OBTAINING SKIN SAMPLES FROM LIVING SPERM WHALES

Samples of sperm whale skin, useful for modern molecular analyses of DNA, can be obtained from living animals either by collecting skin sloughed naturally by the whales, or by using biopsy darts fired from crossbows or compound bows. Sloughed skin was found frequently in warm waters, and particular samples could often be linked to photographs which enabled individuals to be identified. However, sloughed skin seemed less available at higher latitudes. Two types of darts were found to collect skin but collected samples were very small (<4 mm²) and insufficient for repeated DNA fingerprinting analyses. Sperm whales always reacted to darting by "startling" and showing changes of behavior over the next few minutes, but we found no indications of longer-term effects. In warm water studies, collection of sloughed skin seems to be generally effective, but for samples of sperm whale tissue at high latitudes modifications could probably be made to either of the darts in order to obtain larger-sized samples.     

BEHAVIORAL RESPONSE OF FOUR SPECIES OF BALAENOPTERID WHALES TO BIOPSY SAMPLING

Behavioral responses to biopsy sampling of four species of northwestern Atlantic balaenopterid whales summering in the estuary and Gulf of St. Lawrence, Quebec, from 1990 to 1995 were studied to determine if this technique was an important disturbance to the whales. A total of 447 biopsy samples were taken using a small punch-type biopsy tip fired from a crossbow. Biopsies were successfully taken from 91.2% of the whales approached. Whales displayed no reaction to 45.2% of the successful biopsy attempts. Whales that responded to biopsy sampling typically resumed their normal behavior immediately or within a few minutes. Most humpback whales displayed a hard tail flick, and the majority of fin and blue whales submerged following biopsy sampling. Significantly different frequencies and intensities of responses were found between whale species. Minke and humpback whales were found to be more sensitive to biopsy sampling than fin and blue whales. Response frequencies were similar between females and males for all species, with the exception of fin whales where females had a higher response frequency than males. Biopsy sample length, i. e., penetration depth, did not explain variations in response intensity but may influence response frequency to biopsy sampling. Group size, geographical region, and number of biopsies taken per whale were not factors that explained variation in behavioral responses. The biopsy technique was found to be an efficient method for obtaining high-quality whale skin and blubber samples with limited behavioral disturbance to balaenopterid whales.     

The influence of maternal lineages on social affiliations among humpback whales (Megaptera novaeangliae) on their feeding grounds in the southern gulf of Maine

Humpback whales on their feeding grounds in the Gulf of Maine typically form fluid fission/fusion groups of two to three individuals characterized by noncompetitive and, at times, cooperative behavior. Here we test the hypothesis that, despite the apparent absence of close kinship bonds, the fluid associations between feeding whales are influenced by "maternal lineages" as represented by mtDNA haplotypes. Using skin samples collected with a biopsy dart, variation in the hypervariable segment of the mtDNA control region identified 17 unique haplotypes among 159 individually identified whales from the southern Gulf of Maine. The haplotypes of a further 143 individuals were inferred from known direct maternal (cow-calf) relationships. The frequencies of associations among these 302 individuals were calculated from 21,617 sighting records collected from 1980 to 1995, excluding associations between a cow and her dependent calf. For groups of two where the haplotypes of both individuals were known (n = 3,151), individuals with the same haplotype were together significantly more often (26%) than expected by random association (20%). To account for different group sizes and associations with individuals of unknown haplotype and sex, we used Monte Carlo simulations to test for nonrandom associations in the full data set, as well as known female-only (n = 1,512), male-only (n = 730), and mixed-sex (n = 2,745) groups. Within-haplotype associations were significantly more frequent than expected at random for all groups (P = .002) and female-only groups (P = .011) but not male-only groups, while mixed-sex groups approached significance (P = .062). A Mantel test of individual pairwise association indices and haplotype identity confirmed that within-haplotype associations were more frequent than expected for all sex combinations except male-male associations, with females forming within-haplotype associations 1.7 times more often than expected by random assortment. Partial matrix correlations and permutation analyses indicated that the skew toward within-haplotype associations could not be accounted for by short-term temporal co-occurrence or fine-scale spatial distributions of individuals with shared haplotypes. While the mechanism by which individuals with a common mtDNA haplotype assort remains unknown, our results strongly suggest an influence of maternal lineages on the social organization of humpback whales within a regional feeding ground.     

