Search

Summary • Genetic variation was assessed across the UK geographical range of Cirsium acaule and Cirsium heterophyllum. A decline in genetic diversity and increase in population divergence approaching the range edge of these species was predicted based on parallel declines in population density and seed production reported seperately. Patterns were compared with UK populations of the widespread Cirsium arvense. • Populations were sampled along a latitudinal transect in the UK and genetic variation assessed using microsatellite markers. • Cirsium acaule shows strong isolation by distance, a significant decline in diversity and an increase in divergence among range-edge populations. Geographical structure is also evident in C. arvense, whereas no such patterns are seen in C. heterophyllum. • There is a major disparity between patterns of genetic variation in C. acaule and C. heterophyllum despite very similar patterns in seed production and population isolation in these species. This suggests it may be misleading to make assumptions about the geographical structure of genetic variation within species based solely on the present-day reproduction and distribution of populations.

This protocol describes a procedure for sequencing the Spike gene of SARS-CoV-2 using short amplicons (146-208bp) with Oxford Nanopore technology (R9.4.1 MinION/GridION Flow Cell). The method has proved to be successful with both clinical RNA samples and degraded wastewater samples. The primers are unique to the SubARTIC method. The library prep procedure has been heavily adapted from the ncov-2019 sequencing v3 (ARTIC) protocol by Josh Quick (https://www.protocols.io/view/ncov-2019-sequencing-protocol-v3-locost-bh42j8ye) and the "low cost" method from the NEOF Liverpool Illumina ARTIC protocol. See this link for the version of the protocol using Illumina sequencing (https://www.protocols.io/view/sub-artic-illumina-sars-cov-2-spike-sequencing-pro-btpjnmkn).

This protocol describes a procedure for sequencing the Spike region of SARS-CoV-2 using short amplicons (146-208bp). The method has proved to successful with both clinical RNA samples and degraded wastewater samples. The primers are unique to this method. The library prep procedure has been heavily adapted from the ncov-2019 sequencing v3 (ARTIC) protocol by Josh Quick (https://www.protocols.io/view/ncov-2019-sequencing-protocol-v3-locost-bh42j8ye) and the "low cost" method from the NEOF Liverpool Illumina ARTIC protocol.

Offspring of older parents in many species display decreased longevity, a faster ageing rate and lower fecundity than offspring born to younger parents. Biomarkers, such as telomeres, that tend to shorten as individual age, may provide insight into the mechanisms of parental age effects. Parental age could determine telomere length either through inheritance of shortened telomeres or through indirect effects, such as variation in parental care with parent ages, which in turn might lead to variation in offspring telomere length. There is no current consensus as to the heritability of telomere length, and the direction and extent of parental age effects however. To address this, here we experimentally investigate how parental age is associated with telomere length at two time points in early life in a captive population of house sparrows (Passer domesticus). We experimentally separated parental age from sex effects by allowing the parent birds to only mate with young, or old partners. We found that telomere length of the offspring increased between the age of 0.5 and 3 months at the group and individual level, which has been reported previously predominantly in non-avian taxa. We further show that older fathers produced daughters with a greater early-life increase in telomere length, supporting sex-specific inheritance, and or sex-specific non-genetic effects. Overall, our results highlight the need for more studies testing early-life telomere dynamics and sex-specific heritability of telomere length.

Most studies on sexual size dimorphism address proximate and functional questions related to adults, but sexual size dimorphism usually develops during ontogeny and developmental trajectories of sexual size dimorphism are poorly understood. We studied three bird species with variation in adult sexual size dimorphism: black coucals (females 69% heavier than males), white‐browed coucals (females 13% heavier than males) and ruffs (males 70% heavier than females). Using a flexible Bayesian generalized additive model framework (GAMM), we examined when and how sexual size dimorphism developed in body mass, tarsus length and bill length from hatching until fledging. In ruffs, we additionally examined the development of intrasexual size variation among three morphs (Independents, Satellites and Faeders), which creates another level of variation in adult size of males and females. We found that 27–100% of the adult inter‐ and intrasexual size variation developed until fledging although none of the species completed growth during the observational period. In general, the larger sex/morph grew more quickly and reached its maximal absolute growth rate later than the smaller sex/morph. However, when the daily increase in body mass was modelled as a proportion, growth patterns were synchronized between and within sexes. Growth broadly followed sigmoidal asymptotic models, however only with the flexible GAMM approach, residual distributions were homogeneous over the entire observation periods. These results provide a platform for future studies to relate variation in growth to selective pressures and proximate mechanisms in these three species, and they highlight the advantage of using a flexible model approach for examining growth variation during ontogeny.

Delineating conservation units is a complex and often controversial process that is particularly challenging for highly vagile species. Here, we reassess population genetic structure and identify those populations of highest conservation value in the threatened snowy plover (Charadrius nivosus,Cassin, 1858), a partial migrant shorebird endemic to the Americas. We use four categories of genetic data—mitochondrial DNA (mtDNA), microsatellites, Z-linked and autosomal single nucleotide polymorphisms (SNPs)—to: (1) assess subspecies delineation and examine population structure (2) compare the sensitivity of the different types of genetic data to detect spatial genetic patterns, and (3) reconstruct demographic history of the populations analysed. Delineation of two traditionally recognised subspecies was broadly supported by all data. In addition, microsatellite and SNPs but not mtDNA supported the recognition of Caribbean snowy plovers (C. n. tenuirostris) and Floridian populations (easternC. n. nivosus) as distinct genetic lineage and deme, respectively. Low migration rates estimated from autosomal SNPs (m m = 0.26) from the western into the easternnivosusdeme. Within westernnivosus,we found no genetic differentiation between coastal Pacific and inland populations. The correlation between geographic and genetic distances was weak but significant for all genetic data sets. All demes showed signatures of bottlenecks occurring during the past 1000 years. We conclude that at least four snowy plover conservation units are warranted: in addition to subspeciesnivosusandoccidentalis,a third unit comprises the Caribbeantenuirostrislineage and a fourth unit the distinct easternnivosusdeme.

