The International Whaling Commission’s Scientific Committee conducts regular Implementation Reviews (IRs) of the biology, threats and status of whale species subject to aboriginal subsistence whaling. The last IR of plans for hunting eastern North Pacific (ENP) gray whales by the Chukotka Natives of the Russian Federation and the Makah Tribe of the United States of America occurred in 2020. This paper presents a review of new scientific findings on gray whales to assess whether the current status of the stock(s) is within the parameter space tested in the 2020 IR. Updated information on gray whale stock structure hypotheses, abundance and calf productivity, health and strandings, human removals by hunting and non‐hunting sources, population growth rates, immigration into the Pacific Coast Feeding Group, parameterisation of the Makah hunt, and future episodic mortality events (EMEs) were reviewed for this assessment. For almost all factors, it appears that the current dynamics of the ENP gray whale population are within the parameter space evaluated in 2020 IR. The exception is that EMEs affecting whales in the ENP are occurring more frequently and at a greater magnitude than previously evaluated. However, preliminary evaluations suggest that the performances of the Gray Whale Strike Limit Algorithm (SLA) and Makah Management Plan are robust to recent and future EMEs of Northern Feeding Group gray whales and reductions of productivity of the Pacific Coast Feeding Group, at least under the initial parameterisations. We therefore conclude that there is no compelling need for a Special IR prior to the next scheduled IR in 2026, while noting that additional abundance data for 2022/23 and 2023/24 analysed after drafting this paper could strengthen or weaken the evidence for this conclusion.

The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10X, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world’s smallest cetacean, to investigate blue whale’s unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.

Blue whales (Balaenoptera musculus) are the largest living animal and, like other baleen whales, became endangered due to whaling. Here, we used population genomics to infer the number, distribution and other characteristics of subspecies and populations. We used the largest DNA dataset in blue whales, both in terms of genomic markers (16,661 SNPs and mtDNA) and geographic coverage (n = 276 for SNPs; n = 531 for mtDNA). We found greatest divergence among the eastern Pacific, Indo-western Pacific and Antarctic blue whales. There were indications that natural selection in different environments promoted divergence among these groupings. Within these regions, there was divergence between the eastern North and eastern South Pacific, and among the eastern Indian Ocean, the western South Pacific and the northern Indian Ocean. There was no divergence within the Antarctic. These findings are consistent with the current classification of Antarctic and Indo-western Pacific blue whales in the Southern Hemisphere as different subspecies but call into question the subspecies taxonomy of eastern Pacific blue whales. The study shows that opposite breeding seasons on either side of the equator do not necessarily inhibit connectivity across the equator, and reinforces that population structure needs to be well understood to conserve the diversity within species. Blue whales are the largest living animal and became endangered due to whaling. We found three major groupings of blue whales using high-resolution population genomics: the eastern Pacific, Indo-western Pacific, and Antarctic blue whales. Within these groupings, there was divergence between the eastern North and eastern South Pacific; between the eastern Indian Ocean, the western South Pacific, and the northern Indian Ocean; and no divergence within the Antarctic. The study reinforces that population structure needs to be well understood to conserve the diversity within species. image

ABSTRACTReliable estimates of population abundance and demographics are essential for managing harvested species. Ice‐associated phocids, “ice seals,” are a vital resource for subsistence‐dependent coastal Native communities in western and northern Alaska, USA. In 2012, the Beringia distinct population segment of the bearded seal, Erignathus barbatus nauticus, was listed as “threatened” under the US Endangered Species Act requiring greater scrutiny for management assessments. We sought to estimate requisite population parameters from harvested seals by using close‐kin mark‐recapture (CKMR) methods, the first such application for marine mammals. Samples from 1758 bearded seals harvested by Bering, Chukchi, and Beaufort Sea communities during 1998–2020 were genotyped, genetically sexed, and aged by tooth annuli. After rigorous quality control, kin relationships were established for 1484 seals including two parent–offspring pairs (POPs) and 25 potential second‐order kin pairs. Most of the second‐order kin were half‐sibling pairs (HSPs), but four were potential grandparent‐grandchild pairs (GGPs). There were no full sibling pairs, suggesting a lack of mate fidelity. Mitochondrial DNA analysis identified 17 potential HSPs as paternally related, providing substantial evidence of persistent heterogeneity in reproductive success among adult males. The statistical CKMR model incorporates probabilities associated with POPs, HSPs, and GGPs and assumes known ages and a stable population. Our top model accommodates heterogeneity in adult male breeding success and yields an abundance estimate of ~409,000 with a coefficient of variation (CV) = 0.35, which is substantially greater than the “non‐heterogeneity” model estimate of ~232,000 (CV = 0.21), an important difference for managing a harvested species. Using CKMR methods with harvested species provides estimates of abundance with the added opportunity to acquire information about adult survival, fecundity, and breeding success that could be applied to other species of concern, marine and terrestrial.