CpG methylation frequency of TET2, GRIA2, and CDKN2A genes in the North Atlantic fin whale varies with age and between populations

Recovery rates for baleen whales that were decimated by exploitation vary between species and populations. Age determination is critical for the understanding of recovery trends and population structure, but determining age in free-ranging individuals remains challenging. Recent research has suggested that the methylation level of some genes in skin samples may provide age determinations with accuracy. We selected nine CpG sites from three genes (TET2, CDKN2A, and GRIA2) and analyzed them in 40 skin samples from known-age individuals pertaining to two different populations of fin whales from the North Atlantic. We observed significant correlations with age in five CpG sites. We used three of these CpG sites to perform an epigenetic age estimation. Predictions had a standard deviation of 2.94, but regression between observed and predicted ages showed a clear underestimation for older fin whales. For further development, we suggest: (1) screening for new CpG sites associated with age that exhibit higher variability between individuals, and (2) including older animals whenever the sampling allows it. We also observed subtle, but significant differences between the two populations studied in one of the CpG sites (TET2_CpG + 21). We attributed these differences to genetic differences or to the dissimilar environments that affect both populations.     

A BIOPSY SYSTEM FOR SMALL CETACEANS: DARTING SUCCESS AND WOUND HEALING IN TURSIOPS SPP.

Together with PAXARMS (NZ), we developed a biopsy system for small cetaceans and tested it on four populations of bottlenose dolphins ( Tursiops spp.). The system consists of a modified 0.22 caliber rifle, and biopsy darts made out of polycarbonate with stainless steel biopsy tips. Animals were darted at a range of 2–15 m while travelling parallel to the vessel. Overall sampling success for obtaining biopsy samples when an animal was struck ranged from 96.6% to 100% in the four populations. However, hit rate varied for the four different populations. We did not observe a significant difference in strength of the reaction to the darting procedure when an animal was hit or missed, both among and within populations. Data from one population showed no significant difference in the reaction to biopsy sampling by four different age-sex classes. The only factor that had a significant influence on darting success was the hit location. Furthermore, we observed a significant positive correlation between the size of the sample obtained and the reaction to biopsy sampling. Biopsy samples were sufficient for microsatellite and d-loop analysis in 95.8% and for genetic sexing in 99% of all cases. In animals that we observed on a daily basis, wounds were healed after approximately 23 d.     

The simultaneous detection of mitochondrial DNA damage from sun-exposed skin of three whale species and its association with UV-induced microscopic lesions and apoptosis

Due to life history and physiological constraints, cetaceans (whales) are unable to avoid prolonged exposure to external environmental insults, such as solar ultraviolet radiation (UV). The majority of studies on the effects of UV on skin are restricted to humans and laboratory animals, but it is important to develop tools to understand the effects of UV damage on large mammals such as whales, as these animals are long-lived and widely distributed, and can reflect the effects of UV across a large geographical range. We and others have used mitochondrial DNA (mtDNA) as a reliable marker of UV-induced damage particularly in human skin. UV-induced mtDNA strand breaks or lesions accumulate throughout the lifespan of an individual, thus constituting an excellent biomarker for cumulative exposure. Based on our previous studies in human skin, we have developed for the first time in the literature a quantitative real-time PCR methodology to detect and quantify mtDNA lesions in skin from sun-blistered whales. Furthermore the methodology allows for simultaneous detection of mtDNA damage in different species. Therefore using 44 epidermal mtDNA samples collected from 15 blue whales, 10 fin whales, and 19 sperm whales from the Gulf of California, Mexico, we quantified damage across 4.3 kilobases, a large region of the ~ 16,400 base pair whale mitochondrial genome. The results show a range of mtDNA damage in the skin of the three different whale species. This previously unreported observation was correlated with apoptotic damage and microscopic lesions, both of which are markers of UV-induced damage. As is the case in human studies, this suggests the potential use of mtDNA as a biomarker for measuring the effect of cumulative UV exposure in whales and may provide a platform to help understand the effects of changing global environmental conditions.     

