What is physiologging? Introduction to the theme issue, part 2.

The physiological mechanisms by which animals regulate energy expenditure, respond to stimuli and stressors, and maintain homeostasis at the tissue, organ and whole organism levels can be described by 'physiologging'-that is, the use of onboard miniature electronic devices to record physiological metrics of animals in captivity or free-living in the wild. Despite its origins in the 1960s, physiologging has evolved more slowly than its umbrella field of biologging. However, the recording of physiological metrics in free-living animals will be key to solving some of the greatest challenges in biodiversity conservation, issues pertaining to animal health and welfare, and for inspiring future therapeutic strategies for human health. Current physiologging technologies encompass the measurement of physiological variables such as heart rate, brain activity, body temperature, muscle stimulation and dynamic movement, yet future developments will allow for onboard logging of metrics relating to organelle, molecular and genetic function. This article is part of the theme issue 'Measuring physiology in free-living animals (Part II)'.

Future trends in measuring physiology in free-living animals.

Thus far, ecophysiology research has predominantly been conducted within controlled laboratory-based environments, owing to a mismatch between the recording technologies available for physiological monitoring in wild animals and the suite of behaviours and environments they need to withstand, without unduly affecting subjects. While it is possible to record some physiological variables for free-living animals using animal-attached logging devices, including inertial-measurement, heart-rate and temperature loggers, the field is still in its infancy. In this opinion piece, we review the most important future research directions for advancing the field of 'physiologging' in wild animals, including the technological development that we anticipate will be required, and the fiscal and ethical challenges that must be overcome. Non-invasive, multi-sensor miniature devices are ubiquitous in the world of human health and fitness monitoring, creating invaluable opportunities for animal and human physiologging to drive synergistic advances. We argue that by capitalizing on the research efforts and advancements made in the development of human wearables, it will be possible to design the non-invasive loggers needed by ecophysiologists to collect accurate physiological data from free-ranging animals ethically and with an absolute minimum of impact. In turn, findings have the capacity to foster transformative advances in human health monitoring. Thus, we invite biomedical engineers and researchers to collaborate with the animal-tagging community to drive forward the advancements necessary to realize the full potential of both fields. This article is part of the theme issue 'Measuring physiology in free-living animals (Part II)'.

Introduction to the theme issue: Measuring physiology in free-living animals.

By describing where animals go, biologging technologies (i.e. animal attached logging of biological variables with small electronic devices) have been used to document the remarkable athletic feats of wild animals since the 1940s. The rapid development and miniaturization of physiologging (i.e. logging of physiological variables such as heart rate, blood oxygen content, lactate, breathing frequency and tidal volume on devices attached to animals) technologies in recent times (e.g. devices that weigh less than 2 g mass that can measure electrical biopotentials for days to weeks) has provided astonishing insights into the physiology of free-living animals to document how and why wild animals undertake these extreme feats. Now, physiologging, which was traditionally hindered by technological limitations, device size, ethics and logistics, is poised to benefit enormously from the on-going developments in biomedical and sports wearables technologies. Such technologies are already improving animal welfare and yield in agriculture and aquaculture, but may also reveal future pathways for therapeutic interventions in human health by shedding light on the physiological mechanisms with which free-living animals undertake some of the most extreme and impressive performances on earth. This article is part of the theme issue 'Measuring physiology in free-living animals (Part I)'.

Flight muscle and heart phenotypes in the high-flying ruddy shelduck.

