Olfaction and brain size in the bowhead whale (Balaena mysticetus)

Although there are several isolated references to the olfactory anatomy of mysticetes, it is usually thought that olfaction is rudimentary in this group. We investigated the olfactory anatomy of bowhead whales and found that these whales have a cribriform plate and small, but histologically complex olfactory bulb. The olfactory bulb makes up approximately 0.13% of brain weight, unlike odontocetes where this structure is absent. We also determined that 51% of olfactory receptor genes were intact, unlike odontocetes, where this number is less than 25%. This suggests that bowheads have a sense of smell, and we speculate that they may use this to find aggregations of krill on which they feed.     

Characterization of 25 microsatellite loci in bowhead whales (Balaena mysticetus)

Bowhead whales (Balaena mysticetus) experienced a severe demographic population bottleneck caused by commercial whaling that ceased in 1914. Aboriginal subsistence whale harvests have continued and are managed by the International Whaling Commission. In an effort to provide management advice for bowhead whales, 25 microsatellite loci were isolated from genomic DNA libraries. This panel of markers will be utilized to analyse stock structure hypotheses of current bowhead whale populations.     

Behaviour and kinematics of continuous ram filtration in bowhead whales (Balaena mysticetus)

Balaenid whales perform long breath-hold foraging dives despite a high drag from their ram filtration of zooplankton. To maximize the volume of prey acquired in a dive with limited oxygen supplies, balaenids must either filter feed only occasionally when prey density is particularly high, or they must swim at slow speeds while filtering to reduce drag and oxygen consumption. Using digital tags with three-axis accelerometers, we studied bowhead whales feeding off West Greenland and present here, to our knowledge, the first detailed data on the kinematics and swimming behaviour of a balaenid whale filter feeding at depth. Bowhead whales employ a continuous fluking gait throughout the bottom phase of foraging dives, moving at very slow speeds (less than 1 m s⁻¹), allowing them to filter feed continuously at depth. Despite the slow speeds, the large mouth aperture provides a water filtration rate of approximately 3 m³ s⁻¹, amounting to some 2000 tonnes of water and prey filtered per dive. We conclude that a food niche of dense, slow-moving zooplankton prey has led balaenids to evolve locomotor and filtering systems adapted to work against a high drag at swimming speeds of less than 0.07 body length s⁻¹ using a continuous fluking gait very different from that of nekton-feeding, aquatic predators.     

Song sharing and diversity in the Bering‐Chukchi‐Beaufort population of bowhead whales (Balaena mysticetus), spring 2011

Bowhead whales (Balaena mysticetus) of the Bering‐Chukchi‐Beaufort population migrate in nearshore leads through the Chukchi Sea each spring to summering grounds in the Beaufort Sea. As part of a population abundance study, hydrophones were deployed in the Chukchi Sea off Point Barrow, (12 April to 27 May 2011) and in the Beaufort Sea (12 April to 30 June 2011). Data from these sites were analyzed for the presence of bowhead whale song. We identified 12 unique song types sung by at least 32 individuals during ~95 h of recordings off Point Barrow. Six of these songs were detected at the Beaufort MARU site as well as six additional song types that were not analyzed. These results suggest a shared song repertoire among some individuals. This report represents the greatest number of songs to date during the spring migration for this population. We attribute this greater variety to population growth over the 30 yr since acoustic monitoring began in the early 1980s. Singing during early to mid‐spring is consistent with the hypothesis that song is a reproductive display, but further research is necessary to understand the exact function of this complex vocal behavior.     

