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Data & codes for "Changes in abundance and distribution of European forest bird populations depend on biome, ecological specialisation and traits"
<h1>1. Selection of European forest bird species and classification of their biome preferences</h1> <p>We selected all species that are related to forest and woodland based on two data sources: Storchová & Hořák (2018) and Tobias et al. (2022), resulting in 107 bird species studied (Data S1). We defined forest bird species as those using environments ranging from closed-canopy forests to more open-canopy woodlands (A. Lehikoinen & Virkkala, 2018; Storchová & Hořák, 2018; Tobias et al., 2022). We determined their biome specialisation using breeding distribution centroids and the overall breeding distribution of each of the species, using the global map of terrestrial ecoregions from Olson et al. (2001) and range data from European Breeding Bird Atlas 1 and 2 (Hagemeijer & Blair, 1997; Keller et al., 2020). We categorised species as Mediterranean, temperate, or boreal based on their predominant biogeographic region. We considered species commonly occurring over several biomes as “generalists”. For instance, we reclassified the two typically boreal species Glaucidium passerinum Linnaeus and Strix uralensis Pallas as “generalists” due to significant range expansions into central and southern Europe in recent decades, therefore no longer restricted to the boreal region. For the complete list of species, biome specialisation, traits, and specialisation indices, refer to Data S1.</p> <h1>2. Changes in abundance and distribution of European forest bird species</h1> <p>We assessed long-term changes in European forest bird populations through two approaches: (i) changes in estimated total European-level species abundance over a 40-year timeframe; and (ii) changes in species spatial distribution over a 30-year timeframe (Fig. 1).</p> <p>We utilized the estimated trends in European-level population size (i.e., the total number of individuals) for each common native European bird species from 1980 to 2017, as reported by Burns et al. (2021). Three species out of the 107 studied forest species were missing in the original manuscript and we used data generated with the same method from 1980 to 2018 from the European assessment, Article 12 (https://nature-art12.eionet.europa.eu/article12/). These abundance trends were calculated by Burns et al. (2021) using multi-sourced annual times series. For each species, they gathered population estimates and trends from each European country as well as European Union (EU)-level population trends. They analysed these data with a Bayesian hierarchical model to reconstruct EU-level smoothed species population time series. The model outputs include an average annual rate of abundance change and an associated 95% credible interval (Burns et al., 2021). Therefore, we did not directly use the average annual rate of abundance change, as this would have led us to consider species with low uncertainty as similar to those with high uncertainty. To account for the uncertainty, we categorised species as (i) declining, i.e., annual rates below one, (ii) increasing, i.e., annual rates above one and (iii) stable, i.e., annual rate whose 95% CI overlap one, i.e., no significant change. To better acknowledge the magnitude of the abundance change, significant changes with rates below 0.98 were labelled as “strongly declining” (i.e., 6.5% of the 107 species), while those above 1.02 were labelled as “strongly increasing” (i.e., 11% of the 107 species). To evaluate the sensitivity of the decision to categorised abundance change data, we also analysed abundance trend as continuous variable (see Supporting Information Fig. S8).</p> <p>To determine changes in species distributions, we used a comparison of species distributions between two periods (i.e., 1985-1988 and 2013-2017) using the European Breeding Bird Atlas 1 and 2 (EBBA 1 & 2; Hagemeijer & Blair, 1997; Howard et al., 2023; Keller et al., 2020). Howard et al. (2023) provided calculations of observed colonisation and extinction areas at a 50 x 50 km resolution across Europe. We measured changes in range as the difference between colonisations and extinctions of each species, with negative values indicating contracting ranges and positive values indicating expanding ranges. Additionally, we calculated the shift in the centre of gravity of the distribution range between the two periods, as a distance (km) along the south-north gradient for each species (Howard et al., 2023).