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.     

Sourcing Eurasian beaver Castor fiber stock for reintroductions in Great Britain and Western Europe

• 1 Eurasian beavers Castor fiber, formerly threatened with extinction, have been widely reintroduced since the 1920s. Reintroductions and studies of possible reintroductions are continuing.
• 2 The International Union for Conservation of Nature (IUCN) guidelines for reintroductions state that ‘the source population should ideally be closely related genetically to the original native stock’.
• 3 Palaeoecological studies suggest that the species survived the last Ice Age in two refugia: in the west in Iberia and Southern France and in the east in the Black Sea region. The post‐Ice Age population of Western Europe, including Great Britain, recolonized from the western refugium. Recent mitochondrial deoxyribonucleic acid studies strongly support this view, and extant beaver populations are clearly divided into eastern and western evolutionarily significant units (ESUs).
• 4 The western ESU is composed of three stocks which survived the 19th and early 20th century as very small, isolated populations. They are very closely related to each other. Each is genetically depauperate, apparently as a result of genetic drift at low population levels.
• 5 There is evidence of inbreeding depression and of phenotypic abnormalities in beaver populations descended from unmixed stocks.
• 6 The evidence suggests three coherent management options for sourcing reintroduction stock for Great Britain and for unoccupied areas of western continental Europe. These are (i) use animals from a single western ESU stock; (ii) intentionally mix animals from two or all three of the surviving western ESU stocks; (iii) make an informed exception to the IUCN guidelines and reintroduce animals of mixed eastern and western ESU provenance.
• 7 These options are discussed with regard to IUCN guidelines, conservation biology and animal welfare considerations. It would be advantageous if a common policy on the origin of reintroduction stock were agreed by the national agencies responsible.

     

Distribution and movements of fin whales in the North Pacific Ocean

• 1 We summarize fin whale Balaenoptera physalus catch statistics, sighting data, mark recoveries and acoustics data. The annual cycle of most populations of fin whales had been thought to entail regular migrations between high‐latitude summer feeding grounds and lower‐latitude winter grounds. Here we present evidence of more complex and varied movement patterns.
• 2 During summer, fin whales range from the Chukchi Sea south to 35 °N on the Sanriku coast of Honshu, to the Subarctic Boundary (ca. 42 °N) in the western and central Pacific, and to 32 °N off the coast of California. Catches show concentrations in seven areas which we refer to as ‘grounds’, representing productive feeding areas.
• 3 During winter months, whales have been documented over a wide area from 60 °N south to 23 °N. Coastal whalers took them regularly in all winter months around Korea and Japan and they have been seen regularly in winter off southern California and northern Baja California. There are also numerous fin whale sightings and acoustic detections north of 40 °N during winter months. Calves are born during the winter, but there is little evidence for distinct calving areas.
• 4 Whales implanted with Discovery‐type marks were killed in whaling operations, and location data from 198 marked whales demonstrate local site fidelity, consistent movements within and between the main summer grounds and long migrations from low‐latitude winter grounds to high‐latitude summer grounds.
• 5 The distributional data agree with immunogenetic and marking findings which suggest that the migratory population segregates into at least two demes with separate winter mating grounds: a western ground off the coast of Asia and an eastern one off the American coast. Members of the two demes probably mingle in the Bering Sea/Aleutian Islands area.
• 6 Prior research had suggested that there were at least two non‐migratory stocks of fin whale: one in the East China Sea and another in the Gulf of California. There is equivocal evidence for the existence of additional non‐migratory groups in the Sanriku‐Hokkaido area off Japan and possibly the northern Sea of Japan, but this is based on small sample sizes.

     

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.     

Life History and Production of the Western Gray Whale’s Prey,Ampelisca eschrichtii Kr?yer, 1842 (Amphipoda,Ampeliscidae)

