Farmland practices are driving bird population decline across Europe.

Declines in European bird populations are reported for decades but the direct effect of major anthropogenic pressures on such declines remains unquantified. Causal relationships between pressures and bird population responses are difficult to identify as pressures interact at different spatial scales and responses vary among species. Here, we uncover direct relationships between population time-series of 170 common bird species, monitored at more than 20,000 sites in 28 European countries, over 37 y, and four widespread anthropogenic pressures: agricultural intensification, change in forest cover, urbanisation and temperature change over the last decades. We quantify the influence of each pressure on population time-series and its importance relative to other pressures, and we identify traits of most affected species. We find that agricultural intensification, in particular pesticides and fertiliser use, is the main pressure for most bird population declines, especially for invertebrate feeders. Responses to changes in forest cover, urbanisation and temperature are more species-specific. Specifically, forest cover is associated with a positive effect and growing urbanisation with a negative effect on population dynamics, while temperature change has an effect on the dynamics of a large number of bird populations, the magnitude and direction of which depend on species' thermal preferences. Our results not only confirm the pervasive and strong effects of anthropogenic pressures on common breeding birds, but quantify the relative strength of these effects stressing the urgent need for transformative changes in the way of inhabiting the world in European countries, if bird populations shall have a chance of recovering.

Species-specific traits affect bird species' susceptibility to global change.

The current ecological crisis has risen extinction rates to similar levels of ancient mass extinctions. However, it seems to not be acting uniformly across all species but affecting species differentially. This suggests that species' susceptibility to the extinction process is mediated by specific traits. Since understanding this response mechanism at large scales will benefit conservation effort around the world, we used the IUCN global threat status and population trends of 8281 extant bird species as proxies of the extinction risk to identify the species-specific traits affecting their susceptibility to extinction within the biogeographic regions and at the global scale. Using linear mixed effect models and multinomial models, we related the global threat status and the population trends with the following traits: migratory strategy, habitat and diet specialization, body size, and generation length. According to our results and independently of the proxy used, more vulnerable species are sedentary and have larger body size, longer generation time, and higher degree of habitat specialization. These relationships apply globally and show little variation across biogeographic regions. We suggest that such concordant patterns might be caused either by a widespread occurrence of the same threats such as habitat modification or by a uniform capacity of some traits to reflect the impact of different local threats. Regardless of the cause of this pattern, our study identified the traits that affect species' response capability to the current ecological crisis. Conservation effort should focus on the species with trait values indicating the limited response capacity to overcome this crisis.

Covariation in population trends and demography reveals targets for conservation action.

Wildlife conservation policies directed at common and widespread, but declining, species are difficult to design and implement effectively, as multiple environmental changes are likely to contribute to population declines. Conservation actions ultimately aim to influence demographic rates, but targeting actions towards feasible improvements in these is challenging in widespread species with ranges that encompass a wide range of environmental conditions. Across Europe, sharp declines in the abundance of migratory landbirds have driven international calls for action, but actions that could feasibly contribute to population recovery have yet to be identified. Targeted actions to improve conditions on poor-quality sites could be an effective approach, but only if local conditions consistently influence local demography and hence population trends. Using long-term measures of abundance and demography of breeding birds at survey sites across Europe, we show that co-occurring species with differing migration behaviours have similar directions of local population trends and magnitudes of productivity, but not survival rates. Targeted actions to boost local productivity within Europe, alongside large-scale (non-targeted) environmental protection across non-breeding ranges, could therefore help address the urgent need to halt migrant landbird declines. Such demographic routes to recovery are likely to be increasingly needed to address global wildlife declines.

Global population trends in shorebirds: migratory behaviour makes species at risk.

