The great tit HapMap project: A continental-scale analysis of genomic variation in a songbird.

A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.

HPAIV outbreak triggers short-term colony connectivity in a seabird metapopulation.

Disease outbreaks can drastically disturb the environment of surviving animals, but the behavioural, ecological, and epidemiological consequences of disease-driven disturbance are poorly understood. Here, we show that an outbreak of High Pathogenicity Avian Influenza Virus (HPAIV) coincided with unprecedented short-term behavioural changes in Northern gannets (Morus bassanus). Breeding gannets show characteristically strong fidelity to their nest sites and foraging areas (2015-2019; n = 120), but during the 2022 HPAIV outbreak, GPS-tagged gannets instigated long-distance movements beyond well-documented previous ranges and the first ever recorded visits of GPS-tagged adults to other gannet breeding colonies. Our findings suggest that the HPAIV outbreak triggered changes in space use patterns of exposed individuals that amplified the epidemiological connectivity among colonies and may generate super-spreader events that accelerate disease transmission across the metapopulation. Such self-propagating transmission from and towards high density animal aggregations may explain the unexpectedly rapid pan-European spread of HPAIV in the gannet.

Body surface temperature of rats reveals both magnitude and sex differences in the acute stress response.

Understanding how biological markers of stress relate to stressor magnitude is much needed and can be used in welfare assessment. Changes in body surface temperature can be measured using infrared thermography (IRT) as a marker of a physiological response to acute stress. While an avian study has shown that changes in body surface temperature can reflect the intensity of acute stress, little is known about surface temperature responses to stressors of different magnitudes and its sex-specificity in mammals, and how they correlate with hormonal and behavioural responses. We used IRT to collect continuous surface temperature measurements of tail and eye of adult male and female rats (Rattus norvegicus), for 30 minutes after exposure to one of three stressors (small cage, encircling handling or rodent restraint cone) for one minute, and cross-validated the thermal response with plasma corticosterone (CORT) and behavioural assessment. To obtain individual baseline temperatures and thermal responses to stress, rats were imaged in a test arena (to which they were habituated) for 30 seconds before and 30 minutes after being exposed to the stressor. In response to the three stressors, tail temperature initially decreased and then recovered to, or overshot the baseline temperature. Tail temperature dynamics differed between stressors; being restrained in the small cage was associated with the smallest drop in temperature, in male rats, and the fastest thermal recovery, in both sexes. Increases in eye temperature only distinguished between stressors early in the response and only in females. The post stressor increase in eye temperature was greater in the right eye of males and the left eye of females. In both sexes encircling may have been associated with the fastest increase in CORT. These results were in line with observed behavioural changes, with greater movement in rats exposed to the small cage and higher immobility after encircling. The female tail and eye temperature, as well as the CORT concentrations did not return to pre-stressor levels in the observation period, in conjunction with the greater occurrence of escape-related behaviours in female rats. These results suggest that female rats are more vulnerable to acute restraint stress compared to male rats and emphasise the importance of using both sexes in future investigations of stressor magnitude. This study demonstrates that acute stress induced changes in mammalian surface temperature measured with IRT relate to the magnitude of restraint stress, indicate sex differences and correlate with hormonal and behavioural responses. Thus, IRT has the potential to become a non-invasive method of continuous welfare assessment in unrestrained mammals.

Non-invasive assessment of positive affective state using infra-red thermography in rats.