Ampelisca eschrichtii are among the most important prey of the Western North Pacific gray whales, Eschrichtius robustus. The largest and densest known populations of this amphipod occur in the gray whale’s Offshore feeding area on the Northeastern Sakhalin Island Shelf. The remote location, ice cover and stormy weather at the Offshore area have prevented winter sampling. The incomplete annual sampling has confounded efforts to resolve life history and production of A. eschrichtii. Expanded comparisons of population size structure and individual reproductive development between late spring and early fall over six sampling years between 2002 and 2013 however, reveal that A. eschrichtii are gonochoristic, iteroparous, mature at body lengths greater than 15 mm and have a two-year life span. The low frequencies of brooding females, the lack of early stage juveniles, the lack of individual or population growth or biomass increases over late spring and summer, all indicate that growth and reproduction occur primarily in winter, when sampling does not occur. Distinct juvenile and adult size cohorts additionally indicate growth and juvenile production occurs in winter through spring under ice cover. Winter growth thus requires that winter detritus or primary production are critical food sources for these ampeliscid populations and yet, the Offshore area and the Eastern Sakhalin Shelf ampeliscid communities may be the most abundant and productive amphipod population in the world. These A. eschrichtii populations are unlikely to be limited by western gray whale predation. Whether benthic community structure can limit access and foraging success of western gray whales is unclear.     

From the southern right whale hunting decline to the humpback whaling expansion: a review of whale catch records in the tropical western South Atlantic Ocean

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Mysticete migration revisited: are Mediterranean fin whales an anomaly?

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North Atlantic killer whale Orcinus orca populations: a review of current knowledge and threats to conservation

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Baleen whales: conservation issues and the status of the most endangered populations

Most species of baleen whales were subject to intensive overexploitation by commercial whaling in this and previous centuries, and many populations were reduced to small fractions of their original sizes. Here, we review the status of baleen whale stocks, with an emphasis on those that are known or thought to be critically endangered. Current data suggest that, of the various threats potentially affecting baleen whales, only entanglement in fishing gear and ship strikes may be significant at the population level, and then only in those populations which are already at critically low abundance. The impact of some problems (vessel harassment, and commercial or aboriginal whaling) is at present probably minor. For others (contaminants, habitat degradation, disease), existing data either indicate no immediate cause for concern, or are insufficient to permit an assessment. While the prospect for many baleen whales appears good, there are notable exceptions; populations that are of greatest concern are those suffering from low abundance and associated problems, including (in some cases) anthropogenic mortality. These include: all Northern Right Whales Eubalaena glacialis, Bowhead Whales Balaena mysticetus of the Okhotsk Sea and various eastern Arctic populations, western Gray Whales Eschrichtius robustus, and probably many Blue Whale Balaenoptera musculus populations. We review the status of these populations and, where known, the issues potentially affecting their recovery. Although Humpback Whales Megaptera novaeangliae and Southern Right Whales Eubalaena australis were also heavily exploited by whaling, existing data indicate strong recovery in most studied populations of these species.     

The forgotten whale: a bibliometric analysis and literature review of the North Atlantic sei whale Balaenoptera borealis

• 1 A bibliometric analysis of the literature on the sei whale Balaenoptera borealis is presented. Research output on the species is quantified and compared with research on four other whale species. The results show a significant increase in research for all species except the sei whale. Research output is characterized chronologically and by oceanic basin.
• 2 The species' distribution, movements, stock structure, feeding, reproduction, abundance, acoustics, mortality and threats are reviewed for the North Atlantic, and the review is complemented with previously unpublished data.
• 3 Knowledge on the distribution and movements of the sei whale in the North Atlantic is still mainly derived from whaling records. Movement patterns and winter distribution are not clear. Surveys in some known summering areas show that the species has changed its distribution in parts of its previously known range.
• 4 With the present information, it is impossible to determine whether or not the North Atlantic sei whale population is subdivided into biological units. Abundance estimates are fragmentary and cover a restricted part of the summering habitat.
• 5 In the North Atlantic, sei whales seem to be stenophagous, feeding almost exclusively on calanoid copepods and euphausiids. On feeding grounds, they are associated with oceanic frontal systems, but how they find and explore these structures has not been fully investigated.
• 6 The available data on vital rates are based on whaling‐derived studies and are 25 years old or older. Despite increasing human and environmentally induced pressures, there are no current estimates for mortality and population trends.
• 7 Current research needs include the clear definition of stock units, reliable abundance estimates, studies of distribution and migration that incorporate the identification of wintering areas, acquisition of up‐to‐date data on reproduction and mortality, and investigations into the consequences of environmental changes for the species.

