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BackgroundThe 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.ResultsWe 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.ConclusionsThis 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.

Southern Resident killer whales (SRKW) were listed as endangered in 2005, requiring designation of Critical Habitat. At that time little was known about SRKW distribution in winter/spring along the outer coast. From 2004 to 2016, we conducted nine winter/spring surveys aboard NOAA ocean-class vessels to locate and follow SRKW pods using visual sightings, satellite telemetry, and passive acoustic monitoring using towed hydrophone arrays. We present information on the evolution of the towed hydrophone array system, and insights gained on the movements and acoustic behavior of this population. Beginning with a linear two-element hydrophone array system, operations evolved to include a secondary, five-element array towed in parallel, to resolve left-right bearing ambiguity to vocalizing animals. Acoustic localization allowed tracking of vocalizing whales when visual surveys were not possible (e.g., nighttime/inclement weather). When visual and/or satellite tag position data indicated whales were within acoustic range, vocalizations were detected only 45% of the time, a result that has implications for other PAM efforts. These surveys helped fill important gaps in our understanding of SRKW occurrence to inform Critical Habitat in the outer coastal portion of their range. Despite limited monitoring, we established the importance of this key portion of their range in winter/spring.

Although most eastern North Pacific (ENP) gray whales feed in the Bering, Beaufort, and Chukchi Seas during summer and fall, a small number of individuals, referred to as the Pacific Coast Feeding Group (PCFG), show intra- and interseasonal fidelity to feeding areas from northern California through southeastern Alaska. We used both mitochondrial DNA (mtDNA) and 12 microsatellite markers to assess whether stock structure exists among feeding grounds used by ENP gray whales. Significant mtDNA differentiation was found when samples representing the PCFG (n = 71) were compared with samples (n = 103) collected from animals feeding further north (FST = 0.012 ,P = 0.0045). No significant nuclear differences were

Stable isotope analysis in mysticete skin and baleen plates has been repeatedly used to assess diet and movement patterns. Accurate interpretation of isotope data depends on understanding isotopic incorporation rates for metabolically active tissues and growth rates for metabolically inert tissues. The aim of this research was to estimate isotopic incorporation rates in blue whale skin and baleen growth rates by using natural gradients in baseline isotope values between oceanic regions. Nitrogen (δ15N) and carbon (δ13C) isotope values of blue whale skin and potential prey were analyzed from three foraging zones (Gulf of California, California Current System, and Costa Rica Dome) in the northeast Pacific from 1996–2015. We also measured δ15N and δ13C values along the lengths of baleen plates collected from six blue whales stranded in the 1980s and 2000s. Skin was separated into three strata: basale, externum, and sloughed skin. A mean (±SD) skin isotopic incorporation rate of 163±91 days was estimated by fitting a generalized additive model of the seasonal trend in δ15N values of skin strata collected in the Gulf of California and the California Current System. A mean (±SD) baleen growth rate of 15.5±2.2 cm y-1 was estimated by using seasonal oscillations in δ15N values from three whales. These oscillations also showed that individual whales have a high fidelity to distinct foraging zones in the northeast Pacific across years. The absence of oscillations in δ15N values of baleen sub-samples from three male whales suggests these individuals remained within a specific zone for several years prior to death. δ13C values of both whale tissues (skin and baleen) and potential prey were not distinct among foraging zones. Our results highlight the importance of considering tissue isotopic incorporation and growth rates when studying migratory mysticetes and provide new insights into the individual movement strategies of blue whales.

We recorded 62 bird species on Clarion Island, Mexico (Revillagigedo Archipelago, Pacific Ocean) during 1998–2006, eight of which breed there, 52 are considered non-breeders, and breeding is likely but unconfirmed for the Red-billed Tropicbird (Phaethon aethereus), Nazca Booby (Sula granti), and an unidentified shearwater. Thirty species are new for the island. A census of the Clarion Burrowing Owl (Athene cunicularia rostrata) in 2002/03 suggested a maximum total population of ∼850 pairs. At least 46 pairs of Laysan Albatrosses (Phoebastria immutabilis) bred in 2002/03, but the species experienced total breeding failure during our study. This result was unexpected because feral pigs (Sus scrofa) were successfully eradicated from Clarion by 2002; endemic Clarion Ravens (Corvus corax clarionensis), an endemic snake (Clarion Racer, Masticophis anthonyi), and an unidentified ant were associated with egg and hatchling failures. A small colony of an unidentified shearwater could be a recolonization by...