With recent increased focus on positive welfare in animal welfare science, there is demand for objective positive welfare indicators. It is unclear whether changes in body surface temperature can be used to non-invasively identify and quantify positive states in mammals. We recorded continuous measurements of tail surface temperature using infra-red thermography (IRT) and concurrent behavioural observations in male and female Wistar rats (Rattus norvegicus). If tail surface temperature can differentiate between positive and negative experiences, we expect a qualitatively different response compared to negative experiences. Three groups of rats were presented with increasing magnitudes of food rewards (neutral/none, one and three rewards). The rats were placed in an arena to which they were habituated and filmed for 30 s before and 30 min after exposure to different rewards. Tail temperature initially decreased from the pre-reward baseline and subsequently returned towards baseline temperature. The overall pattern of the change was the same as for rats subjected to negative stimuli in previous studies. Nevertheless, dynamic changes in tail temperature, specifically the rate of recovery and the behavioural response (exploration), differed between neutral and rewarded rats but failed to distinguish reward magnitude. Sex differences were found in both thermal and behavioural responses, unrelated to reward magnitudes. Female rats exhibited a greater initial response with a slower recovery than male rats, emphasising the value of using of both sexes in animal welfare research. This study improves our understanding of the effects of positive emotions induced by food reward on peripheral body temperature and behaviour.

The prevalence and source of plastic incorporated into nests of five seabird species on a small offshore island.

There is little evidence documenting the prevalence of plastic nest incorporation for different seabird species and populations, and even less detailing the source of such debris as nesting material. This study presents a baseline dataset on the presence of plastic in the nests of five seabird species on Lady Isle, Scotland using a novel and repeatable methodology for quantifying plastic incorporated into nests. Plastic was found in 24.5% to 80% of nests of all species. We analysed pellets of regurgitated material and the spatial distribution of herring gull nests containing plastic in the context of the tide and nesting habitat. Differences in the types of plastic found in pellets and nests suggests that plastic incorporated into herring gull nests was not derived at foraging sites and likely collected from the local environment. Targeted beach cleans before the breeding season could help minimise the quantity of plastic available to herring gulls.

Eye region surface temperature dynamics during acute stress relate to baseline glucocorticoids independently of environmental conditions.

Reactions to acute stressors are critical for survival. Yet, the challenges of assessing underlying physiological processes in the field limit our understanding of how variation in the acute stress response relates to fitness in free-living animals. Glucocorticoid secretion during acute stress can be measured from blood plasma concentrations, but each blood sample can only provide information for one point in time. Also, the number of samples that can be extracted from an individual in the field is usually limited to avoid compromising welfare. This restricts capacity for repeated assessment, and therefore temporal resolution of findings within- and between-acute stress responses - both of which are important for determining links between acute stress and fitness. Acute stress induces additional body surface temperature changes that can be measured non-invasively, and at high frequencies using thermal imaging, offering opportunities to overcome these limitations. But, this method's usefulness in the field depends on the extent that environmental conditions affect the body surface temperature response, which remains poorly understood. We assessed the relative importance of individual physiology (baseline glucocorticoid concentrations) and environmental conditions (air temperature and relative humidity) in determining the eye region surface temperature (Teye) response to acute stress, in wild blue tits (Cyanistes caeruleus) during trapping, handling and blood sampling. When controlling for between-individual baseline variation, Teye initially dropped rapidly below, and then recovered above baseline, before declining more slowly until the end of the test, 160 s after trap closure. One measure of the amplitude of this response - the size of the initial drop in Teye - was dependent on environmental conditions, but not baseline corticosterone. Whereas, two properties defining response dynamics - the timing of the initial drop, and the slope of the subsequent recovery - were related to baseline corticosterone concentrations, independently of environmental conditions. This suggests inferring the acute stress response using thermal imaging of Teye will be practical under fluctuating environmental conditions in the field.

Effects of interspecific coexistence on laying date and clutch size in two closely related species of hole-nesting birds.

