A standardisation framework for bio‐logging data to advance ecological research and conservation

Bio‐logging data obtained by tagging animals are key to addressing global conservation challenges. However, the many thousands of existing bio‐logging datasets are not easily discoverable, universally comparable, nor readily accessible through existing repositories and across platforms, slowing down ecological research and effective management. A set of universal standards is needed to ensure discoverability, interoperability and effective translation of bio‐logging data into research and management recommendations. We propose a standardisation framework adhering to existing data principles (FAIR: Findable, Accessible, Interoperable and Reusable; and TRUST: Transparency, Responsibility, User focus, Sustainability and Technology) and involving the use of simple templates to create a data flow from manufacturers and researchers to compliant repositories, where automated procedures should be in place to prepare data availability into four standardised levels: (a) decoded raw data, (b) curated data, (c) interpolated data and (d) gridded data. Our framework allows for integration of simple tabular arrays (e.g. csv files) and creation of sharable and interoperable network Common Data Form (netCDF) files containing all the needed information for accuracy‐of‐use, rightful attribution (ensuring data providers keep ownership through the entire process) and data preservation security. We show the standardisation benefits for all stakeholders involved, and illustrate the application of our framework by focusing on marine animals and by providing examples of the workflow across all data levels, including filled templates and code to process data between levels, as well as templates to prepare netCDF files ready for sharing. Adoption of our framework will facilitate collection of Essential Ocean Variables (EOVs) in support of the Global Ocean Observing System (GOOS) and inter‐governmental assessments (e.g. the World Ocean Assessment), and will provide a starting point for broader efforts to establish interoperable bio‐logging data formats across all fields in animal ecology

International consensus statement on nomenclature and classification of the congenital bicuspid aortic valve and its aortopathy, for clinical, surgical, interventional and research purposes

This International Consensus Classification and Nomenclature for the congenital bicuspid aortic valve condition recognizes 3 types of bicuspid valves: 1. The fused type (right-left cusp fusion, right-non-coronary cusp fusion and left-non-coronary cusp fusion phenotypes); 2. The 2-sinus type (latero-lateral and antero-posterior phenotypes); and 3. The partial-fusion (forme fruste) type. The presence of raphe and the symmetry of the fused type phenotypes are critical aspects to describe. The International Consensus also recognizes 3 types of bicuspid valve-associated aortopathy: 1. The ascending phenotype; 2. The root phenotype; and 3. Extended phenotypes.Cardiolog

Animal-borne telemetry: An integral component of the ocean observing toolkit

Animal telemetry is a powerful tool for observing marine animals and the physical environments that they inhabit, from coastal and continental shelf ecosystems to polar seas and open oceans. Satellite-linked biologgers and networks of acoustic receivers allow animals to be reliably monitored over scales of tens of meters to thousands of kilometers, giving insight into their habitat use, home range size, the phenology of migratory patterns and the biotic and abiotic factors that drive their distributions. Furthermore, physical environmental variables can be collected using animals as autonomous sampling platforms, increasing spatial and temporal coverage of global oceanographic observation systems. The use of animal telemetry, therefore, has the capacity to provide measures from a suite of essential ocean variables (EOVs) for improved monitoring of Earth's oceans. Here we outline the design features of animal telemetry systems, describe current applications and their benefits and challenges, and discuss future directions. We describe new analytical techniques that improve our ability to not only quantify animal movements but to also provide a powerful framework for comparative studies across taxa. We discuss the application of animal telemetry and its capacity to collect biotic and abiotic data, how the data collected can be incorporated into ocean observing systems, and the role these data can play in improved ocean management

The Argos-CLS Kalman filter : error structures and state-space modelling relative to Fastloc GPS data

Funding was provided by the Norwegian Polar Institute centre for Ice, Climate and Ecosystems (ICE).Understanding how an animal utilises its surroundings requires its movements through space to be described accurately. Satellite telemetry is the only means of acquiring movement data for many species however data are prone to varying amounts of spatial error; the recent application of state-space models (SSMs) to the location estimation problem have provided a means to incorporate spatial errors when characterising animal movements. The predominant platform for collecting satellite telemetry data on free-ranging animals, Service Argos, recently provided an alternative Doppler location estimation algorithm that is purported to be more accurate and generate a greater number of locations that its predecessor. We provide a comprehensive assessment of this new estimation process performance on data from free-ranging animals relative to concurrently collected Fastloc GPS data. Additionally, we test the efficacy of three readily-available SSM in predicting the movement of two focal animals. Raw Argos location estimates generated by the new algorithm were greatly improved compared to the old system. Approximately twice as many Argos locations were derived compared to GPS on the devices used. Root Mean Square Errors (RMSE) for each optimal SSM were less than 4.25km with some producing RMSE of less than 2.50km. Differences in the biological plausibility of the tracks between the two focal animals used to investigate the utility of SSM highlights the importance of considering animal behaviour in movement studies. The ability to reprocess Argos data collected since 2008 with the new algorithm should permit questions of animal movement to be revisited at a finer resolution.Publisher PDFPeer reviewe