MITOCHONDRIAL DNA VARIATION AND MATERNAL GENE FLOW AMONG HUMPBACK WHALES OF THE SOUTHERN HEMISPHERE

Samples of skin tissue were collected by biopsy darting from humpback whales ( Megaptera novaeangliae ) in six seasonal habitats representing three stocks and four regions: Groups IV (western Australia), V western component (eastern Australia), V eastern component (New Zealand and Tonga) and VI (the Antarctic Peninsula and Gorgona Island, Colombia, South America) of the Southern Hemisphere. A variable section of the mitochondrial DNA control region was amplified and sequenced from 84 of these individuals, distinguishing a total of 48 unique sequences ( i. e. , mtDNA nucleotypes). Phylogenetic reconstructions suggested that these nucleotypes form three clades, corresponding to those previously described in a world-wide survey of humpback whale mtDNA variation, although bootstrap support for two of the clades was relatively low (<50%). An analysis of variance adapted for molecular information showed significant differentiation of nucleotypes among the three Groups (Stocks) and heterogeneity of haplotype diversity among the four regions. A pattern of interchange within and between oceanic basins was demonstrated by the presence of shared identical nucleotypes among humpback whales in regions of the Southern and Northern Hemispheres.     

Epigenetic estimation of age in humpback whales

Age is a fundamental aspect of animal ecology, but is difficult to determine in many species. Humpback whales exemplify this as they have a lifespan comparable to humans, mature sexually as early as 4 years and have no reliable visual age indicators after their first year. Current methods for estimating humpback age cannot be applied to all individuals and populations. Assays for human age have recently been developed based on age‐induced changes in DNA methylation of specific genes. We used information on age‐associated DNA methylation in human and mouse genes to identify homologous gene regions in humpbacks. Humpback skin samples were obtained from individuals with a known year of birth and employed to calibrate relationships between cytosine methylation and age. Seven of 37 cytosines assayed for methylation level in humpback skin had significant age‐related profiles. The three most age‐informative cytosine markers were selected for a humpback epigenetic age assay. The assay has an R² of 0.787 (P = 3.04e?16) and predicts age from skin samples with a standard deviation of 2.991 years. The epigenetic method correctly determined which of parent–offspring pairs is the parent in more than 93% of cases. To demonstrate the potential of this technique, we constructed the first modern age profile of humpback whales off eastern Australia and compared the results to population structure 5 decades earlier. This is the first epigenetic age estimation method for a wild animal species and the approach we took for developing it can be applied to many other nonmodel organisms.     

AN OCEAN-BASIN-WIDE MARK-RECAPTURE STUDY OF THE NORTH ATLANTIC HUMPBACK WHALE (MEGAPTERA NOVAEANGLIAE)