Coexistence between great tits Parus major and blue tits Cyanistes caeruleus, but also other hole-nesting taxa, constitutes a classic example of species co-occurrence resulting in potential interference and exploitation competition for food and for breeding and roosting sites. However, the spatial and temporal variations in coexistence and its consequences for competition remain poorly understood. We used an extensive database on reproduction in nest boxes by great and blue tits based on 87 study plots across Europe and Northern Africa during 1957-2012 for a total of 19,075 great tit and 16,729 blue tit clutches to assess correlative evidence for a relationship between laying date and clutch size, respectively, and density consistent with effects of intraspecific and interspecific competition. In an initial set of analyses, we statistically controlled for a suite of site-specific variables. We found evidence for an effect of intraspecific competition on blue tit laying date (later laying at higher density) and clutch size (smaller clutch size at higher density), but no evidence of significant effects of intraspecific competition in great tits, nor effects of interspecific competition for either species. To further control for site-specific variation caused by a range of potentially confounding variables, we compared means and variances in laying date and clutch size of great and blue tits among three categories of difference in density between the two species. We exploited the fact that means and variances are generally positively correlated. If interspecific competition occurs, we predicted a reduction in mean and an increase in variance in clutch size in great tit and blue tit when density of heterospecifics is higher than the density of conspecifics, and for intraspecific competition, this reduction would occur when density of conspecifics is higher than the density of heterospecifics. Such comparisons of temporal patterns of means and variances revealed evidence, for both species, consistent with intraspecific competition and to a smaller extent with interspecific competition. These findings suggest that competition associated with reproductive behaviour between blue and great tits is widespread, but also varies across large spatial and temporal scales.

Tritrophic phenological match-mismatch in space and time.

Increasing temperatures associated with climate change may generate phenological mismatches that disrupt previously synchronous trophic interactions. Most work on mismatch has focused on temporal trends, whereas spatial variation in the degree of trophic synchrony has largely been neglected, even though the degree to which mismatch varies in space has implications for meso-scale population dynamics and evolution. Here we quantify latitudinal trends in phenological mismatch, using phenological data on an oak-caterpillar-bird system from across the UK. Increasing latitude delays phenology of all species, but more so for oak, resulting in a shorter interval between leaf emergence and peak caterpillar biomass at northern locations. Asynchrony found between peak caterpillar biomass and peak nestling demand of blue tits, great tits and pied flycatchers increases in earlier (warm) springs. There is no evidence of spatial variation in the timing of peak nestling demand relative to peak caterpillar biomass for any species. Phenological mismatch alone is thus unlikely to explain spatial variation in population trends. Given projections of continued spring warming, we predict that temperate forest birds will become increasingly mismatched with peak caterpillar timing. Latitudinal invariance in the direction of mismatch may act as a double-edged sword that presents no opportunities for spatial buffering from the effects of mismatch on population size, but generates spatially consistent directional selection on timing, which could facilitate rapid evolutionary change.

Surface temperature elevated by chronic and intermittent stress.

Stress in homeothermic animals is associated with raised body core temperature and altered patterns of peripheral blood flow. During acute stress, peripheral vasoconstriction causes a short-lived drop in surface temperature that can be detected non-invasively using infrared thermography (IRT). Whether and how skin temperature changes under chronic stress, and hence the potential of IRT in chronic stress detection, is unknown. We explored the impact of withdrawing environmental enrichments and intermittent routine handling on long-term skin temperature in laying hens (Gallus gallus domesticus). Immediately following enrichment withdrawal, comb, face and eye temperature dropped, suggesting this was acutely stressful. In the 3 weeks that followed, barren-housed hens displayed behavioural markers of frustration. Whilst control birds, housed in enriched conditions, showed a decline over weeks in both comb temperature and baseline corticosterone levels, barren-housed hens had no change in comb temperature and an increase in corticosterone. By the trial end, comb temperature (but not corticosterone) was significantly higher in barren-housed hens. This change in parameters over time may reflect cumulative impacts of enrichment withdrawal in barren pens and/or, as hens were young and maturing, age-related changes in controls. Comb, face and eye temperature were also higher on days following routine handling, and comb temperature higher on other days in hens that were regularly handled for blood sampling than for a less intensive weighing protocol. Together, these data support comb, face and eye surface temperature increase as a long-term marker of stress exposure in laying hens. It is important to recognise that the strength and even direction of these effects may vary with thermoregulatory and energetic context. However, in laboratory and indoor-reared farm animals that live in carefully managed environments, IRT of the skin can potentially be used to non-invasively monitor chronic and intermittent stress exposure.

