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

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

The effect of environmental variation on the relationship between survival and risk-taking behaviour in a migratory songbird.

Temporal changes in environmental conditions may play a major role in the year-to-year variation in fitness consequences of behaviours. Identifying environmental drivers of such variation is crucial to understand the evolutionary trajectories of behaviours in natural contexts. However, our understanding of how environmental variation influences behaviours in the wild remains limited. Using data collected over 14 breeding seasons from a collared flycatcher (Ficedula albicollis) population, we examined the effect of environmental variation on the relationship between survival and risk-taking behaviour, a highly variable behavioural trait with great evolutionary and ecological significance. Specifically, using annual recapture probability as a proxy of survival, we evaluated the specific effect of predation pressure, food availability, and mean temperature on the relationship between annual recapture probability and risk-taking behaviour (measured as flight initiation distance [FID]). We found a negative trend, as the relationship between annual recapture probability and FID decreased over the study years and changed from positive to negative. Specifically, in the early years of the study, risk-avoiding individuals exhibited a higher annual recapture probability, whereas in the later years, risk-avoiders had a lower annual recapture probability. However, we did not find evidence that any of the considered environmental factors mediated the variation in the relationship between survival and risk-taking behaviour.

Responses in the breeding parameters of the collared flycatcher to the changing climate.

Global climate change involves various aspects of climate, including precipitation changes and declining surface wind speeds, but studies investigating biological responses have often focused on the impacts of rising temperatures. Additionally, related long-term studies on bird reproduction tend to concentrate on breeding onset, even though other aspects of breeding could also be sensitive to the diverse weather aspects. This study aimed to explore how multiple aspects of breeding (breeding onset, hatching delay, breeding season length, clutch size, fledgling number) were associated with different weather components. We used an almost four-decade-long dataset to investigate the various aspects of breeding parameters of a collared flycatcher (Ficedula albicollis) population in the Carpathian Basin. Analyses revealed some considerable associations, for example, breeding seasons lengthened with the amount of daily precipitation, and clutch size increased with the number of cool days. Parallel and opposing changes in the correlated pairs of breeding and weather parameters were also observed. The phenological mismatch between prey availability and breeding time slightly increased, and fledgling number strongly decreased with increasing mistiming. Our results highlighted the intricate interplay between climate change and the reproductive patterns of migratory birds, emphasizing the need for a holistic approach. The results also underscored the potential threats posed by climate change to bird populations and the importance of adaptive responses to changing environmental conditions.

The estimation of additive genetic variance of body size in a wild passerine is sensitive to the method used to estimate relatedness among the individuals.

Assessing additive genetic variance is a crucial step in predicting the evolutionary response of a target trait. However, the estimated genetic variance may be sensitive to the methodology used, e.g., the way relatedness is assessed among the individuals, especially in wild populations where social pedigrees can be inaccurate. To investigate this possibility, we investigated the additive genetic variance in tarsus length, a major proxy of skeletal body size in birds. The model species was the collared flycatcher (Ficedula albicollis), a socially monogamous but genetically polygamous migratory passerine. We used two relatedness matrices to estimate the genetic variance: (1) based solely on social links and (2) a genetic similarity matrix based on a large array of single-nucleotide polymorphisms (SNPs). Depending on the relatedness matrix considered, we found moderate to high additive genetic variance and heritability estimates for tarsus length. In particular, the heritability estimates were higher when obtained with the genetic similarity matrix instead of the social pedigree. Our results confirm the potential for this crucial trait to respond to selection and highlight methodological concerns when calculating additive genetic variance and heritability in phenotypic traits. We conclude that using a social pedigree instead of a genetic similarity matrix to estimate relatedness among individuals in a genetically polygamous wild population may significantly deflate the estimates of additive genetic variation.

Plumage color degradation indicates reproductive effort: an experiment.

Plumage color has traditionally been regarded as a static ornamental trait, but evidence is accumulating for significant color changes without molt that typically reduce the conspicuousness of ornamentation. In some species, the social partner seems to increase its reproductive investment if the color trait is experimentally enhanced, suggesting that color change could act as a signal. However, the information content of this signal is so far unclear. For example, birds in poor condition or making greater effort may deteriorate more severely. We used brood size manipulations to alter the reproductive effort of male and female collared flycatchers Ficedula albicollis. Both sexes showed less severe decline in some reflectance attribute of their white breast when their brood was experimentally reduced. In each sex, greater deterioration of the reflectance trait affected by the manipulation was accompanied by increased feeding rate by the partner. These feeding patterns do not prove, but are consistent with, a compensatory response by the partner to induced degradation. The manipulation effects on color change we detected confirm for the first time that plumage color deterioration can indicate current reproductive effort, thereby providing a potential fitness advantage to social partners that react to such deterioration.

