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Little is known about the dietary richness and variation of generalist insectivorous species, including birds, due primarily to difficulties in prey identification. Using faecal metabarcoding we provide the most comprehensive analysis of a passerine’s diet to date, identifying the relative magnitudes of biogeographic, habitat and temporal trends in the richness and turnover in diet of Cyanistes caeruleus (blue tit) along a 39-site, 2° latitudinal transect in Scotland. Faecal samples were collected in 2014-15 from adult birds roosting in nestboxes prior to nest building. DNA was extracted from 793 samples and we amplified COI and 16S minibarcodes. We identified 432 molecular operational taxonomic units (MOTUs) that correspond to putative dietary items. Most dietary items were rare, with Lepidoptera being the most abundant and taxon-rich prey order. We present a statistical approach for estimation of gradients and inter-sample variation in taxonomic richness and turnover using a generalised linear mixed model. We discuss the merits of this approach over existing tools and present methods for model-based estimation of repeatability, taxon richness and Jaccard indices. We find that dietary richness increases significantly as spring advances, but changes little with elevation, latitude or local tree composition. In comparison, dietary composition exhibits significant turnover along temporal and spatial gradients and among sites. Our study shows the promise of faecal metabarcoding for inferring the macroecology of food webs, but we also highlight the challenge posed by contamination and make recommendations of laboratory and statistical practices to minimise its impact on inference.

Little is known about the dietary richness and variation of generalist insectivorous species, including birds, due primarily to difficulties in prey identification. Using faecal metabarcoding we provide the most comprehensive analysis of a passerine’s diet to date, identifying the relative magnitudes of biogeographic, habitat and temporal trends in the richness and turnover in diet of Cyanistes caeruleus (blue tit) along a 39-site, 2° latitudinal transect in Scotland. Faecal samples were collected in 2014-15 from adult birds roosting in nestboxes prior to nest building. DNA was extracted from 793 samples and we amplified COI and 16S minibarcodes. We identified 432 molecular operational taxonomic units (MOTUs) that correspond to putative dietary items. Most dietary items were rare, with Lepidoptera being the most abundant and taxon-rich prey order. We present a statistical approach for estimation of gradients and inter-sample variation in taxonomic richness and turnover using a generalised linear mixed model. We discuss the merits of this approach over existing tools and present methods for model-based estimation of repeatability, taxon richness and Jaccard indices. We find that dietary richness increases significantly as spring advances, but changes little with elevation, latitude or local tree composition. In comparison, dietary composition exhibits significant turnover along temporal and spatial gradients and among sites. Our study shows the promise of faecal metabarcoding for inferring the macroecology of food webs, but we also highlight the challenge posed by contamination and make recommendations of laboratory and statistical practices to minimise its impact on inference.

We propose to change the default P-value threshold for statistical significance for claims of new discoveries from 0.05 to 0.005.

We propose to change the default P-value threshold for statistical significance for claims of new discoveries from 0.05 to 0.005.

We propose to change the default P-value threshold for statistical significance from 0.05 to 0.005 for claims of new discoveries.

Cryptic evolution has been defined as adaptive evolutionary change being masked by concurrent environmental change. Empirical studies of cryptic evolution have usually invoked a changing climate and/or increasing population density as the form of detrimental environmental change experienced by a population undergoing cryptic evolution. However, Fisher (1958) emphasized that evolutionary change in itself is likely to be an important component of "environmental deterioration," a point restated by Cooke et al. (1990) in the context of intraspecific competition. In this form, environmental deterioration arises because a winning lineage has to compete against more winners in successive generations as the population evolves. This "evolutionary environmental deterioration" has different implications for the selection and evolution of traits influenced by resource competition than general environmental change. We reformulate Cooke's model as a quantitative genetic model to show that it is identical in form to more recent developments proposed by quantitative geneticists. This provides a statistical framework for discriminating between the alternative hypotheses of environmental change and environmental deterioration caused by evolutionary change. We also demonstrate that in systems where no phenotypic change has occurred, there are many reasonable biological processes that will generate patterns in predicted breeding values that are consistent with what has been interpreted as cryptic evolution, and care needs to be taken when interpreting these patterns. These processes include mutation, sib competition, and invisible fractions.

