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The ever-increasing human demand for fossil fuels has resulted in the expansion of oil exploration efforts to waters over the continental shelf. These waters are largely utilized by a complex biological community. Large baleen whales, in particular, utilize continental shelf waters as breeding and calving grounds, foraging grounds, and also as migration corridors. We developed a dynamic approach to estimate the likelihood that individuals from different populations of blue whales Balaenoptera musculus and humpback whales Megaptera novaeangliae could be exposed to idealized, simulated seismic surveys as they move over the continental shelf. Animal tracking data for the different populations were filtered, and behaviors (transit and foraging) were inferred from the tracks using hidden Markov models. We simulated a range of conditions of exposure by having the source of noise affecting a circular area of different radii (5, 25, 50 and 100 km), moving along a gridded transect of 270 and 2500 km2 at a constant speed of 9 km h-1, and starting the simulated surveys every week of the year. Our approach allowed us to identify the temporal variability in the susceptibility of the different populations under study, as we ran the simulations for an entire year, allowing us to identify periods when the surveys would have an intensified effect on whales. Our results highlight the importance of understanding the behavior and ecology of individuals in a site-specific context when considering the likelihood of exposure to anthropogenic disturbances, as the habitat utilization patterns of each population are highly variable.

Understanding calving rates of wild whale populations is critically important for management and conservation. Reproduction of humpback whales (Megaptera novaeangliae) is difficult to monitor and, even with long-term sighting studies, basic physiological information such as pregnancy rates and calving intervals remain poorly understood in many populations. We hypothesized that pregnant whales have sustained elevations in baleen progesterone that temporally correlate with gestation. To test this hypothesis, baleen progesterone profiles from two adult female North Pacific humpbacks, both with extensive sighting records and documented pregnancies, were compared to those of a nulliparous female (adult female never seen with a calf) and a juvenile male. Baleen specimens recovered during necropsy were subsampled every 2 cm from the base to the tip of the plate, with each interval representing 30–45 days of growth. Homogenized baleen powder was assayed for progesterone using enzyme immunoassays. The date of growth of each sampling location on the baleen plate was estimated based on stable isotope analysis of annual δ15N cycles. Progesterone profiles from both pregnant whales showed sustained high progesterone content (>350 ng/g) in areas corresponding to known pregnancies, inferred from calf sightings and post-mortem data. The younger female, estimated to be 13 years old, had higher progesterone during pregnancy than the 44.5 year old, but levels during non-pregnancy were similar. The nulliparous female and the male had low progesterone throughout their baleen plates. Baleen hormone analysis can determine how progesterone concentrations change throughout gestation and has potential for estimating age at first reproduction, pregnancy intervals, failed pregnancies and early calf mortality. Understanding rates of calving and current and historic reproductive patterns in humpbacks is vital to continuing conservation measures in this species.

Obtaining direct measurements to characterise ecosystem function can be hindered by remote or inaccessible regions. Next-generation satellite tags that inform increasingly sophisticated movement models, and the miniaturisation of animal-borne loggers, have enabled the use of animals as tools to collect habitat data in remote environments, such as the Southern Ocean. Research on the distribution, habitat use and recovery of Oceania’s humpback whales (Megaptera novaeangliae) has been constrained by the inaccessibility to their Antarctic feeding grounds and the limitations of technology. In this multi-disciplinary study, we combine innovative analytical tools to comprehensively assess the distribution and population structure of this marine predator throughout their entire migratory range. We used genotype and photo-identification matches and conducted a genetic mixed-stock analysis to identify the breeding ground origins of humpback whales migrating past the Kermadec Islands, New Zealand. Satellite tracking data and a state-space model were then used to identify the migratory paths and behaviour of 18 whales, and to reveal their Antarctic feeding ground destinations. Additionally, we conducted progesterone assays and epigenetic aging to determine the pregnancy rate and age-profile of the population. Humpback whales passing the Kermadec Islands did not assign to a single breeding ground origin, but instead came from a range of breeding grounds spanning ∼3500 km of ocean. Sampled whales ranged from calves to adults of up to 67 years of age, and a pregnancy rate of 57% was estimated from 30 adult females. The whales migrated to the Southern Ocean (straight-line distances of up to 7000 km) and spanned ∼4500 km across their Antarctic feeding grounds. All fully tracked females with a dependent calf (n = 4) migrated to the Ross Sea region, while 70% of adults without calves (n = 7) travelled further east to the Amundsen and Bellingshausen Seas region. By combining multiple research and analytical tools we obtained a comprehensive understanding of this wide-ranging, remote population of whales. Our results indicate a population recovering from exploitation, and their feeding ground distribution serves as an indicator of the resources available in these environments. The unexpected Kermadec Islands migratory bottle-neck of whales from several breeding grounds, variable distribution patterns by life history stage and high pregnancy rates will be important in informing conservation and management planning, and for understanding how this, as well as other whale populations, might respond to emerging threats such as climate change.