Linking population trends to species' traits is informative for the detection of the most important threatening factors and for assessing the effectiveness of conservation measures. Although some previous studies performed such an analysis at local to continental scales, the global-scale focus is the most relevant for conservation of the entire species. Here we evaluate information on global population trends of shorebirds, a widely distributed and ecologically diversified group, where some species connect different parts of the world by migration, while others are residents. Nowadays, shorebirds face rapid environmental changes caused by various human activities and climate change. Numerous signs of regional population declines have been recently reported in response to these threats. The aim of our study was to test whether breeding and non-breeding habitats, migratory behaviour (migrants vs. residents) and migration distance, breeding latitude, generation time and breeding range size mirror species' global population trends. We found that a majority of shorebird species have declined globally. After accounting for the influence of traits and species taxonomy, linear mixed-effects models showed that populations of migratory shorebirds decreased more than populations of residents. Besides that, declines were more frequent for species breeding at high latitudes of the Northern Hemisphere, but these patterns did not hold after excluding the non-migratory species. Our findings suggest that factors linked to migration, such as habitat loss as well as deterioration at stop-over or wintering sites and a pronounced climate change impact at high latitudes, are possible drivers of the observed worldwide population decreases.

Postcopulatory sexual selection reduces Z-linked genetic variation and might contribute to the large Z effect in passerine birds.

The X and Z sex chromosomes play a disproportionately large role in intrinsic postzygotic isolation. The underlying mechanisms of this large X/Z effect are, however, still poorly understood. Here we tested whether faster rates of molecular evolution caused by more intense positive selection or genetic drift on the Z chromosome could contribute to the large Z effect in two closely related passerine birds, the Common Nightingale (Luscinia megarhynchos) and the Thrush Nightingale (L. luscinia). We found that the two species differ in patterns of molecular evolution on the Z chromosome. The Z chromosome of L. megarhynchos showed lower levels of within-species polymorphism and an excess of non-synonymous polymorphisms relative to non-synonymous substitutions. This is consistent with increased levels of genetic drift on this chromosome and may be attributed to more intense postcopulatory sexual selection acting on L. megarhynchos males as was indicated by significantly longer sperm and higher between-male variation in sperm length in L. megarhynchos compared to L. luscinia. Interestingly, analysis of interspecific gene flow on the Z chromosome revealed relatively lower levels of introgression from L. megarhynchos to L. luscinia than vice versa, indicating that the Z chromosome of L. megarhynchos accumulated more hybrid incompatibilities. Our results are consistent with the view that postcopulatory sexual selection may reduce the effective population size of the Z chromosome and thus lead to stronger genetic drift on this chromosome in birds. This can result in relatively faster accumulation of hybrid incompatibilities on the Z and thus contribute to the large Z effect.

Genomic islands of differentiation in two songbird species reveal candidate genes for hybrid female sterility.

Hybrid sterility is a common first step in the evolution of postzygotic reproductive isolation. According to Haldane's Rule, it affects predominantly the heterogametic sex. While the genetic basis of hybrid male sterility in organisms with heterogametic males has been studied for decades, the genetic basis of hybrid female sterility in organisms with heterogametic females has received much less attention. We investigated the genetic basis of reproductive isolation in two closely related avian species, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (L. luscinia), that hybridize in a secondary contact zone and produce viable hybrid progeny. In accordance with Haldane's Rule, hybrid females are sterile, while hybrid males are fertile, allowing gene flow to occur between the species. Using transcriptomic data from multiple individuals of both nightingale species, we identified genomic islands of high differentiation (FST ) and of high divergence (Dxy ), and we analysed gene content and patterns of molecular evolution within these islands. Interestingly, we found that these islands were enriched for genes related to female meiosis and metabolism. The islands of high differentiation and divergence were also characterized by higher levels of linkage disequilibrium than the rest of the genome in both species indicating that they might be situated in genomic regions of low recombination. This study provides one of the first insights into genetic basis of hybrid female sterility in organisms with heterogametic females.

Interspecific competition promotes habitat and morphological divergence in a secondary contact zone between two hybridizing songbirds.

Interspecific competition is assumed to play an important role in the ecological differentiation of species and speciation. However, empirical evidence for competition's role in speciation remains surprisingly scarce. Here, we studied the role of interspecific competition in the ecological differentiation and speciation of two closely related songbird species, the Common Nightingale (Luscinia megarhynchos) and the Thrush Nightingale (Luscinia luscinia). Both species are insectivorous and ecologically very similar. They hybridize in a secondary contact zone, which is a mosaic of sites where both species co-occur (syntopy) and sites where only one species is present (allotopy). We analysed fine-scale habitat data for both species in both syntopic and allotopic sites and looked for associations between habitat use and bill morphology, which have been previously shown to be more divergent in sympatry than in allopatry. We found that the two nightingale species differ in habitat use in allotopic sites, where L. megarhynchos occurred in drier habitats and at slightly higher elevations, but not in syntopic sites. Birds from allotopic sites also showed higher interspecific divergence in relative bill size compared to birds from syntopic sites. Finally, we found an association between bill morphology and elevation. Our results are consistent with the view that interspecific competition in nightingales has resulted in partial habitat segregation in sympatry and that the habitat-specific food supply has in turn very likely led to bill size divergence. Such ecological divergence may enhance prezygotic as well as extrinsic postzygotic isolation and thus accelerate the completion of the speciation process.