The research examines the growth of home ownership and its tenure dominance in Australia after the Second World War, together with its fading, most notably for younger households (ages 25–44) over the last four decades.

The longitudinal study of populations is a core tool for understanding ecological and evolutionary processes. Long-term studies typically collect samples repeatedly over individual lifetimes and across generations. These samples are then analysed in batches (e.g. qPCR-plates) and clusters (i.e. group of batches) over time in the laboratory. However, these analyses are constrained by cross-classified data structures introduced biologically or through experimental design. The separation of biological variation from the confounding among-batch and among-cluster variation is crucial, yet often ignored. The commonly used approaches to structuring samples for analysis, sequential and randomisation, generate bias due to the non-independence between time of collection and the batch and cluster they are analysed in. We propose a new sample structuring strategy, called slicing, designed to separate confounding among-batch and among-cluster variation from biological variation. Through simulations we tested the statistical power and precision to detect within-individual, between-individual, year and cohort effects of this novel approach. Our slicing approach, whereby recently and previously collected samples are sequentially analysed in clusters together, enables the statistical separation of collection time and cluster effects by bridging clusters together, for which we provide a case study. Our simulations show, with reasonable slicing width and angle, similar precision and similar or greater statistical power to detect year, cohort, within- and between-individual effects when samples are sliced across batches, compared with strategies that aggregate longitudinal samples or use randomised allocation. While the best approach to analysing long-term datasets depends on the structure of the data and questions of interest, it is vital to account for confounding among-cluster and batch variation. Our slicing approach is simple to apply and creates the necessary statistical independence of batch and cluster from environmental or biological variables of interest. Crucially, it allows sequential analysis of samples and flexible inclusion of current data in later analyses without completely confounding the analysis. Our approach maximises the scientific value of every sample, as each will optimally contribute to unbiased statistical inference from the data. Slicing thereby maximises the power of growing biobanks to address important ecological, epidemiological and evolutionary questions.

The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and eco-logical processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change)., To solve data integration issues and enable a new scale of ecological and evolution-ary research based on long-term studies of birds, we have created the SPI-Birds Network and Database (www.spibirds.org)—a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2,000 cumulative years, and counting., SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collab-oration and synthesis. We provide community-derived data and meta-data stand-ards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata lan-guages (e.g. ecological meta-data language)., The encouraging community involvement stems from SPI-Bird's decentralized ap-proach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demogra-phy, etc.) will aid much-needed large-scale ecological data integration., The SPI-Birds have been supported by an NWO personal grant (grant number 016.Veni.181.054) to A.C., and a Research Council of Norway grant: 223257 (SFF-III) and 267511 (EVOCLIM).

Behavioral traits are considered animal personality traits when individuals differ consistently in their expression across time and across context. Here, we test this idea on three metrics derived from social interaction networks (strength, betweenness, closeness). Using experimental data from house sparrows in captive populations, and observational data from house sparrows in a wild population, we show that all three metrics consistently exhibit repeatability across both study populations and two methods of recording interactions. The highest repeatability values were estimated in male-only captive groups, while repeatabilities estimated in single-sex networks subsetted from mixed-sex groups showed no sex-specificity. We also show that changes in social group composition led to a decrease in repeatability for up to six months. This work provides substantial and generalizable support for the notion that social network node-based metrics can be considered animal personalities. Our work suggests that social network traits may be heritable and thus could be selected for. This article is protected by copyright. All rights reserved.

1. In many cooperatively breeding animals, a combination of ecological constraints and benefits of philopatry favours offspring taking a subordinate position on the natal territory instead of dispersing to breed independently. However, in many species individuals disperse to a subordinate position in a non-natal group ("subordinate between-group" dispersal), despite losing the kin-selected and nepotistic benefits of remaining in the natal group. It is unclear which social, genetic and ecological factors drive between-group dispersal. 2. We aim to elucidate the adaptive significance of subordinate between-group dispersal by examining which factors promote such dispersal, whether subordinates gain improved ecological and social conditions by joining a non-natal group, and whether between-group dispersal results in increased lifetime reproductive success and survival. 3. Using a long-term dataset on the cooperatively-breeding Seychelles warbler (Acrocephalus sechellensis), we investigated how a suite of proximate factors (food availability, group composition, age and sex of focal individuals, population density) promote subordinate between-group dispersal by comparing such dispersers with subordinates that dispersed to a dominant position or became floaters. We then analysed whether subordinates that moved to a dominant or non-natal subordinate position, or became floaters, gained improved conditions relative to the natal territory, and compared fitness components between the three dispersal strategies. 4. We show that individuals that joined another group as non-natal subordinates were mainly female and that, similar to floating, between-group dispersal was associated with social and demographic factors that constrained dispersal to an independent breeding position. Between-group dispersal was not driven by improved ecological or social conditions in the new territory and did not result in higher survival. Instead, between-group dispersing females often became co-breeders, obtaining maternity in the new territory, and were likely to inherit the territory in the future, leading to higher lifetime reproductive success compared to females that floated. Males never reproduced as subordinates, which may be one explanation why subordinate between-group dispersal by males is rare. 5. Our results suggest that subordinate between-group dispersal is used by females to obtain reproductive benefits when options to disperse to an independent breeding position are limited. This provides important insight into the additional strategies that individuals can use to obtain reproductive benefits.