Currently, three stocks of sei whales (Balaenoptera borealis) are defined in the North Atlantic; the Nova Scotian, Iceland-Denmark Strait and Eastern North Atlantic stocks, which are mainly based upon historical catch and sighting data. We analyzed mitochondrial control region DNA (mtDNA) sequences and genotypes from 7 to 11 microsatellite loci in 87 samples from three sites in the North Atlantic; Iceland, the Gulf of Maine and the Azores, and compared against the North Pacific using 489 previously published samples. No statistically significant deviations from homogeneity were detected among the North Atlantic samples at mtDNA or microsatellite loci. The genealogy estimated from the mtDNA sequences revealed a clear division of the haplotypes into a North Atlantic and a North Pacific clade, with the exception of one haplotype detected in a single sample from the Azores, which was included in the North Pacific clade. Significant genetic divergence between the North Atlantic and North Pacific Oceans was detected (mtDNA ΦST = 0.72, microsatellite Weir and Cockerham’s ϴ = 0.20; p

Humpback whales (Megaptera novaeangliae) congregate to breed during the austral winter near tropical islands of the South Pacific (Oceania). It has long been assumed that humpback whales from Oceania migrate primarily to Antarctic feeding grounds directly south (International Whaling Commission Management Areas V and VI); however, there are few records of individual movement connecting these seasonal habitats. Based on genetic samples of living whales collected over nearly two decades, we demonstrate interchange between the breeding grounds of Oceania and Antarctic feeding Areas V, VI, and I (i.e., from 130°E to 60°W), as well as with the eastern Pacific (Colombia), and the migratory corridors of eastern Australia and New Zealand. We first compared genotype profiles (up to 16 microsatellite loci) of samples collected from Oceania breeding grounds to each other and to those from the eastern Pacific. The matching profiles documented 47 individuals that were present on more than one breeding ground, including the first record of movement between Oceania and Colombia. We then compared the 1179 genotypes from the breeding grounds to 777 from the migratory corridors of east Australia and New Zealand, confirming the connection of these corridors with New Caledonia. Finally, we compared genotypes from breeding grounds to 166 individuals from Antarctic feeding Areas I–VI. This comparison of genotypes revealed five matches: one between New Caledonia and Area V, one between Tonga and Area VI, two between Tonga and Area I (western edge), and one between Colombia and Area I (Antarctic Peninsula). Despite the relatively small number of samples from the Antarctic, our comparison has doubled the number of recorded connections with Oceania available from previous studies during the era of commercial whaling.

Southern Hemisphere humpback whales breed in tropical waters and migrate to Antarctica to forage. While the breeding grounds are well defined, the population structure on Antarctic feeding grounds is poorly described. The Western Antarctic Peninsula (WAP) is of particular interest, where rapidly changing environmental conditions could alter prey distribution or migration pathways. To examine changes in the population of whales around the WAP, we used mitochondrial DNA (mtDNA) and 15 microsatellite loci. We compared our WAP dataset to a dataset collected 18 years earlier, and identified new haplotypes for the region, but found no significant difference between the datasets. We compared whales from the WAP to breeding populations in Oceania, Colombia, and Brazil. We used an Analysis of Molecular Variance to confirm significant genetic differentiation between the WAP and each breeding ground (overall F ST = 0.035/0.007 mtDNA/microsatellite, p

