Caller identification and characterization of individual humpback whale acoustic behaviour

Acoustic recording tags provide fine-scale data linking acoustic signalling with individual behaviour; however, when an animal is in a group, it is challenging to tease apart calls of conspecifics and identify which individuals produce each call. This, in turn, prohibits a robust assessment of individual acoustic behaviour including call rates and silent periods, call bout production within and between individuals, and caller location. To overcome this challenge, we simultaneously instrumented small groups of humpback whales on a western North Atlantic feeding ground with sound and movement recording tags. This approach enabled a comparison of the relative amplitude of each call across individuals to infer caller identity for 97% of calls. We recorded variable call rates across individuals (mean = 23 calls/h) and groups (mean = 55 calls/h). Calls were produced throughout dives, and most calls were produced in bouts with short inter-call intervals of 2.2 s. Most calls received a likely response from a conspecific within 100 s. This caller identification (ID) method facilitates studying both individual- and group-level acoustic behaviour, yielding novel results about the nature of sequence production and vocal exchanges in humpback whale social calls. Future studies can expand on these caller ID methods for understanding intra-group communication across taxa.

Vulnerability to climate change of United States marine mammal stocks in the western North Atlantic, Gulf of Mexico, and Caribbean

Climate change and climate variability are affecting marine mammal species and these impacts are projected to continue in the coming decades. Vulnerability assessments provide a framework for evaluating climate impacts over a broad range of species using currently available information. We conducted a trait-based climate vulnerability assessment using expert elicitation for 108 marine mammal stocks and stock groups in the western North Atlantic, Gulf of Mexico, and Caribbean Sea. Our approach combined the exposure (projected change in environmental conditions) and sensitivity (ability to tolerate and adapt to changing conditions) of marine mammal stocks to estimate vulnerability to climate change, and categorize stocks with a vulnerability index. The climate vulnerability score was very high for 44% (n = 47) of these stocks, high for 29% (n = 31), moderate for 20% (n = 22), and low for 7% (n = 8). The majority of stocks (n = 78; 72%) scored very high exposure, whereas 24% (n = 26) scored high, and 4% (n = 4) scored moderate. The sensitivity score was very high for 33% (n = 36) of these stocks, high for 18% (n = 19), moderate for 34% (n = 37), and low for 15% (n = 16). Vulnerability results were summarized for stocks in five taxonomic groups: pinnipeds (n = 4; 25% high, 75% moderate), mysticetes (n = 7; 29% very high, 57% high, 14% moderate), ziphiids (n = 8; 13% very high, 50% high, 38% moderate), delphinids (n = 84; 52% very high, 23% high, 15% moderate, 10% low), and other odontocetes (n = 5; 60% high, 40% moderate). Factors including temperature, ocean pH, and dissolved oxygen were the primary drivers of high climate exposure, with effects mediated through prey and habitat parameters. We quantified sources of uncertainty by bootstrapping vulnerability scores, conducting leave-one-out analyses of individual attributes and individual scorers, and through scoring data quality for each attribute. These results provide information for researchers, managers, and the public on marine mammal responses to climate change to enhance the development of more effective marine mammal management, restoration, and conservation activities that address current and future environmental variation and biological responses due to climate change.

PHFinder: assisted detection of point heteroplasmy in Sanger sequencing chromatograms

Heteroplasmy is the presence of two or more organellar genomes (mitochondrial or plastid DNA) in an organism, tissue, cell or organelle. Heteroplasmy can be detected by visual inspection of Sanger sequencing chromatograms, where it appears as multiple peaks of fluorescence at a single nucleotide position. Visual inspection of chromatograms is both consuming and highly subjective, as heteroplasmy is difficult to differentiate from background noise. Few software solutions are available to automate the detection of point heteroplasmies, and those that are available are typically proprietary, lack customization or are unsuitable for automated heteroplasmy assessment in large datasets. Here, we present PHFinder, a Python-based, open-source tool to assist in the detection of point heteroplasmies in large numbers of Sanger chromatograms. PHFinder automatically identifies point heteroplasmies directly from the chromatogram trace data. The program was tested with Sanger sequencing data from 100 humpback whales (Megaptera novaeangliae) tissue samples with known heteroplasmies. PHFinder detected most (90%) of the known heteroplasmies thereby greatly reducing the amount of visual inspection required. PHFinder is flexible and enables explicit specification of key parameters to infer double peaks (i.e., heteroplasmies).

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.

Wild pedigrees inform mutation rates and historic abundance in baleen whales

Phylogeny-based estimates suggesting a low germline mutation rate (μ) in baleen whales have influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. We estimated μ directly from pedigrees in four baleen whale species for both the mitochondrial control region and nuclear genome. The results suggest values higher than those obtained through phylogeny-based estimates and similar to pedigree-based values for primates and toothed whales. Applying our estimate of μ reduces previous genetic-based estimates of preexploitation whale abundance by 86% and suggests that μ cannot explain low cancer rates in gigantic mammals. Our study shows that it is feasible to estimate μ directly from pedigrees in natural populations, with wide-ranging implications for ecological and evolutionary research.

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.

Provision of High Protein Foods Slows the Age-Related Decline in Nutritional Status in Aged Care Residents: A Cluster-Randomised Controlled Trial

OBJECTIVES

Malnutrition, particularly protein insufficiency, is common in institutionalised older adults and increases morbidity, mortality, and costs. We aimed to determine whether 12 months supplementation using high-protein foods (milk, cheese, yoghurt) prevents malnutrition in older adults.

DESIGN

Cluster randomised control study.

SETTING

Sixty Australian aged care facilities.