Competition-driven niche segregation on a landscape scale: Evidence for escaping from syntopy towards allotopy in two coexisting sibling passerine species.

The role of interspecific competition for generating patterns in species' distribution is hotly debated and studies taking into account processes occurring at both large and small spatial scales are almost missing. Theoretically, competition between species with overlapping niches should result in divergence of their niches in sympatry to reduce the costs of competition. Many species show a mosaic distribution within sympatric zones, with the syntopic sites occupied by both species, and allotopic sites where only one species occurs. It is unclear whether such mosaics arise as a consequence of competition-driven niche segregation or due to the decline of their abundances towards range edges driven by environmental gradients. If the interspecific competition matters, we should observe (1) a shift in habitat preferences of one or both species between syntopy and allotopy, and (2) between allopatry and allotopy. Moreover, (3) species should show greater divergence in their habitat preferences in allotopy than in allopatry where (4) no differences in habitat preferences may occur. Finally, (5) shifts should be generally greater in the competitively subordinate species than in the dominant species. We used a unique dataset on abundance of two closely related passerine species, the Common Nightingale (Luscinia megarhynchos) and the Thrush Nightingale (Luscinia luscinia), collected across their syntopy, allotopy and allopatry. The predictions were tested within a generalized mixed-effects modelling framework. After accounting for environmental gradients perpendicular to the species' contact zone, we found a strong support for all but one prediction. Habitat preferences of both species shifted markedly between syntopy and allotopy, as well as between allopatry and allotopy. Whereas the species preferred the same habitats in allopatry, their preferences became strikingly different in allotopy where the abundance of the Common Nightingale increased towards dry and warm sites with low coverage of pastures, while the abundance of the Thrush Nightingale showed exactly opposite trends. Fifth prediction was not supported. Our results indicate that the competition between closely related species can result in considerable changes in habitat use across their geographic ranges accompanied with divergence in their habitat preferences in sympatry. Here, the species "escape" from competition to allotopic sites covered by habitats avoided by the competitor. Therefore, we argue that the interspecific competition is an important driver of species' distribution at both large and small spatial scales.

Patterns of gene flow and selection across multiple species of Acrocephalus warblers: footprints of parallel selection on the Z chromosome.

BACKGROUND: Understanding the mechanisms and selective forces leading to adaptive radiations and origin of biodiversity is a major goal of evolutionary biology. Acrocephalus warblers are small passerines that underwent an adaptive radiation in the last approximately 10 million years that gave rise to 37 extant species, many of which still hybridize in nature. Acrocephalus warblers have served as model organisms for a wide variety of ecological and behavioral studies, yet our knowledge of mechanisms and selective forces driving their radiation is limited. Here we studied patterns of interspecific gene flow and selection across three European Acrocephalus warblers to get a first insight into mechanisms of radiation of this avian group. RESULTS: We analyzed nucleotide variation at eight nuclear loci in three hybridizing Acrocephalus species with overlapping breeding ranges in Europe. Using an isolation-with-migration model for multiple populations, we found evidence for unidirectional gene flow from A. scirpaceus to A. palustris and from A. palustris to A. dumetorum. Gene flow was higher between genetically more closely related A. scirpaceus and A. palustris than between ecologically more similar A. palustris and A. dumetorum, suggesting that gradual accumulation of intrinsic barriers rather than divergent ecological selection are more efficient in restricting interspecific gene flow in Acrocephalus warblers. Although levels of genetic differentiation between different species pairs were in general not correlated, we found signatures of apparently independent instances of positive selection at the same two Z-linked loci in multiple species. CONCLUSIONS: Our study brings the first evidence that gene flow occurred during Acrocephalus radiation and not only between sister species. Interspecific gene flow could thus be an important source of genetic variation in individual Acrocephalus species and could have accelerated adaptive evolution and speciation rate in this avian group by creating novel genetic combinations and new phenotypes. Independent instances of positive selection at the same loci in multiple species indicate an interesting possibility that the same loci might have contributed to reproductive isolation in several speciation events.