Eye region surface temperature reflects both energy reserves and circulating glucocorticoids in a wild bird.

Body temperature of endotherms shows substantial within- and between-individual variation, but the sources of this variation are not fully understood in wild animals. Variation in body temperature can indicate how individuals cope with their environment via metabolic or stress-induced effects, both of which may relate to depletion of energy reserves. Body condition can reflect heat production through changes to metabolic rate made to protect energy reserves. Additionally, changes in metabolic processes may be mediated by stress-related glucocorticoid secretion, which is associated with altered blood-flow patterns that affect regional body temperatures. Accordingly, both body condition and glucocorticoid secretion should relate to body temperature. We used thermal imaging, a novel non-invasive method of temperature measurement, to investigate relationships between body condition, glucocorticoid secretion and body surface temperature in wild blue tits (Cyanistes caeruleus). Individuals with lower body condition had lower eye-region surface temperature in both non-breeding and breeding seasons. Eye-region surface temperature was also negatively correlated with baseline circulating glucocorticoid levels in non-breeding birds. Our results demonstrate that body surface temperature can integrate multiple aspects of physiological state. Consequently, remotely-measured body surface temperature could be used to assess such aspects of physiological state non-invasively in free-living animals at multiple life history stages.

Legacy Pollutants are Declining in Great Skuas (Stercorarius skua) but Remain Higher in Faroe Islands than in Scotland.

To monitor environmental pollutants in Faroese biota, samples from a top predator were analysed and put into a spatial and temporal context. Analysis of 20 Great Skua eggs sampled in 2012 from the Faroe Islands showed >70 % lower concentrations of legacy persistent organic pollutants (POPs) than in samples analysed in 1977. The 2012 Faroese eggs showed higher concentrations than for eggs in Shetland from about the same period (2008). Eggshells were analysed for sub-lethal effects but there were no detectable effects of legacy POP levels on eggshell colour or thickness. A temporal decline in legacy POPs would indicate a reduction in the general pollutant levels present in the environment as has been shown in other areas of the North Atlantic, but there are significant geographic differences in POPs levels likely due to differences in diet resulting in significantly different exposures on a relatively limited spatial scale.

Meta-analysis indicates that oxidative stress is both a constraint on and a cost of growth.

Oxidative stress (OS) as a proximate mechanism for life-history trade-offs is widespread in the literature. One such resource allocation trade-off involves growth rate, and theory suggests that OS might act as both a constraint on and a cost of growth, yet studies investigating this have produced conflicting results. Here, we use meta-analysis to investigate whether increased OS levels impact on growth (OS as a constraint on growth) and whether greater growth rates can increase OS (OS as a cost of growth). The role of OS as a constraint on growth was supported by the meta-analysis. Greater OS, in terms of either increased damage or reduced levels of antioxidants, was associated with reduced growth although the effect depended on the experimental manipulation used. Our results also support an oxidative cost of growth, at least in terms of increased oxidative damage, although faster growth was not associated with a change in antioxidant levels. These findings that OS can act as a constraint on growth support theoretical links between OS and animal life histories and provide evidence for a growth-self-maintenance trade-off. Furthermore, the apparent oxidative costs of growth imply individuals cannot alter this trade-off when faced with enhanced growth. We offer a starting platform for future research and recommend the use of oxidative damage biomarkers in nonlethal tissue to investigate the growth-OS relationship further.

Thermal Imaging to Study Stress Non-invasively in Unrestrained Birds.