</p> <h1>3. Trait and specialisation data for European forest bird species</h1> <p>We extracted data for six functional traits from several sources (Table 1). (i) The species temperature index (STI)represents the long-term average temperature within the species’ breeding range (A. Lehikoinen et al., 2021). (ii) Diet data during the breeding season were obtained from Storchová & Hořák (2018), classifying species into binary variables as vertebrate carnivorous, invertebrate carnivorous, and herbivores (combining the leaf and seed eaters). Storchová & Hořák (2018) classified species into a diet category when the corresponding food resource represented at least 10% of the species diet throughout the breeding season. Therefore, one species can be in several categories (i.e., omnivores). (iii) We obtained nesting site data from Pearman et al. (2014), classifying species into binary variables as ground nesters, tree hole nesters, or elevated nesters (> 1 m in a tree or shrub). We also included data on (iv) species dependence on old-growth forests (Data S1; mostly from Fraixedas et al. (2015) and Mönkkönen et al. (2014), if present on both references, we classified them as “1” and if only in one reference as “0.5”), (v) migration distance (Howard et al., 2023), and (vi) body mass (Tobias et al., 2022).</p> <p>Finally, we extracted and developed seven species specialisation indices. (i) We used an overall specialisation index based on multiple traits (i.e., temperature, diet, foraging behaviour and substrate, habitat, and nesting site), and (ii) a nesting specialisation index, both obtained from Morelli et al. (2019). Both indices represent species specialization based on the dispersion of trait preferences for each species: e.g., nesting specialism equal 0 for species that nest in all habitat type and equal 1 for species that nest in only one habitat type). They are both calculated using the Gini index of inequality, which measures overall dispersion across, e.g., all traits for the overall specialization, based on data from Pearman et al. (2014) and Storchová & Hořák (2018). For additional information, see Morelli et al. (2019). We also used (iii) the diet specialisation index, (iv) the species distribution range during the breeding season (hereafter “breeding range area”) and (v) the climatic niche breadth from Reif et al. (2016). The diet specialisation index was calculated as the coefficient of variation for diet preferences for each species, where high values denotes specialized species (Reif et al., 2016). The breeding range area was evaluated as the number of 50-km squares in the distribution maps in Europe occupied by each species during the reproduction period, and is based on EBBA 1 (Hagemeijer & Blair, 1997). The climatic niche breadth was calculated as the difference between the 5% hottest and the 5% coldest mean temperature between April and June in which each species occurs, using EBBA 1 (Hagemeijer & Blair, 1997; Reif et al., 2016).</p> <p>Additionally, (vi) we calculated a broadleaf forest specialisation index based on binary forest habitat preferences (Storchová & Hořák, 2018), assigning values of one for species found only in broadleaf forests; zero for those in coniferous forests, and 0.5 for those found in both. Lastly, (vii) we created a forest specialisation index based on the species habitat preferences (Storchová & Hořák, 2018). The forest specialisation index was calculated as the mean of species affinity across habitats. We used increasing habitat weights along a gradient of tree dominance: open habitats as 1, shrubland as 1.5, woodland as 2 (i.e., species associated with habitats structured by trees in lower density than in forest), forest generalist (found in both coniferous and broadleaf dense forests) as 3, and forest specialist (found only either in coniferous or broadleaf dense forests) as 4. For instance, the index value for species occurring either in shrubland, woodland or both broadleaf and coniferous forests is 2.167.</p> <h1>4. Data analysis</h1> <p>Data analyses were conducted with R software version 4.4.1. (R Core Team, 2024). Given the non-independence of species due to their genetic relatedness, we accounted for interspecific phylogenetic distance in all models. We constructed the phylogenetic tree for the 107 European forest bird species using ‘rotl’ and ‘ape’ R-packages (Michonneau et al., 2022; Paradis et al., 2023). We used rotl as an interface with the "Open Tree of Life", employing tol_induced_subtree R-function to generate the phylogenetic tree and compute.brlen R-function to set branch lengths using Grafen’s computation. We generated separate phylogenetic trees for boreal (17), temperate (15), Mediterranean (16) and “generalist” (59) species to perform biome-specific analysis (see Supplementary Information, Figs. S1 & S2).