PARTICIPANTS

Older adults living in aged care homes (n=654, mean age 86.7±7.2 years, 72% females). Intervention Facilities randomly allocated to a high-protein (n=30 intervention) or regular (n=30 controls) menu.

MEASUREMENTS

Nutritional status assessed using the Mini Nutrition Assessment (MNA) tool and fasting morning blood samples (n=302) assayed for haemoglobin (Hb) and albumin. Food intake was monitored 3-monthly using visual plate waste assessment. Measurements at baseline and month 12 were analysed using random effects model accounting for clustering (facility), repeated measure and confounders.

RESULTS

Addition of 11g of protein as 1.5 servings of high-protein foods daily preserved nutritional status that deteriorated in controls [MNA screen (-0.68, 95%CI: -1.03, -0.32, p<0.001) and total (-0.90, 95%CI: -1.45, -0.35, p=0.001) scores], resulting in group differences in MNA screen (0.62, 95%CI: 0.17, 1.06, p=0.007) and total (0.81, 95%CI: 0.11, 1.51, p=0.023) scores and group difference in Hb (3.60g/L, 95%CI: 0.18, 7.03, p=0.039), the net result of preservation with intervention (0.19g/L, 95%CI: -2.04, 2.42, p=0.896) and a decline in controls (-3.41g/L, 95%CI: -6.01, -0.82, p=0.010). No group differences were observed for serum albumin.

CONCLUSION

Consumption of high-protein foods is a pragmatic approach to maintaining nutritional status in older adults in aged-care.

Persistent organic pollutants in female humpback whales Megaptera novaeangliae from the Gulf of Maine

Contaminant studies in cetaceans can provide information about pollutant levels and patterns in a given region. Due to the confounding effects of reproductive status and maternal offloading in females, these studies typically focus on males. However, an improved understanding of contaminant burdens in female cetaceans is needed to better assess potential impacts to populations. The objectives of this study were to characterize concentrations of persistent organic pollutants (POPs) in blubber of female humpback whales across age classes and to also better characterize maternal offloading of these pollutants to their offspring. A total of 36 blubber biopsy samples of female humpback whales (Megaptera novaeangliae) from the Gulf of Maine were analyzed to examine contaminant loads across females of different ages. Sampled individuals were individually-identified from longitudinal studies and assigned to age class (i.e., adult, subadult, juvenile, calf). Analysis was performed using gas chromatography/mass spectrometry (GC/MS) of POPs including polychlorinated biphenyls (PCBs), dichlorodiphenyltrichloroethanes (DDTs), chlordanes (CHLDs), polybrominated diphenyl ethers (PBDEs), hexachlorocyclohexanes (HCHs). The most abundant POPs were PCB congeners, with summed values ranging from 280 to 12,000 ng/g, lipid weight, which is above recent estimates of the threshold for adverse health effects. We found significant differences in mean values between adults and juveniles and between adults and subadults, with the exception of the less persistent HCHs for the latter. We also found significant differences in mean levels of ∑HCHs between the juveniles and subadults. Changes over age are consistent with maternal offloading and potentially important for evaluating population health and viability.

Strong and lasting impacts of past global warming on baleen whales and their prey

Global warming is affecting the population dynamics and trophic interactions across a wide range of ecosystems and habitats. Translating these real-time effects into their long-term consequences remains a challenge. The rapid and extreme warming period that occurred after the Last Glacial Maximum (LGM) during the Pleistocene-Holocene transition (7-12 thousand years ago) provides an opportunity to gain insights into the long-term responses of natural populations to periods with global warming. The effects of this post-LGM warming period have been assessed in many terrestrial taxa, whereas insights into the impacts of rapid global warming on marine taxa remain limited, especially for megafauna. In order to understand how large-scale climate fluctuations during the post-LGM affected baleen whales and their prey, we conducted an extensive, large-scale analysis of the long-term effects of the post-LGM warming on abundance and inter-ocean connectivity in eight baleen whale and seven prey (fish and invertebrates) species across the Southern and the North Atlantic Ocean; two ocean basins that differ in key oceanographic features. The analysis was based upon 7032 mitochondrial DNA sequences as well as genome-wide DNA sequence variation in 100 individuals. The estimated temporal changes in genetic diversity during the last 30,000 years indicated that most baleen whale populations underwent post-LGM expansions in both ocean basins. The increase in baleen whale abundance during the Holocene was associated with simultaneous changes in their prey and climate. Highly correlated, synchronized and exponential increases in abundance in both baleen whales and their prey in the Southern Ocean were indicative of a dramatic increase in ocean productivity. In contrast, the demographic fluctuations observed in baleen whales and their prey in the North Atlantic Ocean were subtle, varying across taxa and time. Perhaps most important was the observation that the ocean-wide expansions and decreases in abundance that were initiated by the post-LGM global warming, continued for millennia after global temperatures stabilized, reflecting persistent, long-lasting impacts of global warming on marine fauna.

Effect of dietary sources of calcium and protein on hip fractures and falls in older adults in residential care: cluster randomised controlled trial

OBJECTIVE

To assess the antifracture efficacy and safety of a nutritional intervention in institutionalised older adults replete in vitamin D but with mean intakes of 600 mg/day calcium and <1 g/kg body weight protein/day.

DESIGN

Two year cluster randomised controlled trial.

SETTING

60 accredited residential aged care facilities in Australia housing predominantly ambulant residents.

PARTICIPANTS

7195 permanent residents (4920 (68%) female; mean age 86.0 (SD 8.2) years).

