In most animals, individuals tend to decline in performance in later life, known as ageing. In birds, studies of ageing have traditionally concentrated on metrics of survival and reproductive success, whereas morphological traits have received comparatively little attention. Feather quality is a key morphological trait for passerines as it contributes to flight performance, camouflage and thermoregulation, and is, therefore, important for survival. However, there are, as of yet, very few studies on how feather quality changes with age. In this study, we use a closely monitored natural population of long-lived Seychelles warblers to investigate whether and how three different indices of feather quality change with age within individuals. We found that feather mass-to-length ratio increased with age (indicating improving quality with age), while rachis width declined with age (indicating declining quality), and barbule density showed no ageing pattern. All feather quality indices showed no sex differences in ageing rates. The inconsistent findings of ageing across the three feather quality indices may suggest that life history trade-offs between feather quality and survival or reproduction are not as strong, and feather quality may not be a costly trait to maintain. Age-related improvements of mass-to-length ratio but not the other indices may also suggest that certain aspects of feather quality are more important than others to maintain. Opposite patterns of ageing in rachis width and mass-to-length ratio may also suggest possible trade-offs between different feather quality metrics. Our study highlights the need for further investigation on energetic trade-offs between maintenance of different phenotypic traits and fitness

When altricial birds hatch, they are unable to regulate their own temperature, but by the time they fledge they are thermally independent. Early-life conditions have been shown to be an important factor contributing to fitness. However, it is currently unknown to what extent body temperature during endothermy development is driven by genetic variation or by the early environment. We use thermal images of cross-fostered house sparrows (Passer domesticus) throughout the nestling period to separate genetic and environmental drivers of body temperature. We estimated negligible heritability of body temperature at all ages. We further found that there are effects from the natal environment that carry over into the late nestling stage. A correlation between the early- and mid-nestling periods was explained by the natal environment, and during this period body temperature and growth followed independent developmental trajectories. Furthermore, higher body temperature was under viability selection, independent of body mass. We, therefore, demonstrate that the natal environment influences future offspring phenotype via a novel measure; body temperature. Our study provides a novel investigation into the environmental and genetic drivers of body temperature variation in a wild bird, furthering our understanding of how traits evolve.

Social transmission of microbes has profound impacts on disease epidemiology and host health. However, how social factors influence gut microbiome (GM) transmission in wild populations is not well understood. Here, we use a wild population of the Seychelles warbler, a facultative cooperatively breeding passerine, to determine whether cooperative breeding behaviour influences the GM. Specifically, we hypothesise that close social interactions as part of cooperative breeding should encourage the sharing of anaerobic microbes, which may be less likely to transmit indirectly through the environment. We found that GM composition was more similar within versus between social groups, and this effect was driven by sharing both aerotolerant and anaerobic bacterial genera. As predicted, the similarity of anaerobic, but not aerotolerant, GM communities between pairs of individuals within a group was positively correlated with the strength of their social interactions (defined by their cooperative breeding status). Specifically, anaerobic GM composition was more similar between pairs of individuals that cooperate at the nest (dominant breeders and dominant-helper pairs) than for non-cooperative pairs (involving non-helping subordinate individuals). This is likely because breeders and helpers directly interact while caring for offspring at a nest. This work reveals how cooperative social interactions lead to microbial transmission and thus contribute to shaping specific components of a host's gut microbiome.

It is poorly understood how populations survive extreme bottlenecks despite severe inbreeding. We investigate the genomic architecture of inbreeding in the once critically endangered Seychelles warbler ( Acrocephalus sechellensis ) using 37 years of individual-based monitoring and 1.8 million SNPs. Linkage disequilibrium patterns reveal a historical effective population size of ~270 that plummeted to ~13 coinciding with human colonisation events of the Seychelles archipelago. Contemporary genomes are over one-third inbred from recent inbreeding measured by runs of homozygosity (ROH) formed since human colonisation of the Seychelles, 50 generations ago (mean F ROH < 50 generations ago = 0.38), and we identify significant inbreeding depression across cross key fitness traits. On average, a 17.9% reduction in lifespan and a 15.1% reduction in lifetime offspring production were associated with each 10% increase in individual inbreeding. Genome-wide scans reveal this depression is caused by a polygenic load. Our results suggest that a history of small population size could have facilitated the selective purging of severe genetic load, while mildly deleterious alleles escaped selection via drift. A partitioned genetic load architecture potentially enabled species recovery despite the inbreeding depression that followed near-extinction.