North Atlantic humpback whales (Megaptera novaeangliae) in the Gulf of Maine overlap with both recreational and commercial vessel activity. Vessel strikes are one source of anthropogenic impact that has the potential to inhibit the recovery of this protected species. There are currently no regulations or guidelines specifically devised to reduce the likelihood of collisions for vessels transiting in the vicinity of humpback whales, except for vessels actively engaged in whale watching. To understand interactions between vessels and humpback whales better, we analyzed injuries on 624 individuals photographed in the southern Gulf of Maine from 2004 to 2013. Multiple reviewers evaluated 210,733 photos for five categories of injury consistent with a vessel strike. In total, 14.7% (n = 92) of individuals photographed showed injuries consistent with one or more vessel strikes. These results likely underestimate vessel collision rates and impacts because multiple events, events resulting in mortality, and those that involved only blunt force trauma could not be detected. Nevertheless, our results indicate that vessel strikes are underreported and that healing is dependent on the severity and location of the injury. We recommend that a management strategy be developed for all classes of vessels transiting in the vicinity of whales.

HighlightsMitochondrial monophyly is commonly employed to define evolutionary significant units.Monophyly may be caused by insufficient sampling or a recent common ancestor.Mitogenomic studies are generally based on few samples and prone to sampling issues.Expanded mitogenome sampling negates previous monophyly in fin whales.AbstractThe advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point is illustrated by a re-analysis of a global mitogenomic assessment of fin whales,Balaenoptera physalusspp., published by Archer et al. (2013) which proposed to further subdivide the Northern Hemisphere fin whale subspecies,B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1,676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 358 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para-or polyphyly) can lead to erroneous conclusions due to relatively “trivial” aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to most recent common ancestor and hence the probability that individuals in a sample are monophyletic.

In the context of a changing climate, understanding the environmental drivers of marine megafauna distribution is important for conservation success. The extent of humpback whale breeding habitats and the impact of temperature variation on their availability are both unknown. We used 19 years of dedicated survey data from seven countries and territories of Oceania (1,376 survey days), to investigate humpback whale breeding habitat diversity and adaptability to climate change. At a fine scale (1 km resolution), seabed topography was identified as an important influence on humpback whale distribution. The shallowest waters close to shore or in lagoons were favored, although humpback whales also showed flexible habitat use patterns with respect to shallow offshore features such as seamounts. At a coarse scale (1 degrees resolution), humpback whale breeding habitats in Oceania spanned a thermal range of 22.3-27.8 degrees C in August, with interannual variation up to 2.0 degrees C. Within this range, both fine and coarse scale analyses of humpback whale distribution suggested local responses to temperature. Notably, the most detailed dataset was available from New Caledonia (774 survey days, 1996-2017), where encounter rates showed a negative relationship to sea surface temperature, but were not related to the El Nino Southern Oscillation or the Antarctic Oscillation from previous summer, a proxy for feeding conditions that may impact breeding patterns. Many breeding sites that are currently occupied are predicted to become unsuitably warm for this species (>28 degrees C) by the end of the 21st century. Based on modeled ecological relationships, there are suitable habitats for relocation in archipelagos and seamounts of southern Oceania. Although distribution shifts might be restrained by philopatry, the apparent plasticity of humpback whale habitat use patterns and the extent of suitable habitats support an adaptive capacity to ocean warming in Oceania breeding grounds.

Abandoned, lost or discarded fishing gear (ALDFG) comprises a significant amount of global marine debris, with diverse impacts to marine environments, wildlife, and the fishing industry. Building evidence on ALDFG is critical to holistically understand the marine debris issue, and to inform the development of solutions that reduce amounts of ALDFG sources and recover existing gear. Substantial work has been and continues to be undertaken around the world to collect data on ALDFG, much of which remains unpublished. To provide a global picture of data on ALDFG, we organized a technical session that brought together seven ALDFG leaders to share their expertise in data collection, retrieval, and awareness-raising. This paper summarizes the technical session to highlight: 1) case studies that feature innovative approaches to ALDFG data collection and retrieval; 2) examples of opportunities to fill data gaps and improve our understanding of wildlife ingestion of and entanglement in ALDFG; and 3) awareness-raising through the development of a publicly accessible global ALDFG database.