Although much is known about the humpback whale, Megaptera novaeangliae, regional studies have been unable to answer several questions that are central to the conservation and management of this endangered species. To resolve uncertainties about population size, as well as the spatial and genetic structure of the humpback whale population in the North Atlantic, we conducted a two-year ocean-basin-wide photographic and biopsy study in 1992-1993. Photographic and skin-biopsy sampling was conducted of animals in feeding and breeding areas throughout most of the range of this species in the North Atlantic, from the West Indies breeding grounds through all known feeding areas as far north as arctic Norway. A standardized sampling protocol was designed to maximize sample sizes while attempting to ensure equal probability of sampling, so that estimates of abundance would be as accurate and as precise as possible. During 666 d at sea aboard 28 vessels, 4,207 tail fluke photographs and 2,326 skin biopsies were collected. Molecular analyses of all biopsies included determination of sex, genotype using six microsatellite loci, and mitochondrial control region sequence. The photographs and microsatellite loci were used to identify 2,998 and 2,015 individual whales, respectively. Previously published results from this study have addressed spatial distribution, migration, and genetic relationships. Here, we present new estimates of total abundance in this ocean using photographic data, as well as overall and sex-specific estimates using biopsy data. We identify several potential sampling biases using only breeding-area samples and report a consistent mark-recapture estimate of oceanwide abundance derived from photographic identification, using both breeding and feeding-area data, of 10,600 (95% confidence interval 9,300-12,100). We also report a comparable, but less precise, biopsy-based estimate of 10,400 (95% confidence interval of 8,000-13,600). These estimates are significantly larger and more precise than estimates made for the 1980s, potentially reflecting population growth. In contrast, significantly lower and less consistent estimates were obtained using between-feeding-area or between-breeding-area sampling. Reasons for the lower estimates using the results of sampling in the same areas in subsequent years are discussed. Overall, the results of this ocean-basin-wide study demonstrate that an oceanwide approach to population assessment of baleen whales is practicable and results in a more comprehensive understanding of population abundance and biology than can be gained from smaller-scale efforts.     

DNA methylation-based biomarkers for ageing long-lived cetaceans

Epigenetic approaches for estimating the age of living organisms are revolutionizing studies of long-lived species. Molecular biomarkers that allow age estimates from small tissue biopsies promise to enhance studies of long-lived whales, addressing a fundamental and challenging parameter in wildlife management. DNA methylation (DNAm) can affect gene expression, and strong correlations between DNAm patterns and age have been documented in humans and nonhuman vertebrates and used to construct “epigenetic clocks”. We present several epigenetic clocks for skin samples from two of the longest-lived cetaceans, killer whales and bowhead whales. Applying the mammalian methylation array to genomic DNA from skin samples we validate four different clocks with median errors of 2.3–3.7 years. These epigenetic clocks demonstrate the validity of using cytosine methylation data to estimate the age of long-lived cetaceans and have broad applications supporting the conservation and management of long-lived cetaceans using genomic DNA from remote tissue biopsies.     

Social structure in migrating humpback whales (Megaptera novaeangliae)

Although largely solitary, humpback whales exhibit a number of behaviours where individuals co-operate with one another, for example during bubble net feeding. Such cases could be due to reciprocal altruism brought on by exceptional circumstances, for example the presence of abundant shoaling fish. An alternative explanation is that these behaviours have evolved through kin selection. With little restriction to either communication or movement, diffuse groups of relatives could maintain some form of social organization without the need to travel in tight-nit units. To try to distinguish between these hypotheses, we took advantage of the fact that migrating humpback whales often swim together in small groups. If kin selection is important in humpback whale biology, these groups should be enriched for relatives. Consequently, we analysed biopsy samples from 57 groups of humpback whales migrating off Eastern Australia in 1992. A total of 142 whales were screened for eight microsatellite markers. Mitochondrial DNA sequences (371 bp) were also used to verify and assist kinship identification. Our data add support to the notion that mothers travel with their offspring for the first year of the calf's life. However, beyond the presence of mother-calf/yearling pairs, no obvious relatedness pattern was found among whales sampled either in the same pod or on the same day. Levels of relatedness did not vary between migratory phases (towards or away from the breeding ground), nor between the two sexes considered either overall or in the north or south migrations separately. These findings suggest that, if any social organization does exist, it is formed transiently when needed rather than being a constant feature of the population, and hence is more likely based on reciprocal altruism than kin selection.     

Occurrence and social structure of Baird's beaked whales,Berardius bairdii,in the Commander Islands,Russia

The social structure of Baird's beaked whales is completely unstudied, and it is unknown if either females or males form long‐term social associations or occur in stable groups. In this paper we summarize our observations of individually identified animals over the span of 6 yr to provide insight on their long‐term social structure. We have identified 122 whales, with 28 of them encountered three times or more and thus included in the analysis of social structure. We found that the whales exhibited nonrandom patterns of social associations with some individuals preferentially associating with each other. Whales with more scarred skin had higher maximum association coefficients, which indicates that older animals and/or males were more inclined to form stable associations. Cluster analysis with a modularity test for gregariousness divided the whales into four clusters. Whales from the same clusters did not always occur together, but some individuals retained stable associations over several years. The strength of social relationships decayed over periods of months, with between‐year relationships showing little deviation from what would be expected if association was random. Generally these findings do not correspond to a stable society with fixed groups but instead suggest a fission‐fusion society with some stable alliances.     