Abstract Understanding evolutionary processes is greatly facilitated by high-quality data on genetic variation. We report the development of a genomic toolkit for a recently bottlenecked, long-term studied species, the Seychelles warbler (Ptimerl dezil; Acrocephalus sechellensis ). This toolkit comprises a reference genome assembled into 31 chromosomes, together with functional annotations and reference-panel-free imputation of whole-genome sequences from 1,935 individuals. The genomic data have been used to assign the sequenced individuals into a genetic pedigree. Individual genomic data are associated with a suite of phenotypic metadata, amassed from three decades of fieldwork in this closed, long-term monitored population. We compared sex and parentage assigned using the genomic data with the previously recorded sex and parentage metadata to identify and correct 41 sample DNA samples labelled with the wrong identity. This population resource enables a wide range of analyses, that include, but are not limited to phylogenetics, metabarcoding, recombination rates, linkage patterns, adaptation, heritability, demographic history, selection, and inbreeding estimates. We wish to encourage interest from researchers seeking to collaborate on future analyses and data collection. Overall, our methods demonstrate the potential of next generation sequencing and statistical tools to provide dense genomic datasets at large sample sizes for wild populations.

Conservation translocations are an increasingly common tool used to help combat species extinction and global biodiversity loss. However, their success is dependent on a wide range of abiotic and biotic factors. To date, the potential role of host-associated microbiomes in translocation success has been overlooked despite their fundamental contribution to host health and fitness. Here, we use faecal samples to evaluate how gut microbiome communities vary across the last remnant (source) population, and all four translocated populations (established between 1988 and 2011), of the Seychelles warbler (Acrocephalus sechellensis). Gut microbiome alpha diversity was lower in all translocated populations compared to the source population on Cousin Island. Gut microbiome composition also varied, with several short-chain fatty acid producing bacterial families being lost from the core microbiome in some translocated populations; such taxa have been shown to play an important role in maintaining host metabolic health. Furthermore, the two translocated populations that were established the longest time ago, and with the fewest individuals, had reduced inter-individual gut microbiome variability compared to the source population. While it was not possible to directly assess the specific drivers of these differences due to samples being collected after the translocation event, it is likely that the size of the founding population, subsequent loss of host genetic variation and environmental factors all contribute to shaping gut microbiome variation amongst these populations. Future work should assess whether taxonomic variation translates into differences in gut microbiome function and the possible consequences for host population health and long-term resilience to environmental change.

Anthropogenic noise disturbance on wildlife is of growing concern. Environmental noise exposure during incubation can negatively impact fitness in wild birds. Here, we hypothesised that chronic noise introduces stress through oxidative damage to embryos, reflected in short-term fitness reduction and long-term physiological changes. To test this hypothesis, we investigated the effects of chronic natal noise on chick body condition, fledging success, and adult telomere shortening in a wild house sparrow Passer domesticus population using 13 years of data. We disentangled the effects of noise in the natal and rearing environments using cross-fostering. We found no evidence for the association between natal noise exposure and chick mass, body condition at fledging, and fledging success. However, adults with shorter telomeres were underrepresented in older age groups if they were incubated in chronic noise conditions, suggesting a silver spoon effect of early-life noise exposure, which has implications for the management of wild populations.

Inbreeding depression - wherein an increase in homozygosity due to mating between relatives causes fitness loss - is a well-established phenomenon, and a well-known threat to small and endangered populations. However, few studies have examined intergenerational inbreeding effects, i.e. the effect of parental homozygosity on offspring fitness. Here, we use a dataset of 1,019 individuals from the long-term study of the Seychelles warbler (Acrocephalus sechellensis) population on Cousin Island, to test intergenerational inbreeding depression. We use inbreeding coefficients (FROH) generated from imputed low-coverage whole-genome sequences and assess how parental FROH predicts first-year survival, lifespan, and productivity. High levels of extra-pair paternity combined with accurate molecular parentage assignment allows us to separate the contributions of genetic and social fathers. We find evidence of individual inbreeding depression in lifespan and lifetime reproductive success, but limited evidence of intergenerational effects. Paternal homozygosity was found to have no effect on fitness, while maternal homozygosity reduced first-year survival only when sibling competition was also present. We also found no evidence that environmental conditions or breed group structure mediated inbreeding depression.

