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799 results for “abundance data”
Data from: Weighting effective number of species measures by abundance weakens detection of diversity responses
1. The effective number of species (ENS) has been proposed as a robust measure of species diversity that overcomes several shortcomings of both diversity indices and species richness measures. However, it is not yet clear if ENS improves interpretation and comparison of biodiversity monitoring data, and ultimately resource management decisions. 2. We used simulations of five stream macroinvertebrate assemblages and spatially extensive field data of stream fishes and mussels to show (1) how different ENS formulations respond to stress and (2) how diversity-environment relationships change with values of q, which weight ENS measures by species abundances. 3. Values of ENS derived from whole simulated assemblages with all species weighted equally (true species richness) steadily decreased as stress increased, and ENS-stress relationships became weaker and more different among assemblages with increased weighting. 4. The amount of variation in ENS across the fish and mussel assemblages that was associated with environmental gradients decreased with increasing q. 5. Synthesis and applications: ENS does not improve interpretability of how diversity responds to stress or natural environmental gradients, and incorporating relative abundance into species diversity measures as implemented in ENS can actually weaken detection of diversity responses. Ecologists need to be cautious about use and interpretation of diversity measures whose values are jointly influenced by richness and evenness, including ENS, and instead separately assess species richness, species evenness, and compositional change in ecological communities.
Data from: Integrating abundance and diet data to improve inferences of food web dynamics
1. Both population abundances and chemical tracers are useful tools for studying consumer-resource interactions. Food web models parameterized with abundances are often used to understand how interactions structure communities and to inform management decisions of complex ecological systems. Unfortunately, collecting abundance data to parameterize these models is often expensive and time-consuming. Another approach is to use chemical tracers to estimate the proportional diets of consumers by relating the tracers in their tissues to those found in their food sources. Although tracer data are often inexpensive to collect relative to abundances, diet proportions provide little information on the per-capita consumption rates of consumers. Here, we show how integrating these data sources can be used to better estimate of consumption rates. 2. Our modeling approach informs traditional multispecies population abundance models using proportional diet data. We used simulations to determine whether integrated food web datasets were more informative than traditional abundance datasets and demonstrated the use of our integrated approach by estimating consumption rates of humpback whales (\textit{Megaptera novaeangliae}) in the western Gulf of Alaska using abundances coupled with stable isotopes as a tracer. 3. Our simulations demonstrated that integrated models improved the ability to resolve alternative hypotheses about the functional response and yielded more precise parameter estimates relative to standard food web models. The integrated data approach was especially informative under low sample sizes or high process variance. Our application of the integrated modeling approach to humpback whale indicated that fish averaged about 25\% of whale diets, though this proportion declined over the course of the study. We also found that traditional abundance model estimates of humpback whale consumption were non-estimable and that the integrated food web model led to estimable consumption rates. 4. Our results show that integrating stable isotopes and abundance datasets provides an exciting way forward for parameterizing multispecies models in data-limited systems. We expect that future developments of these integrated approaches will extend current food web theory by allowing ecologists to study predation dynamics over seasonal time scales and at the individual level.
Data from: Large-scale manipulation of the acoustic environment can alter the abundance of breeding birds: evidence from a phantom natural gas field
1. Altered animal distributions are a consequence of human expansion and development. Anthropogenic noise can be an important predictor of abundance declines near human infrastructure, yet more information is needed to understand noise impacts at the spatial and temporal scales necessary to alter populations. 2. Energy development and associated anthropogenic noise are globally pervasive, and expanding. For example, 600,000 new natural gas wells have been drilled across central North America in less than twenty years. 3. We experimentally broadcast energy sector noise (recordings of compressor engines) in Southwest Idaho (USA). We placed arrays of speakers creating a "phantom natural gas field" in a large-scale experiment, and tested the effects of noise alone on breeding songbird abundance. To examine variation in human-caused noise, we broadcast two types of compressor noise, one with a slightly higher sound intensity and greater bandwidth than the other. 4. Our phantom natural gas field encompassed approximately 100 km2. We broadcast noise for over three continuous months, for each of two seasons, and quantified over 20,000 hours of background sound levels. 5. Brewer's sparrows (Spizella breweri) were affected by our narrowband playback, declining 30% 50 m from the speaker arrays. During our broadband playback, all species combined and Brewer's sparrows decreased 20% and 33% respectively at the scale of our sites (~0.5 km2; up to 400 m from speaker arrays). 6. Our results show the importance of incorporating the acoustic structure of noise when estimating the cost of noise exposure for populations and suggest an urgent need for noise mitigation, such as quieting compressor station noise, in energy extraction fields and natural areas broadly.
Data from: Legume abundance along successional and rainfall gradients in neotropical forests
The nutrient demands of regrowing tropical forests are partly satisfied by nitrogen (N)-fixing legume trees, but our understanding of the abundance of those species is biased towards wet tropical regions. Here we show how the abundance of Leguminosae is affected by both recovery from disturbance and large-scale rainfall gradients through a synthesis of forest-inventory plots from a network of 42 Neotropical forest chronosequences. During the first three decades of natural forest regeneration, legume basal area is twice as high in dry compared to wet secondary forests. The tremendous ecological success of legumes in recently disturbed, water-limited forests is likely related to both their reduced leaflet size and ability to fix N2, which together enhance legume drought tolerance and water-use efficiency. Earth system models should incorporate these large-scale successional and climatic patterns of legume dominance to provide more accurate estimates of the maximum potential for natural N fixation across tropical forests.