     

Call types of Bigg’s killer whales (Orcinus orca) in western Alaska: using vocal dialects to assess population structure

Bigg’s killer whales (Orcinus orca; i.e. ‘transient’ ecotype), as apex predators, are important to the dynamics of marine ecosystems, but little is known about their population structure in western Alaska. Currently, all Bigg’s killer whales in western Alaska are ascribed to a single broad stock for management under the US Marine Mammal Protection Act. However, recent nuclear microsatellite and mitochondrial DNA analyses indicate that this stock is likely comprised of genetically distinct sub-populations. In accordance with what is known about killer whale vocal dialects in other locations, we used the spatial distribution of group-specific call types to investigate the population structure of Bigg’s killer whales in this part of Alaska. Digital audio recordings were collected from 33 Bigg’s killer whale encounters throughout the Aleutian and Pribilof Islands in the summers of 2001–2007 and 2009–2010. Recorded calls were qualitatively classified into discrete types and then quantitatively described using 12 structural and time-frequency measures. Resulting call categories were validated using a random forest approach. A total of 36 call types and subtypes were identified across the entire study area, and regional patterns of call type use revealed three distinct dialects which correspond to proposed genetic delineations. Our results suggest that there are at least three acoustically and genetically distinct sub-populations in western Alaska, and we present an initial catalogue for this area describing the regional vocal repertoires of Bigg’s killer whale call types.     

Deep genetic subdivision within a continuously distributed and highly vagile marine mammal, the Steller's sea lion (Eumetopias jubatus)

The Steller's sea lion Eumetopias jubatus is an endangered marine mammal that has experienced dramatic population declines over much of its range during the past five decades. Studies using mitochondrial DNA (mtDNA) have shown that an apparently continuous population includes a strong division, yielding two discrete stocks, western and eastern. Based on a weaker split within the western stock, a third Asian stock has also been defined. While these findings indicate strong female philopatry, a recent study using nuclear microsatellite markers found little evidence of any genetic structure, implying extensive paternal gene flow. However, this result was at odds with mark–recapture data, and both sample sizes and genetic resolution were limited. To address these concerns, we increased analytical power by genotyping over 700 individuals from across the species' range at 13 highly polymorphic microsatellite loci. We found a clear phylogenetic break between populations of the eastern stock and those of the western and Asian stocks. However, our data provide little support for the classification of a separate Asian stock. Our findings show that mtDNA structuring is not due simply to female philopatry, but instead reflects a genuine discontinuity within the range, with implications for both the phylogeography and conservation of this important marine mammal.     

Population genetic structure of Bryde’s whales (<Emphasis Type="Italic">Balaenoptera brydei</Emphasis>) at the inter-oceanic and trans-equatorial levels

Bryde’s whales (Balaenoptera brydei) differ from other typical baleen whale species because they are restricted to tropical and warm temperate waters in major oceans, and frequent trans-equatorial movement has been suggested for the species. We tested this hypothesis by analyzing genetic variation at 17 microsatellite loci (N = 508) and 299 bp of mitochondrial DNA (mtDNA) control region sequences (N = 472) in individuals obtained from the western North Pacific, South Pacific, and eastern Indian Ocean. Combined use of microsatellite and mtDNA markers allowed us to distinguish between contemporary gene flow and ancestral polymorphism and to describe sex-specific philopatry. A high level of genetic diversity was found within the samples. Both nuclear and mtDNA markers displayed similar population structure, indicating a lack of sex-specific philopatry. Spatial structuring was detected using both frequency-based population parameters and individual-based Bayesian approaches. Whales in the samples from different oceanic regions came from genetically distinct populations with evidence of limited gene flow. We observed low mtDNA sequence divergence among populations and a lack of concordance between geographic and phylogenetic position of mtDNA haplotypes, suggesting recent separation of populations rather than frequent trans-equatorial and inter-oceanic movement. We conclude that current gene flow between Bryde’s whale populations is low and that effective management actions should treat them as separate entities to ensure continued existence of the species.     

Spatial-temporal patterns in intra-annual gray whale foraging: Characterizing interactions between predators and prey in Clayquot Sound, British Columbia, Canada

In Clayquot Sound, British Columbia, gray whales (Eschrichtius robustus) forage primarily on mysids (Family Mysideae) and also on crab larvae (Family Porcellanidae) that are constrained to specific habitat, which relate to bathymetric depths. In this paper we characterize the interactions of gray whales and their prey by analyzing fine scale spatial‐temporal patterns in foraging gray whale distribution within a season. Kernel density estimators are applied to two seasons (1998 and 2002) of high‐resolution data on foraging by gray whales. By partitioning data from each foraging season into several time periods (12 in 1998 and 11 in 2002), using a temporal autocorrelation function, and generating kernel density estimated surfaces for each time period, it is possible to identify discrete areas of increasing and declining foraging effort. Our results indicate that gray whales forage on mysids throughout a season and opportunistically forage on crab larvae. The episodic crab larvae feeding may reduce, but not eliminate, pressure to mysid populations enabling mysids to reassemble swarms and continue to support gray whale foraging in the latter part of the season. Results suggest that when managing marine environments, gray whale populations require multiple and connected habitats for summer foraging.     