Cetaceans are a clade of highly specialized aquatic mammals that include the largest animals that have ever lived. The largest whales can have ∼1,000× more cells than a human, with long lifespans, leaving them theoretically susceptible to cancer. However, large-bodied and long-lived animals do not suffer higher risks of cancer mortality than humans—an observation known as Peto’s Paradox. To investigate the genomic bases of gigantism and other cetacean adaptations, we generated a de novo genome assembly for the humpback whale (Megaptera novaeangliae) and incorporated the genomes of ten cetacean species in a comparative analysis. We found further evidence that rorquals (family Balaenopteridae) radiated during the Miocene or earlier, and inferred that perturbations in abundance and/or the interocean connectivity of North Atlantic humpback whale populations likely occurred throughout the Pleistocene. Our comparative genomic results suggest that the evolution of cetacean gigantism was accompanied by strong selection on pathways that are directly linked to cancer. Large segmental duplications in whale genomes contained genes controlling the apoptotic pathway, and genes inferred to be under accelerated evolution and positive selection in cetaceans were enriched for biological processes such as cell cycle checkpoint, cell signaling, and proliferation. We also inferred positive selection on genes controlling the mammalian appendicular and cranial skeletal elements in the cetacean lineage, which are relevant to extensive anatomical changes during cetacean evolution. Genomic analyses shed light on the molecular mechanisms underlying cetacean traits, including gigantism, and will contribute to the development of future targets for human cancer therapies.

The demography of baleen whales and their prey during the past 30 thousand years was assessed to understand the effects of past rapid global warming on marine ecosystems. Mitochondrial and genome-wide DNA sequence variation in eight baleen whale and seven prey species revealed strong, ocean-wide demographic changes that were correlated with changes in global temperatures and regional oceanographic conditions. In the Southern Ocean baleen whale and prey abundance increased exponentially and in apparent synchrony, whereas changes in abundance varied among species in the more heterogeneous North Atlantic Ocean. The estimated changes in whale abundance correlated with increases in the abundance of prey likely driven by reductions in sea-ice cover and an overall increase in primary production. However, the specific regional oceanographic environment, trophic interactions and species ecology also appeared to play an important role. Somewhat surprisingly the abundance of baleen whales and prey continued to increase for several thousand years after global temperatures stabilized. These findings warn of the potential for dramatic, long-term effects of current climate changes on the marine ecosystem.One Sentence SummaryThe effects of past global warming on marine ecosystems were drastic, system-wide and long-lasting.

There are few identifiable external indicators of pregnancy state in live baleen whales. However, progesterone can be quantified from biopsy samples that are collected from free-ranging whales. We use a blubber sample archive and associated calving data from a well-studied population to develop a blubber-based pregnancy test for humpback whales., Baleen whales have few identifiable external indicators of pregnancy state, making it challenging to study essential aspects of their biology and population dynamics. Pregnancy status in other marine mammals has been determined by measuring progesterone concentrations from a variety of sample matrices, but logistical constraints have limited such studies in free-swimming baleen whales. We use an extensive blubber sample archive and associated calving history data to retrospectively identify samples that correspond to pregnant females and develop a progesterone-based pregnancy test for humpback whales. The lowest pregnant blubber progesterone concentration was 54.97 ng g−1, and the mean for the known-pregnant group was 198.74 ± 180.65 ng g−1. Conversely, females known to be below the minimum age of sexual maturity (juvenile females) had an overall low mean progesterone concentration (0.59 ± 0.25 ng g−1), well below the known-pregnant range. Of the mature females that did not return with a calf (n = 11), three fell within the known-pregnant range (320.79 ± 209.34 ng g−1), while the levels for the remaining eight were two orders of magnitude below the lowest known-pregnant level (1.63 ± 1.15 ng g−1). The proportion of females that did not return with a calf but had values similar to known-pregnant females are consistent with rates of calf mortality, but other potential explanations were considered. Our findings support a validated blubber endocrine assignment of pregnancy corroborated with field life history information, a first for any baleen whale species. The progesterone values we measured were similar to those found in different pregnancy states of other cetaceans and support using blubber biopsy samples for assigning pregnancy in humpback whales. This method can be applied to existing archives or new samples to better study life history and population demography broadly across species and populations.