INTERVENTION

Facilities were stratified by location and organisation, with 30 facilities randomised to provide residents with additional milk, yoghurt, and cheese that contained 562 (166) mg/day calcium and 12 (6) g/day protein achieving a total intake of 1142 (353) mg calcium/day and 69 (15) g/day protein (1.1 g/kg body weight). The 30 control facilities maintained their usual menus, with residents consuming 700 (247) mg/day calcium and 58 (14) g/day protein (0.9 g/kg body weight).

MAIN OUTCOME MEASURES

Group differences in incidence of fractures, falls, and all cause mortality.

RESULTS

Data from 27 intervention facilities and 29 control facilities were analysed. A total of 324 fractures (135 hip fractures), 4302 falls, and 1974 deaths were observed. The intervention was associated with risk reductions of 33% for all fractures (121 v 203; hazard ratio 0.67, 95% confidence interval 0.48 to 0.93; P=0.02), 46% for hip fractures (42 v 93; 0.54, 0.35 to 0.83; P=0.005), and 11% for falls (1879 v 2423; 0.89, 0.78 to 0.98; P=0.04). The risk reduction for hip fractures and falls achieved significance at five months (P=0.02) and three months (P=0.004), respectively. Mortality was unchanged (900 v 1074; hazard ratio 1.01, 0.43 to 3.08).

CONCLUSIONS

Improving calcium and protein intakes by using dairy foods is a readily accessible intervention that reduces the risk of falls and fractures commonly occurring in aged care residents.

TRIAL REGISTRATION

Australian New Zealand Clinical Trials Registry ACTRN12613000228785.

Multi-year progesterone profiles during pregnancy in baleen of humpback whales (Megaptera novaeangliae)

Understanding calving rates of wild whale populations is critically important for management and conservation. Reproduction of humpback whales (Megaptera novaeangliae) is difficult to monitor and, even with long-term sighting studies, basic physiological information such as pregnancy rates and calving intervals remain poorly understood in many populations. We hypothesized that pregnant whales have sustained elevations in baleen progesterone that temporally correlate with gestation. To test this hypothesis, baleen progesterone profiles from two adult female North Pacific humpbacks, both with extensive sighting records and documented pregnancies, were compared to those of a nulliparous female (adult female never seen with a calf) and a juvenile male. Baleen specimens recovered during necropsy were subsampled every 2 cm from the base to the tip of the plate, with each interval representing 30-45 days of growth. Homogenized baleen powder was assayed for progesterone using enzyme immunoassays. The date of growth of each sampling location on the baleen plate was estimated based on stable isotope analysis of annual δ¹⁵N cycles. Progesterone profiles from both pregnant whales showed sustained high progesterone content (>350 ng/g) in areas corresponding to known pregnancies, inferred from calf sightings and post-mortem data. The younger female, estimated to be 13 years old, had higher progesterone during pregnancy than the 44.5 year old, but levels during non-pregnancy were similar. The nulliparous female and the male had low progesterone throughout their baleen plates. Baleen hormone analysis can determine how progesterone concentrations change throughout gestation and has potential for estimating age at first reproduction, pregnancy intervals, failed pregnancies and early calf mortality. Understanding rates of calving and current and historic reproductive patterns in humpbacks is vital to continuing conservation measures in this species.

Characterizing the culturable surface microbiomes of diverse marine animals

Biofilm-forming bacteria have the potential to contribute to the health, physiology, behavior and ecology of the host and serve as its first line of defense against adverse conditions in the environment. While metabarcoding and metagenomic information furthers our understanding of microbiome composition, fewer studies use cultured samples to study the diverse interactions among the host and its microbiome, as cultured representatives are often lacking. This study examines the surface microbiomes cultured from three shallow-water coral species and two whale species. These unique marine animals place strong selective pressures on their microbial symbionts and contain members under similar environmental and anthropogenic stress. We developed an intense cultivation procedure, utilizing a suite of culture conditions targeting a rich assortment of biofilm-forming microorganisms. We identified 592 microbial isolates contained within 15 bacterial orders representing 50 bacterial genera, and two fungal species. Culturable bacteria from coral and whale samples paralleled taxonomic groups identified in culture-independent surveys, including 29% of all bacterial genera identified in the Megaptera novaeangliae skin microbiome through culture-independent methods. This microbial repository provides raw material and biological input for more nuanced studies which can explore how members of the microbiome both shape their micro-niche and impact host fitness.

Patterns of cortisol and corticosterone concentrations in humpback whale (Megaptera novaeangliae) baleen are associated with different causes of death

Baleen whales are subject to a myriad of natural and anthropogenic stressors, but understanding how these stressors affect physiology is difficult. Measurement of adrenal glucocorticoid (GC) hormones involved in the vertebrate stress response (cortisol and corticosterone) in baleen could help fill this data gap. Baleen analysis is a powerful tool, allowing for a retrospective re-creation of multiple years of GC hormone concentrations at approximately a monthly resolution. We hypothesized that whales that died from acute causes (e.g. ship strike) would have lower levels of baleen GCs than whales that died from extended illness or injury (e.g. long-term entanglement in fishing gear). To test this hypothesis, we extracted hormones from baleen plates of four humpback whales (Megaptera novaeangliae) with well-documented deaths including multiple and chronic entanglements (n = 1, female), ship strike (n = 2, male and female) and chronic illness with nutritional stress (n = 1, male). Over ~3 years of baleen growth and during multiple entanglements, the entangled whale had average corticosterone levels of 80-187% higher than the other three whales but cortisol levels were similar to two of the other three whales. The nutritionally stressed and chronically ill whale showed a slow increase in both cortisol and corticosterone spanning ~3 years, followed by a sharp decline in both hormones before death, possibly indicative of adrenal failure in this moribund individual. This whale's correlation between cortisol and corticosterone was significant but there were no correlations in the other three whales. Our results show that cortisol and corticosterone concentrations vary according to the type and duration of illness or injury. Single-point GC concentrations should be interpreted with caution as low values can occur in whales experiencing pronounced stress and individual baselines can be highly variable. Baleen analysis is a promising tissue type for retrospective analyses of physiological responses to various stressors affecting baleen whales.

