Whale and dolphin behavioural responses to dead conspecifics

The scientific study of death across animal taxa—comparative thanatology—investigates how animals respond behaviourally, physiologically and psychologically to dead conspecifics, and the processes behind such responses. Several species of cetaceans have been long known to care for, attend to, be aroused by, or show interest in dead or dying individuals. We investigated patterns and variation in cetacean responses to dead conspecifics across cetacean taxa based on a comprehensive literature review. We analysed 78 records reported between 1970 and 2016, involving 20 of the 88 extant cetacean species. We adopted a weighted comparative approach to take observation effort into account and found that odontocetes (toothed cetaceans) were much more likely than mysticetes (baleen whales) to attend to dead conspecifics. Dolphins (Delphinidae) had the greatest occurrence of attentive behaviour (92.3% of all records, with a weighed attendance index 18 times greater than the average of all other cetacean families). Two dolphin genera, Sousa and Tursiops, constituted 55.1% of all cetacean records (N = 43) and showed the highest incidence of attentive behaviour. Results of analyses intended to investigate the reasons behind these differences suggested that encephalisation may be an important predictor, consistent with the "social brain" hypothesis. Among attending individuals or groups of known sex (N = 28), the majority (75.0%) were adult females with dead calves or juveniles (possibly their own offspring, with exceptions), consistent with the strong mother-calf bond, or, in a few cases, with the bond between mothers and other females in the group. The remaining records (25.0%) involved males either showing sexual interest in a dead adult or subadult, or carrying a dead calf in the presence of females. Because an inanimate individual is potentially rescuable, responses to dead conspecifics—especially by females—can be explained at least in part by attempts to revive and protect, having a clear adaptive value. In some cases such responses are followed by apparently maladaptive behaviour such as the long-term carrying of, or standing by, a decomposed carcass, similar to observations of other terrestrial mammals. Among the possible explanations for the observed cetacean behavioural responses to dead conspecifics are strong attachment resulting in a difficulty of "letting go"—possibly related to grieving—or perhaps individuals failing to recognise or accept that an offspring or companion has died. Our current understanding is challenged by small sample size, incomplete descriptions, and lack of information on the physiology and neural processes underpinning the observed behaviour. We provide research recommendations that would improve such understanding.PostprintPeer reviewe

The accessible chromatin landscape of the human genome

DNaseI hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers, and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ~2.9 million DHSs that encompass virtually all known experimentally-validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation, and regulatory factor occupancy patterns. We connect ~580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is choreographed with dozens to hundreds of co-activated elements, and the trans-cellular DNaseI sensitivity pattern at a given region can predict cell type-specific functional behaviors. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation

Distribution and Habitat Associations of Billfish and Swordfish Larvae across Mesoscale Features in the Gulf of Mexico

Ichthyoplankton surveys were conducted in surface waters of the northern Gulf of Mexico (NGoM) over a three-year period (2006–2008) to determine the relative value of this region as early life habitat of sailfish (Istiophorus platypterus), blue marlin (Makaira nigricans), white marlin (Kajikia albida), and swordfish (Xiphias gladius). Sailfish were the dominant billfish collected in summer surveys, and larvae were present at 37.5% of the stations sampled. Blue marlin and white marlin larvae were present at 25.0% and 4.6% of the stations sampled, respectively, while swordfish occurred at 17.2% of the stations. Areas of peak production were detected and maximum density estimates for sailfish (22.09 larvae 1000 m−2) were significantly higher than the three other species: blue marlin (9.62 larvae 1000 m−2), white marlin (5.44 larvae 1000 m−2), and swordfish (4.67 larvae 1000 m−2). The distribution and abundance of billfish and swordfish larvae varied spatially and temporally, and several environmental variables (sea surface temperature, salinity, sea surface height, distance to the Loop Current, current velocity, water depth, and Sargassum biomass) were deemed to be influential variables in generalized additive models (GAMs). Mesoscale features in the NGoM affected the distribution and abundance of billfish and swordfish larvae, with densities typically higher in frontal zones or areas proximal to the Loop Current. Habitat suitability of all four species was strongly linked to physicochemical attributes of the water masses they inhabited, and observed abundance was higher in slope waters with lower sea surface temperature and higher salinity. Our results highlight the value of the NGoM as early life habitat of billfishes and swordfish, and represent valuable baseline data for evaluating anthropogenic effects (i.e., Deepwater Horizon oil spill) on the Atlantic billfish and swordfish populations

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

Understanding the molecular basis for phenotypic differences between humans and other primates remains an outstanding challenge. Mutations in non-coding regulatory DNA that alter gene expression have been hypothesized as a key driver of these phenotypic differences. This has been supported by differential gene expression analyses in general, but not by the identification of specific regulatory elements responsible for changes in transcription and phenotype. To identify the genetic source of regulatory differences, we mapped DNaseI hypersensitive (DHS) sites, which mark all types of active gene regulatory elements, genome-wide in the same cell type isolated from human, chimpanzee, and macaque. Most DHS sites were conserved among all three species, as expected based on their central role in regulating transcription. However, we found evidence that several hundred DHS sites were gained or lost on the lineages leading to modern human and chimpanzee. Species-specific DHS site gains are enriched near differentially expressed genes, are positively correlated with increased transcription, show evidence of branch-specific positive selection, and overlap with active chromatin marks. Species-specific sequence differences in transcription factor motifs found within these DHS sites are linked with species-specific changes in chromatin accessibility. Together, these indicate that the regulatory elements identified here are genetic contributors to transcriptional and phenotypic differences among primate species

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Migration ecology of juvenile Pacific salmon smolts : the role of fish condition and behaviour across landscapes

Migrations are utilized across taxa to exploit spatiotemporal variability across landscapes. The benefits of migrations are balanced with costs, and understanding the factors that limit migratory success is needed for proper management and conservation. Sockeye salmon (Oncorhynchus nerka) are of economic, cultural, and ecological importance and undergo downstream migrations from natal freshwater systems through rivers to the ocean as juvenile smolts. In this thesis, I describe a series of studies investigating the migration behaviour and survival of sockeye smolts emigrating from Chilko Lake, British Columbia, a large population that experiences poor survival in the Chilko River. First, field sampling and bioenergetics models were used to find that short-term feeding on smolts by bull trout (Salvelinus confluentus) in the Chilko River was extreme, not limited by cold temperatures, and resulted in greater exploitation of smolts than expected using traditional bioenergetic assumptions. Examining bull trout stomach contents revealed that consumed smolts had higher rates of infection by hematopoietic necrosis virus and Flavobacterium psychrophilum and were smaller than non-predated smolts. Through acoustic telemetry, I found that smolts traversing the upper Chilko River with higher densities of conspecifics experienced improved survival relative to smolts travelling at times when few smolts were migrating. Thus swamping predators can maximize survival. It is more difficult to conduct field studies in the coastal marine environment such as the Strait of Georgia, and even knowledge on migration routes and behaviour is limited. Aggregating telemetry data collected over ~10 years of research on sockeye and steelhead (Oncorhynchus mykiss) populations determined that contingents of both species exhibited westward lateral movements within the strait, consistent with predicted currents. Steelhead using the eastern migratory route experienced improved survival through the Strait to a location ~250 km further along the migratory corridor - a rare example of migration route impacting fitness. Individually, chapters advanced the fields of migration and feeding ecology and tested long-held ecological hypotheses. Important links were identified between smolt migration behaviour and/or survival and components of the movement ecology framework. This thesis has expanded our understanding of the factors influencing the migration of one of the largest sockeye populations in Canada.Forestry, Faculty ofGraduat