</p> <p>To investigate the effects of functional traits and specialisation indices on abundance, range changes, and distribution shift, we used two regression methods. All methods were based on the relationships between a measure of change and a functional trait or specialisation index. Our sample unit is an individual forest bird species (i.e., one value for each species, either abundance or range change, or distribution shift). Abundance change was a categorical variable (i.e., strong decline – decline – stable – increase – strong increase), while range change (i.e., difference between colonisation and extinction) and distribution shift (i.e., south-north shift) were continuous variables. Therefore, to study abundance changes, we used proportional-odds linear mixed effects model using (Phylo)clmm R-function from the ‘ordinal’ R-package (Christensen, 2022). Interspecific phylogenetic relatedness was included as a random effect, reflecting the correlation between species based on phylogenetic distances (see also Hagge et al. (2021) and Seibold et al. (2015)). For distribution changes, we employed phylogenetic generalised least squares regression (PGLS) using the gls R-function from the ‘nlme’ R-package (Pinheiro et al., 2023). The phylogenetic correlation structure was integrated into PGLS using Pagel’s lambda parameter (λ; Pagel (1999)) a widely used measured of phylogenetic signal strength (see, e.g., Hagge et al., 2021; Triviño et al., 2013).</p> <p>Furthermore, we included latitude, a key driver of bird communities at broad scales (Luoto et al., 2007), as a fixed covariable (centroid latitude of the species’ breeding distribution) in all global models (i.e., species from all biomes together), except for the STI model due to strong correlation. For biome-specific analysis, we included latitude only in boreal species models for range change and distribution shift, as it significantly improved model fit (ΔAIC < -2). We did not add latitude for models specific to temperate, Mediterranean, and generalist species since it did not improve model fits (ΔAIC > -2). Additionally, we included breeding range area in range change and distribution shift models, assuming that species with larger ranges would exhibit larger shifts. We scaled predictors to a mean of 0 and standard deviation of 1 to facilitate effect size comparisons. We adjusted p-values using the Holm method (for n=3) to account for multiple testing of traits and specialisation indices on three response variables.</p>
Ecological traits drive genetic structuring in two open-habitat birds from the morphologically cryptic genus Elaenia (Aves: Tyrannidae)
<p>Understanding the relative contributions of the many factors that shape population genetic structuring is a central theme in evolutionary and conservation biology. Historically, abiotic or extrinsic factors (such as geographic barriers or climatic shifts) have received greater attention than biotic or intrinsic factors (such as dispersal or migration). This focus stems in part from the logistical difficulties in taking a comparative phylogeographic approach that contrasts species that have experienced similar abiotic conditions during their evolution yet differ in the intrinsic attributes that might shape their genetic structure. To explore the effects of intratropical migration on the genetic structuring of Neotropical birds, we chose two congeneric species, the Lesser Elaenia (<em>Elaenia chiriquensis</em>) and the Plain-crested Elaenia (<em>E. cristata</em>), that are largely sympatric, and which have similar plumage, habitat preferences, and breeding phenology. Despite these many commonalities, they differ in migratory behavior: <em>E. chiriquensis</em> is an intratropical migratory species while <em>E. cristata</em> is sedentary. We used a reduced representation genomic approach to test whether migratory behavior is associated with increased gene flow and therefore lower genetic population structure. As predicted, we found notably stronger genetic structuring in the sedentary species than in the migratory ones. <em>E. cristata</em> comprises genetic clusters with geographic correspondence throughout its distribution, while there are no geographic groups within Brazil for <em>E. chiriquensis</em>. This comparison adds to the growing evidence about how intrinsic traits like migration can shape the genetic structuring of birds, and advances our understanding of the diversification patterns of the understudied, open habitat species from South America.</p>
The causes and ecological context of rapid morphological evolution in birds
<p><span>Episodic pulses in morphological diversification are a prominent feature of evolutionary history, driven by factors that remain widely disputed. Resolving this question has proved challenging because comprehensive species-level data are generally unavailable at sufficient scale. Combining global phylogenetic and morphological data for birds, we show that pulses of diversification in lineages and traits tend to occur independently and in different contexts. Speciation pulses are preceded by greater differentiation in overall morphology and habitat niche, then followed by increased rates of beak evolution. Contrary to standard hypotheses, pulses of morphological diversification tend to be associated with habitat niche stability rather than adaptation to different diets and habitat types. These patterns suggest that the timing of diversification varies across traits according to their ecological function, and that pulses of morphological evolution may occur when successful lineages subdivide niche space within particular habitat types. Our results highlight the growing potential of functional trait data sets to refine macroevolutionary models.</span></p>