Ruddy shelduck migrate from wintering grounds in lowland India and Myanmar to breeding grounds in central China and Mongolia, sustaining flight over the Himalayas, where oxygen availability is greatly reduced. We compared phenotypes of the pectoralis muscle and the ventricle of the heart from ruddy shelduck and common shelduck (a closely related low-altitude congener) that were raised in common conditions at sea level, predicting that oxidative capacity would be greater in ruddy shelduck to support high-altitude migration. Fibre-type composition of the pectoralis and the maximal activity of eight enzymes involved in mitochondrial energy metabolism in the pectoralis and heart, were compared between species. Few differences distinguished ruddy shelduck from common shelduck in the flight muscle, with the exception that ruddy shelduck had higher activities of complex II and higher ratios of complex IV (cytochrome c oxidase) and complex II when expressed relative to citrate synthase activity. There were no species differences in fibre-type composition, so these changes in enzyme activity may reflect an evolved modification in the functional properties of muscle mitochondria, potentially influencing mitochondrial respiratory capacity and/or oxygen affinity. Ruddy shelduck also had higher lactate dehydrogenase activity concurrent with lower pyruvate kinase and hexokinase activity in the left ventricle, which likely reflects an increased capacity for lactate oxidation by the heart. We conclude that changes in pathways of mitochondrial energy metabolism in the muscle and heart may contribute to the ability of ruddy shelduck to fly at high altitude.

Germline-focussed analysis of tumour-only sequencing: recommendations from the ESMO Precision Medicine Working Group.

It is increasingly common in oncology practice to perform tumour sequencing using large cancer panels. For pathogenic sequence variants in cancer susceptibility genes identified on tumour-only sequencing, it is often unclear whether they are of somatic or constitutional (germline) origin. There is wide-spread disparity regarding both the extent to which systematic 'germline-focussed analysis' is carried out upon tumour sequencing data and for which variants follow-up analysis of a germline sample is carried out. Here we present analyses of paired sequencing data from 17 152 cancer samples, in which 1494 pathogenic sequence variants were identified across 65 cancer susceptibility genes. From these analyses, the European Society of Medical Oncology Precision Medicine Working Group Germline Subgroup has generated (i) recommendations regarding germline-focussed analyses of tumour-only sequencing data, (ii) indications for germline follow-up testing and (iii) guidance on patient information-giving and consent.

Long-term satellite tracking reveals variable seasonal migration strategies of basking sharks in the north-east Atlantic.

Animal migration is ubiquitous in nature with individuals within a population often exhibiting varying movement strategies. The basking shark (Cetorhinus maximus) is the world's second largest fish species, however, a comprehensive understanding of their long-term wider-ranging movements in the north-east Atlantic is currently lacking. Seventy satellite tags were deployed on basking sharks over four years (2012-2015) off the west coast of Scotland and the Isle of Man. Data from 28 satellite tags with attachment durations of over 165 days reveal post-summer ranging behaviours. Tagged sharks moved a median minimum straight-line distance of 3,633 km; achieving median displacement of 1,057 km from tagging locations. Tagged individuals exhibited one of three migration behaviours: remaining in waters of UK, Ireland and the Faroe Islands; migrating south to the Bay of Biscay or moving further south to waters off the Iberian Peninsula, and North Africa. Sharks used both continental shelf areas and oceanic habitats, primarily in the upper 50-200 m of the water column, spanning nine geo-political zones and the High Seas, demonstrating the need for multi-national cooperation in the management of this species across its range.

The roller coaster flight strategy of bar-headed geese conserves energy during Himalayan migrations.

The physiological and biomechanical requirements of flight at high altitude have been the subject of much interest. Here, we uncover a steep relation between heart rate and wingbeat frequency (raised to the exponent 3.5) and estimated metabolic power and wingbeat frequency (exponent 7) of migratory bar-headed geese. Flight costs increase more rapidly than anticipated as air density declines, which overturns prevailing expectations that this species should maintain high-altitude flight when traversing the Himalayas. Instead, a "roller coaster" strategy, of tracking the underlying terrain and discarding large altitude gains only to recoup them later in the flight with occasional benefits from orographic lift, is shown to be energetically advantageous for flights over the Himalayas.

The paradox of extreme high-altitude migration in bar-headed geese Anser indicus.