In many organisms, especially those of conservation concern, traditional lines of evidence for taxonomic delineation, such as morphological data, are often difficult to obtain. In these cases, genetic data are often the only source of information available for taxonomic studies. In particular, population surveys of mitochondrial genomes offer increased resolution and precision in support of taxonomic decisions relative to conventional use of the control region or other gene fragments of the mitochondrial genome. To improve quantitative guidelines for taxonomic decisions in cetaceans, we build on a previous effort targeting the control region and evaluate, for whole mitogenome sequences, a suite of divergence and diagnosability estimates for pairs of recognized cetacean populations, subspecies, and species. From this overview, we recommend new guidelines based on complete mitogenomes, combined with other types of evidence for isolation and divergence, which will improve resolution for taxonomic decisions, especially in the face of small sample sizes or low levels of genetic diversity. We further use simulated data to assist interpretations of divergence in the context of varying forms of historical demography, culture, and ecology.

The California coastal stock of bottlenose dolphins (Tursiops truncatus) expanded its range north from the Southern California Bight, its historical range, into Central California coincident with the 1982-1983 El Niño event. Since the late 1980s, bottlenose dolphin sightings north of Central California have been increasingly reported. To determine the present-day northern range limit for these dolphins, photo-identification efforts were carried out from 2007 to 2018 in San Francisco Bay and nearby coastal waters during which 84 individuals were identified. The results demonstrate a significant range expansion along the Northern California coast at least as far as Sonoma County (38.7º N). Comparisons with photo-identification catalogs compiled south of San Francisco from 1981 to 2015 revealed that 92% of the 84 dolphins were matched to Monterey Bay (n = 77), Santa Barbara (n = 27), Santa Monica Bay (n = 29), Orange County (n = 9), Corona Del Mar (n = 2), San Diego (n = 31), and Ensenada, Mexico (n = 1). Many of the 84 dolphins (54%) showed long-range movements across the stock’s range between the Southern California Bight and the San Francisco Bay Area. The greatest movement distance recorded was by two individuals first observed in San Diego, California, in the 1980s and subsequently in Puget Sound, Washington (47º N), in 2017, setting a coastal bottlenose dolphin long-distance movement record of at least 2,500 km.

AbstractGray whale sexual behavior and copulation are observed throughout their range. The most prominent period for reproductive behavior is during the southward migration from summer feeding areas to wintering areas where some breeding occurs and calves of the year are reared. The seasonal migrations of gray whales are believed to function, in part, to bring together individuals that are otherwise widely distributed during the period of estrus to facilitate mating and reproduction. Sexual behaviors and sexual strategies for this species appear to align closely with those of balaenid (not rorqual) whales, although such comparisons need further investigation. Gray whales are polygynandrous (multi-mate) breeders. There does not appear to be female choice of mates, as groups of numerous females and males aggregate, and multiple copulations occur. Female estrus begins in mid-November and continues to early December; females may undergo a second estrus, extending into February, if they fail to conceive during their first cycle. Male gray whales have large testes and concomitantly produce large volumes of sperm, so they are believed to be sperm competitors; that is, they rely on multiple copulations (and sperm volume) to produce offspring. Multiple copulations with different males during the female estrus period may increase the likelihood that the timing of conception results in the birth of a calf approximately 13 months later near or in the wintering area(s). Mating bouts can last for minutes to hours, interspersed with surface-active-social-sexual behavior. Some all-male groups have been observed with erect penises engaged in social-sexual behavior in the absence of any females. Instances of male aggression toward postpartum females with calves of the year, sometimes resulting in injury or death, have been reported. As a result of dedicated long-term research in the past several decades, the state of knowledge on gray whale reproduction has greatly expanded and updated information on this topic is summarized in this chapter.