Genomic and phenotypic divergence‐with‐gene‐flow across an ecological and elevational gradient in a neotropical bird
<p>Aim: Along with environmental gradients, some species show significant differences in morphological, ecological-related traits. Those differences are commonly related to past events of allopatry but, alternatively, could be caused by natural selection in the presence of gene flow. We aimed to explore the prevalence of the divergence-with-gene-flow model across the Chaco-Andes dry forest belt, testing competing models of evolution in a Neotropical bird.</p> <p>Location: Central Andes Mountain range and Chaco region of Argentina and Bolivia. </p> <p>Taxon: Phytotoma rutila (Aves, Cotingidae).</p> <p>Methods: We studied ddRADseq loci (4,893 SNPs) of 21 tissue samples and body size variation of 146 specimens. We evaluated population genetic structure and tested the effects of altitude and distance on genomic divergence. To evaluate allopatry and divergence-with-gene-flow, we compared the divergence on phenotypic traits (bill, tarsus, and wing measurements) versus neutral genomic variation, conducted coalescent analyses to estimate gene flow and divergence time among populations, and calculated relative (FST) versus absolute (DXY) genomic divergence.</p> <p>Results: a) there is a genomic and phenotypic differentiation in P. rutila matched the highland-lowland axis, where the altitude variation explains genomic variation; b) A larger phenotypic than neutral genomic variation was found. c) there is an asymmetric gene flow between populations; d) a pattern of relative and absolute genomic differentiation compatible with divergence-with-gene-flow.</p> <p>Main conclusions: The mechanism behind the morphological and genomic diversification along the Chaco-Andes dry forest belt in P. rutila is divergence‐with‐gene‐flow. Far more complex than we traditionally thought, diversification in South America implicates gene flow between populations and also natural selection along with the environmental gradients, as well as vicariance, contrasting with the idea of tropical speciation primarily based on allopatric models.</p> <p> </p>
Ecological and geographical marginality in rear edge populations of Palaearctic forest birds (data)
<p>The centre–periphery hypothesis predicts that habitat suitability will decrease at the edge of a species' range, a pattern often questioned by empirical data. Here we explore if habitat suitability decreases southwards and shapes the abundance distribution of rear edge populations of forest birds within the restricted geographical setting of the south-western Palaearctic. We also test if birds endemic to the area fit more poorly to the latitudinal decrease of habitat suitability due to the putative effect of adaptations to regional conditions. Location: North-western Africa (Morocco) Time period: Present day Major taxa studied: Passerines (11 species) Methods: Bird occurrences were used to model species distribution and line transects were used to estimate bird abundance. Occurrence probabilities provided by species distribution models were used to display the spatial patterning of habitat suitability. Habitat suitability was employed to predict abundance after controlling for the effect of the distance to some regional source areas of forest birds (tree covered large areas). The species were classified as North African endemic according to an updated review of their taxonomic status. Results: Habitat suitability decreased southwards, supporting the predicted relationship between ecological and geographical marginality in most species. Abundance was positively correlated to habitat suitability and negatively correlated to distance to source areas. The taxonomic status of birds did not affect the patterns. Main conclusions: The southward decrease of habitat suitability predicted by the centre–periphery hypothesis shapes the distribution of rear edge populations of forest birds within the south-western Palaearctic. As most of these populations are endemic, the results suggest that they track the gradients in isolation within the geographical setting of north-western Africa. These results support the vulnerability of these isolated, peripheral populations of forest birds to large-scale environmental changes in a region under the effect of increasing drought and temperature.</p>
Dataset on foraging ecology of shrubland bird community