Energetics and mechanics of terrestrial locomotion. IV. Total mechanical energy changes as a function of speed and body size in birds and mammals

This is the final paper in or series examining the link between the energetics and mechanics of terrestrial locomotion. In this paper the kinetic energy of the limbs and body relative to the centre of mass (EKE, tot of paper two) is combined with the potential plus kinetic energy of the centre of mass (ECM, tot of paper three) to obtain the total mechanical energy (excluding elastic energy) of an animal during constant average-speed locomotion. The minimum mass-specific power required of the muscles and tendons to maintain the observed oscillations in total energy, Etot/Mb, can be described by one equation: Etot/Mb = 0.478 . vg 1.53 + 0.685 . vg + 0.072 where Etot/Mb is in W kg-1 and vg is in m s-1. This equation is independent of body size, applying equally as well to a chipmunk or a quail as to a horse or an ostrich. In marked contrast, the metabolic energy consumed by each gram of an animal as it moves along the ground at a constant speed increases linearly with speed and is proportional to Mb-0.3. Thus, we have found that each gram of tissue of a 30 g quail or chipmunk running at 3 m s-1 consumes metabolic energy at a rate about 15 times that of a 100 kg ostrich, horse or human running at the same speed while their muscles are performing work at the same rate. Our measurements demonstrate the importance of storage and recovery of elastic energy in larger animals, but they cannot confirm or exclude the possibility of elastic storage of energy in small animals. It seems clear that the rate at which animals consume energy during locomotion cannot be explained by assuming a constant efficiency between the energy consumed and the mechanical work performed by the muscles. It is suggested that the intrinsic velocity of shortening of the active muscle motor units (which is related to the rate of cycling of the cross bridges between actin and myosin) and the rate at which the muscles are turned on and off are the most important factors in determining the metabolic cost of constant-speed locomotion. Faster motor units are recruited as animals increase speed, and equivalent muscles of small animals have faster fibres than those of larger animals. Also, the muscles are turned on and off more quickly as an animal increases speed, and at the same speed a small animal will be turning muscles on and off at a much higher rate. These suggestions are testable, and future studies should determine if they are correct

Environmental and physiological determinants of successful foraging by naive southern elephant seal pups during their first trip to sea

The ability to forage successfully during their first trip to sea is fundamental to the ultimate survival of newly weaned southern elephant seals (Mirounga leonina). However, there is considerable variation in the body mass and fat content of seal pups at weaning, which results in some individuals having larger energy and oxygen stores than others, which may confer advantages on them. The diving behaviour of 21 newly weaned seals was studied using satellite relayed data loggers. Seals were captured at Macquarie Island in December 1995 and 1996, approximately 4 weeks after weaning. Two groups of seals were specifically targeted: a heavy group from the top quartile of weaning masses (n = 6) and a light group from the lower quartile (n = 15). Most of the seals made dives in excess of 100 m depth and 5 min before final departure from the island. However, for the first 60-80 d, all of the seals exhibited behaviour quite distinct from the patterns reported for older conspecifics, and made relatively shallow (100 +/- 39 m; mean +/- SD) and short (5.7 +/- 1.23 min) dives. During this time the seals spent 74.3 +/- 12.6 of each day diving, and the depth of the dives did not follow any diurnal pattern. The diving behaviour of all seals changed abruptly whenthey started on their return to land. During this time their behaviour was more like that of adults: they made deeper (159 +/- 9 m) and longer dives (9.01 +/- 1.69 min) than previously, and the dives showed a strong diurnal pattern in depth. There is no obvious explanation for this change in behaviour, although its abrupt nature suggests that it is unlikely to have been due to physiological changes in the seals. The size of the seals at weaning was an important influence on diving behaviour. Heavy weaners made significantly deeper (130 +/- 40 m) and longer dives (7.36 +/- 0.55 min) than light weaners (88 +/- 32 m and 5.04 +/- 0.64 min, respectively). This indicates that smaller seals are constrained to some extent by their physiological capabilities, which perhaps requires some individuals to adopt different foraging strategies. VA:IB

Use of a tiletamine-zolazepam mixture to immobolise wild grey seals and southern elephant seals

A mixture of tiletamine and zolazepam at a combined dose of 1 mg/kg was a reliable and safe agent for immobilising wild grey seals (Halichoerus grypus) and southern elephant seals (Mirouga leonina). The agent had a number of advantages over all the other agents used previously