SARS-CoV-2 and the resulting COVID-19 pandemic represents one of the greatest recent threats to human health, wellbeing and economic growth. Wastewater-based epidemiology (WBE) of human viruses can be a useful tool for population-scale monitoring of SARS-CoV-2 prevalence and epidemiology to help prevent further spread of the disease, particularly within urban centres. Here we present a longitudinal analysis (March-July, 2020) of SARS-CoV-2 RNA prevalence in sewage across six major urban centres in the UK (total population equivalent 3 million) by q(RT-)PCR and viral genome sequencing. Our results demonstrate that levels of SARS-CoV-2 RNA generally correlated with the abundance of clinical cases recorded within the community in large urban centres, with a marked decline in SARS-CoV-2 RNA abundance following the implementation of lockdown measures. The strength of this association was weaker in areas with lower confirmed COVID-19 case numbers. Further sequencing analysis of SARS-CoV-2 from wastewater suggested that multiple genetically distinct clusters were co-circulating in the local populations covered by our sample sites, and that the genetic variants observed in wastewater reflected similar SNPs observed in contemporaneous samples from cases tested in clinical diagnostic laboratories. We demonstrate how WBE can be used for both community-level detection and tracking of SARS-CoV-2 and other virus’ prevalence, and can inform public health policy decisions. Although, greater understanding of the factors that affect SARS-CoV-2 RNA concentration in wastewater are needed for the full integration of WBE data into outbreak surveillance. In conclusion, our results lend support to the use of routine WBE for monitoring of SARS-CoV-2 and other human pathogenic viruses circulating in the population and assessment of the effectiveness of disease control measures., Graphical abstract Image, graphical abstract

In most bird species, dispersal distance from the natal territory to a breeding territory is greater for females than for males. Two main hypotheses have been proposed to explain sex-biased dispersal: 1) it serves as an inbreeding-avoidance mechanism or 2) it is linked to a sex difference in resource-holding potential and territory establishment. Additionally, in species where individuals delay dispersal and become subordinates in a natal territory, differences in benefits of philopatry (e.g. territory inheritance, own reproduction) may also affect sex-biased dispersal. We show that in the group-living Seychelles warbler, Acrocephalus sechellensis, females disperse further to obtain a breeding position than males do. However, we found no evidence that female-biased dispersal distance can be explained by the above-mentioned hypotheses: further dispersal does not lead to less-related partners, both sexes defend and can inherit a territory, and subordinate females are more likely to obtain some reproduction than subordinate males. Instead, we provide evidence for a little-explored hypothesis based on sex differences in dispersal costs: namely that extra-territorial forays, pursued to search for limited vacancies, are more costly for males in terms of increased mortality, although the exact mechanism for this is unclear. In line with differential dispersal costs, males foray less far than females and often wait for local dispersal opportunities, ultimately resulting in a shorter average dispersal distance. Our results may help future studies in explaining sex-biased dispersal in social and perhaps also non-social species, and we suggest some mechanisms that may explain why sex-biased dispersal differs between species.

Sperm competition is an important selective force in many organisms. As a result, sperm have evolved to be among the most diverse cells in the animal kingdom. However, the relationship between sperm morphology, sperm motility and fertilization success is only partially understood. The extent to which between-male variation is heritable is largely unknown, and remarkably few studies have investigated the genetic architecture of sperm traits, especially sperm morphology. Here we use high-density genotyping and gene expression profiling to explore the considerable sperm trait variation that exists in the zebra finch Taeniopygia guttata. We show that nearly all of the genetic variation in sperm morphology is caused by an inversion polymorphism on the Z chromosome acting as a ‘supergene’. These results provide a striking example of two evolutionary genetic predictions. First, that in species where females are the heterogametic sex, genetic variation affecting sexually dimorphic traits will accumulate on the Z chromosome. Second, recombination suppression at the inversion allows beneficial dominant alleles to become fixed on whichever haplotype they first arise, without being exchanged onto other haplotypes. Finally, we show that the inversion polymorphism will be stably maintained by heterozygote advantage, because heterozygous males have the fastest and most successful sperm. Sperm morphology is remarkably variable yet its genetic architecture is poorly known. Now, sperm morphology variation in zebra finches is shown to be largely explained by an inversion polymorphism on the Z chromosome acting as a supergene.

Speciation typically involves a stage in which species can still exchange genetic material. Interspecific gene flow is facilitated by the hybrid zones that such species establish upon secondary contact. If one member of a hybridizing species pair displaces the other, their hybrid zone would move across the landscape. Although theory predicts that moving hybrid zones quickly stagnate, hybrid zones tracked over one or a few decades do not always follow such a limitation. This suggests that hybrid zones have the potential to traverse considerable distances over extended periods of time. When hybrid zones move, introgression is predicted to result in biased gene flow of selectively neutral alleles, from the receding species into the advancing species. We test for such a genomic footprint of hybrid zone movement in a pair of crested newt species (genus Triturus) for which we have a priori support for westward hybrid zone movement. We perform a multilocus phylogeographical survey and conduct Bayesian clustering analysis, estimation of ancestry and heterozygosity, and geographical cline analysis. In a 600 km wide area east of the present day hybrid zone a genomic footprint constitutes empirical evidence consistent with westward hybrid zone movement. The crested newt case suggests that hybrid zone movement can occur over an extensive span of time and space. Inferring hybrid zone movement provides fundamental insight into historical biogeography and the speciation process, and we anticipate that hybrid zones will prove to be far more mobile than currently appreciated.

We assembled the great snipe blood transcriptome using data from fourteen lekking males, in order to de novo identify candidate genes related to sexual selection, and determined the expression profiles in relation to mating success. The three most highly transcribed genes were encoding different haemoglobin subunits. All tended to be overexpressed in males with high mating success. We also called single nucleotide polymorphisms (SNPs) from the transcriptome data and found considerable genetic variation for many genes expressed during lekking. Among these, we identified 14 polymorphic candidate SNPs that had a significant genotypic association with mating success (number of females mated with) and/or mating status (mated or not). Four of the candidate SNPs were found in HBAA (encoding the haemoglobin α-chain). Heterozygotes for one of these and one SNP in the gene PABPC1 appeared to enjoy higher mating success compared to males homozygous for either of the alleles. In a larger data set of individuals, we genotyped 38 of the identified SNPs but found low support for consistent selection as only one of the zygosities of previously identified candidate SNPs and none of their genotypes were associated with mating status. However, candidate SNPs generally showed lower levels of spatial genetic structure compared to noncandidate markers. We also scored the prevalence of avian malaria in a subsample of birds. Males infected with avian malaria parasites had lower mating success in the year of sampling than noninfected males. Parasite infection and its interaction with specific genes may thus affect performance on the lek.