Stress, a central concept in biology, describes a suite of emergency responses to challenges. Among other responses, stress leads to a change in blood flow that results in a net influx of blood to key organs and an increase in core temperature. This stress-induced hyperthermia is used to assess stress. However, measuring core temperature is invasive. As blood flow is redirected to the core, the periphery of the body can cool. This paper describes a protocol where peripheral body temperature is measured non-invasively in wild blue tits (Cyanistes caeruleus) using infrared thermography. In the field we created a set-up bringing the birds to an ideal position in front of the camera by using a baited box. The camera takes a short thermal video recording of the undisturbed bird before applying a mild stressor (closing the box and therefore capturing the bird), and the bird's response to being trapped is recorded. The bare skin of the eye-region is the warmest area in the image. This allows an automated extraction of the maximum eye-region temperature from each image frame, followed by further steps of manual data filtering removing the most common sources of errors (motion blur, blinking). This protocol provides a time series of eye-region temperature with a fine temporal resolution that allows us to study the dynamics of the stress response non-invasively. Further work needs to demonstrate the usefulness of the method to assess stress, for instance to investigate whether eye-region temperature response is proportional to the strength of the stressor. If this can be confirmed, it will provide a valuable alternative method of stress assessment in animals and will be useful to a wide range of researchers from ecologists, conservation biologists, physiologists to animal welfare researchers.

Skin temperature reveals the intensity of acute stress.

Acute stress triggers peripheral vasoconstriction, causing a rapid, short-term drop in skin temperature in homeotherms. We tested, for the first time, whether this response has the potential to quantify stress, by exhibiting proportionality with stressor intensity. We used established behavioural and hormonal markers: activity level and corticosterone level, to validate a mild and more severe form of an acute restraint stressor in hens (Gallus gallus domesticus). We then used infrared thermography (IRT) to non-invasively collect continuous temperature measurements following exposure to these two intensities of acute handling stress. In the comb and wattle, two skin regions with a known thermoregulatory role, stressor intensity predicted the extent of initial skin cooling, and also the occurrence of a more delayed skin warming, providing two opportunities to quantify stress. With the present, cost-effective availability of IRT technology, this non-invasive and continuous method of stress assessment in unrestrained animals has the potential to become common practice in pure and applied research.

Female but not male zebra finches adjust heat output in response to increased incubation demand.

In many incubating birds, heat transfer from parent to egg is facilitated by the brood patch, an area of ventral abdominal skin that becomes highly vascularised, swells and loses its down feathers around the time of laying. Only the female develops a brood patch in most passerine species, but males of some species can incubate and maintain the eggs at similar temperatures to females even without a brood patch. Here we used a novel application of infrared thermography to examine sex differences in parental care from a physiological perspective. Using incubating male and female zebra finches (Taeniopygia guttata), a species in which the male lacks a brood patch, we measured the surface temperature of the ventral plumage overlying the abdomen and a reference area that does not contact the eggs (thorax) twice per pair. In half of the pairs, clutch size was experimentally enlarged between the two sets of measurements to increase incubation demand. We found that the temperature differential between abdomen and thorax plumage was greater in females than in males, and that abdomen plumage was warmer after clutch enlargement than before in females but not in males. These findings are consistent with morphological sex differences in brood patch development and suggest that male and female zebra finches differ in the way they regulate abdomen versus general body surface temperature in response to variation in incubation demand.

The effect of maternal state on the steroid and macronutrient content of lesser black-backed gull eggs.

It has been proposed that female birds can influence the phenotype of their offspring by provisioning eggs with variable amounts of nutrients and maternal hormones. Egg quality is strongly influenced by maternal body reserves and the amount of food available at the time of egg formation. This study investigated the effects of maternal state and food availability on the capacity of female lesser black-backed gulls Larus fuscus to provision their eggs with macronutrients and steroid hormones. Maternal state was reduced by increasing egg-production effort, whereas extra food was provided to reverse this effect. Compared with eggs of first clutches, eggs of experimentally induced replacement clutches exhibited a lower yolk/albumen ratio and contained more yolk testosterone. During one of the three years in which the study was performed, replacement eggs also contained more 17ß-estradiol. Food provisioning during the relaying interval did not affect changes in yolk/albumen ratio or steroid concentrations, but fed females produced bigger eggs in their replacement clutch. This study demonstrates significant within-female consistency in egg size, macronutrient content, and yolk steroid concentration, and it shows that these egg characteristics are influenced by maternal state, food availability, and the timing of breeding.

Inbreeding and loss of genetic variation in a reintroduced population of Mauritius Kestrel.

