Characterization of the genomic sequence of a circo-like virus and of three chaphamaparvoviruses detected in mute swan (Cygnus olor)

We report the complete genomes of four ssDNA viruses: a circular replication-associated protein-encoding single-stranded DNA virus belonging to a clade previously detected only in mammals, and three chaphamaparvoviruses, which were detected by viromic surveillance of mute swan (Cygnus olor) fecal samples from the United Kingdom.

Genetic diversity, recombination and cross-species transmission of a waterbird gammacoronavirus in the wild

Viruses emerging from wildlife can cause outbreaks in humans and domesticated animals. Predicting the emergence of future pathogens and mitigating their impacts requires an understanding of what shapes virus diversity and dynamics in wildlife reservoirs. In order to better understand coronavirus ecology in wild species, we sampled birds within a coastal freshwater lagoon habitat across 5 years, focussing on a large population of mute swans (Cygnus olor) and the diverse species that they interact with. We discovered and characterised the full genome of a divergent gammacoronavirus belonging to the Goose coronavirus CB17 species. We investigated the genetic diversity and dynamics of this gammacoronavirus using untargeted metagenomic sequencing of 223 faecal samples from swans of known age and sex, and RT-PCR screening of 1632 additional bird samples. The virus circulated persistently within the bird community; virus prevalence in mute swans exhibited seasonal variations, but did not change with swan age-class or epidemiological year. One whole genome was fully characterised, and revealed that the virus originated from a recombination event involving an undescribed gammacoronavirus species. Multiple lineages of this gammacoronavirus co-circulated within our study population. Viruses from this species have recently been detected in aquatic birds from both the Anatidae and Rallidae families, implying that host species habitat sharing may be important in shaping virus host range. As the host range of the Goose coronavirus CB17 species is not limited to geese, we propose that this species name should be updated to 'Waterbird gammacoronavirus 1'. Non-invasive sampling of bird coronaviruses may provide a tractable model system for understanding the evolutionary and cross-species dynamics of coronaviruses.

Impact of host age on viral and bacterial communities in a waterbird population

Wildlife harbour pathogens that can harm human or livestock health and are the source of most emerging infectious diseases. It is rarely considered how changes in wildlife population age-structures or how age-stratified behaviours might alter the level of pathogen detection within a species, or risk of spillover to other species. Micro-organisms that occur in healthy animals can be an important model for understanding and predicting the dynamics of pathogens of greater health concern, which are hard to study in wild populations due to their relative rarity. We therefore used a metagenomic approach to jointly characterise viral and prokaryotic carriage in faeces collected from a healthy wild bird population (Cygnus olor; mute swan) that has been subject to long-term study. Using 223 samples from known individuals allowed us to compare differences in prokaryotic and eukaryotic viral carriage between adults and juveniles at an unprecedented level of detail. We discovered and characterised 77 novel virus species, of which 21% belong putatively to bird-infecting families, and described the core prokaryotic microbiome of C. olor. Whilst no difference in microbiota diversity was observed between juveniles and adult individuals, 50% (4/8) of bird-infecting virus families (picornaviruses, astroviruses, adenoviruses and bornaviruses) and 3.4% (9/267) of prokaryotic families (including Helicobacteraceae, Spirochaetaceae and Flavobacteriaceae families) were differentially abundant and/or prevalent between juveniles and adults. This indicates that perturbations that affect population age-structures of wildlife could alter circulation dynamics and spillover risk of microbes, potentially including pathogens.

