Bellwethers of change: population modelling of North Pacific humpback whales from 2002 through 2021 reveals shift from recovery to climate response

For the 40 years after the end of commercial whaling in 1976, humpback whale populations in the North Pacific Ocean exhibited a prolonged period of recovery. Using mark-recapture methods on the largest individual photo-identification dataset ever assembled for a cetacean, we estimated annual ocean-basin-wide abundance for the species from 2002 through 2021. Trends in annual estimates describe strong post-whaling era population recovery from 16 875 (± 5955) in 2002 to a peak abundance estimate of 33 488 (± 4455) in 2012. An apparent 20% decline from 2012 to 2021, 33 488 (± 4455) to 26 662 (± 4192), suggests the population abruptly reached carrying capacity due to loss of prey resources. This was particularly evident for humpback whales wintering in Hawai'i, where, by 2021, estimated abundance had declined by 34% from a peak in 2013, down to abundance levels previously seen in 2006, and contrasted to an absence of decline in Mainland Mexico breeding humpbacks. The strongest marine heatwave recorded globally to date during the 2014-2016 period appeared to have altered the course of species recovery, with enduring effects. Extending this time series will allow humpback whales to serve as an indicator species for the ecosystem in the face of a changing climate.

Universal DNA methylation age across mammalian tissues

Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.

DNA methylation networks underlying mammalian traits

Using DNA methylation profiles (n = 15,456) from 348 mammalian species, we constructed phyloepigenetic trees that bear marked similarities to traditional phylogenetic ones. Using unsupervised clustering across all samples, we identified 55 distinct cytosine modules, of which 30 are related to traits such as maximum life span, adult weight, age, sex, and human mortality risk. Maximum life span is associated with methylation levels in HOXL subclass homeobox genes and developmental processes and is potentially regulated by pluripotency transcription factors. The methylation state of some modules responds to perturbations such as caloric restriction, ablation of growth hormone receptors, consumption of high-fat diets, and expression of Yamanaka factors. This study reveals an intertwined evolution of the genome and epigenome that mediates the biological characteristics and traits of different mammalian species.

DNA methylation based biomarkers for aging 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 non-human 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.

Inbreeding depression explains killer whale population dynamics

Understanding the factors that cause endangered populations to either grow or decline is crucial for preserving biodiversity. Conservation efforts often address extrinsic threats, such as environmental degradation and overexploitation, that can limit the recovery of endangered populations. Genetic factors such as inbreeding depression can also affect population dynamics but these effects are rarely measured in the wild and thus often neglected in conservation efforts. Here we show that inbreeding depression strongly influences the population dynamics of an endangered killer whale population, despite genomic signatures of purging of deleterious alleles via natural selection. We find that the 'Southern Residents', which are currently endangered despite nearly 50 years of conservation efforts, exhibit strong inbreeding depression for survival. Our population models suggest that this inbreeding depression limits population growth and predict further decline if the population remains genetically isolated and typical environmental conditions continue. The Southern Residents also had more inferred homozygous deleterious alleles than three other, growing, populations, further suggesting that inbreeding depression affects population fitness. These results demonstrate that inbreeding depression can substantially limit the recovery of endangered populations. Conservation actions focused only on extrinsic threats may therefore fail to account for key intrinsic genetic factors that also limit population growth.

Passive acoustic monitoring of killer whales (Orcinus orca) reveals year-round distribution and residency patterns in the Gulf of Alaska

Killer whales (Orcinus orca) are top predators throughout the world's oceans. In the North Pacific, the species is divided into three ecotypes-resident (fish-eating), transient (mammal-eating), and offshore (largely shark-eating)-that are genetically and acoustically distinct and have unique roles in the marine ecosystem. In this study, we examined the year-round distribution of killer whales in the northern Gulf of Alaska from 2016 to 2020 using passive acoustic monitoring. We further described the daily acoustic residency patterns of three killer whale populations (southern Alaska residents, Gulf of Alaska transients, and AT1 transients) for one year of these data. Highest year-round acoustic presence occurred in Montague Strait, with strong seasonal patterns in Hinchinbrook Entrance and Resurrection Bay. Daily acoustic residency times for the southern Alaska residents paralleled seasonal distribution patterns. The majority of Gulf of Alaska transient detections occurred in Hinchinbrook Entrance in spring. The depleted AT1 transient killer whale population was most often identified in Montague Strait. Passive acoustic monitoring revealed that both resident and transient killer whales used these areas much more extensively than previously known and provided novel insights into high use locations and times for each population. These results may be driven by seasonal foraging opportunities and social factors and have management implications for this species.

