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The 20th century commercial whaling industry severely reduced populations of great whales throughout the Southern Hemisphere. The effect of this exploitation on genetic diversity and population structure remains largely undescribed. Here, we compare pre- and post-whaling diversity of mitochondrial DNA (mtDNA) control region sequences for 3 great whales in the South Atlantic, such as the blue, humpback, and fin whale. Pre-whaling diversity is described from mtDNA extracted from bones collected near abandoned whaling stations, primarily from the South Atlantic island of South Georgia. These bones are known to represent the first stage of 20th century whaling and thus pre-whaling diversity of these populations. Post-whaling diversity is described from previously published studies reporting large-scale sampling of living whales in the Southern Hemisphere. Despite relatively high levels of surviving genetic diversity in the post-whaling populations, we found evidence of a probable loss of mtDNA lineages in all 3 species. This is evidenced by the detection of a large number of haplotypes found in the pre-whaling samples that are not present in the post-whaling samples. A rarefaction analysis further supports a loss of haplotypes in the South Atlantic humpback and Antarctic blue whale populations. The bones from former whaling stations in the South Atlantic represent a remarkable molecular archive for further investigation of the decline and ongoing recovery in the great whales of the Southern Hemisphere. [ABSTRACT FROM AUTHOR]

The New York Bight (NYB) is one of the busiest waterways along the US East Coast, and has recently seen an apparent increase in baleen whale presence. With growing anthropogenic pressures, a better understanding of their distribution and behaviour is needed. Encounter rates (sightings km−1) and behaviour of humpback (Megaptera novaeangliae), fin (Balaenoptera physalus) and minke (Balaenoptera acutorostrata) whales were obtained from dedicated non-systematic small vessel surveys conducted from May–November 2017–2019 in previously under-surveyed coastal areas of the NYB. Humpback whales were the most frequently sighted species, and their distribution in the NYB varied significantly by region and season. Within the mid-shelf region (10–60 km from shore), sightings of all species were generally concentrated spatially and temporally in mixed-species aggregations where feeding on sand lance (Ammodytes spp.) was observed. In the nearshore region (<10 km from shore), sightings of all species were more dispersed and typically occurred in close proximity to Atlantic menhaden (Brevoortia tyrannus). Humpback whales were commonly observed lunge feeding on these prey patches. The prevalence of foraging behaviour throughout the study area supports the hypothesis that the NYB may be an important supplementary feeding area for some species. Encounter rates were generally higher in areas overlapping with anthropogenic activity, suggesting that whales may be particularly vulnerable to anthropogenic impacts in the NYB. The observed species distribution patterns and importance of the NYB as a foraging habitat for baleen whales provides valuable information for the development of new baselines and best management practices within this heavily urbanized region. [ABSTRACT FROM AUTHOR]

Aim: Species distribution modelling is a useful tool for determining important habitats. By accounting for specific animal behaviour in the model, it is possible to identify finer‐scale patterns of habitat use. Together with spatially explicit data on anthropogenic activities, models can be used to assess human impacts and inform conservation management. This study used observations of breeding behaviour to identify fine‐scale breeding habitats of humpback whales (Megaptera novaeangliae), as well as potential overlap of these habitats with cumulative anthropogenic impacts. Location: Eastern Tropical Atlantic, West Africa. Methods: Maxent was used to model humpback distribution using pertinent environmental predictors and an integrated dataset of humpback whale occurrences filtered for breeding‐specific behaviours. In conjunction with multiple anthropogenic activities, a subsequent cumulative utilization and impact analysis assessed the degree of overlap between predicted breeding habitat and potential anthropogenic impacts. Results: Greatest habitat suitability occurred in warm coastal waters of Gabon, and other highly suitable areas occurred off Equatorial Guinea (Bioko Island), Cameroon and Angola. Sea surface temperature and height contributed most to the model. Highest overlap between humpback whales and potential impacts from anthropogenic activities occurred off Gabon, Equatorial Guinea (Bioko Island), Cameroon and Angola. Impacts associated with oil and gas development (where oil and gas platforms serve as an indicator for industry activity) appeared to contribute most to potential cumulative impact. Main Conclusions: Depth and sea surface temperature of predicted breeding habitats were consistent with previous studies. However, lesser known characteristics such as sea surface height and wind speed, resulting in potentially more sheltered areas for breeding whales, may also be important in delineating finer‐scale habitat suitability. Identified areas of high potential cumulative impact occurred within exclusive economic zones of multiple countries and likely represent the minimum level of impact to humpback whales in the region, highlighting the need for additional research and effective management throughout the area. [ABSTRACT FROM AUTHOR]