A re‐evaluation of the role of killer whales Orcinus orca in a population decline of sea otters Enhydra lutris in the Aleutian Islands and a review of alternative hypotheses

• 1 During the past 15–20 years, sea otters Enhydra lutris in the Aleutian Islands, Alaska, USA, experienced a drastic decrease in population size. It has been hypothesized that an increase in killer whale Orcinus orca predation was the primary cause of this decline.
• 2 Causation of the decline by increased killer whale predation is now considered a textbook case of top‐down predator control. The purpose of this review is to re‐evaluate the evidence for killer whale predation and to review evidence for alternative causes.
• 3 The killer whale predation hypothesis is based on three lines of evidence: (i) there was an increase in the number of observed killer whale attacks on sea otters during the 1990s, coincident with a decline in sea otters, (ii) sea otter populations did not decline in areas considered inaccessible to killer whales, while they declined in adjacent areas considered accessible to killer whales, and (iii) the estimated number of attacks necessary to account for the rate of decline is similar to the observed number of attacks. Our re‐evaluation indicates that although the killer whale hypothesis is by no means disproved, the supporting data are limited and inconclusive.
• 4 Increases in shark populations in the Aleutian Islands concurrent with the sea otter population declines indicate the need for further research into the role of alternative marine predators in the population decline.
• 5 High contaminant levels observed in sea otters in the Aleutian Islands warrant further investigation into the impact of these toxins on sea otter health and vital rates, and their possible role on the population decline.
• 6 Disease has not been ruled out as a significant contributor to the population decline, particularly in the early stages of the decline.

     

Using pre- and postexploitation samples to assess the impact of commercial whaling on the genetic characteristics of eastern North Pacific gray and humpback whales and to compare methods used to infer historic demography

Many species of whales went through recent bottlenecks due to commercial whaling. These declines were rapid and recent relative to the life spans and generation times of these species, raising questions regarding to what degree commercial whaling influenced the genetic characteristics of these populations. We analyzed mitochondrial and nuclear DNA from pre- and postwhaling samples from two populations that have arguably shown the greatest degree of recovery: eastern North Pacific gray and humpback whales. We also compare the performance of different methods to test for historic bottlenecks and infer past demography based on genetic data. We found substantially higher levels of genetic diversity in gray than in humpback whales (for both time periods), likely due to recent connectivity between Atlantic and Pacific gray whale populations. Other than mitochondrial diversity in humpback whales, levels of diversity were not lower in contemporary samples relative to prewhaling samples, indicating that commercial whaling had a minimal impact on metrics of genetic diversity themselves. However, it did have large impacts on the patterns of diversity, as evidenced by all coalescent-based methods showing clear evidence of a bottleneck for both populations, whereas all but one method not based on the coalescent failed to detect a bottleneck.     

Spatial patterns of humpback whale (Megaptera novaeangliae) sightings and survey effort: Insight into North Atlantic population structure

Understanding the population structure of a species is critical to its effective management and conservation. The humpback whale ( Megaptera novaeangliae ) has been the target of numerous research projects in several ocean basins, but no clear picture of its population structure has emerged. In the North Atlantic Ocean, genetic analyses and photo-identification movements have shown significant heterogeneity among the summer feeding grounds. Building on this knowledge, we test the hypothesis that the feeding grounds represent distinct populations by analyzing the spatial pattern of summer humpback whale sightings and survey effort. Controlling for the spatial pattern of effort, sightings are clustered, with peaks at radial distances of 300 km, 600 km, and 1,500 km. These results provide insight into the spatial extent of the summer population structure of humpback whales in the North Atlantic Ocean. Fine-scale clustering at distances of 300 km and 600 km is compatible with multiple populations consisting of the Gulf of Maine, eastern Canada, western Greenland, and Iceland. Broad-scale clustering at distances of 1,500 km may represent divisions between the western and eastern North Atlantic populations. These results provide spatial bounds to the feeding grounds of humpback whales and emphasize their distinct nature as management units.     