Concentrations and profiles of organochlorine contaminants in North Pacific resident and transient killer whale (Orcinus orca) populations

Organochlorine (OC) profiles have been used as chemical "fingerprints" to infer an animal's foraging area. North Pacific killer whale (Orcinus orca) populations are exposed to different levels and patterns of OCs based on their prey, distribution, and amount of time spent in a particular area. To characterize concentrations and profiles of OCs found in various populations of North Pacific killer whales, polychlorinated biphenyls (PCBs), including dioxin-like congeners, DDTs, and hexachlorobenzene (HCB), were measured in biopsy blubber samples of photo-identified resident (fish-eating) and transient (mammal-eating) killer whales collected from 1994 through 2002 from Russian Far East waters to the waters of the west coast of the United States, representing 10 populations. We compared blubber OC concentrations based on ecotype (resident vs. transient), sex and reproductive maturity, and geographic area. We also examined OC mixtures to determine if we could detect segregated geographical areas (foraging areas) among the six populations with sufficient sample sizes. Transients had significantly higher OC concentrations than residents and adult male whales had consistently higher OC levels compared to adult females, regardless of ecotype. Our OC profile findings indicate segregated foraging areas for the North Pacific killer whales, consistent with observations of their geographic distributions. Several potential health risks have also been associated with exposure to high levels of contaminants in top-level predators including reproductive impairment, immune suppression, skeletal deformities, and carcinoma. The results of this baseline study provide information on the geographic distribution of OCs found in North Pacific killer whales, results which are crucial for assessing the potential health risks associated with OC exposure in this species.

Physical constraints of cultural evolution of dialects in killer whales

Odontocete sounds are produced by two pairs of phonic lips situated in soft nares below the blowhole; the right pair is larger and is more likely to produce clicks, while the left pair is more likely to produce whistles. This has important implications for the cultural evolution of delphinid sounds: the greater the physical constraints, the greater the probability of random convergence. In this paper the authors examine the call structure of eight killer whale populations to identify structural constraints and to determine if they are consistent among all populations. Constraints were especially pronounced in two-voiced calls. In the calls of all eight populations, the lower component of two-voiced (biphonic) calls was typically centered below 4 kHz, while the upper component was typically above that value. The lower component of two-voiced calls had a narrower frequency range than single-voiced calls in all populations. This may be because some single-voiced calls are homologous to the lower component, while others are homologous to the higher component of two-voiced calls. Physical constraints on the call structure reduce the possible variation and increase the probability of random convergence, producing similar calls in different populations.

Geographic and temporal dynamics of a global radiation and diversification in the killer whale

Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of marine mammals, the killer whale (Orcinus orca), using a global data set of over 450 samples. This marine top predator inhabits coastal and pelagic ecosystems ranging from the ice edge to the tropics, often exhibiting ecological, behavioural and morphological variation suggestive of local adaptation accompanied by reproductive isolation. Results suggest a rapid global radiation occurred over the last 350 000 years. Based on habitat models, we estimated there was only a 15% global contraction of core suitable habitat during the last glacial maximum, and the resources appeared to sustain a constant global effective female population size throughout the Late Pleistocene. Reconstruction of the ancestral phylogeography highlighted the high mobility of this species, identifying 22 strongly supported long-range dispersal events including interoceanic and interhemispheric movement. Despite this propensity for geographic dispersal, the increased sampling of this study uncovered very few potential examples of ancestral dispersal among ecotypes. Concordance of nuclear and mitochondrial data further confirms genetic cohesiveness, with little or no current gene flow among sympatric ecotypes. Taken as a whole, our data suggest that the glacial cycles influenced local populations in different ways, with no clear global pattern, but with secondary contact among lineages following long-range dispersal as a potential mechanism driving ecological diversification.

Killer whale call frequency is similar across the oceans, but varies across sympatric ecotypes

Killer whale populations may differ in genetics, morphology, ecology, and behavior. In the North Pacific, two sympatric populations ("resident" and "transient") specialize on different prey (fish and marine mammals) and retain reproductive isolation. In the eastern North Atlantic, whales from the same populations have been observed feeding on both fish and marine mammals. Fish-eating North Pacific "residents" are more genetically related to eastern North Atlantic killer whales than to sympatric mammal-eating "transients." In this paper, a comparison of frequency variables in killer whale calls recorded from four North Pacific resident, two North Pacific transient, and two eastern North Atlantic populations is reported to assess which factors drive the large-scale changes in call structure. Both low-frequency and high-frequency components of North Pacific transient killer whale calls have significantly lower frequencies than those of the North Pacific resident and North Atlantic populations. The difference in frequencies could be related to ecological specialization or to the phylogenetic history of these populations. North Pacific transient killer whales may have genetically inherited predisposition toward lower frequencies that may shape their learned repertoires.