A dynamic approach to estimate the probability of exposure of marine predators to oil exploration seismic surveys over continental shelf waters

The ever-increasing human demand for fossil fuels has resulted in the expansion of oil exploration efforts to waters over the continental shelf. These waters are largely utilized by a complex biological community. Large baleen whales, in particular, utilize continental shelf waters as breeding and calving grounds, foraging grounds, and also as migration corridors. We developed a dynamic approach to estimate the likelihood that individuals from different populations of blue whales Balaenoptera musculus and humpback whales Megaptera novaeangliae could be exposed to idealized, simulated seismic surveys as they move over the continental shelf. Animal tracking data for the different populations were filtered, and behaviors (transit and foraging) were inferred from the tracks using hidden Markov models. We simulated a range of conditions of exposure by having the source of noise affecting a circular area of different radii (5, 25, 50 and 100 km), moving along a gridded transect of 270 and 2500 km2 at a constant speed of 9 km h-1, and starting the simulated surveys every week of the year. Our approach allowed us to identify the temporal variability in the susceptibility of the different populations under study, as we ran the simulations for an entire year, allowing us to identify periods when the surveys would have an intensified effect on whales. Our results highlight the importance of understanding the behavior and ecology of individuals in a site-specific context when considering the likelihood of exposure to anthropogenic disturbances, as the habitat utilization patterns of each population are highly variable.

Marine mammal skin microbiotas are influenced by host phylogeny

Skin-associated microorganisms have been shown to play a role in immune function and disease of humans, but are understudied in marine mammals, a diverse animal group that serve as sentinels of ocean health. We examined the microbiota associated with 75 epidermal samples opportunistically collected from nine species within four marine mammal families, including: Balaenopteridae (sei and fin whales), Phocidae (harbour seal), Physeteridae (sperm whales) and Delphinidae (bottlenose dolphins, pantropical spotted dolphins, rough-toothed dolphins, short-finned pilot whales and melon-headed whales). The skin was sampled from free-ranging animals in Hawai'i (Pacific Ocean) and off the east coast of the United States (Atlantic Ocean), and the composition of the bacterial community was examined using the sequencing of partial small subunit (SSU) ribosomal RNA genes. Skin microbiotas were significantly different among host species and taxonomic families, and microbial community distance was positively correlated with mitochondrial-based host genetic divergence. The oceanic location could play a role in skin microbiota variation, but skin from species sampled in both locations is necessary to determine this influence. These data suggest that a phylosymbiotic relationship may exist between microbiota and their marine mammal hosts, potentially providing specific health and immune-related functions that contribute to the success of these animals in diverse ocean ecosystems.

Evaluation of fecal hormones for noninvasive research on reproduction and stress in humpback whales (Megaptera novaeangliae)

Fecal hormone analysis shows high potential for noninvasive assessment of population-level patterns in stress and reproduction of marine mammals. However, the marine environment presents unique challenges for fecal sample collection. Data are still lacking on collection methodology and assay validations for most species, particularly for those mysticete whales that have variable diets. In this study we tested collection techniques for fecal samples of free-swimming humpback whales (Megaptera novaeangliae), and validated immunoassays for five steroid and thyroid hormones. Resulting data were used for preliminary physiological validations, i.e., comparisons to independently confirmed sex and reproductive state. Pregnant females had significantly higher fecal progestins and glucocorticoids than did other demographic categories of whales. Two possible cases of previously undetected pregnancies were noted. Males had significantly higher fecal testosterone metabolites than nonpregnant females. Fecal glucocorticoids were significantly elevated in pregnant females and mature males compared to nonpregnant females. Calf fecal samples had elevated concentrations of all fecal hormones. Fecal thyroid hormones showed a significant seasonal decline from spring to summer. Though sample sizes were small, and sampling was necessarily opportunistic, these patterns indicate that noninvasive fecal hormone analysis may facilitate studies of reproduction, stress and potentially energetics in humpback whales.

A-35 Assessing the Impact of Expressive Language on Performance on Conners’ Continuous Performance Test 3rd Edition (CPT3) in Inpatients with Aphasia

Objective

The current study examined the impact of expressive language difficulties, assessed by the Neuropsychological Assessment Battery (NAB) naming subtest, on the Conners’ Continuous Performance Test-Third edition (CPT3) in an inpatient acquired brain injury (ABI) population.

Method

A sample of 19 individuals (female n = 3, male n = 16) was evaluated through an inpatient ABI rehabilitation program. Two groups based on diagnosed aphasia (n = 7) versus no aphasia (n = 12) were used. Ages ranged from 15 to 67 (M = 38.37, SD = 16.55) and had an average level of education of 14.9 years.

Results

One-way ANOVAs were used to determine how expressive language impacts performance on the CPT3. As expected, statistically significant results revealed that having aphasia yields a lower score on NAB naming F(1,17) = 11.435, p = .004. Individuals who did not have aphasia had a higher number of Perseverations, F(1,17) = 5.295, p = .034. No differences were noted between Omissions F(1,17) = 2.060, p = .169, Commissions F(1,17) = 3.090, p = .097, and Hit Reaction Time F(1,17) = .434, p = .519.

