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In recent years, humpback whales (Megaptera novaeangliae) have been observed in the waters of the US mid-Atlantic states (USMA; New Jersey to North Carolina), notably in winter. The level of the mortality in this area (52 recorded deaths from 1990-2000), makes it important to understand the nature and population identity of this aggregation. Of the approximately 100 humpback whales documented in this study, photographs of 41 (live or dead) were of sufficient quality to be compared to catalogues from the Gulf of Maine (GOM, the closest feeding ground) and elsewhere in the North Atlantic. Of 22 live whales, 10 (45.5%) matched to the GOM, 5 (22.7%) to Newfoundland and 1 (4.5%) to the Gulf of St Lawrence (GSL). Of 19 dead whales, 6 (31.6%) were known GOM whales. Although the population composition of the USMA is dominated by GOM whales, lack of recent photographic effort in Newfoundland makes it likely that the observed match rates under represent the true presence of Canadian whales in the region. Length data from 48 stranded whales (18 females, 22 males and 8 of unknown sex) suggest that 39 (81.2%) were first-year animals, 7 (14.6%) were immature and 2 (4.2%) were adults. However, sighting histories of five of the dead whales indicate that some were small for their age and histories of live whales further indicate that the population contains a greater percentage of mature animals than is suggested by the stranded sample. The authors suggest that the study area primarily represents a supplemental winter feeding ground that is used by humpbacks for more than one purpose. From a management perspective, although the only successful matches of mortalities to date have been to the GOM, the observed mixing of live whales from different summer stocks might suggest that the high numbers of mortalities occurring there may not be impacting this single stock alone. Although further data are required before conclusions can be drawn, the mortality rate may be significant for the GOM population and this warrants further investigation.

The Gulf of Maine is one of the principal summer feeding grounds for humpback whales (Megaptera novaeangliae) in the North Atlantic, and was one focus of effort in an ocean-basin-wide study known as the Years of the North Atlantic Humpback (YoNAH) project. Data from that project and from subsequent surveys were used to assess stock boundaries, abundance and demographic parameters for Gulf of Maine humpbacks. Surveys on the Scotian Shelf in the summers of 1998 and 1999 produced the first substantial dataset of identified individual humpbacks observed in this region, which lies between the well-studied areas of the Gulf of Maine and Newfoundland. The results gave a match rate of approximately 27% (14 of 52 individuals) between the Scotian Shelf and the Gulf of Maine, with evidence that many of the matched whales were transient in the Gulf of Maine; there were no matches to any other location in the North Atlantic. These data suggest that the range of most whales from the Gulf of Maine usually does not extend as far east as the Scotian Shelf or Newfoundland. Only one whale was observed on the Scotian Shelf in both the 1998 and 1999 surveys, and another seen in 1998 had also been sighted there in 1994. This low inter-annual match rate suggests that the abundance of humpback whales on the Scotian Shelf is larger than previously recognised. Three different but overlapping estimates of abundance for the Gulf of Maine population were calculated. Mark-recapture data from 1992/93 gave an estimate of abundance of 652 (CV = 0.29); however, this estimate is likely biased because of heterogeneity in sampling and in animal distribution. Photo-id data also provided a minimum population estimate of 497 humpbacks known to be alive in 1997; this estimate is also likely to be negatively biased because of heterogeneity. Finally, line-transect surveys conducted in 1999 yielded estimates of 816 (CV = 0.45) or 902 humpback whales (CV = 0.41, including a portion of the eastern Scotian Shelf stratum); these transect-based estimates are more consistent with the number of humpbacks (1,273, including dead animals) in the current photo-id catalogue for the Gulf of Maine. Overall, the size of the Gulf of Maine population is likely to be in the high hundreds, but no more precise estimate can be calculated at this time. The growth rate for the Gulf of Maine population was estimated using an interbirth interval method using data from 1992-2000. The estimate was either 1.00 (for a calf survival rate of 0.51) or 1.04 (for a calf survival rate of 0.875). Although confidence limits are not available (because maturation parameters could not be estimated), both estimates of population growth rate are outside the 95% confidence intervals of the previous estimate of 1.065 for the period 1979-1991 (Barlow and Clapham, 1997). It is unclear whether this apparent decline is an artefact resulting from a shift in distribution or is a real phenomenon; if the latter, it may be related to known high mortality among young-of-the-year whales in the waters of the US mid-Atlantic states. However, calf survival appears to have increased since 1996, presumably accompanied by an increase in population growth.