Ultrasonic whistles of killer whales (Orcinus orca) recorded in the North Pacific (L)

Ultrasonic whistles were previously found in North Atlantic killer whales and were suggested to occur in eastern North Pacific killer whales based on the data from autonomous recorders. In this study ultrasonic whistles were found in the recordings from two encounters with the eastern North Pacific offshore ecotype killer whales and one encounter with the western North Pacific killer whales of unknown ecotype. All ultrasonic whistles were highly stereotyped and all but two had downsweep contours. These results demonstrate that specific sound categories can be shared by killer whales from different ocean basins.

Use of chemical tracers in assessing the diet and foraging regions of eastern North Pacific killer whales

Top predators in the marine environment integrate chemical signals acquired from their prey that reflect both the species consumed and the regions from which the prey were taken. These chemical tracers-stable isotope ratios of carbon and nitrogen; persistent organic pollutant (POP) concentrations, patterns and ratios; and fatty acid profiles-were measured in blubber biopsy samples from North Pacific killer whales (Orcinus orca) (n=84) and were used to provide further insight into their diet, particularly for the offshore group, about which little dietary information is available. The offshore killer whales were shown to consume prey species that were distinctly different from those of sympatric resident and transient killer whales. In addition, it was confirmed that the offshores forage as far south as California. Thus, these results provide evidence that the offshores belong to a third killer whale ecotype. Resident killer whale populations showed a gradient in stable isotope profiles from west (central Aleutians) to east (Gulf of Alaska) that, in part, can be attributed to a shift from off-shelf to continental shelf-based prey. Finally, stable isotope ratio results, supported by field observations, showed that the diet in spring and summer of eastern Aleutian Island transient killer whales is apparently not composed exclusively of Steller sea lions.

Vocal repertoire and acoustic behavior of the isolated AT1 killer whale subpopulation in southern Alaska

Killer whales, Orcinus orca (L., 1758), in the North Pacific are classified as three genetically distinct ecotypes: residents (fish-eaters), transients (mammal-eaters), and offshores (probable fish-eaters). Within the transient ecotype, three putative subpopulations have been identified by genetic analysis: West Coast transients, Gulf of Alaska transients, and AT1 transients. Here, we examine the behavior and vocalizations of the AT1 transients, which are found only in the Prince William Sound/Kenai Fjords region, to determine if their acoustic behavior distinguishes them from other genetically distinct transient subpopulations. We identified 14 discrete, pulsed calls in the vocal repertoire of the AT1 transients. These calls were entirely different than those of West Coast and sympatric Gulf of Alaska transients. Despite their large call repertoire, AT1 transients were silent most of the time, utilizing a foraging strategy of stealth, acoustic crypsis, and passive listening for locating marine-mammal prey. Unlike resident killer whales, AT1 transient vocalization types were context specific. For example, lone AT1 transients produced long-distance, high-amplitude pulsed calls in stereotyped sequences to locate other AT1 whales. In contrast, hunting individuals emitted low-amplitude pulsed calls to maintain contact with group members. The repertoire and call-usage patterns of the AT1 transients are consistent with genetic evidence that they are a unique, reproductively and socially isolated subpopulation in danger of extinction.

Influence of life-history parameters on organochlorine concentrations in free-ranging killer whales (Orcinus orca) from Prince William Sound, AK

Certain populations of killer whales (Orcinus orca) have been extensively studied over the past 30 years, including populations that use Puget Sound, WA, the inside waters of British Columbia, Southeastern Alaska and Kenai Fjords/Prince William Sound, Alaska. Two eco-types of killer whales, 'transient' and 'resident', occur in all of these regions. These eco-types are genetically distinct and differ in various aspects of morphology, vocalization patterns, diet and habitat use. Various genetic and photo-identification studies of eastern North Pacific killer whales have provided information on the male-female composition of most of these resident pods and transient groups, as well as the approximate ages, reproductive status and putative recruitment order (birth order) of the individual whales. Biopsy blubber samples of free-ranging resident and transient killer whales from the Kenai Fjords/Prince William Sound, AK region were acquired during the 1994-1999 field seasons and analyzed for selected organochlorines (OCs), including dioxin-like CB congeners and DDTs. Concentrations of OCs in transient killer whales (marine mammal-eating) were much higher than those found in resident animals (fish-eating) apparently due to differences in diets of these two killer whale eco-types. Certain life-history parameters such as sex, age and reproductive status also influenced the concentrations of OCs in the Alaskan killer whales. Reproductive female whales contained much lower levels of OCs than sexually immature whales or mature male animals in the same age class likely due to transfer of OCs from the female to her offspring during gestation and lactation. Recruitment order also influenced the concentrations of OCs in the Alaskan killer whales. In adult male residents, first-recruited whales contained much higher OC concentrations than those measured in non-first-recruited (e.g. second recruited, third recruited) resident animals in the same age group. This study provides baseline OC data for free ranging Alaskan killer whales for which there is little contaminant information.