We examined the incidence of rake mark scars from killer whales Orcinus orca on the flukes of humpback whales Megaptera novaeangliae throughout the North Pacific to assess geo- graphic variation in predation pressure. We used 3650 identification photographs from 16 wintering or feeding areas collected during 1990 to 1993 to determine conservative estimates in the percentage of whales with rake mark scarring. Dramatic differences were seen in the incidence of rake marks among regions, with highest rates on wintering grounds off Mexico (26 vs. 14% at others) and feed- ing areas off California (20 vs. 6% at others), 2 areas between which humpback whales migrate. Although attacks are rarely witnessed, the prevalence of scars demonstrates that a substantial por- tion of animals are attacked, particularly those that migrate between California and Mexico. Our data also suggest that most attacks occur at or near the wintering grounds in the eastern North Pacific. The prevalence of attacks indicates that killer whale predation has the potential to be a major cause of mortality and a driving force in migratory behavior; however, the location of the attacks is inconsis- tent with the hypothesis that animals migrate to tropical waters to avoid predation. Our conclusion is that, at least in recent decades, attacks are made primarily on calves at the wintering grounds; this contradicts the hypothesis that killer whales historically preyed heavily on large whales in high- latitude feeding areas in the North Pacific.

Springer et al. (2003) contend that sequential declines occurred in North Pacific populations of harbor and fur seals, Steller sea lions, and sea otters. They hypothesize that these were due to increased predation by killer whales, when industrial whaling's removal of large whales as a supposed primary food source precipitated a prey switch. Using a regional approach, we reexamined whale catch data, killer whale predation observations, and the current biomass and trends of potential prey, and found little support for the prey-switching hypothesis. Large whale biomass in the Bering Sea did not decline as much as suggested by Springer et al., and much of the reduction occurred 50–100 yr ago, well before the declines of pinnipeds and sea otters began; thus, the need to switch prey starting in the 1970s is doubtful. With the sole exception that the sea otter decline followed the decline of pinnipeds, the reported declines were not in fact sequential. Given this, it is unlikely that a sequential megafaunal collapse from whales to sea otters occurred. The spatial and temporal patterns of pinniped and sea otter population trends are more complex than Springer et al. suggest, and are often inconsistent with their hypothesis. Populations remained stable or increased in many areas, despite extensive historical whaling and high killer whale abundance. Furthermore, observed killer whale predation has largely involved pinnipeds and small cetaceans; there is little evidence that large whales were ever a major prey item in high latitudes. Small cetaceans (ignored by Springer et al.) were likely abundant throughout the period. Overall, we suggest that the Springer et al. hypothesis represents a misleading and simplistic view of events and trophic relationships within this complex marine ecosystem.

Mating system theory predicts that differences between the sexes in potential reproductive rate and an operational sex ratio skewed strongly towards males should result in intense male competition, polygynous mating and high variance in male reproductive success. Accordingly, humpback whales are thought to be polygynous with differences in reproduction among males related to alternative mating tactics. However, there is currently a lack of data on male reproductive success. We tested predictions regarding male reproductive success in humpback whales using molecular assessment of paternity in a population in the Mexican Pacific. Parentage analysis was conducted for 125 mother–calf pairs and a sample of 297 males using 13 microsatellite loci. Two separate analyses were conducted, based upon conservative and relaxed criteria for the assignment of paternity. In the conservative analysis, 40 paternities (32.5% of tested calves) were assigned among 33 males, whereas in the relaxed analysis, 62 paternities (49.6% of calves) were assigned among 51 males. Regardless of analysis, the distribution of male reproductive success deviated from a random mating model, with significantly larger than expected variance (conservative, P = 0.011; relaxed, P = 0.022), and significantly more than expected males siring three calves (conservative, P = 0.021; relaxed, P = 0.011). However, most successful males sired only one calf and no male was assigned more than three calves, so reproductive skew was not severe. Therefore we conclude that this population has a polygynous mating system, but without the large variation in male reproductive success expected by apparent skew in the operational sex ratio and degree of male competition for mates.