Little is known about the species composition, distribution, abundance or stock structure of odontocetes in the central and western tropical Pacific Ocean, including those inhabiting the US Exclusive Economic Zone (EEZ) waters of American Samoa. While some information on species presence in this region has been gleaned from anecdotal sightings and whaling and stranding records, odontocete diversity in the waters of American Samoa has never been formally investigated. This lack of information precludes efforts to determine the sustainability of cetacean populations within US EEZ waters. This paper reports on the first dedicated surveys to document the presence and distribution of odontocete cetaceans in the waters of American Samoa. A series of small-boat photo-identification and biopsy surveys for cetaceans were conducted in the nearshore waters of Tutuila during 2003-06. In addition, ship-based visual surveys were conducted in the waters surrounding the Manu‘a Islands, Rose Atoll and Swains Island in summer 2006. A total of 58 groups of odontocete cetaceans were encountered during both small-boat and ship-based surveys: spinner dolphins (Stenella longirostris, n=34), rough-toothed dolphins (Steno bredanensis, n=10), sperm whales (Physeter macrocephalus, n=3), false killer whales (Pseudorca crassidens, n=5), bottlenose dolphins (Tursiops truncatus., n=1), dwarf sperm whales (Kogia sima, n=1), short-finned pilot whales (Globicephala macrorhynchus, n=1), and three groups of unidentified odontocetes. Photographs were analysed for quality and individuals with distinctive markings were selected for entry into a photo-identification catalogue. The resultant catalogue included 46 spinner dolphins, 41 rough-toothed dolphins, 2 bottlenose dolphins, 5 false killer whales, 4 pilot whales, 1 dwarf sperm whale and 4 sperm whales. Thirteen spinner dolphins and 14 rough-toothed dolphins were sighted in multiple years. To investigate stock structure, spinner dolphin genetic data were used to compare mitochondrial control region genetic diversity and allele frequencies between American Samoa and the Hawaiian Islands. American Samoa had a higher genetic diversity, and populations at the two locations were genetically distinct (FST = 0.21). The high diversity at American Samoa indicates that spinner dolphins at this location are not reproductively isolated, but the data do not rule out the possibility that these dolphins may be demographically isolated on ecological timescales.

Discovery mark tagging provided the first evidence of linkages between eastern Australian and Oceania Humpback whale breeding grounds and the Antarctic Area V feeding areas. Early investigation of movements of humpback whales in the Western Pacific led to the view that the Balleny Islands and the Ross Sea were the summer destinations for humpback whales from eastern Australia and the Oceania breeding grounds. Recent photo-identification (ID) studies provided further evidence of low levels of migratory interchange and complex linkages within Oceania and between eastern Australia and Oceania. We report here the migratory movement of three humpback whales (Megaptera novaeangliae) between Eastern Australia (E(i) breeding stock) and the Area V Antarctic feeding area in the vicinity of the Balleny Islands. Using photo-ID techniques, comparisons between a Balleny Island fluke catalogue (n = 11 individuals) and existing fluke catalogues from eastern Australia (n = 3,120 individuals) and Oceania (n = 725 individuals), yielded three matches to Hervey Bay, Byron Bay and Ballina in eastern Australia and no matches to Oceania. The eastern Australia catalogue (n = 3,120) was made up of Hervey Bay (n = 1,556), Byron Bay, (n = 916) and Ballina (n = 648). The Oceania catalogue (n = 725) is made up of Tonga (n = 282); New Caledonia (n = 160); French Polynesia (n = 159); New Zealand (n = 41); Cook Islands (n = 36); American Samoa (n = 31); Vanuatu, Niue, Samoa and Fiji (n = 11) and Norfolk Island (n = 5). Only three previous individual photo-ID matches have been reported between eastern Australia Breeding Stock E(i) and Antarctic Area V feeding areas in the vicinity of the Balleny Islands and the Ross Sea. Only one genotype match has been reported between Antarctic Area V feeding areas and Oceania breeding grounds. An analysis of the frequencies of whales seen and not seen in the Balleny Islands, Oceania and eastern Australia, relative to the expected frequencies, based on the estimated population sizes and the sizes of the catalogues, supports the hypothesis that Antarctic Area V waters, in the vicinity of the Balleny islands, is a summer feeding area for some eastern Australian humpback whales.