Delayed offspring dispersal, the prolonged residence in the natal territory after reaching independence and before dispersing to breed elsewhere, is an important aspect of the evolution of cooperative breeding. By applying a path analysis approach to the long-term Seychelles warbler (Acrocephalus sechellensis) dataset, we studied whether and how delayed dispersal is affected by territory quality, the presence of helpers and non-helping subordinates, maternal breeding status, age and fecundity, and offspring sex ratio. We found that offspring are more likely to disperse when their genetic mothers are co-breeders, helpers are absent, and territory quality is high, highlighting that a complex interplay of ecological and social factors shapes dispersal decisions. In contrast to earlier findings, our analysis does not support the idea that the offspring sex ratio is affected by territory quality and helper presence. Collectively, this study underscores the importance of considering proximate factors in understanding cooperative breeding dynamics, and it shows that path analyses offer valuable insights into dissecting the intricate relationships influencing dispersal in wild populations.

Social organization and contributions to reproduction vary widely within and between species that breed in groups. Such variation often arises from the process of group formation, which drives patterns of relatedness and hence the degree of social conflict and co-operation between group members. Using field observations and molecular genetics, we investigated breeding behaviour in an urban population of the highly social Monk Parakeet Myiopsitta monachus to address two objectives. First, we investigated breeding-group frequency, composition and formation, finding that 19% of breeding units were co-operative groups, ranging in size from three to five birds, the remainder being pairs (81%). Group composition was variable with multi-male, multi-female and multi-male-female groups. Relatedness in breeding groups also varied with many containing kin, but some groups containing only non-kin. This variation reflected alternative routes to group formation, including offspring retention by pairs, sibling coalitions and aggregation of unrelated individuals. Secondly, we investigated productivity, reproductive investment and patterns of parentage in relation to the size of breeding units. Productivity did not differ significantly between pairs and groups. We detected extra-pair paternity in 27% of broods raised by pairs, and parentage shared among more than two members of most breeding groups, with joint-nesting by females detected in multi-female groups. In conclusion, the breeding system of the Monk Parakeet defies simple definition, instead showing variable reproductive roles, with potential for both indirect and direct fitness benefits.

Studies on wild animals, mostly undertaken using 16S metabarcoding, have yielded ambiguous evidence regarding changes in the gut microbiome (GM) with age and senescence. Furthermore, variation in GM function has rarely been studied in such wild populations, despite GM metabolic characteristics potentially being associated with host senescent declines. Here, we used 7 years of repeated sampling of individuals and shotgun metagenomic sequencing to investigate taxonomic and functional changes in the GM of Seychelles warblers (Acrocephalus sechellensis) with age. Our results suggest that taxonomic GM species richness declines with age and in the terminal year, with this terminal decline occurring consistently across all ages. Taxonomic and functional GM composition also shifted with host age. However, the changes we identified occurred linearly with age (or even mainly during early years prior to the onset of senescence in this species) with little evidence of accelerated change in later life or during their terminal year. Therefore, the results suggest that changes in the GM with age are not linked to senescence. Interestingly, we found a significant increase in the abundance of a group of transposase genes with age, which may accumulate passively or due to increased transposition induced as a result of stressors that arise with age. These findings reveal taxonomic and functional GM changes with age, but not senescence, in a wild vertebrate and provide a blueprint for future wild functional GM studies linked to age and senescence.

Plastic phenotypes may often be subject to conflicting demands, which should generate nonlinear selection favoring intermediate optima. However, investigating complex patterns of selection on reaction norms has been challenging. We leveraged data on clutch size from 2 long-term studies (25 and 19 years) of individually marked house sparrows (Passer domesticus). We used a novel multivariate technique for examining linear and nonlinear selection acting on clutch size reaction norms via the fitness components of hatchling number, nestling survival, and nestling body mass at the end of the main parental period. Reaction norm slopes were highly canalized and lacked sufficient among-female variation to detect selection. Stabilizing selection and opposing patterns of directional selection occurred on both intercepts and individual residual variation via hatchling counts and nestling body mass. We also observed changes in these gradients as a function of laying date. Our results support Lack's hypothesis that quantity-quality tradeoffs shape selection on both mean clutch size and the variability of clutch sizes across breeding seasons. Our findings are also consistent with models of adaptation on asymmetric fitness landscapes, where tradeoffs near a local fitness ridge or cliff favor distinct patterns of clutch size plasticity in response to unpredictable environmental variability.