Continent-scale global change attribution in European birds - combining annual and decadal time scales.

Species attributes are commonly used to infer impacts of environmental change on multiyear species trends, e.g. decadal changes in population size. However, by themselves attributes are of limited value in global change attribution since they do not measure the changing environment. A broader foundation for attributing species responses to global change may be achieved by complementing an attributes-based approach by one estimating the relationship between repeated measures of organismal and environmental changes over short time scales. To assess the benefit of this multiscale perspective, we investigate the recent impact of multiple environmental changes on European farmland birds, here focusing on climate change and land use change. We analyze more than 800 time series from 18 countries spanning the past two decades. Analysis of long-term population growth rates documents simultaneous responses that can be attributed to both climate change and land-use change, including long-term increases in populations of hot-dwelling species and declines in long-distance migrants and farmland specialists. In contrast, analysis of annual growth rates yield novel insights into the potential mechanisms driving long-term climate induced change. In particular, we find that birds are affected by winter, spring, and summer conditions depending on the distinct breeding phenology that corresponds to their migratory strategy. Birds in general benefit from higher temperatures or higher primary productivity early on or in the peak of the breeding season with the largest effect sizes observed in cooler parts of species' climatic ranges. Our results document the potential of combining time scales and integrating both species attributes and environmental variables for global change attribution. We suggest such an approach will be of general use when high-resolution time series are available in large-scale biodiversity surveys.

Long-term population trends of 48 urban bird species correspond between urban and rural areas.

Colonization of urban areas by wild species is a widespread phenomenon investigated from various ecological and evolutionary perspectives, yet long-term population trends of organisms in urban areas remain understudied. To fill this knowledge gap, we used data from a large-scale breeding bird monitoring scheme and computed population trends in 48 urban bird species in urban and rural areas of a central European country, Czechia. In most species, trends were similar in both environments, indicating common drivers and/or connections between urban and rural populations. In species with significant trends, the positive trends prevailed, suggesting good performance of urbanized species. This may result from wildlife-friendly environmental changes in cities, such as the expansion of green areas and the maturing of woody vegetation. In respect to species traits, more positive trends were found in larger species than in smaller species in both habitats, likely due to the recovery of previously depleted populations.

Sympatry in a nightingale contact zone has no effect on host-specific blood parasite prevalence and lineage diversity.

Parasites are a key driving force behind many ecological and evolutionary processes. Prevalence and diversity of parasites, as well as their effects on hosts, are not uniform across host species. As such, the potential parasite spillover between species can significantly influence outcomes of interspecific interactions. We screened two species of Luscinia nightingales for haemosporidian blood parasites (Plasmodium, Leucocytozoon and Haemoproteus) along an approximately 3000 km transect in Europe, incorporating areas of host distant allopatry, close allopatry and sympatry. We found significant differences in infection rates between the two host species, with common nightingales having much lower parasite prevalence than thrush nightingales (36.7% versus 83.8%). This disparity was mostly driven by Haemoproteus prevalence, which was significantly higher in thrush nightingales while common nightingales had a small, but significantly higher, Plasmodium prevalence. Furthermore, we found no effect of proximity to the contact zone on infection rate in either host species. Despite having lower infection prevalence, common nightingales were infected with a significantly higher diversity of parasite lineages than thrush nightingales, and lineage assemblages differed considerably between the two species, even in sympatry. This pattern was mostly driven by the large diversity of comparatively rare lineages, while the most abundant lineages were shared between the two host species. This suggests that, despite the close evolutionary relationships between the two nightingales, there are significant differences in parasite prevalence and diversity, regardless of the distance from the contact zone. This suggests that spillover of haemosporidian blood parasites is unlikely to contribute towards interspecific interactions in this system.

Accelerated farmland bird population declines in European countries after their recent EU accession.