In species with biparental care, behavioural coordination in the provisioning of the progeny is hypothesized to increase the number of offspring that survive to independence. Coordination is often quantified by two metrics, alternation and synchrony. Turn-taking (leading to an alternation pattern) can result when one parent’s investment strategy is based on the investment of its partner (i.e. conditional cooperation). This should increase the overall provisioning rate and improve offspring body condition. Synchrony might equalise food delivery among offspring and therefore decrease the variance in offspring body condition within the brood. Overall, offspring survival could be increased by parental coordination. Finally, pairs with low coordination, and with potentially lower reproductive success, are expected to be more likely to divorce. In this study, we use a dataset on 473 pairs of house sparrows in a natural insular population to test these hypotheses. We found no effect of the pair’s apparent coordination on offspring condition, offspring survival, or divorce rate, questioning the adaptive significance of this behaviour. We argue that, in this species, the detection of a higher frequency of alternation and synchrony, when compared to chance expectation, might be induced by the environment, rather than result from an emergent pair behaviour selected for fitness benefits.

The role of sexual selection in natural populations has long been the subject of debate in evolutionary biology. Ornaments are sexually selected traits, which means they should vary within a population, have a genetic basis, and be associated with fitness. Despite evidence of ornaments meeting these criteria, evolutionary responses to sexual selection are rare in nature. This study focuses on two ornaments in a population of house sparrows; the plumage badge has been well-studied but remains poorly understood and the mask has been largely neglected in the literature. Using quantitative genetic techniques, we estimate the heritability of both traits and test for age-dependency of the heritability estimates. We also estimate the strength and direction of any selection acting upon the traits. We found that both ornaments have low, significant heritability, which does not vary with age. Selection only occurs in a small number of years, although when it does it is positive in both ornaments. We also found that early social environment plays a role in badge size variation. The results of this study suggest that an evolutionary response in the ornaments of this population is unlikely, but we highlight the importance of long-term research to improve our understanding of evolution in natural populations. Studies like these will add to our understanding of sexual selection, the causes of trait variation and the evolutionary potential of traits, which could help us to predict how populations will evolve.

Offspring from elderly parents often have lower survival due to parental senescence. In cooperatively breeding species, where offspring care is shared between breeders and helpers, the alloparental care provided by helpers is predicted to mitigate the impact of parental senescence on offspring provisioning and, subsequently, offspring survival. We test this prediction using data from a long-term study on cooperatively breeding Seychelles warblers (Acrocephalus sechellensis). We find that the nestling provisioning rate of female breeders declines with their age. Further, the total brood provisioning rate and the first-year survival probability of offspring decline progressively with age of the female breeder, but these declines are mitigated when helpers are present. This effect does not arise because individual helpers provide more care in response to the lower provisioning of older dominant females, but because older female breeders have recruited more helpers, thereby receiving more overall care for their brood. We do not find such effects for male breeders. These results indicate that alloparental care can alleviate the fitness costs of senescence for breeders, which suggests an interplay between age and cooperative breeding.

Behavioural traits are considered animal personality traits when individuals differ consistently in trait expression across time and context. Previous research has primarily focused on the shy-bold continuum, with research on sociability as potential proxy for animal personality traits only recently being considered. Here, we test the hypothesis that three node-based metrics derived from social association networks between individuals (strength, betweenness, closeness) can be considered proxies for animal personality traits in a passerine bird. Using experimental data from house sparrows in captive populations, and observational data from house sparrows in a wild population, we show that all three traits exhibit repeatability. The highest repeatability values were estimated in male-only captive groups, while repeatabilities estimated in single-sex networks subsets from mixed-sex groups showed no sex-specificity. We also show that changes in social group composition led to a decrease in repeatability for up to six months. Concluding, this work provides substantial and generalizable support for the notion that social network node-based traits map animal personalities.

Extra-pair paternity (EPP) is often linked to male age in socially monogamous vertebrates; that is, older males are more likely to gain EPP and less likely to be cuckolded. However, whether this occurs because males improve at gaining paternity as they grow older, or because “higher quality” males that live longer are preferred by females, has rarely been tested, despite being central to our understanding of the evolutionary drivers of female infidelity. Moreover, how extra-pair reproduction changes with age within females has received even less attention. Using 18 years of longitudinal data from an individually marked population of Seychelles warblers (Acrocephalus sechellensis), we found considerable within-individual changes in extra-pair reproduction in both sexes: an early-life increase and a late-life decline. Furthermore, males were cuckolded less as they aged. Our results indicate that in this species age-related patterns of extra-pair reproduction are determined by within-individual changes with age, rather than differences among individuals in longevity. These results challenge the hypothesis—based on longevity reflecting intrinsic quality—that the association between male age and EPP is due to females seeking high-quality paternal genes for offspring. Importantly, EPP accounted for up to half of male reproductive success, emphasizing the male fitness benefits of this reproductive strategy. Finally, the occurrence of post-peak declines in extra-pair reproduction provides explicit evidence of senescence in infidelity in both males and females.

Evolutionary theory predicts that females seek extra‐pair fertilizations from high‐quality males. In socially monogamous bird species, it is often old males that are most successful in extra‐pair fertilizations. Adaptive models of female extra‐pair mate choice suggest that old males may produce offspring of higher genetic quality than young males because they have proven their survivability. However, old males are also more likely to show signs of reproductive senescence, such as reduced sperm quality. To better understand why old males account for a disproportionally large number of extra‐pair offspring and what the consequences of mating with old males are, we compared several sperm traits of both captive and wild house sparrows, Passer domesticus. Sperm morphological traits and cloacal protuberance volume (a proxy for sperm load) of old and young males did not differ substantially. However, old males delivered almost three times more sperm to the female's egg than young males. We discuss the possibility of a post‐copulatory advantage for old over young males and the consequences for females mated with old males., We found that old male house sparrows delivered almost three times more sperm to a female's egg than young males. Our result supports the observation that old males robustly gain more extra‐pair paternity, and we discuss the reproductive consequences for females mated with old males.

