern gray whales return to their major breeding range each winter along the Pacific coast of Baja California, Mexico, concentrating in 3 major calving lagoons, but it is unknown whether genetic differences exist between lagoons. Previous photo-identification studies and genetic studies suggest that gray whales may return to their natal lagoons to breed, potentially resulting in the buildup of genetic differences. However, an earlier genetic study used only one genetic marker and did not include samples from Bahia Magdalena, a major calving lagoon not currently designated as a wildlife refuge. To expand on this previous study, we collected genetic data from the mitochondrial control region (442 bp) and 9 microsatellite markers from 112 individuals across all 3 major calving lagoons. Our data suggest that migration rates between calving lagoons are high but that a small but significant departure from panmixia exists between Bahia Magdalena and Laguna San Ignacio (Fisher's Exact test, P < 0.0001; F(ST) = 0.006, P = 0.025). Coalescent simulations show that the lack of extensive population structure may result from the disruption of structure due to whaling. Another possibility is that rates of migration have always been high (>10% per generation). In addition, microsatellite data showed evidence of a severe population bottleneck. Eastern gray whales are still recovering from the impacts of whaling on their breeding grounds, and these populations should be protected and monitored for future genetic changes.     

CATCHES OF HUMPBACK AND OTHER WHALES FROM SHORE STATIONS AT MOSS LANDING AND TRINIDAD, CALIFORNIA, 1919–1926

Logbook data from California shore whaling stations at Moss Landing (1919–1922 and 1924) and Trinidad (1920 and 1922–1926) are analyzed. The logs for the two stations record the taking of 2,111 whales, including 1,871 humpbacks, 177 fin whales, 26 sei whales, 3 blue whales, 12 sperm whales, 7 gray whales, 1 right whale, 1 Baird's beaked whale, and 13 whales of unspecified type (probably humpbacks). Most whales were taken from spring to autumn, but catches were made in all months of some years. The sex ratios of humpback, fin, and sei whales (the three species with sufficient sample sizes to test) did not differ from parity. Primary prey, determined from stomach contents, included sardines and euphausiids for both humpback and fin whales, and 'plankton' (probably euphausiids) for sei whales. The prevalence of pregnancy was 0.46 among mature female humpbacks and 0.43 among mature female fin whales, although these values are reported with caution. Information on length distribution for all species is summarized. Analysis of the catch data for this and other areas supports the current view that humpback whales along the west coast of the continental United States comprise a single feeding stock and also suggests that the present population is well below pre-exploitation levels.     

Genetic Characteristics of Western North Pacific Sei Whales, Balaenoptera borealis, as Revealed by Microsatellites

Genetic characteristics of sei whales, Balaenoptera borealis, inhabiting the western North Pacific were analyzed at 17 microsatellite loci in a total of 89 whales obtained from the area between 37°N–45°N and 147°E–166°E in 2002 (N = 39) and 2003 (N = 50). All the loci analyzed were polymorphic over the samples, some of the loci had more than 10 alleles, indicating a high level of genetic variation within samples. No significant deviation from the expected Hardy–Weinberg genotypic proportion was observed at the 17 loci in the samples. No evidence of genetic heterogeneity in allele frequencies was observed between sexes within samples as well as between the two temporally different samples, indicating a single population of sei whales inhabiting the western North Pacific. We finally tested and demonstrated that the population appeared not to suffer from genetic bottleneck as a result of population decline from past commercial whaling.     

The World's Most Isolated and Distinct Whale Population? Humpback Whales of the Arabian Sea

A clear understanding of population structure is essential for assessing conservation status and implementing management strategies. A small, non-migratory population of humpback whales in the Arabian Sea is classified as “Endangered” on the IUCN Red List of Threatened Species, an assessment constrained by a lack of data, including limited understanding of its relationship to other populations. We analysed 11 microsatellite markers and mitochondrial DNA sequences extracted from 67 Arabian Sea humpback whale tissue samples and compared them to equivalent datasets from the Southern Hemisphere and North Pacific. Results show that the Arabian Sea population is highly distinct; estimates of gene flow and divergence times suggest a Southern Indian Ocean origin but indicate that it has been isolated for approximately 70,000 years, remarkable for a species that is typically highly migratory. Genetic diversity values are significantly lower than those obtained for Southern Hemisphere populations and signatures of ancient and recent genetic bottlenecks were identified. Our findings suggest this is the world''s most isolated humpback whale population, which, when combined with low population abundance estimates and anthropogenic threats, raises concern for its survival. We recommend an amendment of the status of the population to “Critically Endangered” on the IUCN Red List.     