Agricultural intensification is a major driver of global biodiversity loss. In Europe, intensification progressed over the 20th century and was accelerated by instruments of the EU's Common Agricultural Policy. Central and Eastern European (CEE) countries standing outside the EU until the beginning of the 21st century employed less intensive farming and are considered one of the continent's farmland biodiversity strongholds. Their recent EU accession might be either viewed as a threat to farmland biodiversity due to the availability of funds to increase agricultural production or as an opportunity to implement conservation measures aimed to preserve biodiversity. Here we assessed these possibilities using long-term monitoring data on farmland bird populations in seven CEE countries. We tested whether mean relative abundance and population trends changed after countries' EU accession, and whether such changes also occurred in agricultural management and conservation measures. Both agricultural intensity and spending for agri-environmental and climatic schemes increased when the CEE countries joined the EU. At the same time, farmland bird populations started to decline and their relative abundance was lower after than before EU accession. In addition, increases in fertilizer application were negatively associated with annual changes in relative farmland bird population sizes, indicating a negative impact of intensive agriculture. Taken together, these results indicate that despite the great power of the EU's environmental legislation to improve the population status of species at risk, this does not apply to farmland birds. In their case, the adverse impacts of agricultural intensification most likely overrode the possible benefits of conservation measures. To secure this region as one of the continent's farmland biodiversity strongholds, policy and management actions are urgently needed.

Dense city centers support less evolutionary unique bird communities than sparser urban areas.

Urbanization alters avian communities, generally lowering the number of species and contemporaneously increasing their functional relatedness, leading to biotic homogenization. Urbanization can also negatively affect the phylogenetic diversity of species assemblages, potentially decreasing their evolutionary distinctiveness. We compare species assemblages in a gradient of building density in seventeen European cities to test whether the evolutionary distinctiveness of communities is shaped by the degree of urbanization. We found a significant decline in the evolutionary uniqueness of avian communities in highly dense urban areas, compared to low and medium-dense areas. Overall, communities from dense city centers supported one million years of evolutionary history less than communities from low-dense urban areas. Such evolutionary homogenization was due to a filtering process of the most evolutionarily unique birds. Metrics related to evolutionary uniqueness have to play a role when assessing the effects of urbanization and can be used to identify local conservation priorities.

Sperm competition in tropical versus temperate zone birds.

Sperm competition represents an important component of post-copulatory sexual selection. It has been argued that the level of sperm competition declines in birds towards the equator. However, to date, sperm competition estimates have been available mainly for avian species inhabiting the northern temperate zone. Here we apply a novel approach, using the coefficient of between-male variation (CV(bm)) in sperm size as an index for sperm competition risk, in a comparative analysis of 31 Afrotropical and 99 northern temperate zone passerine species. We found no difference in sperm competition risk between the two groups, nor any relationship with migration distance. However, a multivariate model indicated that sperm competition risk was highest in species with a combination of low body mass and few eggs per clutch. The effect of clutch size was most pronounced in tropical species, which indicates that sperm competition risk in tropical and temperate species is differently associated with particular life-history traits. Although tropical species had lower sperm competition risk than temperate zone species for overlapping clutch sizes, the idea of a generally reduced risk of sperm competition in tropical birds was not supported by our analysis.

Ambient ozone - New threat to birds in mountain ecosystems?

Mountain ecosystems are inhabited by species with specific characteristics enabling survival at high altitudes, which make them at risk from various pressures. In order to study these pressures, birds represent excellent model organisms due to their high diversity and position at the top of food chains. The pressures upon mountain bird populations include climate change, human disturbance, land abandonment, and air pollution, whose impacts are little understood. Ambient ozone (O3) is one of the most important air pollutants occurring in elevated concentrations in mountain conditions. Although laboratory experiments and indirect course-scale evidence suggest its negative effects on birds, population-level impacts remain unknown. To fill this knowledge gap, we analysed a unique 25-years long time series of annual monitoring of bird populations conducted at fixed sites under constant effort in a Central European mountain range, the Giant Mountains, Czechia. We related annual population growth rates of 51 bird species to O3 concentrations measured during the breeding season and hypothesized (i) an overall negative relationship across all species, and (ii) more negative O3 effects at higher altitudes due to increasing O3 concentration along altitudinal gradient. After controlling for the influence of weather conditions on bird population growth rates, we found an indication of the overall negative effect of O3 concentration, but it was insignificant. However, the effect became stronger and significant when we performed a separate analysis of upland species occupying the alpine zone above treeline. In these species, populations growth rates were lower after the years experiencing higher O3 concentration indicating an adverse impact of O3 on bird breeding. This impact corresponds well to O3 behaviour and mountain bird ecology. Our study thus represents the first step towards mechanistic understanding of O3 impacts on animal populations in nature linking the experimental results with indirect indications at the country-level.