Microflora associated with the skin of the bowhead whale (Balaena mysticetus)

A study of the microbiological flora isolated from cultures of normal and lesional skin tissue samples collected from 19 bowhead whales (Balaena mysticetus) over a 4 yr period is presented. These cultures were obtained from 30 tissue samples (17 normal, 13 lesion) and 248 swab samples (157 normal, 91 lesion). Seven hundred-thirty bacterial and yeast isolations were made (285 normal, 445 lesion). Distribution revealed that 56% of the gram positive bacterial isolates, 75% of the gram negative bacterial isolates and 64% of the yeast isolates recovered were associated with lesional skin. It was found that 80% of one group of Corynebacterium sp. isolates, 90% of the Acinetobacter sp. isolates and 94% of the Moraxella sp. isolates were associated with lesional skin. Although the primary yeasts recovered were Candida spp., they were found on both normal and lesional skin. Enzymatic assays of isolates from normal and lesional skin demonstrated production of enzymes capable of causing necrosis. The majority of the microorganisms recovered were facultative anaerobes and many of them could be considered potential pathogens of mammalian hosts.     

Serology and virology of the bowhead whale (Balaena mysticetus L.)

Sera from four bowhead whales (Balaena mysticetus L.) were examined for the presence of specific antibodies, and tissue and swab samples from six and four animals respectively were processed for isolation of viruses and for initiation of bowhead whale cell cultures. All sera were negative for antibodies to nine serovars of Leptospira interrogans and to 21 orthomyxovirus subtypes and a paramyxovirus (Newcastle disease virus). All sera were positive, however, for neutralizing antibodies to one or more calicivirus serotypes. Two untyped adenoviruses were isolated from colon samples of two different whales, but neutralizing antibodies to the agents could not be demonstrated in any sera. Three primary bowhead whale cell cultures were derived from kidney (two cultures) and testis (one culture), from three individual whales.     

Fractured mandible and associated oral lesions in a subsistence-harvested bowhead whale (Balaena mysticetus)

A fractured right mandible with midlength nonunion and oral lesions were noted in a subsistence-harvested female bowhead whale (Balaena mysticetus) near Wainwright, Alaska (USA). The cause of the fracture was not apparent. The fracture resulted in misalignment of the mandible. The abnormal mobility at the fracture site probably caused irregular baleen stowage within the oral cavity, leading to breakage of many baleen plates and extensive ulceration of the tongue and lips. Good body condition suggested the fracture was not debilitating.     

Stomach contents of bowhead whales (Balaena mysticetus) from four locations in the Canadian Arctic

The stomach contents of four bowhead whales (Balaena mysticetus) harvested between 1994 and 2008 from the Canadian Arctic were examined to assess diet composition. Three samples were collected from bowhead whales of the Eastern Canada–West Greenland (EC–WG) population and represent, according to our knowledge, the first diet analysis from this bowhead whale stock. We also examined the stomach content of one bowhead whale from the Bering-Chukchi-Beaufort (BCB) population hunted in 1996. All four whales had food in their stomachs and their diet varied from exclusively pelagic (BCB whale), with Limnocalanus macrurus being the main prey, to epibenthic and benthic (EC–WG) with Mysis oculata playing an important role. These results indicate broad foraging spectrum of the bowhead whales and add to a basic knowledge of their diet.     

Recent sightings of the bowhead whale (Balaena mysticetus) in Northeast Greenland and the Greenland Sea

By the end of the 19th century, European whalers had brought the bowhead whale (Balaena mysticetus) in the “Spitsbergen stock” ranging the waters between eastern Greenland and the western Russian Arctic to the verge of extinction. This paper presents observations of this species in Northeast Greenland and in the Greenland Sea between 1940 and 2004. The number of observations has increased in Northeast Greenland since the mid-1980s. Only three observations are known for the period 1940–1979 but during the 1980s, the 1990s and between 2000 and 2004, six, six and eight observations of bowhead whales were made, involving an absolute minimum of three, five and eight to ten different individuals, respectively. It remains uncertain whether this represents an increase in survey effort, an immigration from other areas, a recent recovery of an eastern Greenland relict “tribe” belonging to the Spitsbergen stock, or a combination of these factors.     