Highly polymorphic single tandem repeat loci (STR, also known as microsatellite loci) remain a familiar, cost efficient class of markers for genetic analyses in ecology, behavior and conservation. We characterize a new universal set of ten STR loci (from 28 potential candidate loci) in seven baleen whale species, which are optimized for PCR amplification in two multiplex reactions along with a Y chromosome marker for sex determination. The optimized, universal set of STR loci provides an ideal starting point for new studies in baleen whales aimed at individual-based and population genetic studies, and facilitates data sharing among research groups. Data from the new STR loci were combined with genotypes from other published STR loci to assess the power to assign parentage (paternity) using exclusion in four species: fin whales, humpback whales, blue whales and bowhead whales. We argue that parentage studies should present a power analysis to demonstrate that the specific data are sufficiently informative to assign parentage with statistical rigor.

Current low germline mutation rate (μ) estimates in baleen whales have greatly influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. However, the reported rates were subject to methodological errors and uncertainty. We estimated μ directly from pedigrees in natural populations of four baleen whale species and the results were similar to primates. The implications of revised μ values include pre-exploitation population sizes at 14% of previous genetic diversity-based estimates and the conclusion that μ in itself is insufficient to explain low cancer rates in gigantic mammals (i.e., Peto’s Paradox). We demonstrate the feasibility of estimating μ from whole genome pedigree data in natural populations, which has wide-ranging implications for the many ecological and evolutionary inferences that rely on μ.

Heteroplasmy is the presence of two or more organellar genomes (mitochondrial or plastid DNA) in an organism, tissue, cell or organelle. Heteroplasmy can be detected by visual inspection of Sanger sequencing chromatograms, where it appears as multiple peaks of fluorescence at a single nucleotide position. Visual inspection of chromatograms is both consuming and highly subjective, as heteroplasmy is difficult to differentiate from background noise. Few software solutions are available to automate the detection of point heteroplasmies, and those that are available are typically proprietary, lack customization or are unsuitable for automated heteroplasmy assessment in large datasets.Here, we present PHFinder, a Python-based, open source tool to assist in the detection of point heteroplasmies in large numbers of Sanger chromatograms. PHFinder automatically identifies point heteroplasmies directly from the chromatogram trace data. The program was tested with Sanger sequencing data from 100 humpback whale (Megaptera novaeangliae) tissue samples with known heteroplasmies.PHFinder detected most (90%) of the known heteroplasmies thereby greatly reducing the amount of visual inspection required. PHFinder is flexible, enabling explicit specification of key parameters to infer double peaks (i.e., heteroplasmies).

Several previous studies have described epigenetic clocks for whale and dolphin species. Here we present a novel and highly robust epigenetic clock for the humpback whale based on methylation levels measured using the Mammalian Methylation Array platform. Skin samples were obtained from 76 individuals that had been studied since their birth year and known to range in age from

Contaminant studies in cetaceans can provide information about pollutant levels and patterns in a given region. Due to the confounding effects of reproductive status and maternal offloading in females, these studies typically focus on males. However, an improved understanding of contaminant burdens in female cetaceans is needed to better assess potential impacts to populations. The objectives of this study were to characterize concentrations of persistent organic pollutants (POPs) in blubber of female humpback whales across age classes and to also better characterize maternal offloading of these pollutants to their offspring. A total of 36 blubber biopsy samples of female humpback whales (Megaptera novaeangliae) from the Gulf of Maine were analyzed to examine contaminant loads across females of different ages. Sampled individuals were individually-identified from longitudinal studies and assigned to age class (i.e., adult, subadult, juvenile, calf). Analysis was performed using gas chromatography/mass spectrometry (GC/MS) of POPs including polychlorinated biphenyls (PCBs), dichlorodiphenyltrichloroethanes (DDTs), chlordanes (CHLDs), polybrominated diphenyl ethers (PBDEs), hexachlorocyclohexanes (HCHs). The most abundant POPs were PCB congeners, with summed values ranging from 280 to 12,000 ng/g, lipid weight, which is above recent estimates of the threshold for adverse health effects. We found significant differences in mean values between adults and juveniles and between adults and subadults, with the exception of the less persistent HCHs for the latter. We also found significant differences in mean levels of ∑HCHs between the juveniles and subadults. Changes over age are consistent with maternal offloading and potentially important for evaluating population health and viability.

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.