Early 'Discovery mark' data together with recent photo-identification, acoustic, genetic and satellite-radio tag data revealed linkages between humpback whales migrating from breeding grounds (C) off East Africa and the Area III feeding area, from Western Australian breeding grounds (D) and the Antarctic Area IV feeding area and the East Australian breeding grounds (E1) and Antarctic Area V feeding area. These data also revealed low levels of intermingling between (E1) and (D) humpback whales in the Antarctic Area IV feeding area consistent with these being separate populations. Greenpeace photographed the ventral tail flukes of 30 individual humpback whales in the Antarctic Area IV feeding area (70°E-130°E) from 2 to 9 January 2008, between 62°47'S and 64°14'S latitude and 80°00'E and 112°57'E longitude. Comparisons of the Antarctic Area IV Greenpeace fluke catalogue (n = 30) with existing reconciled fluke catalogues from East Africa (n = 842), Western Australia (n = 1,558) and Eastern Australia (n = 1,964), yielded no photo-identification matches. An analysis of the frequencies of whales seen and not seen in Antarctica, East Africa, Western Australia and Eastern Australia relative to the frequencies expected to have been seen and not seen, based on the estimated population sizes and the sizes of the catalogues, provided evidence that the Antarctic whales photographed are from a different population to the East African and East Australian populations. There was weak evidence supporting the hypothesis that the Antarctic whales are from the Western Australian population but insufficient data were available to determine a clear outcome. A comparison of the Antarctic Area IV Greenpeace catalogue (n = 30) with other existing African, Indian Ocean, Western and Eastern Australian and/or Antarctic catalogues, together with increased sampling across the humpback whale feeding season in Antarctica and along the Western and Eastern Australian coastline during their winter migration, is likely to provide further evidence of the migratory destination of these humpback whales. It will also add to our limited knowledge of the extent of population overlap within the Antarctic Area III, IV and V feeding areas. [ABSTRACT FROM AUTHOR]

Elucidating patterns of population structure for species with complex life histories, and disentangling the processes driving such patterns, remains a significant analytical challenge. Humpback whale ( Megaptera novaeangliae) populations display complex genetic structures that have not been fully resolved at all spatial scales. We generated a data set of nuclear markers for 3575 samples spanning the seven breeding stocks and substocks found in the South Atlantic and western and northern Indian Oceans. For the total sample, and males and females separately, we assessed genetic diversity, tested for genetic differentiation between putative populations and isolation by distance, estimated the number of genetic clusters without a priori population information and estimated rates of gene flow using maximum-likelihood and Bayesian approaches. At the ocean basin scale, structure is governed by geographical distance ( IBD P < 0.05) and female fidelity to breeding areas, in line with current understanding of the drivers of broadscale population structure. Consistent with previous studies, the Arabian Sea breeding stock was highly genetically differentiated ( FST 0.034-0.161; P < 0.01 for all comparisons). However, the breeding stock boundary between west South Africa and east Africa was more porous than expected based on genetic differentiation, cluster and geneflow analyses. Instances of male fidelity to breeding areas and relatively high rates of dispersal for females were also observed between the three substocks in the western Indian Ocean. The relationships between demographic units and current management boundaries may have ramifications for assessments of the status and continued protections of populations still in recovery from commercial whaling. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Humpback whales ( Megaptera novaeangliae) from a breeding ground off Gabon (0-4°S) and a migratory corridor/feeding ground on the west coast of South Africa (WSA; 33°S) differ genetically and in catch histories. Interpretation of the population structure is hampered by the lack of data from the intervening 3,500 km of coastline or to the north of Gabon. Here we collate all relevant nongenetic data on humpback whales from Namibia (∼23°S) from 2005 to 2012 and compare these with corresponding data from Gabon (2000-2006) and WSA (1983-2008). Data from Namibia include photographic catalogs of dorsal fin and tail fluke images, seasonal presence, and a photographic assessment of scarring and wounds from cookiecutter sharks ( Isistius sp.). No confirmed photographic identification matches could be made between Namibia and Gabon and only 2 potential matches were made between Namibia and WSA from dorsal fins. Humpback whales in Namibia show a bimodal seasonality in occurrence, with a primary peak in austral winter (July) and a secondary peak in spring (September), but generally low directionality of movement. Whales were never recorded to sing, competitive groups were rarely sighted, and very few calves were observed, making it unlikely that this is a breeding area. The prevalence of killer whale bite scars on flukes was similar at all sites. Fresh bites from cookiecutter sharks were highest in Namibia, intermediate in Gabon, but almost nonexistent in WSA. We propose that animals seen in Namibia in winter are on their northward migration and have intercepted the coast from farther offshore (where cookiecutter sharks occur), whereas animals seen in WSA in spring-summer, where they are feeding during their southward migration, have followed a slow coastwise route within the cold Benguela Ecosystem, thus allowing time for cookiecutter bites to heal. [ABSTRACT FROM AUTHOR]