Song Competition Affects Monoamine Levels in Sensory and Motor Forebrain Regions of Male Lincoln's Sparrows (Melospiza lincolnii)

Male animals often change their behavior in response to the level of competition for mates. Male Lincoln''s sparrows (Melospiza lincolnii) modulate their competitive singing over the period of a week as a function of the level of challenge associated with competitors'' songs. Differences in song challenge and associated shifts in competitive state should be accompanied by neural changes, potentially in regions that regulate perception and song production. The monoamines mediate neural plasticity in response to environmental cues to achieve shifts in behavioral state. Therefore, using high pressure liquid chromatography with electrochemical detection, we compared levels of monoamines and their metabolites from male Lincoln''s sparrows exposed to songs categorized as more or less challenging. We compared levels of norepinephrine and its principal metabolite in two perceptual regions of the auditory telencephalon, the caudomedial nidopallium and the caudomedial mesopallium (CMM), because this chemical is implicated in modulating auditory sensitivity to song. We also measured the levels of dopamine and its principal metabolite in two song control nuclei, area X and the robust nucleus of the arcopallium (RA), because dopamine is implicated in regulating song output. We measured the levels of serotonin and its principal metabolite in all four brain regions because this monoamine is implicated in perception and behavioral output and is found throughout the avian forebrain. After controlling for recent singing, we found that males exposed to more challenging song had higher levels of norepinephrine metabolite in the CMM and lower levels of serotonin in the RA. Collectively, these findings are consistent with norepinephrine in perceptual brain regions and serotonin in song control regions contributing to neuroplasticity that underlies socially-induced changes in behavioral state.     

Presence and behavior of bowhead whales (Balaena mysticetus) in the Alaskan Beaufort Sea in July 2011

The Western Arctic bowhead whale (Balaena mysticetus) is highly adapted to sea ice and annually migrates through the Bering, Chukchi, and Beaufort seas. While the overall distribution and seasonal movements of bowhead whales are mostly understood, information about their distribution in the Alaskan Beaufort Sea in early to mid-summer has not been well documented. In July 2011, we conducted an exploratory flight in the Alaskan Beaufort Sea, north of Camden Bay (71°N 144°W), near the location of a single satellite-tagged bowhead whale. Eighteen bowhead whales were observed, and behavior consistent with feeding was documented. To our knowledge, this is the first documentation of behavior consistent with feeding north of Camden Bay in mid-July. Few studies have focused on bowhead whale distribution in the Alaskan Beaufort Sea in early to mid-summer, and no long-term, region-wide surveys have been conducted during summer. Bowhead whales are already exposed to anthropogenic disturbance in the Canadian Beaufort Sea in summer, the Alaskan Beaufort Sea in fall, and the Chukchi and Bering seas from fall through spring. The presence of bowhead whale aggregations in the Alaskan Beaufort Sea in summer should be considered when assessing the cumulative effects of human-related activities.     

Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource

Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.     

Examination of ten thousand years of mitochondrial DNA diversity and population demographics in bowhead whales (Balaena mysticetus) of the Central Canadian Arctic

Mitochondrial DNA (mtDNA) sequences were analyzed from 106 bowhead whale (Balaena mysticetus) specimens dating 471 ± 44 ¹⁴C b.p. –10,290 ± 150 ¹⁴C b.p. to evaluate whether historical changes in distribution and connectivity were detectable in levels of diversity and population structuring in the Central Canadian Arctic. The species has maintained levels of mtDNA diversity over 10,000 yr comparable to other nonbottlenecked large whale species. When compared to data from the Holocene East Greenland/Spitsbergen and contemporary Bering‐Chuckchi‐Beaufort populations, differentiation was low (F_ST≤ 0.005, Φ_ST≤ 0.003) and no temporal or geographical genetic structuring was evident. A combination of analyses suggests that the population has expanded over the past 30,000 ¹⁴C yr. This genetic signature of expansion could result from population growth, admixture of multiple gene pools, or a combination of both scenarios. Despite known climatic change that altered bowhead distribution and led to isolation of populations, there is no detectable population structuring or change in genetic diversity during the Holocene. This may be due to long generation time, occasional population connectivity and a historically large global population. These characteristics warrant caution when interpreting contemporary bowhead whale DNA data, as it is unlikely that any population will be in mutation‐drift equilibrium.     