Fecal hormone analysis shows high potential for noninvasive assessment of population-level patterns in stress and reproduction of marine mammals. However, the marine environment presents unique challenges for fecal sample collection. Data are still lacking on collection methodology and assay validations for most species, particularly for those mysticete whales that have variable diets. In this study we tested collection techniques for fecal samples of free-swimming humpback whales (Megaptera novaeangliae), and validated immunoassays for five steroid and thyroid hormones. Resulting data were used for preliminary physiological validations, i.e., comparisons to independently confirmed sex and reproductive state. Pregnant females had significantly higher fecal progestins and glucocorticoids than did other demographic categories of whales. Two possible cases of previously undetected pregnancies were noted. Males had significantly higher fecal testosterone metabolites than nonpregnant females. Fecal glucocorticoids were significantly elevated in pregnant females and mature males compared to nonpregnant females. Calf fecal samples had elevated concentrations of all fecal hormones. Fecal thyroid hormones showed a significant seasonal decline from spring to summer. Though sample sizes were small, and sampling was necessarily opportunistic, these patterns indicate that noninvasive fecal hormone analysis may facilitate studies of reproduction, stress and potentially energetics in humpback whales.

Publisher's version (útgefin grein), Entanglement in fishing gear is a significant anthropogenic source of large whale injury and mortality. Although entanglements have been reported in the eastern North Atlantic, their frequency has not been previously estimated. This study used systematic scar analysis to estimate the frequency of non-lethal entanglements among individual humpback whales Megaptera novaeangliae off coastal Iceland, from 2005 through 2017. Images of the caudal peduncle and fluke insertions of 379 individuals were analyzed for wrapping injuries and notches known to be indicative of entanglement. The results indicated that at least 24.8% (n = 94, 95% confidence intervals [95% CI]: 20.5-29.1%) of individuals had a history of prior entanglement when first encountered. Depending on the metric used, the whales subsequently acquired new entanglement-related injuries at an average rate of 1.9% (95% CI: 0.6-3.2%) or 16.3% (95% CI: 3.0-29.3%) per year, with no statistically significant change over time. Furthermore, evidence suggests that at least some entanglements occurred locally. Observations of whales with gear still entangling the body confirmed the patterns of injury studied here. These results are lower than scar-based estimates from other parts of the world, but the cause of this difference requires further study. Scar-based methods underestimate the frequency of prior entanglement because some injuries heal beyond recognition, do not involve the caudal peduncle, and may occur on whales that die before they are studied. Long-term monitoring of humpback whale entanglement in Icelandic coastal waters is important for evaluating the local effects of fisheries, as well as the viability of the endangered Cape Verde breeding population., This work was funded in part by a National Geographic Explorer Grant awarded by the National Geographic Society, a PhD sponsorship grant awarded by Gentle Giants Whale Watching, and a Doctoral Grant awarded by Rannís Icelandic Research Fund. We thank all the students at the University of Iceland’s Húsavík Research Center for contributing data, the Faxaflói Ceta - cean Research volunteers (in Húsavík and Reykjavík), and all the whale-watching companies in Iceland who showed interest in the project and contributed photographs and/or space onboard their vessels for data collection. Furthermore, we thank the anonymous reviewers, who provided valuable input into the manuscript. Photographs used in the figures are copyright of University of Iceland (Figs. 2,3,4a1,b,c, 5 & 6a,b,d) Elding Adventures at Sea (Fig. 6c), and Charlie Frank Lavin (Elding Whale Watching Akureyri) (Fig. 4a2).

Maximum lifespan of a species is the oldest that individuals can survive, reflecting the genetic limit of longevity in an ideal environment. Here we report methylation-based models that accurately predict maximum lifespan (r=0.89), gestational time (r=0.96), and age at sexual maturity (r=0.87), using cytosine methylation patterns collected from over 12,000 samples derived from 192 mammalian species. Our epigenetic maximum lifespan predictor corroborated the extended lifespan in growth hormone receptor knockout mice and rapamycin treated mice. Across dog breeds, epigenetic maximum lifespan correlates positively with breed lifespan but negatively with breed size. Lifespan-related cytosines are located in transcriptional regulatory regions, such as bivalent chromatin promoters and polycomb-repressed regions, which were hypomethylated in long-lived species. The epigenetic estimators of maximum lifespan and other life history traits will be useful for characterizing understudied species and for identifying interventions that extend lifespan.