Knowledge of the parentage of individuals is required to address a variety of questions concerning the evolutionary dynamics of wild populations. A major advance in parentage inference in natural populations has been the use of molecular markers and the development of statistical methods to analyse these data. Cervus, one of the most widely used parentage inference programs, uses molecular data to determine parent-offspring relationships. However, Cervus does not make use of all available information: additional phenotypic information may exist predicting parent-offspring relationships, and additional genetic information may be exploited by simultaneously considering multiple types of relationships rather than just pairwise or just parent-offspring relationships. Here we reanalyse data from a wild red deer population using two programs capable of using this additional information, MasterBayes and COLONY2, and quantify the impact of these alternative approaches by comparison with a 'known pedigree' estimated using a larger suite of microsatellite makers for a subset of the population. The use of phenotypic information and multiple relationships increased the number of correct assignments. We highlight the differences between programs, particularly the use of population- rather than individual-level statistical confidence in Cervus. We conclude that the use of additional information allows MasterBayes and COLONY2 to assign more correct paternities, whereas their use of individual- rather than population-level confidence generates fewer erroneous assignments. We suggest that maximal information may be gained by combining outputs from different programs. Higher accuracy and completeness of pedigree information will improve parameters estimated from pedigree information in studies of natural populations.

Best linear unbiased prediction (BLUP) is a method for obtaining point estimates of a random effect in a mixed effect model. Over the past decade it has been used extensively in ecology and evolutionary biology to predict individual breeding values and reaction norms. These predictions have been used to infer natural selection, evolutionary change, spatial-genetic patterns, individual reaction norms, and frailties. In this article we show analytically and through simulation and example why BLUP often gives anticonservative and biased estimates of evolutionary and ecological parameters. Although some concerns with BLUP methodology have been voiced before, the scale and breadth of the problems have probably not been widely appreciated. Bias arises because BLUPs are often used to estimate effects that are not explicitly accounted for in the model used to make the predictions. In these cases, predicted breeding values will often say more about phenotypic patterns than the genetic patterns of interest. An additional problem is that BLUPs are point estimates of quantities that are usually known with little certainty. Failure to account for this uncertainty in subsequent tests can lead to both bias and extreme anticonservatism. We demonstrate that restricted maximum likelihood and Bayesian solutions exist for these problems and show how unbiased and powerful tests can be derived that adequately quantify uncertainty. Of particular utility is a new test for detecting evolutionary change that not only accounts for prediction error in breeding values but also accounts for drift. To illustrate the problem, we apply these tests to long-term data on the Soay sheep (Ovis aries) and the great tit (Parus major) and show that previously reported temporal trends in breeding values are not supported.

Global warming has had numerous effects on populations of animals and plants, with many species in temperate regions experiencing environmental change at unprecedented rates. Populations with low potential for adaptive evolutionary change and plasticity will have little chance of persistence in the face of environmental change. Assessment of the potential for adaptive evolution requires the estimation of quantitative genetic parameters, but it is as yet unclear what impact, if any, global warming will have on the expression of genetic variances and covariances. Here we assess the impact of a changing climate on the genetic architecture underlying three reproductive traits in a wild bird population. We use a large, long-term, data set collected on great tits (Parus major) in Wytham Woods, Oxford, and an 'animal model' approach to quantify the heritability of, and genetic correlations among, laying date, clutch size and egg mass during two periods with contrasting temperature conditions over a 40-year period (1965-1988 [cooler] vs. 1989-2004 [warmer]). We found significant additive genetic variance and heritability for all traits under both temperature regimes. We also found significant negative genetic covariances and correlations between clutch size and egg weight during both periods, and among laying date and clutch size in the colder years only. The overall G matrix comparison among periods, however, showed only a minor difference among periods, thus suggesting that genotype by environment interactions are negligible in this context. Our results therefore suggest that despite substantial changes in temperature and in mean laying date phenotype over the last decades, and despite the large sample sizes available, we are unable to detect any significant change in the genetic architecture of the reproductive traits studied.