Photographic and genetic studies have revealed the complex population structure of migratory large whales. Most research and management are geographically based, focusing on either wintering or summering areas, which in most cases fails to capture this complexity. We use examples from humpback whales (Megaptera novaeangliae) and gray whales (Eschrichtius robustus) to illustrate the concept of migratory herds, defined here as conspecific whales that migrate between the same wintering and feeding ground. In cases where individuals show strong fidelity to both feeding and wintering grounds, and therefore to a herd, dispersal between herds can be low enough to render them as demographically independent populations, where population dynamics are determined more by net internal recruitment (births minus deaths) than by immigration from outside sources. In these cases, the migratory whale herd is the appropriate unit to conserve under the ecological paradigm that focuses on groups united by demographic forces. We suggest that when addressing questions focused on ecological timescales for whale species with strong fidelity to migratory destinations, the migratory whale herd is a better initial working hypothesis rather than one based on geographically defined strata.

The goal of the present study was to carry out a thorough methodological validation and describe baseline profiles for glucocorticoid hormones (cortisol and corticosterone) in blubber from blue (n = 77) and gray (n = 103) whales from the eastern North Pacific Ocean. For each species, we modelled cortisol and corticosterone concentrations in response to life history parameters (age, sex, reproductive status) and season or geographic location. In blue whales, cortisol concentrations did not vary significantly by age class, sex, or reproductive status, whereas corticosterone was significantly lower in immature than in adult females (p < .001). In gray whales, cortisol concentrations were significantly higher in lactating whales (p < .05), while corticosterone was significantly different between females and males (p = .001) and elevated in calves (p = .003). In gray whales, corticosterone concentrations were significantly lower in males sampled later in the year (August to November) compared to both sexes sampled between March and August (p = .05), but no seasonal trend occurred in blue whales. Our results indicate that glucocorticoid actions vary between species and sex in large whales. Analysis of multiple hormones improves our understanding of the physiology of maintaining metabolic homeostasis or coping with chronic stressors.

Background The blue whale, Balaenoptera musculus , is the largest animal known to have ever existed. Body size is tightly coupled to cell metabolism and environmental adaptations. A high-quality genome assembly of this magnificent animal will aid our understanding of body size regulation and related biological processes. Results We report a reference-quality, long read based assembly of the blue whale genome. We sequenced genomic DNA using PacBio long-read, Illumina short-read, and 10X Genomics synthetic long-read technologies. We also obtained long-range mapping information using Bionano optical mapping and Dovetail Hi-C. Additionally, we sequenced the transcriptome of blue whale fibroblasts using Illumina RNA-seq and PacBio Iso-seq technologies. We also measured genome size using a flow cytometry technique. We report on: (1) comparison of alternative long-read and short-read-based assemblies; (2) segmental duplications within the blue whale genome, which have resulted in dramatic amplifications of several genes; (3) sites in IGF1 gene correlated to body size in cetaceans; and (4) heterozygosity and historical demography of Pacific and Atlantic blue whale populations. Conclusions This is one of the first high-quality reference genomes of a cetacean and the first baleen whale sequenced using a long-read technology. A high quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.

Exposure to persistent organic pollutants (POPs) can significantly impact marine mammal health, reproduction, and fitness. This study addresses a significant 20-year gap in gray whale contaminant monitoring through analysis of POPs in 120 blubber biopsies. The scope of this substantial sample set is noteworthy in its range and diversity with collection between 2003 and 2017 along North America's west coast and across diverse sex, age, and reproductive parameters, including paired mothers and calves. Mean blubber concentrations of polychlorinated biphenyls (∑PCBs), dichlorodiphenyltrichloroethanes (∑DDTs), and chlordanes (∑CHLs) generally decreased since previous reports (1968–1999). This is the first report of polybrominated diphenyl ethers (PBDEs) and select hexachlorocyclohexanes (HCHs) in this species. Statistical modeling of the 19 most frequently detected compounds in this dataset revealed sex-, age-, and reproductive status-related patterns, predominantly attributed to maternal offloading. Mean POP concentrations differed significantly by sex in adults (17 compounds, up to 3-fold higher in males) but not in immatures (all 19 compounds). Mean POP concentrations were significantly greater in adults versus immatures in both males (17 compounds, up to 12-fold) and females (13 compounds, up to 3-fold). POP concentrations were detected with compound-specific patterns in nursing calves, confirming maternal offloading for the first time in this species.