Theory predicts that individuals behave altruistically towards their relatives. Hence, some form of kin recognition is useful for individuals to optimize their behavior. In species that display bi-parental care and are subject to extra-pair matings, kin recognition theoretically can allow cuckolded fathers to reduce their parental investment, and thus optimize their fitness. Whether this is possible remains unclear in birds. This study investigates whether males provide differential parental care depending on relatedness, as a proxy to recognizing chicks in their nest as kin or not. We cross-fostered House sparrow (Passer domesticus) chicks after hatching, and then expected that fathers would show a decrease in their parental efforts when tending to a clutch of unrelated offspring. House sparrow males are able to adjust their parental care to the identity of their partner, making them an ideal study species. However, there was no significant effect of relatedness on provisioning rates. This suggests that sparrows may not be capable of kin recognition, or at least do not display kin discrimination despite its apparent evolutionary advantage.

The social environment can influence phenotypes through indirect genetic effects (IGEs), whereby genetic variance among interacting individuals explains some of the phenotypic variance. Empirical studies of wild populations often ignore IGEs especially among unrelated individuals, probably due to data limitations. This is problematic because IGEs can crucially affect estimates of heritable variation and subsequently influence the predicted evolutionary change. We here present a quantitative genetic analysis of biparental care in a natural bird population using a genetic pedigree. For both sexes, the conventionally calculated repeatability (15% in the female trait and 19% in the male trait) was lower than the total heritable variation including IGEs (24% in the female trait, and 25% in the male trait). These estimates of total heritable variation was also larger compared to conventionally calculated heritability (13% in both sexes), suggesting that parental care can evolve through social selection. Furthermore, we detected statistically significant genetic covariance between direct genetic effects, and between IGEs and direct genetic effects. Our work showcases how IGEs can represent substantial and important hidden heritable variance and highlights the importance of considering IGEs for theoretical models of parental care for ecology and evolution.

Finding a high quality territory is essential for many animals to reproduce successfully. Despite its importance for fitness, we know little about the process of territory prospecting in wild birds, and whether individual traits and behaviours, such as personality, co-vary with territory prospecting. Here, we use long-term data from a wild, insular house sparrow Passer domesticus population to test three hypotheses about territory fidelity and prospecting: (1) House sparrows show high territory fidelity between years and also during winter. (2) Individuals will prospect for a breeding territory during their first winter whereas older, more experienced individuals will keep a territory from previous years and will, therefore, show no or reduced winter territory prospecting. (3) More active behavioural types will prospect more than less active behavioural types. We use data from four winters from automatically, daily recorded nest-box visits of 188 birds of known age. The number of nest-boxes that each individual visited within each winter was used as a proxy of winter territory prospecting. We show that house sparrows visit multiple nest-boxes during their first winter, whereas older individuals keep territories year-round and, potentially because of this, indeed show reduced winter territory prospecting. Activity was not associated with the number of nest-boxes visited. Further research is needed to investigate whether time of territory and mate acquisition differs among individuals and the possible effect on lifetime fitness.

This study identified five Australian housing markets that could be made more efficient using online technology to match highly specific ‘buyers’ and ‘sellers’. The five markets considered are: swaps in public housing; disability accessible housing; low-cost private rental housing brokerage; apartment presales for low/mid income earners; and precinct-level urban redevelopment. The research also proposed solutions to how the matching markets could best operate.

Why so much variation in extra-pair parentage occurs within and among populations remains unclear. Often the fitness costs and benefits of extra-pair parentage are hypothesised to explain its occurrence; therefore, linking extra-pair parentage with traits such as personality (behavioural traits that can be heritable and affect reproductive behaviour) may help our understanding. Here, we investigate whether reproductive outcomes and success are associated with exploratory behaviour in a natural population of cooperatively breeding Seychelles warblers (Acrocephalus sechellensis) on Cousin Island. Exploratory behaviour correlates positively with traits such as risk-taking behaviour and activity in other wild bird species and might promote extra-pair mating by increasing the rate at which potential extra-pair partners are encountered. We therefore predicted that fast-exploring individuals would have more extra-pair offspring. There is also a potential trade-off between pursuing extra-pair parentage and mate guarding in males. We therefore also predicted that fast-exploring males would be more likely to pursue extra-pair parentage and that this would increase the propensity of their mate to gain extra-pair parentage. We found that neither the total number of offspring nor the number of extra-pair offspring were associated with a male’s or female’s exploratory behaviour. However, there was a small but significant propensity for females to have extra-pair fertilisations in pairs that were behaviourally disassortative. Overall, we conclude that, due to the small effect size, the association between exploratory behaviour and extra-pair paternity is unlikely to be biologically relevant. Significance statement True genetic monogamy is rare, even in socially monogamous systems, and multiple factors, such as behaviour, social structure, morphology and physiology, determined by the biological system can cause variation in extra-pair parentage (EPP). Therefore, investigating the inherent differences in these factors among individuals could be informative. We investigated whether reproductive outcomes/success are associated with differences in the propensity to explore novel environments/objects in a promiscuous, island-dwelling cooperatively breeding bird, the Seychelles warbler. Our results showed that exploratory behaviour was not associated with the number of offspring produced by an individual, and thus the long-term fitness consequences of different exploratory tendencies did not differ. We also found that the propensity to engage in EPP in females was higher in dissimilar behavioural pairs, but due to the small effect size, we hesitate to conclude that there are personality-dependent mating outcomes in the population. Electronic supplementary material The online version of this article (10.1007/s00265-018-2448-z) contains supplementary material, which is available to authorized users.