Are brood sex ratios adaptive?-The effect of experimentally altered brood sex ratio on nestling growth, mortality and recruitment.

Brood sex ratios (BSRs) have often been found to be nonrandom in respect of parental and environmental quality, and many hypotheses suggest that nonrandom sex ratios can be adaptive. To specifically test the adaptive value of biased BSRs, it is crucial to disentangle the consequences of BSR and maternal effects. In multiparous species, this requires cross-fostering experiments where foster parents rear offspring originating from multiple broods, and where the interactive effect of original and manipulated BSR on fitness components is tested. To our knowledge, our study on collared flycatchers (Ficedula albicollis) is the first that meets these requirements. In this species, where BSRs had previously been shown to be related to parental characteristics, we altered the original BSR of the parents shortly after hatching by cross-fostering nestlings among trios of broods and examined the effects on growth, mortality and recruitment of the nestlings. We found that original and experimental BSR, as well as the interaction of the two, were unrelated to the fitness components considered. Nestling growth was related only to background variables, namely brood size and hatching rank. Nestling mortality was related only to hatching asynchrony. Our results therefore do not support that the observed BSRs are adaptive in our study population. However, we cannot exclude the possibility of direct effects of experimentally altered BSRs on parental fitness, which should be evaluated in the future. In addition, studies similar to ours are required on various species to get a clearer picture of the adaptive value of nonrandom BSRs.

Temperature synchronizes temporal variation in laying dates across European hole-nesting passerines.

Identifying the environmental drivers of variation in fitness-related traits is a central objective in ecology and evolutionary biology. Temporal fluctuations of these environmental drivers are often synchronized at large spatial scales. Yet, whether synchronous environmental conditions can generate spatial synchrony in fitness-related trait values (i.e., correlated temporal trait fluctuations across populations) is poorly understood. Using data from long-term monitored populations of blue tits (Cyanistes caeruleus, n = 31), great tits (Parus major, n = 35), and pied flycatchers (Ficedula hypoleuca, n = 20) across Europe, we assessed the influence of two local climatic variables (mean temperature and mean precipitation in February-May) on spatial synchrony in three fitness-related traits: laying date, clutch size, and fledgling number. We found a high degree of spatial synchrony in laying date but a lower degree in clutch size and fledgling number for each species. Temperature strongly influenced spatial synchrony in laying date for resident blue tits and great tits but not for migratory pied flycatchers. This is a relevant finding in the context of environmental impacts on populations because spatial synchrony in fitness-related trait values among populations may influence fluctuations in vital rates or population abundances. If environmentally induced spatial synchrony in fitness-related traits increases the spatial synchrony in vital rates or population abundances, this will ultimately increase the risk of extinction for populations and species. Assessing how environmental conditions influence spatiotemporal variation in trait values improves our mechanistic understanding of environmental impacts on populations.

Reducing data dimension boosts neural network-based stage-specific malaria detection.

Although malaria has been known for more than 4 thousand years1, it still imposes a global burden with approx. 240 million annual cases2. Improvement in diagnostic techniques is a prerequisite for its global elimination. Despite its main limitations, being time-consuming and subjective, light microscopy on Giemsa-stained blood smears is still the gold-standard diagnostic method used worldwide. Autonomous computer assisted recognition of malaria infected red blood cells (RBCs) using neural networks (NNs) has the potential to overcome these deficiencies, if a fast, high-accuracy detection can be achieved using low computational power and limited sets of microscopy images for training the NN. Here, we report on a novel NN-based scheme that is capable of the high-speed classification of RBCs into four categories-healthy ones and three classes of infected ones according to the parasite age-with an accuracy as high as 98%. Importantly, we observe that a smart reduction of data dimension, using characteristic one-dimensional cross-sections of the RBC images, not only speeds up the classification but also significantly improves its performance with respect to the usual two-dimensional NN schemes. Via comparative studies on RBC images recorded by two additional techniques, fluorescence and atomic force microscopy, we demonstrate that our method is universally applicable for different types of microscopy images. This robustness against imaging platform-specific features is crucial for diagnostic applications. Our approach for the reduction of data dimension could be straightforwardly generalised for the classification of different parasites, cells and other types of objects.

Functional Integration of Multiple Sexual Ornaments: Signal Coherence and Sexual Selection.