Recent findings that some gray whales that feed off Sakhalin Island (SI), Russia, in the western North Pacific (WNP) overwinter in the eastern North Pacific (ENP) indicate that population structure in this species is more complex than originally thought. We generated mitochondrial DNA (mtDNA) control region sequences and microsatellite genotypes (n = 12 loci) from 156 whales sampled off SI and compared them to available data from 106 ENP whales. Significant mitochondrial and nuclear genetic differentiation between the SI and ENP whales was found. Genetic cluster analysis identified two groups among the SI whales, one of which was genetically similar to ENP whales. Photographs collected from the biopsied SI whales showed that both groups comprised whales known to migrate to the ENP, suggesting that the clustering pattern was not reflective of some SI whales interbreeding while overwintering in the WNP. Instead, the genetic differentiation observed between the SI and ENP whales may be due to assortative mating of SI whales while west of eastern migratory routes. The rare but continued reports of gray whales off the coasts of Japan and China, however, confirm that some gray whales overwinter in the WNP and highlight the need to collect additional data from these whales.

Most of our knowledge on reproductive biology of gray whales dates back to scientific research conducted during commercial whaling in the late 1950s and 1960s. The goal of the present study was to provide updated insights on reproductive physiology of gray whales, using progesterone and testosterone as biomarkers. We measured hormone concentrations using enzyme immunoassay (EIA) techniques in blubber biopsies collected from 106 individual whales from March to November over a span of 12 years (2004-2016) between California and Alaska. We found testosterone concentrations in males to increase significantly with age (P = 0.03). Adult males showed significantly elevated testosterone concentrations when sampled in the fall compared to the summer (P = 0.01), likely indicating physiological preparation for mating. We measured testosterone concentrations in females of different age classes, but no statistical differences were found. We found significantly higher progesterone concentrations in pregnant females compared to non-pregnant females and adult males (P< 0.001), indicating progesterone is a valid biomarker for pregnancy in gray whales. Both female and male calves had elevated progesterone concentrations, suggesting maternal transfer via lactation. We fit a mixture of two normal distributions to progesterone data from all non-calf females to identify clusters of high and low progesterone and estimated the probability of being pregnant for whales of unknown reproductive status. With this approach we identified likely pregnant and non-pregnant animals. This study represents an important milestone on reproductive profiles in this population, that can be used to estimate more accurate and precise reproductive parameters to be used for better understanding population dynamics of gray whales.

Although Arctic ringed seals Phoca hispida hispida are currently abundant and broadly distributed, their numbers are projected to decline substantially by the year 2100 due to climate warming. While understanding population structure could provide insight into the impact of environmental changes on this subspecies, detecting demographically important levels of exchange can be difficult in taxa with high abundance. We used a next-generation sequencing approach (DArTseq) to genotype ~5700 single nucleotide polymorphisms in 79 seals from 4 Pacific Arctic regions. Comparison of the 2 most geographically separated strata (eastern Bering vs. northeastern Chukchi-Beaufort Seas) revealed a statistically significant level of genetic differentiation (FST = 0.001, p = 0.005) that, while small, was 1 to 2 orders of magnitude greater than expected based on divergence estimated for similarly sized populations connected by low (1% yr-1) dispersal. A relatively high proportion (72 to 88%) of individuals within these strata could be genetically assigned to their stratum of origin. These results indicate that demographically important structure may be present among Arctic ringed seals breeding in different areas, increasing the risk that declines in the number of seals breeding in areas most negatively affected by environmental warming could occur.