Movement of individuals, or their genes, can influence eco-evolutionary processes in structured populations. We have limited understanding of the extent to which spatial behavior varies among groups and individuals within populations. Here, we use genetic pedigree reconstruction in a long-term study of European badgers (Meles meles) to characterize the extent of extra-group paternity, occurring as a consequence of breeding excursions, and to test hypothesized drivers of variation at multiple levels. We jointly estimate parentage and paternity distance (PD; distance between a cub’s natal and its father’s social group), and test whether population density and sex ratio influence mean annual PD. We also model cub-level PD and extra-group paternity (EGP) to test for variation among social groups and parental individuals. Mean PD varied among years but was not explained by population density or sex ratio. However, cub-level analysis shows strong effects of social group, and parental identities, with some parental individuals being consistently more likely to produce cubs with extra-group partners. Group effects were partially explained by local sex ratio. There was also a strong negative correlation between maternal and paternal social group effects on cub paternity distance, indicating source-sink dynamics. Our analyses of paternity distance and EGP indicate variation in extra-group mating at multiple levels—among years, social groups and individuals. The latter in particular is a phenomenon seldom documented and suggests that gene flow among groups may be disproportionately mediated by a nonrandom subset of adults, emphasizing the importance of the individual in driving eco-evolutionary dynamics., Variation in breeding behavior exists at multiple levels. Based on indirect observations from a genetic pedigree, we found that individual badgers show consistent differences in their tendency to mate with the members of other groups and the distance they travelled to breed. Social groups also differ from each other, with some acting as sinks, both attracting and retaining genes. Average distance travelled also varied annually, but not because of changes in population density or sex ratio.

Understanding how species have replaced each other in the past is important to predicting future species turnover. While past species replacement is difficult to detect after the fact, the process may be inferred from present-day distribution patterns. Species with abutting ranges sometimes show a characteristic distribution pattern, where a section of one species range is enveloped by that of the other. Such an enclave could indicate past species replacement: when a species is partly supplanted by a competitor, but a population endures locally while the invading species moves around and past it, an enclave forms. If the two species hybridize and backcross, the receding species is predicted to leave genetic traces within the expanding one under a scenario of species replacement. By screening dozens of genes in hybridizing crested newts, we uncover genetic remnants of the ancestral species, now inhabiting an enclave, in the range of the surrounding invading species. This independent genetic evidence supports the past distribution dynamics we predicted from the enclave. We suggest that enclaves provide a valuable tool in understanding historical species replacement, which is important because a major conservation concern arising from anthropogenic climate change is increased species replacement in the future.

The Gouldian finch (Erythrura gouldiae) went through a huge population decline in the last century. To address questions on conservation genetics, ecology and evolutionary biology we characterised 120 microsatellite markers (30 Z-linked) in this species using four methods: designing primers from the reference genome of a confamilial species (the zebra finch Taeniopygia guttata, n = 15); Sanger (n = 47) and 454-sequencing (n = 5) of microsatellite-enriched Gouldian finch libraries; and characterisation of cross-species markers (n = 53). We also identified 1992 primer-designable microsatellites for this species.

Lay Summary We manipulated factors that normally constrain the social mate choice of female Seychelles warblers to test if, when less constrained, these females chose partners based on variation at specific immune genes that have been linked to mate choice in other species. We found that older and more generally genetically diverse males were more likely to end up paired with females, but contrary to our predictions, variation at the immune genes did not appear to influence social pairing., The prevalence and significance of precopulatory mate choice remains keenly debated. The major histocompatibility complex (MHC) plays a key role in vertebrate adaptive immunity, and variation at the MHC influences individual survival. Although MHC-dependent mate choice has been documented in certain species, many other studies find no such pattern. This may be, at least in part, because in natural systems constraints may reduce the choices available to individuals and prevent full expression of underlying preferences. We used translocations to previously unoccupied islands to experimentally reduce constraints on female social mate choice in the Seychelles warbler (Acrocephalus sechellensis), a species in which patterns of MHC-dependent extrapair paternity (EPP), but not social mate choice, have been observed. We find no evidence of MHC-dependent social mate choice in the new populations. Instead, we find that older males and males with more microsatellite heterozygosity are more likely to have successfully paired. Our data cannot resolve whether these patterns in pairing were due to male–male competition or female choice. However, our research does suggest that female Seychelles warblers do not choose social mates using MHC class I to increase fitness. It may also indicate that the MHC-dependent EPP observed in the source population is probably due to mechanisms other than female precopulatory mate choice based on MHC cues.

Understanding the distribution of genetic diversity in exploited species is fundamental to successful conservation. Genetic structure and the degree of gene flow among populations must be assessed to design appropriate strategies to prevent the loss of distinct populations. The cephalopod Nautilus pompilius is fished unsustainably in the Philippines for the ornamental shell trade and has limited legislative protection, despite the species' recent dramatic decline in the region. Here, we use 14 microsatellite markers to evaluate the population structure of N. pompilius around Australia and the Philippines. Despite their relative geographical proximity, Great Barrier Reef individuals are genetically isolated from Osprey Reef and Shark Reef in the Coral Sea (FST = 0.312, 0.229, respectively). Conversely, despite the larger geographical distances between the Philippines and west Australian reefs, samples display a small degree of genetic structure (FST = 0.015). Demographic scenarios modelled using approximate Bayesian computation analysis indicate that this limited divergence is not due to contemporary gene flow between the Philippines and west Australia. Instead, present-day genetic similarity can be explained by very limited genetic drift that has occurred due to large average effective population sizes that persisted at both locations following their separation. The lack of connectivity among populations suggests that immigrants from west Australia would not facilitate natural recolonization if Philippine populations were fished to extinction. These data help to rectify the paucity of information on the species' biology currently inhibiting their conservation classification. Understanding population structure can allow us to facilitate sustainable harvesting, thereby preserving the diversity of genetically distinct stocks.

The major histocompatibility complex (MHC) plays a crucial role in the immune system, and in some species, it is a target by which individuals choose mates to optimize the fitness of their offspring, potentially mediated by olfactory cues. Under the genetic compatibility hypothesis, individuals are predicted to choose mates with compatible MHC alleles, to increase the fitness of their offspring. Studies of MHC-based mate choice in wild mammals are under-represented currently, and few investigate more than one class of MHC genes. We investigated mate choice based on the compatibility of MHC class I and II genes in a wild population of European badgers (Meles meles). We also investigated mate choice based on microsatellite-derived pairwise relatedness, to attempt to distinguish MHC-specific effects from genomewide effects. We found MHC-assortative mating, based on MHC class II, but not class I genes. Parent pairs had smaller MHC class II DRB amino acid distances and smaller functional distances than expected from random pairings. When we separated the analyses into within-group and neighbouring-group parent pairs, only neighbouring-group pairs showed MHC-assortative mating, due to similarity at MHC class II loci. Our randomizations showed no evidence of genomewide-based inbreeding, based on 35 microsatellite loci; MHC class II similarity was therefore the apparent target of mate choice. We propose that MHC-assortative mate choice may be a local adaptation to endemic pathogens, and this assortative mate choice may have contributed to the low MHC genetic diversity in this population.