SummaryEpigenetics has hitherto been studied and understood largely at the level of individual organisms. Here, we report a multi-faceted investigation of DNA methylation across 11,117 samples from 176 different species. We performed an unbiased clustering of individual cytosines into 55 modules and identified 31 modules related to primary traits including age, species lifespan, sex, adult species weight, tissue type and phylogenetic order. Analysis of the correlation between DNA methylation and species allowed us to construct phyloepigenetic trees for different tissues that parallel the phylogenetic tree. In addition, while some stable cytosines reflect phylogenetic signatures, others relate to age and lifespan, and in many cases responding to anti-aging interventions in mice such as caloric restriction and ablation of growth hormone receptors. Insights uncovered by this investigation have important implications for our understanding of the role of epigenetics in mammalian evolution, aging and lifespan.

Biofilm-forming bacteria have the potential to contribute to the health, physiology, behavior and ecology of the host and serve as its first line of defense against adverse conditions in the environment. While metabarcoding and metagenomic information furthers our understanding of microbiome composition, fewer studies use cultured samples to study the diverse interactions among the host and its microbiome, as cultured representatives are often lacking. This study examines the surface microbiomes cultured from three shallow-water coral species and two whale species. These unique marine animals place strong selective pressures on their microbial symbionts and contain members under similar environmental and anthropogenic stress. We developed an intense cultivation procedure, utilizing a suite of culture conditions targeting a rich assortment of biofilm-forming microorganisms. We identified 592 microbial isolates contained within 15 bacterial orders representing 50 bacterial genera, and two fungal species. Culturable bacteria from coral and whale samples paralleled taxonomic groups identified in culture-independent surveys, including 29% of all bacterial genera identified in the Megaptera novaeangliae skin microbiome through culture-independent methods. This microbial repository provides raw material and biological input for more nuanced studies which can explore how members of the microbiome both shape their micro-niche and impact host fitness., This study captures a diverse range of cultured microorganisms from the surface microbiomes of marine animals, which fills necessary gaps in the availability of cultured isolates from this important environment.

Baleen of two pregnant humpback whales contains areas of high progesterone that span the duration of pregnancy (determined from sighting records), while baleen from a non-pregnant female and juvenile male had low progesterone through the baleen. Thus, baleen hormone analysis can identify pregnancies and inter-calving intervals of female humpback whales., 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.

Baleen whales are subject to a myriad of natural and anthropogenic stressors, but understanding how these stressors affect physiology is difficult. Measurement of adrenal glucocorticoid (GC) hormones involved in the vertebrate stress response (cortisol and corticosterone) in baleen could help fill this data gap. Baleen analysis is a powerful tool, allowing for a retrospective re-creation of multiple years of GC hormone concentrations at approximately a monthly resolution. We hypothesized that whales that died from acute causes (e.g. ship strike) would have lower levels of baleen GCs than whales that died from extended illness or injury (e.g. long-term entanglement in fishing gear). To test this hypothesis, we extracted hormones from baleen plates of four humpback whales (Megaptera novaeangliae) with well-documented deaths including multiple and chronic entanglements (n = 1, female), ship strike (n = 2, male and female) and chronic illness with nutritional stress (n = 1, male). Over ~3 years of baleen growth and during multiple entanglements, the entangled whale had average corticosterone levels of 80–187% higher than the other three whales but cortisol levels were similar to two of the other three whales. The nutritionally stressed and chronically ill whale showed a slow increase in both cortisol and corticosterone spanning ~3 years, followed by a sharp decline in both hormones before death, possibly indicative of adrenal failure in this moribund individual. This whale’s correlation between cortisol and corticosterone was significant but there were no correlations in the other three whales. Our results show that cortisol and corticosterone concentrations vary according to the type and duration of illness or injury. Single-point GC concentrations should be interpreted with caution as low values can occur in whales experiencing pronounced stress and individual baselines can be highly variable. Baleen analysis is a promising tissue type for retrospective analyses of physiological responses to various stressors affecting baleen whales.

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.

Supplementary Table 3. PERMANOVA and PERMDISP pair-wise comparison analysis of the effect of species on the composition of the skin microbiota (PERMANOVA *p0.05 ).

Specific MED sequencing groupings from SIMPER analysis that contribute to host family microbiome similarity.

Specific MED sequencing groupings from SIMPER analysis that contribute to microbiome similarity within a species.

NCBI accessions for reference mitochondrial genomes sequences used to infer host phylogeny.

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.