Townsend's shearwater ( Puffinus auricularis auricularis ) is an endangered seabird endemic to the Revillagigedo Archipelago. It nested on Socorro, Clarion, and San Benedicto Islands. It was extirpated by the Barcena volcano on San Benedicto in 1952, and there are no recent indications of nesting. Introduced mammals—pigs and rabbits—preyed on them and destroyed habitat at Clarion; shearwaters were extirpated by 1988, and no breeding attempts have been reported since. Our results confirm that Socorro holds the last breeding grounds. We found breeding colonies above 800 m and a minimum population of 1100 individuals. This represents a significant reduction in distribution and population size. Intensive cat predation at Socorro could potentially kill ca. 350 females per season, and sheep progressively destroy nesting areas. Population projections suggest that demographic instability could occur in less than 100 years under severe predation and habitat degradation. Only low predation rates would allow population persistence for more than 150 years in spite of a declining population. Thus, the immediate eradication of all introduced mammals is necessary to prevent the extinction of this seabird.

Humpback whale song, a male breeding display, shows a remarkable degree of similarity among distant breeding assemblages, despite constant progressive change. It has been hypothesized that whales maintain continuity through cultural transmission via migratory movements of males. We examined songs of whales breeding off Hawaii and Mexico to determine whether they changed similarly in both areas during the course of a breeding season. Songs recorded off Kauai, Hawaii (11 individuals) and Isla Socorro, Mexico (13 individuals) during winter and spring of 1991, were compared qualitatively and quantitatively. We measured 44 acoustic variables describing all known levels of song structure for each singer and we grouped these variables into six categories. We used two-factor analyses of variance to assess change across the season in each area, comparing the two regions and two 3-week periods (January/February and April). Twenty-seven variables changed significantly during the 12-week study in at least one area. Variables within categories displayed similar trends of change. Time and frequency characteristics describing the structure of song elements (units and phrases) changed synchronously in each area, with 21 of 25 variables displaying significant differences between periods and no interaction with region. Structures of song patterns, as defined by frequency of occurrence and number of unit and phrase types, changed differently in each area, with five of 12 variables indicating a significant interaction between region and period. Our results may suggest cultural transmission during the season, since many variables changed in similar manners. We propose an alternative hypothesis, that whales may be predisposed to gradually change certain features of song independently of cultural influences; change of structural elements may be governed by a discrete set of rules, or according to an innate template. Therefore, continuity of song patterns across the ocean basin may be due to a combination of mechanisms, only partially involving cultural transmission. We assess these hypotheses in relation to humpback whale behaviour and population structure, and cultural transmission and evolution of avian song.

Sighting histories of individually identified female humpback whales (Megaptera novaeangliae) in their win- ter and summer ranges were used to investigate mortality of North Pacific humpback whale calves. We compiled re- cords collected between 1979 and 1995 by eight independent research groups, which yielded 29 cases where 25 different mothers sighted in Hawaii were identified later the same year in Alaska. In 7 of 29 cases, a calf sighted with its mother in Hawaii was missing from its mother's Alaska sighting(s). After investigating many factors, we deter - mined that the largest potential bias would occur in late-autumn observations, when calf absences might indicate wean- ing or temporary mother-calf separation rather than calf mortality. Our minimal and most robust estimate excluded all mortalities and survivals based on sightings of the mother after October 31; 3 of 20 cases or 0.150 (95% confidence intervals (CI) = 0.032, 0.378). The maximal calf mortality rate, derived from all the available data, was 7 of 29 cases or 0.241 (95% CI = 0.103, 0.434). An intermediate estimate that excluded all cases based on single Alaska sightings and omitted late-season sightings (2 of 11 cases or 0.182; 95% CI = 0.023, 0.518) is perhaps closest to the actual first- year mortality rate for humpback whale calves, although it is compromised by its small sample size. Our results dem- onstrate both the value and the limitations of using longitudinal data to determine the life-history parameters that are essential for documenting the recovery of endangered populations. 600 Resume : L'observation suivie de Baleines a bosse (Megaptera novaeangliae) femelles identifiees individuellement dans leurs aires d'hiver et d'ete a permis d'etudier la mortalite des petits dans la population du Pacifique Nord. Nous avons compile des donnees obtenues de 1979 a 1995 par huit groupes independants de chercheurs et l'operation a revele 29 cas ou 25 meres differentes apercues dans les eaux hawaiennes ont ete observees de nouveau en Alaska plus tard la meme annee. Dans 7 des 29 cas, une mere apercue a Hawaii avec son petit a ete revue en Alaska sans son petit. Apres avoir examine plusieurs facteurs, nous avons determine que la cause la plus probable d'erreur potentielle etait reliee aux observations de fin d'automne, alors que l'absence du petit pourrait s'expliquer par le sevrage ou par la separation temporaire du petit d'avec sa mere, plutot que par la mortalite. Notre estimation minimale la plus robuste ne tient pas compte des taux de mortalite et de survie bases sur les observations des meres apres le 31 octobre; 3 cas sur 20 ou 0,150 (95 % IC = 0,032, 0,378). Le taux maximal de mortalite des petits, base sur toutes les donnees, etait de 7 cas sur 29 ou 0,241 (95 % IC = 0,103, 0,434). Une estimation moyenne excluant tous les cas d'observations uniques en Alaska et les observations de fin de saison (2 cas sur 11 ou 0,182; 95 % IC = 0,023, 0,518) est peut etre plus pres de la mortalite reelle des petits au cours de la premiere annee, bien que les resultats soient compromis par la taille