Future recovery of baleen whales is imperiled by climate change

Historical harvesting pushed many whale species to the brink of extinction. Although most Southern Hemisphere populations are slowly recovering, the influence of future climate change on their recovery remains unknown. We investigate the impacts of two anthropogenic pressures—historical commercial whaling and future climate change—on populations of baleen whales (blue, fin, humpback, Antarctic minke, southern right) and their prey (krill and copepods) in the Southern Ocean. We use a climate–biological coupled “Model of Intermediate Complexity for Ecosystem Assessments” (MICE) that links krill and whale population dynamics with climate change drivers, including changes in ocean temperature, primary productivity and sea ice. Models predict negative future impacts of climate change on krill and all whale species, although the magnitude of impacts on whales differs among populations. Despite initial recovery from historical whaling, models predict concerning declines under climate change, even local extinctions by 2100, for Pacific populations of blue, fin and southern right whales, and Atlantic/Indian fin and humpback whales. Predicted declines were a consequence of reduced prey (copepods/krill) from warming and increasing interspecific competition between whale species. We model whale population recovery under an alternative scenario whereby whales adapt their migratory patterns to accommodate changing sea ice in the Antarctic and a shifting prey base. Plasticity in range size and migration was predicted to improve recovery for ice‐associated blue and minke whales. Our study highlights the need for ongoing protection to help depleted whale populations recover, as well as local management to ensure the krill prey base remains viable, but this may have limited success without immediate action to reduce emissions.     

A surplus no more? Variation in krill availability impacts reproductive rates of Antarctic baleen whales

The krill surplus hypothesis of unlimited prey resources available for Antarctic predators due to commercial whaling in the 20th century has remained largely untested since the 1970s. Rapid warming of the Western Antarctic Peninsula (WAP) over the past 50 years has resulted in decreased seasonal ice cover and a reduction of krill. The latter is being exacerbated by a commercial krill fishery in the region. Despite this, humpback whale populations have increased but may be at a threshold for growth based on these human-induced changes. Understanding how climate-mediated variation in prey availability influences humpback whale population dynamics is critical for focused management and conservation actions. Using an 8-year dataset (2013–2020), we show that inter-annual humpback whale pregnancy rates, as determined from skin-blubber biopsy samples (n = 616), are positively correlated with krill availability and fluctuations in ice cover in the previous year. Pregnancy rates showed significant inter-annual variability, between 29% and 86%. Our results indicate that krill availability is in fact limiting and affecting reproductive rates, in contrast to the krill surplus hypothesis. This suggests that this population of humpback whales may be at a threshold for population growth due to prey limitations. As a result, continued warming and increased fishing along the WAP, which continue to reduce krill stocks, will likely impact this humpback whale population and other krill predators in the region. Humpback whales are sentinel species of ecosystem health, and changes in pregnancy rates can provide quantifiable signals of the impact of environmental change at the population level. Our findings must be considered paramount in developing new and more restrictive conservation and management plans for the Antarctic marine ecosystem and minimizing the negative impacts of human activities in the region.     

The potential beginning of a postwhaling recovery in New Zealand humpback whales (Megaptera novaeangliae)

Between the 1940s and 1970s Southern Hemisphere populations of humpback whales (including eastern Australia and Oceania populations) were hunted to near extinction by extensive commercial whaling activities in Antarctica, with fewer whales taken in shore whaling operations in New Zealand, Australia (including Norfolk Island) and Tonga. Variable rates of recovery of these populations have been documented, ranging from recovery to prewhaling numbers in eastern Australian humpbacks to very little sign of recovery in many Oceania populations. Here we analyze recent sighting data collected over 12 yr, from annual surveys in Cook Strait, New Zealand. The data show an increase in sightings, at an estimated rate of 13% (95% CI of 4.9% and 21.7%) in 2015, of humpback whales migrating through Cook Strait. The wide confidence intervals preclude substantive conclusions about the rate of increase but suggest humpback whales are returning to this region in increasing numbers, indicating an influx of immigrants from neighboring areas, namely eastern Australia.     

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.     

Spatial and seasonal distribution of American whaling and whales in the age of sail

American whalemen sailed out of ports on the east coast of the United States and in California from the 18(th) to early 20(th) centuries, searching for whales throughout the world's oceans. From an initial focus on sperm whales (Physeter macrocephalus) and right whales (Eubalaena spp.), the array of targeted whales expanded to include bowhead whales (Balaena mysticetus), humpback whales (Megaptera novaeangliae), and gray whales (Eschrichtius robustus). Extensive records of American whaling in the form of daily entries in whaling voyage logbooks contain a great deal of information about where and when the whalemen found whales. We plotted daily locations where the several species of whales were observed, both those caught and those sighted but not caught, on world maps to illustrate the spatial and temporal distribution of both American whaling activity and the whales. The patterns shown on the maps provide the basis for various inferences concerning the historical distribution of the target whales prior to and during this episode of global whaling.     