<p>Habitat loss due to increasing anthropogenic disturbance is the major driver for bird population declines across the globe. Within the Eastern Ghats of India, shrubland bird communities are threatened by shrinking of suitable habitats due to increased anthropogenic disturbance and climate change. Development of an effective habitat management strategy is hampered by the absence of data for this bird community. To address this knowledge gap, we examined foraging sites for 14 shrubland bird species, including three declining species, in three study areas representing the shrubland type of forest community in the Eastern Ghats. We recorded microhabitat features within an 11 m radius of observed foraging points and compared these data with similar data from random plots. We used chi-square to test the association between plant species and bird species for sites where they were observed foraging. We observed significant differences between foraging sites of all the study species and random plots, thus indicating selection for foraging habitat. Using linear discriminant analysis, we found that the microhabitat features important for the bird species were shrub density, vegetational height, vertical foliage stratification, grass height, and percent rock cover. Our results show that diet guild and foraging strata influence the foraging microhabitat selection of a species (e.g., ground-foraging species differed significantly from other species). Except for two species, all focal birds were associated with at least one plant species. The plant-bird association was based on foraging, structural, or behavioral preferences. Several key factors affecting foraging habitat such as shrub density can be actively managed at the local scale. Strategic and selective harvesting of forest products and a spatially and temporally controlled livestock grazing regime may allow regeneration of scrubland and create conditions favorable to birds.</p>
Figure 5 in Knowledge gaps regarding frugivorous ecological networks between birds and plants in Brazil
Figure 5. Complex ecological network constructed from information about interactions between frugivorous birds (triangles) and non-native plants (circles) in the Brazilian Atlantic Forest (A) and Cerrado (B). Each color represents an agglomerate of species that are more connected among themselves than with species of other agglomerates. Names in triangles and circles represent are abbreviations of species names. Abbreviations are defined in the supplementary material (S1).
Figure 3 in Knowledge gaps regarding frugivorous ecological networks between birds and plants in Brazil
Figure 3. Complex ecological network constructed with information about interactions between frugivorous birds (triangles) and plants (circles) in the Brazilian Atlantic Forest. Each color represents an agglomerate of species that are more connected among themselves than with species of other agglomerates. Species with the highest values of connectivity and centrality are circled. Names in triangles and circles are abbreviations of species names. Abbreviations are defined in the supplementary material (S1).
Figure 4 in Knowledge gaps regarding frugivorous ecological networks between birds and plants in Brazil
Figure 4. Complex ecological network constructed with information about interactions between frugivorous birds (triangles) and plants (circles) in the Brazilian Cerrado. Each color represents an agglomerate of species that are more connected among themselves than with species of other agglomerates. Species with the highest values of connectivity and centrality are circled. Names in triangles and circles are abbreviations of species names. Abbreviations are defined in the supplementary material (S1).
Depleted lean body mass after crossing an ecological barrier differentially affects stopover duration and refueling rate among species of long-distance migratory birds
<p>During the long-distance migratory flights of birds, lean mass breakdown occurs in concert with fat catabolism and is expected to have repercussions on total stopover duration because birds require time to rebuild lean tissue before accumulating fat reserves. Despite this, little is known about the role of in-flight lean mass breakdown on stopover duration because direct measurements are restricted by the destructive nature of traditional body composition analysis and the technological limitations of tracking small birds over large expanses. We used non-lethal, non-invasive Quantitative Magnetic Resonance technology and plasma metabolite profiling to measure the body composition and physiological state of free-living birds captured at a migratory stopover site after flight across the Gulf of Mexico, and an automated radiotelemetry array covering ~5000 km<sup>2</sup> to track stopover duration and regional movements. We tested whether stopover duration is prolonged in individuals arriving with lower lean mass and investigated how lean mass affects regional movements. Stopover duration decreased by 22% for each additional gram of lean mass in Northern Waterthrush (Parkesia noveboracensis), but this relationship was not apparent in Swainson's Thrush (Catharus ustulatus), Gray-cheeked Thrush (Catharus minimus), or Yellow-billed Cuckoo (Coccyzus americanus), even though these species also arrived with depleted lean mass. Stopover duration increased for Swainson's Thrush with higher plasma uric acid, a marker of protein catabolism. Northern Waterthrush with higher plasma triglycerides had longer stopovers. Our findings suggest that migratory birds may compensate for substantial lean mass losses by increasing refueling rate or relocating habitat, and highlights species-level differences in lean mass breakdown and the associated impacts on physiological function. Our results highlight the strategies used by different species to recover from a trans-Gulf of Mexico flight and resume migration, which improves our understanding of the annual cycle of migratory birds.</p>