Rapid gene content turnover on the germline-restricted chromosome in songbirds.

The germline-restricted chromosome (GRC) of songbirds represents a taxonomically widespread example of programmed DNA elimination. Despite its apparent indispensability, we still know very little about the GRC's genetic composition, function, and evolutionary significance. Here we assemble the GRC in two closely related species, the common and thrush nightingale. In total we identify 192 genes across the two GRCs, with many of them present in multiple copies. Interestingly, the GRC appears to be under little selective pressure, with the genetic content differing dramatically between the two species and many GRC genes appearing to be pseudogenized fragments. Only one gene, cpeb1, has a complete coding region in all examined individuals of the two species and shows no copy number variation. The acquisition of this gene by the GRC corresponds with the earliest estimates of the GRC origin, making it a good candidate for the functional indispensability of the GRC in songbirds.

Effects of light and noise pollution on avian communities of European cities are correlated with the species' diet.

Urbanization affects avian community composition in European cities, increasing biotic homogenization. Anthropic pollution (such as light at night and noise) is among the most important drivers shaping bird use in urban areas, where bird species are mainly attracted by urban greenery. In this study, we collected data on 127 breeding bird species at 1349 point counts distributed along a gradient of urbanization in fourteen different European cities. The main aim was to explore the effects of anthropic pollution and city characteristics, on shaping the avian communities, regarding species' diet composition. The green cover of urban areas increased the number of insectivorous and omnivorous bird species, while slightly decreasing the overall diet heterogeneity of the avian communities. The green heterogeneity-a measure of evenness considering the relative coverage of grass, shrubs and trees-was positively correlated with the richness of granivorous, insectivorous, and omnivorous species, increasing the level of diet heterogeneity in the assemblages. Additionally, the effects of light pollution on avian communities were associated with the species' diet. Overall, light pollution negatively affected insectivorous and omnivorous bird species while not affecting granivorous species. The noise pollution, in contrast, was not significantly associated with changes in species assemblages. Our results offer some tips to urban planners, managers, and ecologists, in the challenge of producing more eco-friendly cities for the future.

Spatial Overlap and Habitat Selection of Corvid Species in European Cities.

Understanding habitat and spatial overlap in sympatric species of urban areas would aid in predicting species and community modifications in response to global change. Habitat overlap has been widely investigated for specialist species but neglected for generalists living in urban settings. Many corvid species are generalists and are adapted to urban areas. This work aimed to determine the urban habitat requirements and spatial overlap of five corvid species in sixteen European cities during the breeding season. All five studied corvid species had high overlap in their habitat selection while still having particular tendencies. We found three species, the Carrion/Hooded Crow, Rook, and Eurasian Magpie, selected open habitats. The Western Jackdaw avoided areas with bare soil cover, and the Eurasian Jay chose more forested areas. The species with similar habitat selection also had congruent spatial distributions. Our results indicate that although the corvids had some tendencies regarding habitat selection, as generalists, they still tolerated a wide range of urban habitats, which resulted in high overlap in their habitat niches and spatial distributions.

More and more generalists: two decades of changes in the European avifauna.

Biotic homogenization (BH) is a process whereby some species (losers) are systematically replaced by others (winners). While this process has been related to the effects of anthropogenic activities, whether and how BH is occurring across regions and the role of native species as a driver of BH has hardly been investigated. Here, we examine the trend in the community specialization index (CSI) for 234 native species of breeding birds at 10,111 sites in six European countries from 1990 to 2008. Unlike many BH studies, CSI uses abundance information to estimate the balance between generalist and specialist species in local assemblages. We show that bird communities are more and more composed of native generalist species across regions, revealing a strong, ongoing BH process. Our result suggests a rapid and non-random change in community composition at a continental scale is occurring, most likely driven by anthropogenic activities.