A METHOD TO COLLECT AND PROCESS SKIN BIOPSIES FOR CELL CULTURE FROM FREE-RANGING GRAY WHALES (ESCHRICHTIUS ROBUSTUS)

For researchers studying mysticere whales few methods for determining gender or for collecting biochemical and genetic information from unrestrained animals are available. The objective of this study was to develop a reliable method for collecting viable tissue samples for establishing continuous cell cultures from skin biopsies of free-ranging whales. A method to collect and process these samples is presented. Six of seven skin biopsies from gray whales were established in cell culture. Our results suggest that the viability of the samples is improved by (1) sterile processing in the field, (2) minimizing the time between collection and delivery to the cell culture facility, (3) reducing the concentration of antifungal agent, and (4) placing tissue explants under a coverslip. While the results reported in this paper are based on a small sample size, we believe that if the procedures are followed, they will increase the probability of successfully culturing cetacean tissue. Established cell lines can supply replenishable material from identified whales still living in the wild. These cultures can then be used for determination of sex from karyotypes, and for assessing genetic relationships of cetaceans from inherited protein, chromosomal and DNA polymorphisms. These much needed analytical tools can be used to determine familial and populational relationships, leading to a better understanding of mating systems, stock identification and effective population sizes of wild cetaceans.     

Molecular identification of individual North Atlantic right whales (Eubalaena glacialis) using free-floating feces

During the 1990s, North Atlantic right whales had significantly decreased reproduction and showed signs of compromised health, prompting the initiation of noninvasive fecal-based studies to investigate potential causal factors. The interpretation of these studies is enhanced when the defecator is identified, as data can then be linked to individual life history information. Fecal samples (n= 118) were either collected from single photoidentified whales, associated with several individuals by photoidentification of whales in the vicinity upon sample collection, or were collected when no whales were in the vicinity. Genetic profiles from fecal DNA comprising sex, mitochondrial haplotype, and five microsatellite loci helped assign specific samples to individual right whales based on existing genetic profiles. Profiles were informative in assigning 61 fecal samples to known individuals, 24 of which were collected when no whales were in the vicinity. Whales identified genetically were typically photographed in the same habitat area and on the same day of sample collection (n= 35/48). Twelve profiles new to the genetic database were identified, suggesting fecal sampling provides a means to obtain genetic profiles from previously unsampled individuals, which may help refine estimates of population size and habitat use patterns if annual fecal sampling continues.     

Population biology, social behavior and communication in whales and dolphins

The baleen whales differ from the toothed whales and dolphins in life history and in social organization. Even though they grow to a larger size, young baleen whales tend to develop more rapidly than dolphins and toothed whales. Except for the mother-calf bond, most groups of baleen whales are short-lived, lasting only for hours, and individual-specific associations appear to be exceptions to the norm. Most toothed whales live in more structured groups, in which young animals have a long period of dependency and social learning. The communication signals described for different cetacean species have functions suited to the interactions that predominate in their societies.     

Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin

Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro‐organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.     