Conclusions

In our sample, patients with and without aphasia had similar reaction times and similar performances for omissions and commissions. The aphasia group, with significantly worse expressive language abilities, did not score significantly worse on any of the CPT3-related indices. Our study supports previous literature that CPT3 is an appropriate attention measure for individuals with aphasia but adds to the literature in providing evidence for use of the measure with an acute inpatient population with aphasia. While the results are promising, our sample is small and future research would be stronger with a larger sample with more specific information provided regarding the types of aphasia.

Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae)

Cetaceans are a clade of highly specialized aquatic mammals that include the largest animals that have ever lived. The largest whales can have ∼1,000× more cells than a human, with long lifespans, leaving them theoretically susceptible to cancer. However, large-bodied and long-lived animals do not suffer higher risks of cancer mortality than humans-an observation known as Peto's Paradox. To investigate the genomic bases of gigantism and other cetacean adaptations, we generated a de novo genome assembly for the humpback whale (Megaptera novaeangliae) and incorporated the genomes of ten cetacean species in a comparative analysis. We found further evidence that rorquals (family Balaenopteridae) radiated during the Miocene or earlier, and inferred that perturbations in abundance and/or the interocean connectivity of North Atlantic humpback whale populations likely occurred throughout the Pleistocene. Our comparative genomic results suggest that the evolution of cetacean gigantism was accompanied by strong selection on pathways that are directly linked to cancer. Large segmental duplications in whale genomes contained genes controlling the apoptotic pathway, and genes inferred to be under accelerated evolution and positive selection in cetaceans were enriched for biological processes such as cell cycle checkpoint, cell signaling, and proliferation. We also inferred positive selection on genes controlling the mammalian appendicular and cranial skeletal elements in the cetacean lineage, which are relevant to extensive anatomical changes during cetacean evolution. Genomic analyses shed light on the molecular mechanisms underlying cetacean traits, including gigantism, and will contribute to the development of future targets for human cancer therapies.

Whales in warming water: Assessing breeding habitat diversity and adaptability in Oceania's changing climate

In the context of a changing climate, understanding the environmental drivers of marine megafauna distribution is important for conservation success. The extent of humpback whale breeding habitats and the impact of temperature variation on their availability are both unknown. We used 19 years of dedicated survey data from seven countries and territories of Oceania (1,376 survey days), to investigate humpback whale breeding habitat diversity and adaptability to climate change. At a fine scale (1 km resolution), seabed topography was identified as an important influence on humpback whale distribution. The shallowest waters close to shore or in lagoons were favored, although humpback whales also showed flexible habitat use patterns with respect to shallow offshore features such as seamounts. At a coarse scale (1° resolution), humpback whale breeding habitats in Oceania spanned a thermal range of 22.3-27.8°C in August, with interannual variation up to 2.0°C. Within this range, both fine and coarse scale analyses of humpback whale distribution suggested local responses to temperature. Notably, the most detailed dataset was available from New Caledonia (774 survey days, 1996-2017), where encounter rates showed a negative relationship to sea surface temperature, but were not related to the El Niño Southern Oscillation or the Antarctic Oscillation from previous summer, a proxy for feeding conditions that may impact breeding patterns. Many breeding sites that are currently occupied are predicted to become unsuitably warm for this species (>28°C) by the end of the 21st century. Based on modeled ecological relationships, there are suitable habitats for relocation in archipelagos and seamounts of southern Oceania. Although distribution shifts might be restrained by philopatry, the apparent plasticity of humpback whale habitat use patterns and the extent of suitable habitats support an adaptive capacity to ocean warming in Oceania breeding grounds.

Building evidence around ghost gear: Global trends and analysis for sustainable solutions at scale

Abandoned, lost or discarded fishing gear (ALDFG) comprises a significant amount of global marine debris, with diverse impacts to marine environments, wildlife, and the fishing industry. Building evidence on ALDFG is critical to holistically understand the marine debris issue, and to inform the development of solutions that reduce amounts of ALDFG sources and recover existing gear. Substantial work has been and continues to be undertaken around the world to collect data on ALDFG, much of which remains unpublished. To provide a global picture of data on ALDFG, we organized a technical session that brought together seven ALDFG leaders to share their expertise in data collection, retrieval, and awareness-raising. This paper summarizes the technical session to highlight: 1) case studies that feature innovative approaches to ALDFG data collection and retrieval; 2) examples of opportunities to fill data gaps and improve our understanding of wildlife ingestion of and entanglement in ALDFG; and 3) awareness-raising through the development of a publicly accessible global ALDFG database.

High pregnancy rates in humpback whales (Megaptera novaeangliae) around the Western Antarctic Peninsula, evidence of a rapidly growing population

Antarctic humpback whales are recovering from near extirpation from commercial whaling. To understand the dynamics of this recovery and establish a baseline to monitor impacts of a rapidly changing environment, we investigated sex ratios and pregnancy rates of females within the Western Antarctic Peninsula (WAP) feeding population. DNA profiling of 577 tissue samples (2010-2016) identified 239 males and 268 females. Blubber progesterone levels indicated 63.5% of the females biopsied were pregnant. This proportion varied significantly across years, from 36% in 2010 to 86% in 2014. A comparison of samples collected in summer versus fall showed significant increases in the proportion of females present (50% to 59%) and pregnant (59% to 72%), consistent with demographic variation in migratory timing. We also found evidence of annual reproduction among females; 54.5% of females accompanied by a calf were pregnant. These high pregnancy rates are consistent with a population recovering from past exploitation, but appear inconsistent with recent estimates of WAP humpback population growth. Thus, our results will help to better understand population growth potential and set a current baseline from which to determine the impact of climate change and variability on fecundity and reproductive rates.