Dispersal is a fundamental but poorly understood process in ecology, evolution and conservation. Natal dispersal patterns are a major determinant of population kin structure and thus may play a key role in social evolution. We studied natal dispersal in the cooperatively breeding long-tailed tit Aegithalos caudatus, a non-territorial species that does not exhibit delayed dispersal. We investigated the factors associated with local recruitment and dispersal distance using 11 years of data, and generated dispersal distance distributions (DDDs) before and after correcting for sampling bias. We also examined how dispersal direction varied between and within nests, using a novel randomisation method to correct for bias. Recruitment was male-biased and increased with nestling weight, and there were significant nest and year effects. Neither sex nor weight had a significant effect on dispersal distance, but distance increased with brood size and there was a significant nest effect. The observed DDD was right-skewed but the corrected DDD was almost symmetrical, and this correction more than doubled estimates of mean dispersal distance and fledgling recruitment rate. There was no tendency across nests for birds to disperse in a particular direction, but siblings dispersed in similar directions. These results provide a detailed description of natal dispersal in long-tailed tits with minimal bias. They also demonstrate the importance of studying the different aspects of dispersal in combination, and show that direction is an important component of dispersal that is usually overlooked. The pattern of natal dispersal is consistent with the nature of helping behaviour in long-tailed tits, and may play an important role in the evolution and maintenance of cooperation despite the absence of delayed dispersal.

Dispersal is a fundamental but poorly understood process in ecology, evolution and conservation. Natal dispersal patterns are a major determinant of population kin structure and thus may play a key role in social evolution. We studied natal dispersal in the cooperatively breeding long-tailed tit Aegithalos caudatus, a non-territorial species that does not exhibit delayed dispersal. We investigated the factors associated with local recruitment and dispersal distance using 11 years of data, and generated dispersal distance distributions (DDDs) before and after correcting for sampling bias. We also examined how dispersal direction varied between and within nests, using a novel randomisation method to correct for bias. Recruitment was male-biased and increased with nestling weight, and there were significant nest and year effects. Neither sex nor weight had a significant effect on dispersal distance, but distance increased with brood size and there was a significant nest effect. The observed DDD was right-skewed but the corrected DDD was almost symmetrical, and this correction more than doubled estimates of mean dispersal distance and fledgling recruitment rate. There was no tendency across nests for birds to disperse in a particular direction, but siblings dispersed in similar directions. These results provide a detailed description of natal dispersal in long-tailed tits with minimal bias. They also demonstrate the importance of studying the different aspects of dispersal in combination, and show that direction is an important component of dispersal that is usually overlooked. The pattern of natal dispersal is consistent with the nature of helping behaviour in long-tailed tits, and may play an important role in the evolution and maintenance of cooperation despite the absence of delayed dispersal.

Aim The laying of eggs and the building of a nest structure to accommodate them are two of the defining characteristics of members of the class Aves. Nest structures vary considerably across avian taxa and for many species the design of the completed nest can have important consequences for both parents and their offspring. While nest characteristics are expected to vary adaptively in response to environmental conditions, large-scale spatial variation in nest characteristics has been largely overlooked. Here, we examined the effects of latitudinal variation in spring temperatures on nest characteristics, including insulatory properties, and reproductive success of blue tits, Cyanistes caeruleus, and great tits, Parus major. Location Great Britain. Methods Nests and reproductive data were collected from seven study sites, spread over five degrees of latitude. Then, the nest insulatory properties were determined before the nests were separated into either nest base material or cup lining material. Results As spring temperatures increased with decreasing latitude, the mass of the nest base material did not vary in either species, whilst the mass of the cup lining material and nest insulatory properties decreased in both species. This suggests that in response to increasing temperatures the breeding female reduces the mass of the cup lining material thereby maintaining an appropriate microclimate for incubating and brooding. The mean laying dates of both species advanced with decreasing latitude and increasing spring temperatures, although reproductive success did not vary. Main conclusions This is the first study to demonstrate that birds are systematically adjusting their nest structure in response to variation in ambient temperatures across large spatial scales. Therefore, nest composition reliably indicates environmental conditions and we suggest that studies of nest structure may be sentinels for the early signs of rapid climate change.