The post-copulation withdrawal response in female baboons: A functional analysis

Rapid withdrawal of females from males at the end of the copulatory sequence (prior to male dismounting) characterizes several primate species. The purpose of this paper is to make a preliminary investigation into possible functional aspects of these “copulatory darts.” Two hypotheses are proposed; (1) females use darts to aid competing males to locate the source of copulation calls; and (2) females dart in order to promote re-mating with the same male. Both hypotheses postulate that darts may thus enhance male-male competition, although acquisition of other benefits may be the primary drive to darting according to the re-mating hypothesis. Using data from 157 copulations collected from six females spread across four groups in a wild population of chacma baboonsPapio cynocephalus ursinus, darting behaviour is described. Within females, darting distance is highly variable. Darting distance is greatest at the time of ovulation (and maximal sexual swelling), and there is some evidence that darting may also be more frequent, and cover greater distances, when the mating male is adult rather than juvenile. While darting behaviour appears unrelated to the presence or absence of ejaculation, it tends to correlate positively with the duration of the female copulation call. These preliminary results are consistent with a mediating role in male-male competition and therefore provide support for both hypotheses.     

Fine‐scale spatial differences in humpback whale diet composition near Kodiak,Alaska

On the North Pacific feeding grounds, humpback whales (Megaptera novaeangliae) are recovering from commercial whaling at a rapid rate (6.8%). The potential effect that this recovery will have on trophic dynamics involving these predators is currently unknown. To better elucidate complex trophic dynamics, variability in diet composition of apex predators on their respective feeding grounds needs to be understood. Thus, we explored the diet composition of two defined subaggregations of humpback whales of the Kodiak Archipelago population (“North,” “South”) using stable carbon (δ¹³C) and nitrogen (δ¹⁵N) isotope ratios of humpback whale skin and regional prey samples in Bayesian dietary mixing models. Humpback whales in the “North” region consumed proportionally more fish, dominated by capelin (Mallotus villosus), whereas, whales in the “South” region consumed predominantly krill. The difference in diet composition appears to reflect regional differences in prey availability. Thus, regional variability in diet composition by humpback whales may have disproportionate impacts on prey resources of sympatric predators depending on available prey biomass. As a result, we suggest fine‐scale studies of apex predator diets are needed to better model trophic dynamics with accuracy.     

Trophic level and fatty acids in harp seals compared with common minke whales in the Barents Sea

The objectives of this study were to explore trophic levels and possible diet overlap between harp seals (Pagophilus groenlandicus) and common minke whales (Balaenoptera acutoroostrata) in the Barents Sea using stable isotopes of nitrogen (δ¹⁵N) and carbon (δ¹³C) and fatty acid analyses, and to explore the energy pathways from the plankton to the top predators. Blubber and muscle samples from 93 harp seals and 20 minke whales were collected in the southern Barents Sea in May 2011. The study showed that harp seals were at a higher trophic level than minke whales during spring. This supported previous diet studies suggesting a more fish-dominant diet for seals, as compared with the whales, at this time of the year. The stable isotopes and fatty acids indicated niche separation between the seals and the whales, and between different age groups of the harp seals. Older seals had fatty acid profiles more equal to minke whales as compared with younger seals. Furthermore, while the fatty acid profiles suggested that krill were of particular importance for the young seals, the profiles from older seals and whales suggested that fish dominated their diets.     

Dietary variation within and between populations of northeast Atlantic killer whales,Orcinus orca,inferred from δ13C and δ15N analyses

Epidermal skin samples from eastern North Atlantic killer whales, Orcinus orca, were analyzed for carbon and nitrogen stable isotope ratios. From those, comparisons within a data set of 17 samples collected from Tysfjord, Norway, in November suggested that diet is relatively specialized during this time period at this location. There were significant differences between a small set of samples from Iceland and those collected from Norway, which had all been assigned to the same population by a previous population genetics study. The results would be consistent with matrilines feeding on either the Norwegian or Icelandic stocks of Atlantic herring (Clupea harengus). There was no significant difference within Icelandic samples between those assigned to the population known to feed upon herring and those assigned to a population hypothesized to follow Atlantic mackerel (Scomber scombrus). The greatest differences were between the epidermal samples analyzed in this study and tooth and bone collagen samples from the North Sea that were analyzed previously, which also showed significantly more variation in isotopic ratios than found for skin samples. These differences could reflect differences in turnover rate, differences in diet‐tissue fractionation and discrimination due to the amino acid composition of the different tissues, and/or greater competition promoting dietary variation between groups in the North Sea.