Validation of a blubber-based endocrine pregnancy test for humpback whales

Baleen whales have few identifiable external indicators of pregnancy state, making it challenging to study essential aspects of their biology and population dynamics. Pregnancy status in other marine mammals has been determined by measuring progesterone concentrations from a variety of sample matrices, but logistical constraints have limited such studies in free-swimming baleen whales. We use an extensive blubber sample archive and associated calving history data to retrospectively identify samples that correspond to pregnant females and develop a progesterone-based pregnancy test for humpback whales. The lowest pregnant blubber progesterone concentration was 54.97 ng g^-1, and the mean for the known-pregnant group was 198.74 ± 180.65 ng g^-1. Conversely, females known to be below the minimum age of sexual maturity (juvenile females) had an overall low mean progesterone concentration (0.59 ± 0.25 ng g^-1), well below the known-pregnant range. Of the mature females that did not return with a calf (n = 11), three fell within the known-pregnant range (320.79 ± 209.34 ng g^-1), while the levels for the remaining eight were two orders of magnitude below the lowest known-pregnant level (1.63 ± 1.15 ng g^-1). The proportion of females that did not return with a calf but had values similar to known-pregnant females are consistent with rates of calf mortality, but other potential explanations were considered. Our findings support a validated blubber endocrine assignment of pregnancy corroborated with field life history information, a first for any baleen whale species. The progesterone values we measured were similar to those found in different pregnancy states of other cetaceans and support using blubber biopsy samples for assigning pregnancy in humpback whales. This method can be applied to existing archives or new samples to better study life history and population demography broadly across species and populations.

Multiple steroid and thyroid hormones detected in baleen from eight whale species

Recent studies have demonstrated that some hormones are present in baleen powder from bowhead (Balaena mysticetus) and North Atlantic right (Eubalaena glacialis) whales. To test the potential generalizability of this technique for studies of stress and reproduction in large whales, we sought to determine whether all major classes of steroid and thyroid hormones are detectable in baleen, and whether these hormones are detectable in other mysticetes. Powdered baleen samples were recovered from single specimens of North Atlantic right, bowhead, blue (Balaenoptera [B.]musculus), sei (B. borealis), minke (B. acutorostrata), fin (B. physalus), humpback (Megaptera novaeangliae) and gray (Eschrichtius robustus) whales. Hormones were extracted with a methanol vortex method, after which we tested all species with commercial enzyme immunoassays (EIAs, Arbor Assays) for progesterone, testosterone, 17β-estradiol, cortisol, corticosterone, aldosterone, thyroxine and tri-iodothyronine, representing a wide array of steroid and thyroid hormones of interest for whale physiology research. In total, 64 parallelism tests (8 species × 8 hormones) were evaluated to verify good binding affinity of the assay antibodies to hormones in baleen. We also tested assay accuracy, although available sample volume limited this test to progesterone, testosterone and cortisol. All tested hormones were detectable in baleen powder of all species, and all assays passed parallelism and accuracy tests. Although only single individuals were tested, the consistent detectability of all hormones in all species indicates that baleen hormone analysis is likely applicable to a broad range of mysticetes, and that the EIA kits tested here perform well with baleen extract. Quantification of hormones in baleen may be a suitable technique with which to explore questions that have historically been difficult to address in large whales, including pregnancy and inter-calving interval, age of sexual maturation, timing and duration of seasonal reproductive cycles, adrenal physiology and metabolic rate.

Effects of fishing rope strength on the severity of large whale entanglements

Entanglement in fixed fishing gear affects whales worldwide. In the United States, deaths of North Atlantic right (Eubalaena glacialis) and humpback whales (Megaptera novaeangliae) have exceeded management limits for decades. We examined live and dead whales entangled in fishing gear along the U.S. East Coast and the Canadian Maritimes from 1994 to 2010. We recorded whale species, age, and injury severity and determined rope polymer type, breaking strength, and diameter of the fishing gear. For the 132 retrieved ropes from 70 cases, tested breaking strength range was 0.80-39.63 kN (kiloNewtons) and the mean was 11.64 kN (SD 8.29), which is 26% lower than strength at manufacture (range 2.89-53.38 kN, mean = 15.70 kN [9.89]). Median rope diameter was 9.5 mm. Right and humpback whales were found in ropes with significantly stronger breaking strengths at time of manufacture than minke whales (Balaenoptera acuturostrata) (19.30, 17.13, and 10.47 mean kN, respectively). Adult right whales were found in stronger ropes (mean 34.09 kN) than juvenile right whales (mean 15.33 kN) and than all humpback whale age classes (mean 17.37 kN). For right whales, severity of injuries increased since the mid 1980s, possibly due to changes in rope manufacturing in the mid 1990s that resulted in production of stronger ropes at the same diameter. Our results suggest that broad adoption of ropes with breaking strengths of ≤ 7.56 kN (≤ 1700 lbsf) could reduce the number of life-threatening entanglements for large whales by at least 72%, and yet could provide sufficient strength to withstand the routine forces involved in many fishing operations. A reduction of this magnitude would achieve nearly all the mitigation legally required for U.S. stocks of North Atlantic right and humpback whales. Ropes with reduced breaking strength should be developed and tested to determine the feasibility of their use in a variety of fisheries.