Extra-pair paternity is the result of copulation between a female and a male other than her social partner. In socially monogamous birds, old males are most likely to sire extra-pair offspring. The male manipulation and female choice hypotheses predict that age-specific male mating behaviour could explain this old-over-young male advantage. These hypotheses have been difficult to test because copulations and the individuals involved are hard to observe. Here, we studied the mating behaviour and pairing contexts of captive house sparrows, Passer domesticus. Our set-up mimicked the complex social environment experienced by wild house sparrows. We found that middle-aged males, which would be considered old in natural populations, gained most extra-pair paternity. However, both, female solicitation behaviour and subsequent extra-pair matings were not associated with male age. Further, copulations were more likely when solicited by females than when initiated by males (i.e. unsolicited copulations). Male initiated within-pair copulations were more common than male initiated extra-pair copulations. To conclude, our results did not support either hypothesis regarding age-specific male mating behaviour. Instead, female choice, independent of male age, governed copulation success, especially in an extra-pair context. Post-copulatory mechanisms might determine why older males sire more extra-pair offspring.

Background High-throughput sequencing enables high-resolution genotyping of extremely duplicated genes. 454 amplicon sequencing (454) has become the standard technique for genotyping the major histocompatibility complex (MHC) genes in non-model organisms. However, illumina MiSeq amplicon sequencing (MiSeq), which offers a much higher read depth, is now superseding 454. The aim of this study was to quantitatively and qualitatively evaluate the performance of MiSeq in relation to 454 for genotyping MHC class I alleles using a house sparrow (Passer domesticus) dataset with pedigree information. House sparrows provide a good study system for this comparison as their MHC class I genes have been studied previously and, consequently, we had prior expectations concerning the number of alleles per individual. Results We found that 454 and MiSeq performed equally well in genotyping amplicons with low diversity, i.e. amplicons from individuals that had fewer than 6 alleles. Although there was a higher rate of failure in the 454 dataset in resolving amplicons with higher diversity (6–9 alleles), the same genotypes were identified by both 454 and MiSeq in 98% of cases. Conclusions We conclude that low diversity amplicons are equally well genotyped using either 454 or MiSeq, but the higher coverage afforded by MiSeq can lead to this approach outperforming 454 in amplicons with higher diversity. Electronic supplementary material The online version of this article (doi:10.1186/s13104-017-2654-1) contains supplementary material, which is available to authorized users.

Inbreeding results in more homozygous offspring that should suffer reduced fitness, but it can be difficult to quantify these costs for several reasons. First, inbreeding depression may vary with ecological or physiological stress and only be detectable over long time periods. Second, parental homozygosity may indirectly affect offspring fitness, thus confounding analyses that consider offspring homozygosity alone. Finally, measurement of inbreeding coefficients, survival and reproductive success may often be too crude to detect inbreeding costs in wild populations. Telomere length provides a more precise measure of somatic costs, predicts survival in many species and should reflect differences in somatic condition that result from varying ability to cope with environmental stressors. We studied relative telomere length in a wild population of Seychelles warblers (Acrocephalus sechellensis) to assess the lifelong relationship between individual homozygosity, which reflects genome‐wide inbreeding in this species, and telomere length. In juveniles, individual homozygosity was negatively associated with telomere length in poor seasons. In adults, individual homozygosity was consistently negatively related to telomere length, suggesting the accumulation of inbreeding depression during life. Maternal homozygosity also negatively predicted offspring telomere length. Our results show that somatic inbreeding costs are environmentally dependent at certain life stages but may accumulate throughout life.

Understanding individual‐level variation in response to the environment is fundamental to understanding life‐history evolution and population dynamics. Telomeres, the protective caps at the ends of chromosomes, shorten in response to oxidative stress, and telomere shortening is correlated with reduced survival and life span. Investigating telomere dynamics may help us quantify individual variation in the costs experienced from social and ecological factors, and enhance our understanding of the dynamics of natural populations.Here, we study spatio‐temporal variation in lifelong telomere dynamics in the Seychelles warbler, Acrocephalus sechellensis. We combine long‐term life history and ecological data with a large longitudinal dataset of mean telomere lengths, consisting of 1,808 samples from 22 cohorts born between 1993 and 2014. We provide a detailed analysis of how telomere dynamics vary over individual life spans and cohorts, and with spatio‐temporal variation in the social and ecological environment.We found that telomere length decreases with cross‐sectional and longitudinal measures of age, and most rapidly very early in life. However, both cross‐sectional and longitudinal data suggested that against this overall pattern of shortening, bouts of telomere length increase occur in some individuals. Using a large number of repeated measurements we show statistically that these increases are unlikely to be explained solely by qPCR measurement error.Telomere length varied markedly among cohorts. Telomere length was positively associated with temporal variation in island‐wide insect abundance—a key resource for the insectivorous Seychelles warbler—suggesting that the costs associated with living in harsher environments can be studied by investigating telomere dynamics. We also found evidence for sex‐specific relationships between telomeres and tarsus length, potentially reflecting differential costs of growth.Our long‐term data show that in a natural population, telomere dynamics vary in a complex manner over individual life spans, and across space and time. Variance in telomere dynamics among individuals is the product of a wide array of genetic, parental and environmental factors. Explaining this variation more fully will require the integration of comprehensive long‐term ecological and genetic data from multiple populations and species.

We analysed the spatial and temporal pattern of egg laying in great spotted cuckoo females using microsatellite typing to determine parentage of the eggs and nestlings found in host (magpie) nests. The results showed that there were no exclusive laying territories in the study area. Cases of multiparasitism could be due to single females laying two or more eggs in a nest, or to several females using the same nest. In the latter case multiparasitism was due to a shortage of available host nests. We argue that the need for very large laying areas and the likely small cost of sharing parental care for chicks make the costs of defending territories higher than the benefits, which has constrained the evolution of territoriality in this species.