Data from: Nocturnal giants: evolution of the sensory ecology in elephant birds and other palaeognaths inferred from digital brain reconstructions
The recently-extinct Malagasy elephant birds (Palaeognathae, Aepyornithiformes) included the largest birds that ever lived. Elephant bird neuroanatomy is understudied but can shed light on the lifestyle of these enigmatic birds. Paleoneurological studies can provide clues to the ecologies and behaviors of extinct birds because avian brain shape is correlated with neurological function. We digitally reconstruct endocasts of two elephant bird species, Aepyornis maximus and A. hildebrandti, and compare them with representatives of all major extant and recently-extinct palaeognath lineages. Among palaeognaths, we find large olfactory bulbs in taxa generally occupying forested environments where visual cues used in foraging are likely to be limited. We detected variation in olfactory bulb size among elephant bird species, possibly indicating interspecific variation in habitat. Elephant birds exhibited extremely reduced optic lobes, a condition also observed in the nocturnal kiwi. Kiwi, the sister taxon of elephant birds, have effectively replaced their visual systems with hyperdeveloped olfactory, somatosensory and auditory systems useful for foraging. We interpret these results as evidence for nocturnality among elephant birds. Vision was likely deemphasized in the ancestor of elephant birds and kiwi. These results show a previously unreported trend toward decreased visual capacity apparently exclusive to flightless, nocturnal taxa endemic to predator-depauperate islands.
Ecological and evolutionary drivers of geographic variation in songs of a Neotropical suboscine bird: The Drab-breasted Bamboo Tyrant (Hemitriccus diops, Rhynchocyclidae)
<p>Understanding the evolutionary and ecological mechanisms that shape the spatial divergence of signals involved in reproductive isolation is a central goal in studies of speciation. For birds with innate songs, such as the suboscine passerine birds, the integration and comparison of both genetic and ecological factors in explaining song variation at the microevolutionary scale is rare. Here we evaluated the evolutionary and ecological processes underlying the variation in the songs of the Atlantic Forest endemic Drab-breasted Bamboo Tyrant (<i>Hemitriccus diops</i>), testing the effects of both stochastic and adaptive processes, namely the Stochastic and Adaptation Acoustic Hypotheses, respectively. We combined vocal, genetic and ecological (climate and forest cover) data across the species' range. To this end, we analyzed 89 samples of long and short songs. We performed analyses on raw and synthetic data song variables with linear mixed models and multivariate statistics. Our results show that both song types differ in spectral features between the two extant phylogeographic lineages of this species, but such vocal divergence is weak and subtle in both song types. Overall, there is a positive relationship of acoustic distances with the amount of forest cover in long songs. Our results suggest that there is cryptic geographical variation in both song types and that this variation is associated with low levels of genetic divergence in both songs and with ecological factors in long songs.</p>
Remote sensing and ecological variables related to Influenza A prevalence and subtype diversity in wild birds in the Lluta wetland of northern Chile
<p>Supplemental material for manuscript, tables 1 and 2</p>
Ecological and geographical marginality in rear edge populations of Palaearctic forest birds (data)
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Code from: Climate, ecological dynamics, and the seasonal distribution of birds in mountains
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Depleted lean body mass after crossing an ecological barrier differentially affects stopover duration and refueling rate among species of long-distance migratory birds
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Data from: Nocturnal giants: evolution of the sensory ecology in elephant birds and other palaeognaths inferred from digital brain reconstructions
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Dataset on foraging ecology of shrubland bird community
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The causes and ecological context of rapid morphological evolution in birds
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Genomic and phenotypic divergence‐with‐gene‐flow across an ecological and elevational gradient in a neotropical bird
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Allen Brain Atlas
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