Molecular biomarkers for chronological age in animal ecology

The chronological age of an individual animal predicts many of its biological characteristics, and these in turn influence population-level ecological processes. Animal age information can therefore be valuable in ecological research, but many species have no external features that allow age to be reliably determined. Molecular age biomarkers provide a potential solution to this problem. Research in this area of molecular ecology has so far focused on a limited range of age biomarkers. The most commonly tested molecular age biomarker is change in average telomere length, which predicts age well in a small number of species and tissues, but performs poorly in many other situations. Epigenetic regulation of gene expression has recently been shown to cause age-related modifications to DNA and to cause changes in abundance of several RNA types throughout animal lifespans. Age biomarkers based on these epigenetic changes, and other new DNA-based assays, have already been applied to model organisms, humans and a limited number of wild animals. There is clear potential to apply these marker types more widely in ecological studies. For many species, these new approaches will produce age estimates where this was previously impractical. They will also enable age information to be gathered in cross-sectional studies and expand the range of demographic characteristics that can be quantified with molecular methods. We describe the range of molecular age biomarkers that have been investigated to date and suggest approaches for developing the newer marker types as age assays in nonmodel animal species.

Relationships Among Rheological, Sensory Texture, and Swallowing Pressure Measurements of Hydrocolloid-Thickened Fluids

The objective of this study was to examine the relationships among three categories of measurements (rheological, sensory texture, and swallowing pressure) from fluids thickened to two different viscosities with 15 different hydrocolloids. Fluids at viscosities of 300 and 1500 cP (at 30 s(-1)) were targeted because these are the viscosities corresponding to the barium standards used in radiographic dysphagia diagnosis. Within the low viscosity (nectar) fluids (300 cP), the sensory properties thickness, stickiness, adhesiveness, mouth coating, and number of swallows were highly positively correlated with each other and highly positively correlated with the flow behavior index, n value (an indicator of shear-thinning behavior). Within the higher viscosity (thin honey) fluids (1500 cP), the sensory textures of adhesiveness, stickiness, mouth coating, and number of swallows correlated positively with rheological measures of n value. Swallowing pressures measured in the anterior oral cavity correlated negatively with the consistency coefficient k [shear stress/(shear rate) (n) ]. Samples that were more shear thinning (lower n values, higher k values) were generally perceived as less thick, with less adhesive properties (stickiness, adhesiveness, mouthcoating, and number of swallows). This information can be useful for selecting thickeners for people with dysphagia. A desirable thickener for many dysphagic patients would be one that allowed for a safe swallow by being viscous enough to reduce airway penetration, yet pleasant to drink, having the minimal perceived thickness and mouthcoating associated with greater shear thinning.

Population structure of humpback whales in the western and central South Pacific Ocean as determined by vocal exchange among populations

For cetaceans, population structure is traditionally determined by molecular genetics or photographically identified individuals. Acoustic data, however, has provided information on movement and population structure with less effort and cost than traditional methods in an array of taxa. Male humpback whales (Megaptera novaeangliae) produce a continually evolving vocal sexual display, or song, that is similar among all males in a population. The rapid cultural transmission (the transfer of information or behavior between conspecifics through social learning) of different versions of this display between distinct but interconnected populations in the western and central South Pacific region presents a unique way to investigate population structure based on the movement dynamics of a song (acoustic) display. Using 11 years of data, we investigated an acoustically based population structure for the region by comparing stereotyped song sequences among populations and years. We used the Levenshtein distance technique to group previously defined populations into (vocally based) clusters based on the overall similarity of their song display in space and time. We identified the following distinct vocal clusters: western cluster, 1 population off eastern Australia; central cluster, populations around New Caledonia, Tonga, and American Samoa; and eastern region, either a single cluster or 2 clusters, one around the Cook Islands and the other off French Polynesia. These results are consistent with the hypothesis that each breeding aggregation represents a distinct population (each occupied a single, terminal node) in a metapopulation, similar to the current understanding of population structure based on genetic and photo-identification studies. However, the central vocal cluster had higher levels of song-sharing among populations than the other clusters, indicating that levels of vocal connectivity varied within the region. Our results demonstrate the utility and value of using culturally transmitted vocal patterns as a way of defining connectivity to infer population structure. We suggest vocal patterns be incorporated by the International Whaling Commission in conjunction with traditional methods in the assessment of structure.

Population structure of humpback whales in the western and central South Pacific Ocean as determined by vocal exchange among populations

For cetaceans, population structure is traditionally determined by molecular genetics or photographically identified individuals. Acoustic data, however, has provided information on movement and population structure with less effort and cost than traditional methods in an array of taxa. Male humpback whales (Megaptera novaeangliae) produce a continually evolving vocal sexual display, or song, that is similar among all males in a population. The rapid cultural transmission (the transfer of information or behavior between conspecifics through social learning) of different versions of this display between distinct but interconnected populations in the western and central South Pacific region presents a unique way to investigate population structure based on the movement dynamics of a song (acoustic) display. Using 11 years of data, we investigated an acoustically based population structure for the region by comparing stereotyped song sequences among populations and years. We used the Levenshtein distance technique to group previously defined populations into (vocally based) clusters based on the overall similarity of their song display in space and time. We identified the following distinct vocal clusters: western cluster, 1 population off eastern Australia; central cluster, populations around New Caledonia, Tonga, and American Samoa; and eastern region, either a single cluster or 2 clusters, one around the Cook Islands and the other off French Polynesia. These results are consistent with the hypothesis that each breeding aggregation represents a distinct population (each occupied a single, terminal node) in a metapopulation, similar to the current understanding of population structure based on genetic and photo-identification studies. However, the central vocal cluster had higher levels of song-sharing among populations than the other clusters, indicating that levels of vocal connectivity varied within the region. Our results demonstrate the utility and value of using culturally transmitted vocal patterns as a way of defining connectivity to infer population structure. We suggest vocal patterns be incorporated by the International Whaling Commission in conjunction with traditional methods in the assessment of structure.