The MHC (Major Histocompatibility Complex) plays an important role in the immune system of vertebrates. MHC genes are extremely polymorphic and this variation is considered to be maintained by selection from pathogens. We investigate whether MHC diversity (number of different alleles per individual) affects the survival and recruitment of nestling house sparrows. We hypothesize that individuals with higher MHC diversity can recognize and combat a wider range of pathogens, and therefore are more likely to survive and recruit into the breeding population. Additionally, we hypothesize that specific MHC class I alleles (MHC-I) could be associated with survival and recruitment. We screened MHC-I genotypes in 518 house sparrow chicks hatched on Lundy Island but we found no evidence for a relationship between nestling survival, post-fledging survival or recruitment success with MHC diversity. Then we investigated effects of specific MHC-I alleles in 195 individuals from a single cohort. Twenty-one MHC-I alleles were tested for relationships with nestling survival, post-fledging survival and recruitment, and we detected associations with survival for three different alleles. This pattern was, however, not different to what would be expected from random, so we could not conclude that particular MHC-I alleles are associated with survival in house sparrows on Lundy Island. Nonetheless, one of these alleles (1105) showed both a tendency for a higher probability of surviving in nestlings, and a significant association with survival in fledglings. We envision that allele 1105 could be an interesting candidate gene for testing associations with survival in house sparrows in the future.

Extra-group paternity (EGP) occurs commonly among group-living mammals and plays an important role in mating systems and the dynamics of sexual selection; however, socio-ecological and genetic correlates of EGP have been underexplored. We use 23years of demographic and genetic data from a high-density European badger (Meles meles) population, to investigate the relationship between the rate of EGP in litters and mate availability, mate incompatibility and mate quality (heterozygosity). Relatedness between within-group assigned mothers and candidate fathers had a negative quadratic effect on EGP, whereas the number of neighbouring-group candidate fathers had a linear positive effect. We detected no effect of mean or maximum heterozygosity of within-group candidate fathers on EGP. Consequently, EGP was associated primarily with mate availability, subject to within-group genetic effects, potentially to mitigate mate incompatibility and inbreeding. In badgers, cryptic female choice, facilitated by superfecundation, superfoetation and delayed implantation, prevents males from monopolizing within-group females. This resonates with a meta-analysis in group-living mammals, which proposed that higher rates of EGP occur when within-group males cannot monopolize within-group females. In contrast to the positive meta-analytic association, however, we found that EGP associated negatively with the number of within-group assigned mothers and the number of within-group candidate fathers; potentially a strategy to counter within-group males committing infanticide. The relationship between the rate of EGP and socio-ecological or genetic factors can therefore be intricate, and the potential for cryptic female choice must be accounted for in comparative studies.

This paper uses the release of the 2011 Australian Bureau of Statistics (ABS) census results and other recent and historical data sets to explore how Australian public housing has changed over the period 1981-2011. It summarises the contextual factors that have influenced housing provision and consumption in Australia over the past thirty years. The overall supply trends by tenure for Australia and each capital city are set out, followed by analysis of the demographics of public housing tenants, including age, household type, income, mobility, and workforce participation. Issues identified in the paper include insufficient stock and increasingly targeted households, representing a social and financial problem for housing agencies. The current stock is ill-adapted to tenants' needs; if housing agencies re-profile the housing to meet such needs, then they risk creating inflexible stock. The paper concludes with reflection on the future of public housing in Australia.

Atlantic forest is a biome of high diversity that is increasingly under threat from habitat clearance. This habitat contains a large number of endemic species, many of which are currently endangered. Here, we consider the genetic population structure of a Brazilian endemic bird restricted to Atlantic forest, the Brazilian tanager, Ramphocelus bresilius. While currently not threatened, this narrow range endemic faces future habitat reductions, potentially serving as a model species for other birds reliant on this biome. We sampled six populations, three on the mainland (Rio de Janeiro state), and three on a neighbouring continental island (Ilha Grande), to compare the genetic diversity and population structure in these two regions. Using microsatellite data from eight loci generated for 177 individuals, we found that the short ocean crossing significantly restricted gene flow (20–150 km between populations, FCT = 0.057 P

We assessed whether adult House Sparrows Passer domesticus adjusted their provisioning in response to an experimental increase in the nutritional condition of their nestlings. When we supplemented chicks directly with additional food, male parents, but not female parents, reduced their provisioning. The results for males, but not females, run contrary to a previous experiment in this species. In addition, female provisioning was positively associated with both brood size and the age of the brood. In contrast, whereas male provisioning was positively associated with brood size, males did not increase provisioning as their chicks grew older. Males, but not females, exhibited repeatability in their provisioning. Food supplementation had a larger positive effect upon nestling survival in smaller broods than in larger broods. Overall, there appear to be fundamental differences between males and females in how decisions regarding the level of parental investment in the current brood are made.

Hybridization between wild species and their domestic relatives can be an important conservation and management problem. Genetic purity of the wild species is desirable per se and the phenomenon can have unpredictable evolutionary consequences. Declining European wild boar populations were frequently restocked with farmed wild boars that sometimes had been crossed with domestic pigs. We used simple polymerase chain reaction-based diagnostic tests to detect the presence of mitochondrial DNA and coat colour alleles of domestic origin in wild boars from Belgium, Luxembourg, and western Germany. Microsatellite genotypes were used to test for genetic admixture between the wild boars and domestic pigs. Although almost one-third of all Luxembourg wild boars carried Asian mitochondrial DNA haplotypes originating from domestic pigs, microsatellite-based clustering only identified four putatively admixed individuals in Luxembourg. By contrast, clustering identified wild boar × domestic hybrids in most sampling locations in Belgium. We interpret these results as evidence of releases of hybrid captive-reared wild boars. Our results emphasize the need (if working with classical markers) to use different systems to obtain an understanding as to whether hybridization between wild and domestic relatives might have affected the genetic make-up of a local population. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110, 104–115.