Disentangling the causes of age‐assortative mating in bird populations with contrasting life‐history strategies

Age shapes fundamental processes related to behaviour, survival and reproduction, where age influences reproductive success, non-random mating with respect to age can magnify or mitigate such effects. Consequently, the correlation in partners' age across a population may influence its productivity. Despite widespread evidence for age-assortative mating, little is known about what drives this assortment and its variation. Specifically, the relative importance of active (same-age mate preference) and passive processes (assortment as a consequence of other spatial or temporal effects) in driving age assortment is not well understood. In this paper, we compare breeding data from a great tit and mute swan population (51- and 31-year datasets, respectively) to tease apart the contributions of pair retention, cohort age structure and active age-related mate selection to age assortment in species with contrasting life histories. Both species show age-assortative mating and variable assortment between years. However, we demonstrate that the drivers of age assortment differ between the species, as expected from their life histories and resultant demographic differences. In great tits, pair fidelity has a weak effect on age-assortative mating through pair retention; variation in age assortment is primarily driven by fluctuations in age structure from variable juvenile recruitment. Age-assortative mating is, therefore, largely passive, with no evidence consistent with active age-related mate selection. In mute swans, age assortment is partly explained by pair retention, but not population age structure, and evidence exists for active age-assortative pairing. This difference is likely to result from shorter life-spans in great tits compared with mute swans, leading to fundamental differences in their population age structure, whereby a larger proportion of great tit populations consist of a single age cohort. In mute swans, age-assortative pairing through mate selection may also be driven by greater age-dependent variation in fitness. The study highlights the importance of considering how different life histories and demographic differences arising from these affect population processes that appear congruent across species. We suggest that future research should focus on uncovering the proximate mechanisms that lead to variation in active age-assortative mate selection (as seen in mute swans); and the consequences of variation in age structure on the ecological and social functioning of wild populations.

Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild bird population

Understanding the epidemiological dynamics of highly pathogenic avian influenza virus (HPAIV) in wild birds is crucial for guiding effective surveillance and control measures. The spread of H5 HPAIV has been well characterized over large geographical and temporal scales. However, information about the detailed dynamics and demographics of individual outbreaks in wild birds is rare and important epidemiological parameters remain unknown. We present data from a wild population of long-lived birds (mute swans; Cygnus olor) that has experienced three outbreaks of related H5 HPAIVs in the past decade, specifically, H5N1 (2007), H5N8 (2016) and H5N6 (2017). Detailed demographic data were available and intense sampling was conducted before and after the outbreaks; hence the population is unusually suitable for exploring the natural epidemiology, evolution and ecology of HPAIV in wild birds. We show that key epidemiological features remain remarkably consistent across multiple outbreaks, including the timing of virus incursion and outbreak duration, and the presence of a strong age-structure in morbidity that likely arises from an equivalent age-structure in immunological responses. The predictability of these features across a series of outbreaks in a complex natural population is striking and contributes to our understanding of HPAIV in wild birds.

This article is part of the theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes’. This issue is linked with the subsequent theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control’.

Breeding phenology and winter activity predict subsequent breeding success in a trans-global migratory seabird

Inter-seasonal events are believed to connect and affect reproductive performance (RP) in animals. However, much remains unknown about such carry-over effects (COEs), in particular how behaviour patterns during highly mobile life-history stages, such as migration, affect RP. To address this question, we measured at-sea behaviour in a long-lived migratory seabird, the Manx shearwater (Puffinus puffinus) and obtained data for individual migration cycles over 5 years, by tracking with geolocator/immersion loggers, along with 6 years of RP data. We found that individual breeding and non-breeding phenology correlated with subsequent RP, with birds hyperactive during winter more likely to fail to reproduce. Furthermore, parental investment during one year influenced breeding success during the next, a COE reflecting the trade-off between current and future RP. Our results suggest that different life-history stages interact to influence RP in the next breeding season, so that behaviour patterns during winter may be important determinants of variation in subsequent fitness among individuals.

Interspecific variation in the relationship between clutch size, laying date and intensity of urbanization in four species of hole-nesting birds