Bar-headed geese are renowned for migratory flights at extremely high altitudes over the world's tallest mountains, the Himalayas, where partial pressure of oxygen is dramatically reduced while flight costs, in terms of rate of oxygen consumption, are greatly increased. Such a mismatch is paradoxical, and it is not clear why geese might fly higher than is absolutely necessary. In addition, direct empirical measurements of high-altitude flight are lacking. We test whether migrating bar-headed geese actually minimize flight altitude and make use of favourable winds to reduce flight costs. By tracking 91 geese, we show that these birds typically travel through the valleys of the Himalayas and not over the summits. We report maximum flight altitudes of 7290 m and 6540 m for southbound and northbound geese, respectively, but with 95 per cent of locations received from less than 5489 m. Geese travelled along a route that was 112 km longer than the great circle (shortest distance) route, with transit ground speeds suggesting that they rarely profited from tailwinds. Bar-headed geese from these eastern populations generally travel only as high as the terrain beneath them dictates and rarely in profitable winds. Nevertheless, their migration represents an enormous challenge in conditions where humans and other mammals are only able to operate at levels well below their sea-level maxima.

Spatial dynamics of bar-headed geese migration in the context of H5N1.

Virulent outbreaks of highly pathogenic avian influenza (HPAI) since 2005 have raised the question about the roles of migratory and wild birds in the transmission of HPAI. Despite increased monitoring, the role of wild waterfowl as the primary source of the highly pathogenic H5N1 has not been clearly established. The impact of outbreaks of HPAI among species of wild birds which are already endangered can nevertheless have devastating consequences for the local and non-local ecology where migratory species are established. Understanding the entangled dynamics of migration and the disease dynamics will be key to prevention and control measures for humans, migratory birds and poultry. Here, we present a spatial dynamic model of seasonal migration derived from first principles and linking the local dynamics during migratory stopovers to the larger scale migratory routes. We discuss the effect of repeated epizootic at specific migratory stopovers for bar-headed geese (Anser indicus). We find that repeated deadly outbreaks of H5N1 on stopovers during the autumn migration of bar-headed geese could lead to a larger reduction in the size of the equilibrium bird population compared with that obtained after repeated outbreaks during the spring migration. However, the opposite is true during the first few years of transition to such an equilibrium. The age-maturation process of juvenile birds which are more susceptible to H5N1 reinforces this result.

Predicting the impacts of climate change on a globally distributed species: the case of the loggerhead turtle.

Marine turtles utilise terrestrial and marine habitats and several aspects of their life history are tied to environmental features that are altering due to rapid climate change. We overview the likely impacts of climate change on the biology of these species, which are likely centred upon the thermal ecology of this taxonomic group. Then, focusing in detail on three decades of research on the loggerhead turtle (Caretta caretta L.), we describe how much progress has been made to date and how future experimental and ecological focus should be directed. Key questions include: what are the current hatchling sex ratios from which to measure future climate-induced changes? What are wild adult sex ratios and how many males are necessary to maintain a fertile and productive population? How will climate change affect turtles in terms of their distribution?

Hereditary mixed polyposis syndrome due to a BMPR1A mutation.

The conditions Juvenile Polyposis Syndrome (JPS) and Hereditary Mixed Polyposis Syndrome (HMPS) are associated with an increased risk of colorectal carcinoma. The genetic mechanisms which explain these conditions have until recently been poorly understood. Recent interest has focused on the transforming growth factor (TGF)-beta signalling pathway and, in particular, on mutations in the SMAD4 gene. However, not all cases of JPS and HMPS have mutations in SMAD4 and focus has now shifted to other components of the TGF-beta pathway to clarify the genetic mechanisms involved in these conditions. In this report, we describe the significance of a bone morphogenetic protein receptor type 1A gene mutation in an Irish family.

A simplified method for fabrication of a die holder.

A technique is described for fabricating a simple and inexpensive holder for dies to be used during the process of die spacer application.

Linear responses.