Clinical features, microbiology and surgical outcomes of infective endocarditis: a 13-year study from a UK tertiary cardiothoracic referral centre

BACKGROUND

Infective endocarditis (IE) causes substantial morbidity and mortality. Patient and pathogen profiles, as well as microbiological and operative strategies, continue to evolve. The impact of these changes requires evaluation to inform optimum management and identify individuals at high risk of early mortality.

AIM

Identification of clinical and microbiological features, and surgical outcomes, among patients presenting to a UK tertiary cardiothoracic centre for surgical management of IE between 1998 and 2010.

DESIGN

Retrospective observational cohort study.

METHODS

Clinical, biochemical, microbiological and echocardiographic data were identified from clinical records. Principal outcomes were all-cause 28-day mortality and duration of post-operative admission.

RESULTS

Patients (n = 336) were predominantly male (75.0%); median age 52 years (IQR = 41-67). Most cases involved the aortic (56.0%) or mitral (53.9%) valves. Microbiological diagnoses, obtained in 288 (85.7%) patients, included streptococci (45.2%); staphylococci (34.5%); Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, Kingella (HACEK) organisms (3.0%); and fungi (1.8%); 11.3% had polymicrobial infection. Valve replacement in 308 (91.7%) patients included mechanical prostheses (69.8%), xenografts (24.0%) and homografts (6.2%). Early mortality was 12.2%, but fell progressively during the study (P = 0.02), as did median duration of post-operative admission (33.5 to 10.5 days; P = 0.0003). Multivariable analysis showed previous cardiothoracic surgery (OR = 3.85, P = 0.03), neutrophil count (OR = 2.27, P = 0.05), albumin (OR = 0.94, P = 0.04) and urea (OR = 2.63, P < 0.001) predicted early mortality.

CONCLUSIONS

This study demonstrates reduced post-operative early mortality and duration of hospital admission for IE patients over the past 13 years. Biomarkers (previous cardiothoracic surgery, neutrophil count, albumin and urea), predictive of early post-operative mortality, require prospective evaluation to refine algorithms, further improve outcomes and reduce healthcare costs associated with IE.

Utility of telomere length measurements for age determination of humpback whales

This study examines the applicability of telomere length measurements by quantitative PCR as a tool for minimally invasive age determination of free-ranging cetaceans. We analysed telomere length in skin samples from 28 North Atlantic humpback whales (Megaptera novaeangliae), ranging from 0 to 26 years of age. The results suggested a significant correlation between telomere length and age in humpback whales. However, telomere length was highly variable among individuals of similar age, suggesting that telomere length measured by quantitative PCR is an imprecise determinant of age in humpback whales. The observed variation in individual telomere length was found to be a function of both experimental and biological variability, with the latter perhaps reflecting patterns of inheritance, resource allocation trade-offs, and stochasticity of the marine environment.

Management of impacted wisdom teeth: teaching of undergraduate students in UK dental schools

INTRODUCTION

Wisdom tooth removal is one of the most common oral surgical procedures performed across the world. The aim of this study was to gauge the teaching and training of impacted wisdom teeth in undergraduate dental programmes across the UK. The objectives were to identify consistencies and variations in theoretical instructions and clinical training as well as approaches to management of impacted wisdom teeth.

METHODS

This was a cross-sectional survey utilising an online questionnaire. A purposefully designed pro forma with open- as well as closed-ended questions was used. The questionnaire was hosted online on the school's blackboard academic suite (Emily). Prior to conducting the study, approval was gained from the Research and Ethics Committee, and all the ethical principles pertaining to data protection were strictly followed. E-mail invitations were sent to oral surgery leads in all dental schools in the UK. The participants were provided with an information sheet, and an informed consent was obtained. The participants were invited by e-mail to complete the questionnaire online voluntarily.

RESULTS

A total of 16 dental schools offering an undergraduate course in dentistry in the UK, 13 responded positively. (response rate = 81.25%). In majority of dental schools, this subject is taught in the 4th and 5th years. A pre-clinical competency on phantom heads is a requirement in six schools, whilst only one school requires the students to pass a clinical competency. The clinical exposure of students to wisdom tooth surgery is quite variable. Although the dental schools are fairly consistent in their teaching with regard to the indications for surgical intervention, diagnostic/treatment modalities as well as the post-operative care, interesting variations were also observed.

CONCLUSIONS

This study, perhaps the first of its kind, provides useful insights into management of impacted wisdom teeth, as taught in the undergraduate dental programmes across the UK.

Epigenetic estimation of age in humpback whales

Age is a fundamental aspect of animal ecology, but is difficult to determine in many species. Humpback whales exemplify this as they have a lifespan comparable to humans, mature sexually as early as 4 years and have no reliable visual age indicators after their first year. Current methods for estimating humpback age cannot be applied to all individuals and populations. Assays for human age have recently been developed based on age-induced changes in DNA methylation of specific genes. We used information on age-associated DNA methylation in human and mouse genes to identify homologous gene regions in humpbacks. Humpback skin samples were obtained from individuals with a known year of birth and employed to calibrate relationships between cytosine methylation and age. Seven of 37 cytosines assayed for methylation level in humpback skin had significant age-related profiles. The three most age-informative cytosine markers were selected for a humpback epigenetic age assay. The assay has an R(2) of 0.787 (P = 3.04e-16) and predicts age from skin samples with a standard deviation of 2.991 years. The epigenetic method correctly determined which of parent-offspring pairs is the parent in more than 93% of cases. To demonstrate the potential of this technique, we constructed the first modern age profile of humpback whales off eastern Australia and compared the results to population structure 5 decades earlier. This is the first epigenetic age estimation method for a wild animal species and the approach we took for developing it can be applied to many other nonmodel organisms.