AbstractThe sexual ornamentation of animals typically consists of multiple distinct traits. The classical research approach focuses on differences among these traits, but this approach may often be misleading because of correlations among distinct sexual traits of similar origins. There are many published studies on the correlation structures of sexual traits, but the way receivers take into account the components of an integrated, multicomponent trait system remains mostly unknown. Here, we propose a general analytical framework to assess the possible sexual selection consequences of within-individual coherence in the expression of multiple correlated sexual traits. We then apply this framework to a long-term mutual plumage coloration data set from a wild bird population. The results suggest that the coherence of component plumage color traits is not sexually selected. However, component trait coherence affects sexual selection on integrated plumage color. When assessing across-spectrum plumage reflectance, receivers choosing mates apparently disregard a component trait if it is inconsistent with the overall expression of other components. This indicates that separately examining and manipulating distinct sexual traits may often be misleading. Theoretical and empirical studies should further explore the effects of coherence on the ornament-preference coevolution.

Bird populations most exposed to climate change are less sensitive to climatic variation.

The phenology of many species shows strong sensitivity to climate change; however, with few large scale intra-specific studies it is unclear how such sensitivity varies over a species' range. We document large intra-specific variation in phenological sensitivity to temperature using laying date information from 67 populations of two co-familial European songbirds, the great tit (Parus major) and blue tit (Cyanistes caeruleus), covering a large part of their breeding range. Populations inhabiting deciduous habitats showed stronger phenological sensitivity than those in evergreen and mixed habitats. However, populations with higher sensitivity tended to have experienced less rapid change in climate over the past decades, such that populations with high phenological sensitivity will not necessarily exhibit the strongest phenological advancement. Our results show that to effectively assess the impact of climate change on phenology across a species' range it will be necessary to account for intra-specific variation in phenological sensitivity, climate change exposure, and the ecological characteristics of a population.

Deep Learning Exploration of Agent-Based Social Network Model Parameters.

Interactions between humans give rise to complex social networks that are characterized by heterogeneous degree distribution, weight-topology relation, overlapping community structure, and dynamics of links. Understanding these characteristics of social networks is the primary goal of their research as they constitute scaffolds for various emergent social phenomena from disease spreading to political movements. An appropriate tool for studying them is agent-based modeling, in which nodes, representing individuals, make decisions about creating and deleting links, thus yielding various macroscopic behavioral patterns. Here we focus on studying a generalization of the weighted social network model, being one of the most fundamental agent-based models for describing the formation of social ties and social networks. This generalized weighted social network (GWSN) model incorporates triadic closure, homophilic interactions, and various link termination mechanisms, which have been studied separately in the previous works. Accordingly, the GWSN model has an increased number of input parameters and the model behavior gets excessively complex, making it challenging to clarify the model behavior. We have executed massive simulations with a supercomputer and used the results as the training data for deep neural networks to conduct regression analysis for predicting the properties of the generated networks from the input parameters. The obtained regression model was also used for global sensitivity analysis to identify which parameters are influential or insignificant. We believe that this methodology is applicable for a large class of complex network models, thus opening the way for more realistic quantitative agent-based modeling.

Triparental care in the collared flycatcher (Ficedula albicollis): Cooperation of two females with a cuckolded male in rearing a brood.

Certain predominant forms of mating and parental care systems are assumed in several model species among birds, but the opportunistic and apparently infrequent variations of "family structures" may often remain hidden due to methodological limitations with regard to genetic or behavioral observations. One of the intensively studied model species, the collared flycatcher (Ficedula albicollis), is usually characterized by social monogamy with polyterritorial, facultative social polygyny, and frequent extrapair mating and extrapair paternity. During a brood-size manipulation experiment, we observed two females and a male delivering food at an enlarged brood. A combination of breeding phenology data (egg laying and hatching date), behavioral data (feeding rates) from video recordings at 10 days of nestling age, and microsatellite genotyping for maternity and paternity suggests a situation of an unrelated female helping a pair in chick rearing. Such observations highlight the relevance of using traditional techniques and genetic analyses together to assess the parental roles within a population, which becomes more important where individuals may dynamically switch from their main and presupposed roles according to the actual environmental conditions.

Interacting jammed granular systems.