Population genetic studies of non-model organisms often rely on initial ascertainment of genetic markers from a single individual or a small pool of individuals. This initial screening has been a significant barrier to beginning population studies on non-model organisms (Aitken et al., Mol Ecol 13:1423-1431, 2004; Morin et al., Trends Ecol Evol 19:208-216, 2004). As genomic data become increasingly available for non-model species, SNP ascertainment from across the genome can be performed directly from published genome contigs and short-read archive data. Alternatively, low to medium genome coverage from shotgun NGS library sequencing of single or pooled samples, or from reduced-representation libraries (e.g., capture enrichment; see Ref. "Hancock-Hanser et al., Mol Ecol Resour 13:254-268, 2013") can produce sufficient new data for SNP discovery with limited investment. We describe protocols for assembly of short read data to reference or related species genome contig sequences, followed by SNP discovery and filtering to obtain an optimal set of SNPs for population genotyping using a variety of downstream high-throughput genotyping methods.

The population assessment of gray whales Eschrichtius robustus feeding off Sakhalin and Kamchatka is updated, using a population model that alows for multiple feeding and breeding areas. The model is fit to photo-id data collected of Sakhalin during 1995-2015 (Burdin et al. 2015), tracking of whales from Sakhalin to the eastern North Pacific (Mate et al. 2015), photo-id matches of gray whales between the Sakhalin and Mexico catalogues (Urbán et al. 2013) and reported photo-id results from Kamchatka collected during 2004-12 (Yakovlev et al. 2013),. The results show that the Sakhalin and Kamchatka feeding populations have been increasing at 2-5% per year over the 10 or 20 years to 2015. The number of non-calf whales in 2016 is estimated to be 320−410, of which 130−170 are predominantly Sakhalinfeeding whales or 180−220 are whales that feed at least occasionally off Sakhalin. A test of the population model output against the results of a paternity analysis by Lang (2010) just rejects the hypothesis of genetic closure of the Sakhalin feeding population (p < 0.05) but does not reject the hypothesis of genetic closure of the Sakhalin and Kamchatka feeding populations combined. Of the predominantly Sakhalin-feeding whales, an estimated 0-50 belong to a possible relict western North Pacific breeding population (which may or may not be genetically closed). Using the IUCN Red List criteria, the Sakhalin and Kamchatka populations, if assessed as a subpopulation, either separately or together, would be classified as Endangered, on the basis of there being between 50 and 250 mature individuals (i.e. ~100-500 individuals when juveniles but not calves are included). If the relict western North Pacific breeding population were assessed as a subpopulation, it would be classified as Critically Endangered, on the basis of there being less than 50 mature individuals.

Taxonomy is an imprecise science that delimits the evolutionary continuum into discrete categories. For marine mammals, this science is complicated by the relative lack of morphological data for taxa that inhabit remote and often vast ranges. We provide guidelines to promote consistency in studies relying primarily on molecular genetic data to delimit cetacean subspecies from both populations and species. These guidelines identify informational needs: basis for the taxonomic hypothesis being tested, description of current taxonomy, description of relevant life history, sample distribution, sample size, number and sequence length of genetic markers, description of measures taken to ensure data quality, summary statistics for the genetic markers, and analytical methods used to evaluate the genetic data. We propose an initial set of quantitative and qualitative standards based on the types of data and analytical methods most readily available at present. These standards are not expected to be rigidly applied. Rather, they are meant to encourage taxonomic arguments that are consistent and transparent. We hope professional societies, such as the Society for Marine Mammalogy, will adopt quantitative standards that evolve as new data types and analytical methods become widely available.

Uncertainty in marine mammal taxonomy is increasingly being addressed using molecular genetic data. We examined 32 peer-reviewed articles published between 1994 and 2011to review methodological practices, consistency of markers and analytical methods, and overall quality of arguments used when genetic data have been employed to delimit new species and subspecies of marine mammals. The mitochondrial DNA (mtDNA) control region was the primary genetic marker used in these studies, but analytical methods varied greatly across studies. Diagnosability, a common metric for delimiting subspecies with morphological data, was only used through citing of fixed differences in mtDNA sequences. Assignment tests based on microsatellite data were less common but were applied at both taxonomic levels. Nuclear DNA sequence data were rarely used. Basic background material needed to evaluate the strength of arguments, such as distribution and sampling maps, were often missing. For most studies, sample sizes were good, but adequate geographic sampling for broadly distributed taxa was often lacking, diminishing the strength of evidence for taxonomic distinctness. Examining these empirical cases revealed a mixture of sound and inadequate practices for genetic studies of cetacean taxonomy and suggested that improvements could be made to the field by developing standard guidelines.