Evidence of two subaggregations of humpback whales on the Kodiak,Alaska, feeding ground revealed from stable isotope analysis

Knowledge of humpback whale (Megaptera novaeangliae) foraging on feeding grounds is becoming increasingly important as the growing North Pacific population recovers from commercial whaling and consumes more prey, including economically important fishes. We explored spatial and temporal (interannual, within‐season) variability in summer foraging by humpback whales along the eastern side of the Kodiak Archipelago as described by stable carbon (δ¹³C) and nitrogen (δ¹⁵N) isotope ratios of humpback whale skin (n = 118; 2004–2013). The trophic level (TL) of individual whales was calculated using basal food web δ¹⁵N values collected within the study area. We found evidence for the existence of two subaggregations of humpback whales (“North,” “South”) on the feeding ground that fed at different TLs throughout the study period. Linear mixed models suggest that within an average year, Kodiak humpback whales forage at a consistent TL during the feeding season. TL estimates support mixed consumption of fish and zooplankton species in the “North” (mean ± SE; 3.3 ± 0.1) and predominant foraging on zooplankton in the “South” (3.0 ± 0.1). This trend appears to reflect spatial differences in prey availability, and thus, our results suggest North Pacific humpback whales may segregate on feeding aggregations and target discrete prey species.     

Incomplete reporting of whale, dolphin and porpoise 'bycatch' revealed by molecular monitoring of Korean markets

We report the results of molecular monitoring of 'whalemeat' markets in the Republic of (South) Korea based on nine systematic surveys from February 2003 to February 2005. As Korea has no programme of commercial or scientific whaling and there is a closure on the hunting of dolphins and porpoises, the only legal source of these products was assumed to be incidental fisheries mortalities ('bycatch') as reported by the government to the International Whaling Commission. Species identification of 357 products using mitochondrial DNA control region or cytochrome b sequences and the web-based programme DNA-surveillance revealed three species of baleen whales (North Pacific minke, common form Bryde's and humpback), three species of beaked whales (Cuvier's, Stejneger's and Blainville's), seven species of dolphins (short-finned pilot, false killer and killer whales; Risso's, bottlenose, common and Pacific white-sided dolphins) and two species of porpoises (harbour and finless). Comparison of market products with official records revealed a number of discrepancies. Of the eight species identified on the markets in 2003, three were not reported in official records for that year. Of the 11 species identified in 2004, five were not reported as bycatch, although one species, a humpback whale, was reported as 'stranded'. We also found significant inconsistencies in the expected frequencies of products from most species, including a large over-representation of finless porpoises and false killer whales. We suggest ways in which market surveys could be improved to provide better information on the magnitude of fisheries bycatch and other illegal, unregulated and unreported (IUU) exploitation of wildlife.     

Gene flow on ice: the role of sea ice and whaling in shaping Holarctic genetic diversity and population differentiation in bowhead whales (Balaena mysticetus)

Sea ice is believed to be a major factor shaping gene flow for polar marine organisms, but it remains unclear to what extent it represents a true barrier to dispersal for arctic cetaceans. Bowhead whales are highly adapted to polar sea ice and were targeted by commercial whalers throughout Arctic and subarctic seas for at least four centuries, resulting in severe reductions in most areas. Both changing ice conditions and reductions due to whaling may have affected geographic distribution and genetic diversity throughout their range, but little is known about range‐wide genetic structure or whether it differed in the past. This study represents the first examination of genetic diversity and differentiation across all five putative stocks, including Baffin Bay‐Davis Strait, Hudson Bay‐Foxe Basin, Bering‐Beaufort‐Chukchi, Okhotsk, and Spitsbergen. We also utilized ancient specimens from Prince Regent Inlet (PRI) in the Canadian Arctic and compared them with modern stocks. Results from analysis of molecular variance and demographic simulations are consistent with recent and high gene flow between Atlantic and Pacific stocks in the recent past. Significant genetic differences between ancient and modern populations suggest PRI harbored unique maternal lineages in the past that have been recently lost, possibly due to loss of habitat during the Little Ice Age and/or whaling. Unexpectedly, samples from this location show a closer genetic relationship with modern Pacific stocks than Atlantic, supporting high gene flow between the central Canadian Arctic and Beaufort Sea over the past millennium despite extremely heavy ice cover over much of this period.     

SPATIAL AND SEASONAL DISTRIBUTION OF THE HUMPBACK WHALE, MEGAPTERA NOVAEANGLIAE, IN THE MEXICAN PACIFIC

From observations of the spatial distribution of humpback whales in the Mexican Pacific between 1981 and 1986, it is possible to recognize four subregions: 1) the southern coast of Baja California; 2) the northern Gulf of California, including the Midriff Islands; 3) the mainland coast of Mexico, including the Isla Isabel and Islas Tres Marias and 4) the Revillagigedo Archipelago. The seasonal distribution of whales near the Mexican mainland and the Revillagigedo Archipelago extends from November to May and is similar to that of other winter breeding grounds, including the Hawaiian Islands. Along the southern coast of Baja California, whales have been observed from September to April, possibly indicating a shorter migratory route. In the northern Gulf of California, however, humpback whales have been reported throughout the year and are occasionally observed feeding during both summer and winter months. The degree of individual movement between the four subregions is still unknown. The number of individual humpback whales identified photographically in recent years suggests that there ate more whales in the Mexican Pacific than previously reported.