More than 30 years ago Edwards and co-authors proposed a model to describe the statistics of granular packings by an ensemble of equiprobable jammed states. Experimental tests of this model remained scarce so far. We introduce a simple system to analyze statistical properties of jammed granular ensembles to test Edwards theory. Identical spheres packed in a nearly two-dimensional geometrical confinement were studied in experiments and numerical simulations. When tapped, the system evolves toward a ground state, but due to incompatible domain structures it gets trapped. Analytical calculations reproduce relatively well our simulation results, which allows us to test Edwards theory on a coupled system of two subsystems with different properties. We find that the joint system can only be described by the Edwards theory if considered as a single system due to the constraints in the stresses. The results show counterintuitive effects as in the coupled system the change in the order parameter is opposite to what is expected from the change in the compactivity.

Sequential organization of birdsong: relationships with individual quality and fitness.

Many vocalizing animals produce the discrete elements of their acoustic signals in a specific sequential order, but we know little about the biological relevance of this ordering. For that, we must characterize the degree by which individuals differ in how they organize their signals sequentially and relate these differences to variation in quality and fitness. In this study, we fulfilled these tasks in male collared flycatchers (Ficedula albicollis). We characterized the sequential order of syllables with a network analysis approach and studied the consistency of network variables on distinct time scales (within day, between days, and between years), and assessed their relationship with such quality indicators like age, body condition, arrival date, and fitness related proxies like survival to the next year and pairing success. We found that the syllables were associated nonrandomly with one another and both the frequency differences of consecutive syllables and the number of motif types were higher in the original than in randomized syllable sequences. Average degree and small-worldness showed considerable among-individual differences and decreasing repeatability with increasing time scale. Furthermore, we found relationships between male age and average degree among and within individuals. Accordingly, older males produce syllable sequences by using common syllables less often than younger individuals. However, the network variables showed no relationship with fitness-related variables. In conclusion, the sequential organization of birdsong has the potential to encode individual-specific characteristics, which thus could be used as signal in social interactions and thus potentially could be subject to sexual selection.

Sex-dependent risk-taking behaviour towards different predatory stimuli in the collared flycatcher.

Prey animals may react differently to predators, which can thus raise plasticity in risk-taking behaviour. We assessed the behavioural responses of nestling-feeding collared flycatcher (Ficedula albicollis) parents towards different avian predator species (Eurasian sparrowhawk, long-eared owl) and a non-threatening songbird (song thrush) by measuring the latency to resume feeding activity. We found that the sexes differed in their responses towards the different stimuli, as males resumed nestling-provisioning sooner after the songbird than after the predator stimuli, while latency of females was not affected by the type of stimulus. Parents breeding later in the season took less risk than early breeders, and mean response also varied across the study years. We detected a considerable repeatability at the within-brood level across stimuli, and a correlation between the latency of parents attending the same nest, implying that they may adjust similarly their risk-taking behaviour to the brood value. Repeated measurements at the same brood suggested that risk-taking behaviour of flycatcher parents is a plastic trait, and sex-specific effects might be the result of sex-specific adjustments of behaviour to the perceived environmental challenge as exerted by different predators. Furthermore, the nest-specific effects highlighted that environmental effects can render consistently similar responses between the parents.

Evolution of shear zones in granular packings under pressure.

Stress transmission in realistic granular media often occurs under external load and in the presence of boundary slip. We investigate shear localization in a split-bottom Couette cell with smooth walls subject to a confining pressure experimentally and by means of numerical simulations. We demonstrate how the characteristics of the shear zone, such as its center position and width, evolve as the confining pressure and wall slip modify the local effective friction coefficient of the material. For increasing applied pressure, the shear zone evolves toward the center of the cylinder and grows wider and the angular velocity reduces compared to the driving rate of the bottom disk. Moreover, the presence of slip promotes the transition from open shear zones at the top surface to closed shear zones inside the bulk. We also systematically vary the ratio of the effective friction near the bottom plate and in the bulk in simulations and observe the resulting impact on the surface flow profile. Besides the boundary conditions and external load, material properties such as grain size are also known to influence the effective friction coefficient. However, our numerical results reveal that the center position and width of the shear zone are insignificantly affected by the choice of the grain size as far as it remains small compared to the radius of the rotating bottom disk.

Gravity Governs Shear Localization in Confined Dense Granular Flows.