The interconnecting links between individuals in an animal social network are often defined by discrete, directed behaviours, but where these are difficult to observe, a network link (edge) may instead be defined by individuals sharing a space at the same time, which can then be used to infer a social association. The method by which these associations are defined should be informed by the biological significance of edges, and therefore often vary between studies. Identifying an appropriate measure of association remains a challenge to behavioural ecologists. Here, we use automatically recorded feeder visit data from four bird systems to compare three methods to identify a social association: (1) strict time-window, (2) co-occurrence in a group, and (3) arrival-time. We tested the similarity of the resulting networks by comparing the repeatability and sensitivity of individuals’ social traits (network degree, strength, betweenness). We found that networks constructed using different methods but applying similar, ecologically relevant definitions of associations based on individuals’ spatio-temporal co-occurrence, showed similar characteristics. Our findings suggest that the different methods to construct animal social networks are comparable, but result in subtle differences driven by species biology and feeder design. We urge researchers to carefully evaluate the ecological context of their study systems when making methodological decisions. Specifically, researchers in ecology and evolution should carefully consider the biological relevance of an edge in animal social networks, and the implications of adopting different definitions.

Migratory birds are inherently vagile, a strategy that may reduce the impacts of habitat loss and fragmentation on genetic diversity. However, specialist resource requirements and range-edge distribution can counteract these benefits. The European nightjar (Caprimulgus europaeus) is a long-distance migratory bird and resource specialist. Like other long-distance migrants, nightjar populations have declined across the British Isles and Northwestern Europe over the past century. With this decline well documented in the British Isles, there is a need to quantify its genetic impacts. We applied full genome resequencing to 60 historic (1841-1980) and 36 contemporary British nightjars. Nightjars exhibited a statistically significant 34.8% loss in heterozygosity and an increase in inbreeding over the last ~180 years, showing a departure from panmixia towards weak spatial structure in the modern population. Such fine-scale structuring in migratory birds is rare. Our results provide a case study of fragmentation's impact on a species with specialist resource requirements at its range limit. Similar demographic declines in nightjars and other long-distance migrants across Northern and Western Europe suggest that genetic patterns seen in the British population may reflect those in other nightjar populations and European avifauna. Whilst our results indicate no immediate conservation concern, they depict a trajectory of declining genetic diversity, increasing inbreeding and genetic structure, potentially shared with other migratory species. Our study highlights the value of applying spatiotemporal population genetics analysis to migratory birds, despite their inherent vagility.

Sex-linked meiotic drivers limit the inheritance of the alternate sex chromosome in the heterogametic sex, subsequently skewing the offspring sex ratio. They consequently have large impacts on genome evolution, adaptation, and the emergence and maintenance of sexually selected traits. Despite this, our understanding of their molecular basis and consequences for gametogenesis and sex chromosome regulation more broadly has focused on a handful of model organisms, primarily Drosophila and mouse, which are not representative of the broad diversity of reproductive modes and drive systems in nature. Here, we employ single-cell RNA sequencing (scRNA-seq) to investigate a sex-linked meiotic driver in the Malaysian stalk-eyed fly, Teleopsis dalmanni. First, we produce a comprehensive single-cell atlas of the male T. dalmanni gonad and identify major testis cell types. We then provide a comprehensive profile of the cellular and transcriptional landscape of the testis, providing evidence for a lack of complete meiotic sex chromosome inactivation and complex trajectory of dosage compensation. Second, by contrasting single-cell expression data between drive and standard testes, we provide insight into the consequences of a meiotic driver for the transcriptomic landscape of the testis and sex chromosome regulation. Importantly, we show that the presence of a meiotic driver does not perturb fundamental patterns of X-linked regulation. Our results provide insight into how the meiotic driver might bias its transmission to the next generation and highlight genes with perturbed expression as a potential consequence of the disruption of spermatogenesis.