In 2008 two male sperm whales (Physeter macrocephalus) stranded along the northern California coast with large amounts of fishing net scraps, rope, and other plastic debris in their stomachs. One animal had a ruptured stomach, the other was emaciated, and gastric impaction was suspected as the cause of both deaths. There were 134 different types of nets in these two animals, all made of floating material, varying in size from 10 cm2 to about 16 m2. The variability in size and age of the pieces suggests the material was ingested from the surface as debris rather than bitten off from active gear. These strandings demonstrate that ingestion of marine debris can be fatal to large whales, in addition to the well documented entanglements known to impact these species.

The migratory destinations of humpback whales that feed off California. Oregon and Washington were determined using photo-identification. Fluke photographs of 594 individuals were taken between 1981 and 1992 and compared to collections from 9 wintering regions in the North Pacific: Ogasawara (162) and Okinawa (17) islands of Japan; the Big Island and Maui (634 for both) and Kauai (384) of Hawaii; the Revillagigedo Archipelago (450), the mainland coast (383) and Baja Peninsula (471) of Mexico; and Central America (31). A total of 160 matches were found to 6 central and eastern North Paclfic wintering regions, with most from Central America, Baja, and mainland Mexico. Of whales identified off Central America, 84 % were resighted off California-Washington, this high rate of interchange suggests that whales in these tropical waters appear to be comprised entirely of animals from the California-Washington feeding aggregation. Humpback whales seen off Central America were reslghted disproportionately off southern California while those from mainland ~Vexico tended to be seen off northern California-Washington. From 157 same-season migratory transits documented, the shortest were 29 d to Baja and 56 d to Costa Rica and the longest distance was 5322 km. Of the California-Washington whales with known sex, the proportion of males identified at a wintering region was significantly higher than females (2.2:1, p < 0.05).

Songs of humpback whales off Hawaii and Mexico were examined to determine whether they changed similarly in both areas during a breeding season. Songs of 24 individuals were recorded off Kauai, Hawaii and Isla Socorro, Mexico during winter and spring of 1991. Forty‐seven acoustic variables describing all levels of song structure were measured for each singer. Similar variables were grouped together into six categories. Mean values for each singer were compared among regions and time periods using two‐factor ANOVAs. All but three variables changed between winter and spring in at least one area. Groups of similar variables displayed similar trends. Quantitative characteristics of song elements often changed during the breeding season by the same amount in each area, with little variation within and among individuals. Structures of song patterns often changed differently in each area. Results indicated cultural transmission may have occurred during the season. Alternatively, whales may be predisposed to gradually change features of song independent of cultural influences. Given the low level of variability exhibited by many variables, the latter seems more likely; therefore, temporal change, like song structure, may be governed by a discrete set of rules. Further research on a longer time scale is needed.