Four experiments established complex choice responses a few seconds in duration. A response was reinforced if it sufficiently approximated a `target' response. The two target responses in each experiment were linear in the sense that they involved either constant rates, or constant rates of change, in component key pecking by pigeons. For example, in Experiment 4, one target response consisted of the linearly increasing pattern of 0, 1, 2, and 3 pecks per s in four successive seconds, and the other response consisted of 3, 2, 1, and 0 pecks per s. Contingencies were `tolerant' in the sense that they permitted variability across different reinforced exemplars of a response. Responses approximated target responses, at least crudely in terms of overall cumulative records, and sometimes even quantitatively in terms of within-trial, local sequential organization. In this sense, the `contents' of at least some choice responses, like their `envelopes', can be shaped. That is, patterning within their boundaries, in addition to their relative and absolute durations, can be shaped. Some responses may have emerged from variability inherent in component pecking occurring at a constant probability, thereby demonstrating a few cases where the relation between molecular and molar analyses fully legitimizes a molar analysis.

Reinforcement of behavioral patterns: shaping a scallop.

Temporal patterns of key pecking by pigeons were shaped by a schedule in which the delivery of food was contingent upon a measure of the overall extent to which the temporal pattern of behavior within a 5-sec trial conformed to a required pattern. This pattern approximated a constant rate of change in the rate of key pecking throughout the 5-sec trial. In comparison with behavior maintained by a classical fixed-interval 5-sec schedule, the new schedule controlled a better approximation to a "scallop" within individual trials and greatly reduced intersubject variability. These results are consistent with the view that the delivery of a reinforcer after a behavioral pattern a few seconds in duration may strengthen the entire pattern as a unit, or operant. The response topography contiguous with reinforcement may be a negligible fraction of the strengthened operant. One implication of this view is that mean response rate for such brief responses as key pecks and lever presses is a byproduct of whatever patterns are strengthened, and generally will not reveal fundamental controlling relationships, whenever a reinforcer is not contiguous with all the behavior on which it is contingent.

Time-allocation, matching, and contrast.

A variable-interval schedule arranged food reinforcement for key pecking by pigeons on a single operandum at two rates, corresponding to two classes of reinforced interresponse times ranging from 1.5 to 2.5 sec and from 3.5 to 4.5 sec. The scheduled reinforcement rate for the higher component response rate was constant and equivalent to that of a variable-interval 4-min schedule. The scheduled reinforcement rate for the lower component response rate varied from zero to over 100 per hour. The number of occurrences of the constant component response rate varied inversely with the reinforcement rate for the variable component. This result, by definition a concurrent reinforcement interaction, or contrast, was the combined effect of two time-allocation functions, which together determine mean response rate: the time allocated to both component rates as a function of the total reinforcement rate, and the time allocated to a particular component rate as a function of the percentage of reinforcements for that component. The present experiment reveals a further parallel between the controlling relations for free responding on a single operandum and those for choice between two operanda; in each case, a concurrent reinforcement interaction can be found that corresponds to matching.

Choice between response rates.

Three pigeons were required to peck a single key at a higher and a lower rate, corresponding to two classes of shorter and longer concurrently reinforced interresponse times. Food reinforcers arranged by a single variable-interval schedule were randomly allocated to the two reinforced interresponse times. The absolute durations of reinforced interresponse times were varied while the total reinforcements per hour was held constant and the relative duration, i.e., the relative reciprocal, of the shorter reinforcer class was held constant at 0.70. Preference for the higher rate of responding, as measured by the relative frequency of responses terminating interresponse times in the shorter reinforced class, depended on the absolute reinforced response rates. Preference for the higher reinforced rate increased from a level of near-indifference (0.50) at high reinforced response rates, through the matching level (0.70) at intermediate reinforced response rates, to a virtually exclusive preference (>0.90) at low reinforced response rates. These results resemble corresponding preference functions obtained with two-key concurrent-chains schedules and thereby provide another sense in which it may be said that interresponse-time distributions from interval schedules estimate preference functions for the component response rates corresponding to different classes of reinforced interresponse times.