Entanglement in fixed fishing gear affects whales worldwide. In the United States, deaths of North Atlantic right (Eubalaena glacialis) and humpback whales (Megaptera novaeangliae) have exceeded management limits for decades. We examined live and dead whales entangled in fishing gear along the U.S. East Coast and the Canadian Maritimes from 1994 to 2010. We recorded whale species, age, and injury severity and determined rope polymer type, breaking strength, and diameter of the fishing gear. For the 132 retrieved ropes from 70 cases, tested breaking strength range was 0.80-39.63 kN (kiloNewtons) and the mean was 11.64 kN (SD 8.29), which is 26% lower than strength at manufacture (range 2.89-53.38 kN, mean = 15.70 kN [9.89]). Median rope diameter was 9.5 mm. Right and humpback whales were found in ropes with significantly stronger breaking strengths at time of manufacture than minke whales (Balaenoptera acuturostrata) (19.30, 17.13, and 10.47 mean kN, respectively). Adult right whales were found in stronger ropes (mean 34.09 kN) than juvenile right whales (mean 15.33 kN) and than all humpback whale age classes (mean 17.37 kN). For right whales, severity of injuries increased since the mid 1980s, possibly due to changes in rope manufacturing in the mid 1990s that resulted in production of stronger ropes at the same diameter. Our results suggest that broad adoption of ropes with breaking strengths of ≤ 7.56 kN (≤ 1700 lbsf) could reduce the number of life-threatening entanglements for large whales by at least 72%, and yet could provide sufficient strength to withstand the routine forces involved in many fishing operations. A reduction of this magnitude would achieve nearly all the mitigation legally required for U.S. stocks of North Atlantic right and humpback whales. Ropes with reduced breaking strength should be developed and tested to determine the feasibility of their use in a variety of fisheries.

Progesterone, testosterone, 17β-estradiol, cortisol, corticosterone, aldosterone, thyroxine and tri-iodothyronine are detectable in baleen of eight whale species. The presence of a broad array of hormones in baleen of multiple species indicates that baleen hormone analysis may be widely applicable for studies of reproduction, stress and metabolism of the large whales., Recent studies have demonstrated that some hormones are present in baleen powder from bowhead (Balaena mysticetus) and North Atlantic right (Eubalaena glacialis) whales. To test the potential generalizability of this technique for studies of stress and reproduction in large whales, we sought to determine whether all major classes of steroid and thyroid hormones are detectable in baleen, and whether these hormones are detectable in other mysticetes. Powdered baleen samples were recovered from single specimens of North Atlantic right, bowhead, blue (Balaenoptera [B.]musculus), sei (B. borealis), minke (B. acutorostrata), fin (B. physalus), humpback (Megaptera novaeangliae) and gray (Eschrichtius robustus) whales. Hormones were extracted with a methanol vortex method, after which we tested all species with commercial enzyme immunoassays (EIAs, Arbor Assays) for progesterone, testosterone, 17β-estradiol, cortisol, corticosterone, aldosterone, thyroxine and tri-iodothyronine, representing a wide array of steroid and thyroid hormones of interest for whale physiology research. In total, 64 parallelism tests (8 species × 8 hormones) were evaluated to verify good binding affinity of the assay antibodies to hormones in baleen. We also tested assay accuracy, although available sample volume limited this test to progesterone, testosterone and cortisol. All tested hormones were detectable in baleen powder of all species, and all assays passed parallelism and accuracy tests. Although only single individuals were tested, the consistent detectability of all hormones in all species indicates that baleen hormone analysis is likely applicable to a broad range of mysticetes, and that the EIA kits tested here perform well with baleen extract. Quantification of hormones in baleen may be a suitable technique with which to explore questions that have historically been difficult to address in large whales, including pregnancy and inter-calving interval, age of sexual maturation, timing and duration of seasonal reproductive cycles, adrenal physiology and metabolic rate.