Life-history theory, central to our understanding of diversity in morphology, behaviour, and senescence, describes how traits evolve through the optimisation of trade-offs in investment. Despite considerable study, there is only minimal support for trade-offs within species between the two traits most closely linked to fitness – reproductive effort and survival – questioning the theory’s general validity. We used a meta-analysis to separate the effects of individual quality (positive survival/reproduction correlation) from the costs of reproduction (negative survival/reproduction correlation) using studies of reproductive effort and parental survival in birds. Experimental enlargement of brood size caused reduced parental survival. However, the effect size of brood size manipulation was small and opposite to the effect of phenotypic quality, as we found that individuals that naturally produced larger clutches also survived better. The opposite effects on parental survival in experimental and observational studies of reproductive effort provide the first meta-analytic evidence for theory suggesting that quality differences mask trade-offs. Fitness projections using the overall effect size revealed that reproduction presented negligible costs, except when reproductive effort was forced beyond the maximum level observed within species, to that seen between species. We conclude that there is little support for the most fundamental life-history trade-off, between reproductive effort and survival, operating within a population. We suggest that within species the fitness landscape of the reproduction–survival trade-off is flat until it reaches the boundaries of the between-species fast–slow life-history continuum. Our results provide a quantitative explanation as to why the costs of reproduction are not apparent and why variation in reproductive effort persists within species.

Environmental variation is a key factor shaping microbial communities in wild animals. However, most studies have focussed on separate populations distributed over large spatial scales. How ecological factors shape inter-individual microbiome variation within a single landscape and host population remains poorly understood. Here, we use dense sampling of individuals in a natural, closed population of Seychelles warblers (Acrocephalus sechellensis) on Cousin Island (<0.7 km diameter, 0.34 km2 total area) to determine whether gut microbiome communities exhibit high-resolution spatial variation over fine scales (average territory area is 0.0023 km2). We identified a small but highly significant quadratic relationship between geographic distance and gut microbiome beta diversity across the island. Microbiome composition initially diverged with increasing geographic distance between territories. However, after ca. >300 m, microbiome composition became increasingly similar amongst individuals situated on different sides of the island. This relationship was robust to the effects of host relatedness, age, and sex. Further analysis showed that microbiome composition differed between individuals inhabiting coastal and inland territories. Warblers in coastal territories harboured greater abundances of marine bacteria and lower abundances of anaerobic taxa commonly linked to host metabolic health, suggesting that exposure to different environmental microbes and variation in host condition (which is lower in coastal territories) could drive spatial patterns of gut microbiome variation across the island. This work demonstrates that host-microbe interactions can be labile even at very fine spatial scales. Such variability may have implications for how species respond to anthropogenic disturbance in wild habitats.

There is intraspecific variation in reproduction and survival, which has been hypothesised to be the result of trade-offs in investment. However, we lack compelling evidence that trade- offs drive variation within species, perhaps because genetic trade-offs are masked by environmental variation. We used a long-term dataset of breeding records for a closed population of house sparrows ( Passer domesticus ) and its associated pedigree to separate the genetic and environmental covariance between fecundity and survival. We measured age-specific changes in reproductive outputs and estimated the heritability of both offspring production and survival in multivariate animal models. Our results show no evidence for survival costs to reproductive output. Nor did we find evidence that individuals’ fecundity and survival are correlated either the genetic or permanent environment level. Our findings show no evidence that variation in fecundity is driven by the offspring-production/survival trade-off. Instead, our results show that individuals are only somewhat consistent in their reproductive output, and suggest this is a possible mechanism why selection cannot act on individual quality. ### Competing Interest Statement The authors have declared no competing interest.

Studies on wild animals, mostly undertaken using 16S metabarcoding, have yielded ambigous evidence regarding changes in the gut microbiome (GM) with age and senescence. Furthermore, variation in GM function has rarely been studied in such wild populations, despite GM metabolic characteristics potentially being associated with host senescent declines. Here, we used seven years of longitudinal sampling and shotgun metagenomic sequencing to investigate taxonomic and functional changes in the GM of Seychelles warblers (Acrocephalus sechellensis) with age and senescence. Our results suggest that taxonomic GM species richness declines with age and in the terminal year, with this terminal decline occurring consistently across all ages. Taxonomic and functional GM composition also shifted with host age. However, all the changes we identified occurred linearly with adult age, with little evidence of accelerated change in late life or during their terminal year. Therefore, the results suggest changes that changes in the GM with age are not linked to senescence. Interestingly, we found an increase in the abundance of a group of transposase genes with age, which may accumulate passively or due to increased transposition induced as a result of stressors that arise with age. These findings reveal taxonomic and functional GM changes with age in a wild vertebrate and provide a blueprint for future wild functional GM studies linked to age and senescence.