The increase in size of human populations in urban and agricultural areas has resulted in considerable habitat conversion globally. Such anthropogenic areas have specific environmental characteristics, which influence the physiology, life history, and population dynamics of plants and animals. For example, the date of bud burst is advanced in urban compared to nearby natural areas. In some birds, breeding success is determined by synchrony between timing of breeding and peak food abundance. Pertinently, caterpillars are an important food source for the nestlings of many bird species, and their abundance is influenced by environmental factors such as temperature and date of bud burst. Higher temperatures and advanced date of bud burst in urban areas could advance peak caterpillar abundance and thus affect breeding phenology of birds. In order to test whether laying date advance and clutch sizes decrease with the intensity of urbanization, we analyzed the timing of breeding and clutch size in relation to intensity of urbanization as a measure of human impact in 199 nest box plots across Europe, North Africa, and the Middle East (i.e., the Western Palearctic) for four species of hole‐nesters: blue tits (Cyanistes caeruleus), great tits (Parus major), collared flycatchers (Ficedula albicollis), and pied flycatchers (Ficedula hypoleuca). Meanwhile, we estimated the intensity of urbanization as the density of buildings surrounding study plots measured on orthophotographs. For the four study species, the intensity of urbanization was not correlated with laying date. Clutch size in blue and great tits does not seem affected by the intensity of urbanization, while in collared and pied flycatchers it decreased with increasing intensity of urbanization. This is the first large‐scale study showing a species‐specific major correlation between intensity of urbanization and the ecology of breeding. The underlying mechanisms for the relationships between life history and urbanization remain to be determined. We propose that effects of food abundance or quality, temperature, noise, pollution, or disturbance by humans may on their own or in combination affect laying date and/or clutch size.

The involvement of prolactin in avian molt: the effects of gender and breeding success on the timing of molt in Mute swans (Cygnus olor)

The aim of the study was to test the hypothesis that decreasing plasma prolactin stimulates or permits the initiation of avian molt. Changes in the concentration of plasma prolactin in Mute swans (Cygnus olor) were compared in non-breeding singletons and breeding pairs. In breeding swans, the onset of molt is delayed compared to non-breeders, and is delayed further in breeding males compared to their female partners. The seasonal decrease in prolactin in non-breeding birds of both sexes started at the end of May and was associated with the initiation of molt 4 weeks later. The decrease in plasma prolactin in incubating females was more pronounced, as a consequence of increased prolactin secretion associated with incubation behavior, but also started at end of May, and was associated the onset of molt 6 weeks later. In breeding males, plasma prolactin increased at the end of May when they started to care for their newly hatched cygnets. Correspondingly, prolactin began to decrease 3-5 weeks later in males than in females. These males started to molt in mid August, at least 4 weeks later than females. It is concluded that molt is related to decreasing plasma prolactin, and is inhibited when plasma prolactin is increasing or high.

Migration and stopover in a small pelagic seabird, the Manx shearwater Puffinus puffinus: insights from machine learning

The migratory movements of seabirds (especially smaller species) remain poorly understood, despite their role as harvesters of marine ecosystems on a global scale and their potential as indicators of ocean health. Here we report a successful attempt, using miniature archival light loggers (geolocators), to elucidate the migratory behaviour of the Manx shearwater Puffinus puffinus, a small (400 g) Northern Hemisphere breeding procellariform that undertakes a trans-equatorial, trans-Atlantic migration. We provide details of over-wintering areas, of previously unobserved marine stopover behaviour, and the long-distance movements of females during their pre-laying exodus. Using salt-water immersion data from a subset of loggers, we introduce a method of behaviour classification based on Bayesian machine learning techniques. We used both supervised and unsupervised machine learning to classify each bird's daily activity based on simple properties of the immersion data. We show that robust activity states emerge, characteristic of summer feeding, winter feeding and active migration. These can be used to classify probable behaviour throughout the annual cycle, highlighting the likely functional significance of stopovers as refuelling stages.

Age-specific reproduction in a long-lived species: the combined effects of senescence and individual quality

Apparent changes in breeding performance with age measured at the population level can be due to changes in individual capacity at different ages, or to the differential survival of individuals with different capabilities. Estimating the relative importance of the two is important for understanding ageing patterns in natural populations, but there are few studies of such populations in which these effects have been disentangled. We analysed laying date and clutch size as measures of individual performance in a population of mute swans (Cygnus olor) studied over 25 years at Abbotsbury, UK. On both measures of breeding performance, individuals tended to improve up to the age of 6 or 7, and to decline after about the age of 12. Individuals with longer lifespans performed better at all ages (earlier laying, larger clutches) than animals that ceased breeding earlier. We conclude that the apparent mean increase in performance with age in mute swans is due to both individual improvement and differential survival of individuals who perform well, while the decline in older age groups is due to individual loss of function. Our results underline the need to take individual differences into account when testing hypotheses about life histories in wild populations.