Blubber lipid concentrations of 14 organochlorine compounds and 10 polychlorinated biphenyls (PCB) were measured by gas chromatography with electron-capture detection in eastern North Atlantic humpback whales Megaptera novaeangliae from Cape Verde (n = 20) and Ireland (n = 4). Concentrations were statistically compared to those from 20 samples collected from the Gulf of Maine in the western North Atlantic. Pollutant burdens were compared using males only, in order to circum- vent biases associated with reproductive offloading. Lipid-normalised PCB concentrations were below the estimated threshold toxicity value of 17 000 ng g �1 for blubber in marine mammals. Dichlorodiphenyltrichloroethane (DDT), PCB and chlordane concentrations were an order of mag - nitude lower than those previously reported for Gulf of Maine humpback whales and higher than those reported from the North Pacific Ocean. Higher concentrations of lower-chlorinated PCB con- geners (28, 31 and 52), hexachlorocyclohexanes and hexachlorobenzene in males in eastern North At- lantic sites is consistent with higher latitude feeding grounds. Lower p,p'-DDE (dich loro di phe nyl - dichloroethane):ΣDDT ratios suggest that whales from the eastern North Atlantic harbour more recent inputs of DDT. The ΣDDTs:ΣPCBs ratio was higher for males from Cape Verde (1.69) and Ireland (1.44), indicating proportionately greater sources of agricultural rather than industrial sources of pol- lutants than for the Gulf of Maine whales (0.75). We demonstrate potential for persistent organochlo- rine pollutants (POPs) as tracers to determine foraging ground provenance for samples collected on breeding grounds in the North Atlantic. Low concentrations suggest that POPs are unlikely to be a factor in the poor recovery rate of humpback whales in Cape Verde.

Antarctic humpback whales are recovering from near extirpation from commercial whaling. To understand the dynamics of this recovery and establish a baseline to monitor impacts of a rapidly changing environment, we investigated sex ratios and pregnancy rates of females within the Western Antarctic Peninsula (WAP) feeding population. DNA profiling of 577 tissue samples (2010–2016) identified 239 males and 268 females. Blubber progesterone levels indicated 63.5% of the females biopsied were pregnant. This proportion varied significantly across years, from 36% in 2010 to 86% in 2014. A comparison of samples collected in summer versus fall showed significant increases in the proportion of females present (50% to 59%) and pregnant (59% to 72%), consistent with demographic variation in migratory timing. We also found evidence of annual reproduction among females; 54.5% of females accompanied by a calf were pregnant. These high pregnancy rates are consistent with a population recovering from past exploitation, but appear inconsistent with recent estimates of WAP humpback population growth. Thus, our results will help to better understand population growth potential and set a current baseline from which to determine the impact of climate change and variability on fecundity and reproductive rates.

Understanding the dynamics of population recovery is particularly complex when an organism has multiple, remote breeding and feeding grounds separated by one of the longest known migration routes. This study reports on the most comprehensive assessment of humpback whale (Megaptera novaeangliae) movements between remote Antarctic waters south of New Zealand and east Australia (EA), and the migratory corridors and breeding grounds of Australia and Oceania. A total of 112 individual whales were identified; 57 from microsatellites and 61 by fluke with 23 % (n = 26) matched to sites outside Antarctica. Despite large datasets from other southern regions being included in the comparison, the whales were predominantly linked to EA (n = 24). Only two matches to the Oceania catalogues directly north was surprising; therefore the primary feeding grounds of these endangered whales still remain unknown. The confirmation of the Balleny Islands as an important feeding ground for EA whales could provide an insight into reasons behind the rapid recovery of this population. Determining the feeding grounds of Oceania’s whales may explain whether prey energetics or migration length are limiting factors to their recovery and will allow an understanding of future ecosystem changes in these whales.