Evaluating a Putative Bottleneck in a Population of Bowhead Whales from Patterns of Microsatellite Diversity and Genetic Disequilibria

A size-selected Balaena mysticetus genomic library was screened for clones containing simple sequence repeat, or microsatellite, loci. A total of 11 novel loci was identified. These loci were combined with a set of 9 published loci, for a total of 20 markers, and were scored across a sample of 108 bowhead whales from the Bering–Chukchi–Beaufort Seas population of bowhead whales. Genetic variability was measured in terms of polymorphism information content values and unbiased heterozygosity. From the latter, estimates of long-term effective population size were obtained. In addition, gametic phase disequilibrium among loci was investigated. Moderate to high levels of polymorphism were found overall, and the long-term effective size estimates were large relative to total population size. Tests of heterozygosity excess (Cornuet and Luikart 1996) and allele frequency distribution (Luikart et al. 1998) indicated that the possibility of a recent genetic bottleneck in the Bering–Chukchi–Beaufort Seas population of bowhead whales is highly unlikely. However, the fact that five loci displayed a statistically significant heterozygote deficiency remains to be explained. Received: 3 November 1998 / Accepted: 28 April 1999     

Essential Role of a Trypanosome U4-Specific Sm Core Protein in Small Nuclear Ribonucleoprotein Assembly and Splicing