Components of variance underlying fitness in a natural population of the great tit Parus major

Traits that are closely associated with fitness tend to have lower heritabilities (h2) than those that are not. This has been interpreted as evidence that natural selection tends to deplete genetic variation more rapidly for traits more closely associated with fitness (a corollary of Fisher's fundamental theorem), but Price and Schluter (1991) suggested the pattern might be due to higher residual variance in traits more closely related to fitness. The relationship between 10 different traits for females, seven traits for males, and overall fitness (lifetime recruitment) was quantified for great tits (Parus major) studied in their natural environment of Wytham Wood, England, using data collected over 39 years. Heritabilities and the coefficients of additive genetic and residual variance (CVA and CVR, respectively) were estimated using an "animal model." For both males and females, a trait's correlation (r) with fitness was negatively related to its h2 but positively related to its CVR. The CVA was not related to the trait's correlation with fitness in either sex. This is the third study using directly measured fitness in a wild population to show the important role of residual variation in determining the pattern of lower heritabilities for traits more closely related to fitness.

A survey of blood lead levels in Mute Swans Cygnus olor

Following bans on the use of most lead angling weights, the incidence of lead poisoning cases in Mute Swans started to fall and the population started to increase. However, surveys of lead levels in blood of rescued swans continue to show that a high proportion of the birds are carrying levels in excess of 1.21 mol/l. Since rescued swans, although rescued for many different reasons, might be a biased sample, a survey was made of apparently healthy birds living in flocks in the summer. These too showed that a high percentage of the birds in most of the flocks sampled had blood lead levels in excess of 1.21 mol/l. No source of this lead has been identified other than lead fishing weights; these may be long-lost leads, current, but illegally used weights or "dust-shot" which it is still legal to use. Although many of the birds sampled are carrying lead burdens that are probably not harmful, others are seriously affected. Except in the most serious cases, it is not possible to recognise birds with elevated lead levels without taking a blood sample for assay.

The prevalence and ecology of the haematozoan parasites of European blackbirds, Turdus merula

The prevalence and ecology of the haematozoan parasites of a rural population of European blackbirds, Turdus merula, were investigated. Parasites belonging to eight species from four genera (Leucocytozoon, Plasmodium, Haemoproteus, and Trypanosoma) were identified. Prevalence was high: 83% of adults and 80% of juveniles were infected by at least one species of haematozoa, but no parasites were detected in 8-day-old nestlings. There were no sex differences in infection rates and only Plasmodium infection varied with age among adult blackbirds. Haemo proteus infections increased and Plasmodium infections decreased through the sampling period (January to July), but infections with other haematozoa showed no seasonal change. Haemoproteus and Plasmodium were negatively associated with each other, even during the period when infections by both genera were frequent in the study population.

Is clutch size in birds affected by environmental conditions during growth?

Only environmental conditions occurring at the time of breeding have been shown to affect clutch size in birds, even though conditions experienced during growth are known to affect body size or egg size. We show here that environmental conditions experienced during early life can affect clutch size in captive zebra finches (Taeniopygia guttata) and wild great tits (Parus major). Not only do factors outside the immediate breeding season affect clutch size, but clutch size control mechanism is permanently influenced by conditions experienced during ontogeny.

Hematology of fledgling Manx shearwaters (Puffinus puffinus) with and without 'puffinosis'

Hematological parameters were measured in 14 fledgling Manx shearwaters (Puffinus puffinus), with the disease puffinosis and in 10 birds that did not have the disease, on the Island of Skomer between 2 and 11 September 1991. The mean plasma fibrinogen concentration was significantly higher in the diseased birds and some of these had abnormally elevated monocyte counts. No other significant differences were observed.