The prediction of flow profiles of slowly sheared granular materials is a major geophysical and industrial challenge. Understanding the role of gravity is particularly important for future planetary exploration in varying gravitational environments. Using the principle of minimization of energy dissipation, and combining experiments and variational analysis, we disentangle the contributions of the gravitational acceleration, confining pressure, and layer thickness on shear strain localization induced by moving fault boundaries at the bottom of a granular layer. The flow profile is independent of the gravity for geometries with a free top surface. However, under a confining pressure or if the sheared layer withstands the weight of the upper layers, increasing gravity promotes the transition from closed shear zones buried in the bulk to open ones that intersect the top surface. We show that the center position and width of the shear zone and the axial angular velocity at the top surface follow universal scaling laws when properly scaled by the gravity, applied pressure, and layer thickness. Our finding that the flow profiles lie on a universal master curve opens the possibility to predict the quasistatic shear flow of granular materials in varying gravitational environments.

Plato's cube and the natural geometry of fragmentation.

Plato envisioned Earth's building blocks as cubes, a shape rarely found in nature. The solar system is littered, however, with distorted polyhedra-shards of rock and ice produced by ubiquitous fragmentation. We apply the theory of convex mosaics to show that the average geometry of natural two-dimensional (2D) fragments, from mud cracks to Earth's tectonic plates, has two attractors: "Platonic" quadrangles and "Voronoi" hexagons. In three dimensions (3D), the Platonic attractor is dominant: Remarkably, the average shape of natural rock fragments is cuboid. When viewed through the lens of convex mosaics, natural fragments are indeed geometric shadows of Plato's forms. Simulations show that generic binary breakup drives all mosaics toward the Platonic attractor, explaining the ubiquity of cuboid averages. Deviations from binary fracture produce more exotic patterns that are genetically linked to the formative stress field. We compute the universal pattern generator establishing this link, for 2D and 3D fragmentation.

Host dispersal shapes the population structure of a tick-borne bacterial pathogen.

Birds are hosts for several zoonotic pathogens. Because of their high mobility, especially of longdistance migrants, birds can disperse these pathogens, affecting their distribution and phylogeography. We focused on Borrelia burgdorferi sensu lato, which includes the causative agents of Lyme borreliosis, as an example for tick-borne pathogens, to address the role of birds as propagation hosts of zoonotic agents at a large geographical scale. We collected ticks from passerine birds in 11 European countries. B. burgdorferi s.l. prevalence in Ixodes spp. was 37% and increased with latitude. The fieldfare Turdus pilaris and the blackbird T. merula carried ticks with the highest Borrelia prevalence (92 and 58%, respectively), whereas robin Erithacus rubecula ticks were the least infected (3.8%). Borrelia garinii was the most prevalent genospecies (61%), followed by B. valaisiana (24%), B. afzelii (9%), B. turdi (5%) and B. lusitaniae (0.5%). A novel Borrelia genospecies "Candidatus Borrelia aligera" was also detected. Multilocus sequence typing (MLST) analysis of B. garinii isolates together with the global collection of B. garinii genotypes obtained from the Borrelia MLST public database revealed that: (a) there was little overlap among genotypes from different continents, (b) there was no geographical structuring within Europe, and (c) there was no evident association pattern detectable among B. garinii genotypes from ticks feeding on birds, questing ticks or human isolates. These findings strengthen the hypothesis that the population structure and evolutionary biology of tick-borne pathogens are shaped by their host associations and the movement patterns of these hosts.

Relationship between oxidative stress and sexual coloration of lizards depends on thermal habitat.

Sexual signals serve as an honest indicator of individual quality, reflecting either developmental and/or maintenance costs. A possible underlying physiological mechanism is oxidative stress, which could mediate energy trade-offs between sexual signals and other quality traits. In ectotherms, thermal performance acts as a key indicator of individual quality and influence signal intensity. We investigated how oxidative state is reflected in visual signals of lizards from different thermal habitats. According to our hypothesis, efficient thermoregulation requires different strategies in different thermal environments. In a habitat with predictable temperature changes, animals are less exposed to suboptimal temperature ranges and selection will, therefore, be stronger on the maximum oxidative damage at optimal body temperature. Contrarily, in a habitat with rather stochastic thermal shifts, individuals are often constricted by suboptimal thermal conditions, and oxidative damage can be limiting on a wide temperature range. We used Iberolacerta cyreni and Psammodromus algirus inhabiting stochastic and predictable thermal environments respectively. We examined two aspects of oxidative stress: the level of reactive oxygen metabolites at the preferred temperature (maximal ROM) and the temperature range in which animals produce at least 80% of the maximum level of reactive oxygen metabolites (effective ROM range). In I. cyreni, we found that duller coloration was related to a wider effective ROM range, while expression of coloration in P. algirus was negatively correlated with the maximal ROM. Our results suggest that different thermal constraints affect different aspects of oxidative damage which can indicate individual quality and are, therefore, represented in sexual ornaments.