Spliceosomal small nuclear ribonucleoproteins (snRNPs) in trypanosomes contain either the canonical heptameric Sm ring or variant Sm cores with snRNA-specific Sm subunits. Here we show biochemically by a combination of RNase H cleavage and tandem affinity purification that the U4 snRNP contains a variant Sm heteroheptamer core in which only SmD3 is replaced by SSm4. This U4-specific, nuclear-localized Sm core protein is essential for growth and splicing. As shown by RNA interference (RNAi) knockdown, SSm4 is specifically required for the integrity of the U4 snRNA and the U4/U6 di-snRNP in trypanosomes. In addition, we demonstrate by in vitro reconstitution of Sm cores that under stringent conditions, the SSm4 protein suffices to specify the assembly of U4 Sm cores. Together, these data indicate that the assembly of the U4-specific Sm core provides an essential step in U4/U6 di-snRNP biogenesis and splicing in trypanosomes.The excision of intronic sequences from precursor mRNAs is a critical step during eukaryotic gene expression. This reaction is catalyzed by the spliceosome, a macromolecular complex composed of small nuclear ribonucleoproteins (snRNPs) and many additional proteins. Spliceosome assembly and splicing catalysis occur in an ordered multistep process, which includes multiple conformational rearrangements (35). Spliceosomal snRNPs are assembled from snRNAs and protein components, the latter of which fall into two classes: snRNP-specific and common proteins. The common or canonical core proteins are also termed Sm proteins, specifically SmB, SmD1, SmD2, SmD3, SmE, SmF, and SmG (10; reviewed in reference 9), which all share an evolutionarily conserved bipartite sequence motif (Sm1 and Sm2) required for Sm protein interactions and the formation of the heteroheptameric Sm core complex around the Sm sites of the snRNAs (3, 7, 29). Prior to this, the Sm proteins form three heteromeric subcomplexes: SmD3/SmB, SmD1/SmD2, and SmE/SmF/SmG (23; reviewed in reference 34). Individual Sm proteins or Sm subcomplexes cannot stably interact with the snRNA. Instead, a stable subcore forms by an association of the subcomplexes SmD1/SmD2 and SmE/SmF/SmG with the Sm site on the snRNA; the subsequent integration of the SmD3/SmB heterodimer completes Sm core assembly.In addition to the canonical Sm proteins, other proteins carrying the Sm motif have been identified for many eukaryotes. Those proteins, termed LSm (like Sm) proteins, exist in distinct heptameric complexes that differ in function and localization. For example, a complex composed of LSm1 to LSm7 (LSm1-7) accumulates in cytoplasmic foci and participates in mRNA turnover (4, 8, 31). Another complex, LSm2-8, binds to the 3′ oligo(U) tract of the U6 snRNA in the nucleus (1, 15, 24). Finally, in the U7 snRNP, which is involved in histone mRNA 3′-end processing, the Sm proteins SmD1 and SmD2 are replaced by U7-specific LSm10 and LSm11 proteins, respectively (20, 21; reviewed in reference 28).This knowledge is based primarily on the mammalian system, where spliceosomal snRNPs are biochemically well characterized (34). In contrast, for trypanosomes, comparatively little is known about the components of the splicing machinery and their assembly and biogenesis. In trypanosomes, the expression of all protein-encoding genes, which are arranged in long polycistronic units, requires trans splicing. Only a small number of genes are additionally processed by cis splicing (reviewed in reference 11). During trans splicing, a short noncoding miniexon, derived from the spliced leader (SL) RNA, is added to each protein-encoding exon. Regarding the trypanosomal splicing machinery, the U2, U4/U6, and U5 snRNPs are considered to be general splicing factors, whereas the U1 and SL snRNPs represent cis- and trans-splicing-specific components, respectively. In addition to the snRNAs, many protein splicing factors in trypanosomes have been identified based on sequence homology (for example, see references 14 and 19).Recent studies revealed variations in the Sm core compositions of spliceosomal snRNPs from Trypanosoma brucei. Specifically, in the U2 snRNP, two of the canonical Sm proteins, SmD3 and SmB, are replaced by two novel, U2 snRNP-specific proteins, Sm16.5K and Sm15K (33). In this case, an unusual purine nucleotide, interrupting the central uridine stretch of the U2 snRNA Sm site, discriminates between the U2-specific and the canonical Sm cores. A second case of Sm core variation was reported for the U4 snRNP, in which a single protein, SmD3, was suggested to be replaced by the U4-specific LSm protein initially called LSm2, and later called SSm4, based on a U4-specific destabilization after SSm4 knockdown (30). A U4-specific Sm core variation was also previously suggested and discussed by Wang et al. (33), based on the inefficient pulldown of U4 snRNA through tagged SmD3 protein. However, neither of these two studies conclusively demonstrated by biochemical criteria that the specific Sm protein resides in the U4 Sm core; a copurification of other snRNPs could not be unequivocally ruled out.By using a combination of RNase H cleavage, tandem affinity purification, and mass spectrometry, we provide here direct biochemical evidence that in the variant Sm core of the U4 snRNP, only SmD3 is replaced by the U4-specific SSm4. SSm4 is nuclear localized, and the silencing of SSm4 leads to a characteristic phenotype: dramatic growth inhibition, general trans- and cis-splicing defects, a loss of the integrity of the U4 snRNA, as well as a destabilization of the U4/U6 di-snRNP. Furthermore, in vitro reconstitution assays revealed that under stringent conditions, SSm4 is sufficient to specify U4-specific Sm core assembly. In sum, our data establish SSm4 as a specific component of the U4 Sm core and demonstrate its importance in U4/U6 di-snRNP biogenesis, splicing function, and cell viability.     

Molecular genetic analysis of the Shantar summer group of bowhead whales (Balaena mysticetus L.) in the Okhotsk Sea

The results of molecular genetic analysis (full-length sequences of the mtDNA cytochrome b gene and control region and the allelic composition of 14 microsatellite loci) of 65 tissue samples from the endangered bowhead whale (Balaena mysticetus) population of the Sea of Okhotsk are presented. The data obtained enable the suggestion that at present, the state of the Sea of Okhotsk bowhead whale population is relatively stable.