Many populations have recovered from severe bottlenecks either naturally or through intensive conservation management. In the past, however, few conservation programs have monitored the genetic health of recovering populations. We conducted a conservation genetic assessment of a small, reintroduced population of Mauritius Kestrel (Falco punctatus) to determine whether genetic deterioration has occurred since its reintroduction. We used pedigree analysis that partially accounted for individuals of unknown origin to document that (1) inbreeding occurred frequently (2.6% increase per generation; N(eI)= 18.9), (2) 25% of breeding pairs were composed of either closely or moderately related individuals, (3) genetic diversity has been lost from the population (1.6% loss per generation; N(eV)= 32.1) less rapidly than the corresponding increase in inbreeding, and (4) ignoring the contribution of unknown individuals to a pedigree will bias the metrics derived from that pedigree, ultimately obscuring the prevailing genetic dynamics. The rates of inbreeding and loss of genetic variation in the subpopulation of Mauritius Kestrel we examined were extreme and among the highest yet documented in a wild vertebrate population. Thus, genetic deterioration may affect this population's long-term viability. Remedial conservation strategies are needed to reduce the impact of inbreeding and loss of genetic variation in this species. We suggest that schemes to monitor genetic variation after reintroduction should be an integral component of endangered species recovery programs.

The perils and prospects of using phytohaemagglutinin in evolutionary ecology.

Several techniques are available for quantifying the vertebrate immune response, information that is particularly useful for understanding the contribution of immunity to the evolution of life-history strategies. The most widely used is the phytohaemagglutinin (PHA) skin-swelling technique, which is usually regarded as an index of acquired immunity. However, our understanding of the effects of PHA in skin is poor, despite the fact that it has implications for what the test can tell us about immune activity. As we discuss here, a recent study by Martin and colleagues on the response to PHA at the cellular level in wild birds has highlighted the relative extent to which PHA-induced swelling, as most commonly applied, measures innate immunity versus acquired immunity.

Compensatory growth impairs adult cognitive performance.

Several studies have demonstrated that poor early nutrition, followed by growth compensation, can have negative consequences later in life. However, it remains unclear whether this is attributable to the nutritional deficit itself or a cost of compensatory growth. This distinction is important to our understanding both of the proximate and ultimate factors that shape growth trajectories and of how best to manage growth in our own and other species following low birth weight. We reared sibling pairs of zebra finches on different quality nutrition for the first 20 d of life only and examined their learning performance in adulthood. Final body size was not affected. However, the speed of learning a simple task in adulthood, which involved associating a screen colour with the presence of a food reward, was negatively related to the amount of growth compensation that had occurred. Learning speed was not related to the early diet itself or the amount of early growth depression. These results show that the level of compensatory growth that occurs following a period of poor nutrition is associated with long-term negative consequences for cognitive function and suggest that a growth-performance trade-off may determine optimal growth trajectories.

Prenatal developmental conditions have long-term effects on offspring fecundity.

Maternal effects, in which differences in parental state cause differences in offspring fitness, are important in trade-offs influencing an individual's optimal reproductive strategy. In zebra finches (Taeniopygia guttata) we manipulated the nutritional state for four weeks before the start of breeding through protein supplementation. Zebra finches were kept on identical diets during the rest of the experiment. We then tested the effects of maternal state on offspring size, survival and fecundity. In order to separate the effects of maternal state occurring through egg production, incubation and chick-rearing, we used a cross-fostering experiment. We show that a protein-rich diet prior to laying improved maternal body weight prior to breeding compared with birds on a protein-poor diet. Poorer maternal state prior to breeding gave rise to offspring with lower fecundity than offspring from birds in a better nutritional state. Maternal state is thought to affect the conditions developing offspring experience through the bird's ability to produce and incubate eggs. Male and female embryos differed in their responses to conditions at different developmental stages. This shows that embryonic developmental conditions and sex differences in vulnerability to these conditions need to be incorporated into future models of selection, life-history evolution and sex-ratio theory.