Machine learning algorithms are often used to model and predict animal habitat selection—the relationships between animal occurrences and habitat characteristics. For broadly distributed species, habitat selection often varies among populations and regions; thus, it would seem preferable to fit region- or population-specific models of habitat selection for more accurate inference and prediction, rather than fitting large-scale models using pooled data. However, where the aim is to make range-wide predictions, including areas for which there are no existing data or models of habitat selection, how can regional models best be combined? We propose that ensemble approaches commonly used to combine different algorithms for a single region can be reframed, treating regional habitat selection models as the candidate models. By doing so, we can incorporate regional variation when fitting predictive models of animal habitat selection across large ranges. We test this approach using satellite telemetry data from 168 humpback whales across five geographic regions in the Southern Ocean. Using random forests, we fitted a large-scale model relating humpback whale locations, versus background locations, to 10 environmental covariates, and made a circumpolar prediction of humpback whale habitat selection. We also fitted five regional models, the predictions of which we used as input features for four ensemble approaches: an unweighted ensemble, an ensemble weighted by environmental similarity in each cell, stacked generalization, and a hybrid approach wherein the environmental covariates and regional predictions were used as input features in a new model. We tested the predictive performance of these approaches on an independent validation dataset of humpback whale sightings and whaling catches. These multiregional ensemble approaches resulted in models with higher predictive performance than the circumpolar naive model. These approaches can be used to incorporate regional variation in animal habitat selection when fitting range-wide predictive models using machine learning algorithms. This can yield more accurate predictions across regions or populations of animals that may show variation in habitat selection. [ABSTRACT FROM AUTHOR]

Humpback whales (Megaptera novaeangliae) annually undertake the longest migrations between seasonal feeding and breeding grounds of any mammal. Despite this dispersal potential, discontinuous seasonal distributions and migratory patterns suggest that humpbacks form discrete regional populations within each ocean. To better understand the worldwide population history of humpbacks, and the interplay of this species with the oceanic environment through geological time, we assembled mitochondrial DNA control region sequences representing approximately 2700 individuals (465 bp, 219 haplotypes) and eight nuclear intronic sequences representing approximately 70 individuals (3700 bp, 140 alleles) from the North Pacific, North Atlantic and Southern Hemisphere. Bayesian divergence time reconstructions date the origin of humpback mtDNA lineages to the Pleistocene (880 ka, 95% posterior intervals 550-1320 ka) and estimate radiation of current Northern Hemisphere lineages between 50 and 200 ka, indicating colonization of the northern oceans prior to the Last Glacial Maximum. Coalescent analyses reveal restricted gene flow between ocean basins, with long-term migration rates (individual migrants per generation) of less than 3.3 for mtDNA and less than 2 for nuclear genomic DNA. Genetic evidence suggests that humpbacks in the North Pacific, North Atlantic and Southern Hemisphere are on independent evolutionary trajectories, supporting taxonomic revision of M. novaeangliae to three subspecies. [ABSTRACT FROM AUTHOR]