Ecotype and geographical variation in carbon and nitrogen stable isotope values in western North Pacific killer whales (Orcinus orca)

Killer whales are top predators in marine trophic chains, and therefore their feeding preferences can substantially affect the abundance of species on the lower trophic levels. Killer whales are known to feed on many different types of prey from small fish to large whales, but a given killer whale population usually focuses on a specific type of prey. Stable isotope analysis is widely used to study whale diets, because direct observations are often impossible. Killer whale feeding habits in the western North Pacific are poorly studied, and the large-scale stable isotope analysis provides a unique opportunity to gain insights into the trophic links of this top predator. In this study, we compare the δ¹³C and δ¹⁵N stable isotope values from killer whale skin samples obtained in different areas of the western North Pacific from fish-eating (R-type) and mammal-eating (T-type) killer whale ecotypes. The effect of ecotype was highly significant: both carbon and nitrogen stable isotope values were lower in R-type whales than in T-type whales. The geographical variation also affected killer whale stable isotope values due to both the differences in killer whale diet and the variation in baseline stable isotope values across the study areas.     

A genetic analysis of the beluga whale Delphinapterus leucas (Cetacea: Monodontidae) from summer aggregations in the Russian Far East

The genetic structure of four summer aggregations of the Beluga Whale, Delphinapterus leucas, in Sakhalin Bay and Udskaya Bay, off the western coast of Kamchatka in the Sea of Okhotsk and in the Anadyr Estuary of the Bering Sea was analyzed through nucleotide sequencing of the mtDNA control region and detection of the allelic composition of nine microsatellite loci in nuclear DNA. It has been shown that each of the aggregations features a unique set of maternal lines, which indicates a high degree of philopatry in this species. Beluga whales of the Anadyr Estuary are genetically isolated from those of the Sea of Okhotsk. Beluga whales of the summer aggregations of Sakhalin Bay and those from Udskaya Bay share a common gene pool and belong to a single population, while the whales that summer off western Kamchatka with great consistency may be attributed to a different population. Comparison of nucleotide sequences of the mtDNA in beluga whales from various waters of the Russian Far East and North America allowed us to propose a hypothesis about how the structure of beluga whale populations formed in the North Pacific during the postglacial period.     

Past and present distribution, densities and movements of blue whales Balaenoptera musculus in the Southern Hemisphere and northern Indian Ocean

• 1 Blue whale locations in the Southern Hemisphere and northern Indian Ocean were obtained from catches (303 239), sightings (4383 records of ≥8058 whales), strandings (103), Discovery marks (2191) and recoveries (95), and acoustic recordings.
• 2 Sighting surveys included 7 480 450 km of effort plus 14 676 days with unmeasured effort. Groups usually consisted of solitary whales (65.2%) or pairs (24.6%); larger feeding aggregations of unassociated individuals were only rarely observed. Sighting rates (groups per 1000 km from many platform types) varied by four orders of magnitude and were lowest in the waters of Brazil, South Africa, the eastern tropical Pacific, Antarctica and South Georgia; higher in the Subantarctic and Peru; and highest around Indonesia, Sri Lanka, Chile, southern Australia and south of Madagascar.
• 3 Blue whales avoid the oligotrophic central gyres of the Indian, Pacific and Atlantic Oceans, but are more common where phytoplankton densities are high, and where there are dynamic oceanographic processes like upwelling and frontal meandering.
• 4 Compared with historical catches, the Antarctic (‘true’) subspecies is exceedingly rare and usually concentrated closer to the summer pack ice. In summer they are found throughout the Antarctic; in winter they migrate to southern Africa (although recent sightings there are rare) and to other northerly locations (based on acoustics), although some overwinter in the Antarctic.
• 5 Pygmy blue whales are found around the Indian Ocean and from southern Australia to New Zealand. At least four groupings are evident: northern Indian Ocean, from Madagascar to the Subantarctic, Indonesia to western and southern Australia, and from New Zealand northwards to the equator. Sighting rates are typically much higher than for Antarctic blue whales.
• 6 South‐east Pacific blue whales have a discrete distribution and high sighting rates compared with the Antarctic. Further work is needed to clarify their subspecific status given their distinctive genetics, acoustics and length frequencies.
• 7 Antarctic blue whales numbered 1700 (95% Bayesian interval 860–2900) in 1996 (less than 1% of original levels), but are increasing at 7.3% per annum (95% Bayesian interval 1.4–11.6%). The status of other populations in the Southern Hemisphere and northern Indian Ocean is unknown because few abundance estimates are available, but higher recent sighting rates suggest that they are less depleted than Antarctic blue whales.