Data from: Reciprocal abundance shifts of the intertidal sea stars, Evasterias troschelii and Pisaster ochraceus, following sea star wasting disease
Disease emergence occurs within the context of ecological communities, and disease driven declines in host populations can lead to complex direct and indirect ecological effects. Varying effects of a single disease among multiple susceptible hosts could benefit relatively resistant species. Beginning in 2013, an outbreak of sea star wasting disease (SSWD) led to population declines of many sea star species along the west coast of North America. Through field surveys and laboratory experiments, we investigated how and why the relative abundances of two co-occurring sea star species, Evasterias troschelii and Pisaster ochraceus, shifted during the ongoing wasting epidemic in Burrard Inlet, British Columbia, Canada. We hypothesized that Evasterias is competitively inferior to Pisaster but more resistant to SSWD. Thus, we predicted that SSWD-induced declines of Pisaster could mitigate the negative effects of SSWD on Evasterias, as the latter would experience competitive release. We document shifts in sea star abundance from 2007-2017: Pisaster abundance and mean size declined during the outbreak, while Evasterias abundance increased from relatively rare to numerically dominant within the intertidal. When exposed to symptomatic sea stars, Pisaster and Evasterias both showed signs of SSWD, but transmission and susceptibility was lower in Evasterias. Despite diet overlap documented in our field surveys, Evasterias was not outcompeted by Pisaster in laboratory trails conducted with the relatively small Pisaster available after the outbreak. Interference competition with larger Pisaster, or prey exploitation by Pisaster during summer when Evasterias is primarily subtidal, may explain the rarity of Evasterias prior to Pisaster declines. Our results suggest that indirect effects mediated by competition can mask some of the direct effects of disease outbreaks, and the combination of direct and indirect effects will determine the restructuring of a community after disturbance.
Data and metadata dealing with prokaryote and viral abundances from a variety of ecosystems
<p>Data from 210 articles and five unpublished studies were used for the meta-analysis. Articles were gathered using on-line databases (ScienceDirect, Wiley Online Library, Springer Link, PubMed and Google), using the keywords "virus-to-prokaryote ratio", "virus-to-bacterium ratio", "VPR", "VBR" and "viral abundance". Interesting reports were also found within the references of publications dealing with viral ecology. Publications were chosen according to the data they contained with a priority on articles containing VPR values (184 out of the 210 publications and four out of five unpublished studies) and viral abundance data. Articles lacking information on VPR and viral numbers were discarded (e.g. reports with only prokaryotic abundance, but lacking data on viral numbers, etc.), as the focus was on the ratio between viruses and prokaryotes. When data of interest were not available in the analysed reports, authors were contacted for more detail. When VPR values were not cited as such given within a publication, they were calculated according to the given viral and prokaryotic abundances provided therein. The file corresponding to our database was created by KJ Parikka. The doi was obtained by S Jacquet with INRA services.</p>
Data and code for: "Large reductions in tropical bird abundance attributable to heat extreme intensification "
<p>Data and code necessary to reproduce results of paper:</p> <p>Large reductions in tropical bird abundance attributable to heat extreme intensification</p> <p>By Maximilan Kotz, Tatsuya Amanon and James Watson.</p> <p>Please contact maximilian.kotz@bsc.es / maxkotz@pik-potsdam.de for questions.</p> <p> </p>
Multitrophic metacommunity dataset, with metapopulation level butterfly data, in addition to predation pressure and floral abundance
<p>This dataset includes metapopulation level butterfly data within a butterfly metacommunity sampled across 15 sites at Burnt Lands Provincial Park in Ontario, Canada, during the summer of 2019. It includes floral abundance at each site for each sampling round. It also includes information on the number of predator attacks on experimental clay butterfly models at each site. It contains data on site size and connectivity for the 15 sites, as well as the length of butterfly survey transects sampled in each site.</p>
Data from: Plastic mulches reduce abundance of some arthropods but are not detrimental to pollinators in primocane raspberries
<p>Cultural practices modify agroecosystems to prevent or reduce pest outbreaks, but they may be detrimental to beneficial arthropods and non-target effects are not commonly evaluated. Plastic mulches are an effective management practice for spotted-wing drosophila (<em>Drosophila suzukii </em>Matsumura) since they increase UV radiance in the plant canopy to reduce larval infestation of fruit. In this two-year study, we evaluated how black, white, and metallic plastic mulches impact populations of arthropods, including predators of <em>D. suzukii </em>and raspberry pollinators in Wisconsin. The three plastic mulches did not affect arthropod richness and did not affect the abundance of about 65% of arthropod groups identified. In the raspberry canopy, the black mulch decreased the abundance of Orthoptera and Thysanoptera and increased <em>Orius </em>spp.; the white mulch increased Diptera, Thysanoptera, and <em>Orius </em>spp.; and the metallic mulch decreased Coleoptera, micro-Hymenoptera, Orthoptera, and Thysanoptera. On the ground, all mulches decreased the abundance of Gryllidae, the black and metallic increased Formicidae, and the white increased Staphylinidae. We reported ten insect groups visiting raspberry flowers. <em>Bombus impatiens </em>Cresson<em> </em>was the most common, accounting for 82% of flower visits. The plastic mulches did not reduce flower visitation, though the white plastic mulch increased the abundance of <em>B. impatiens</em> compared to the other mulch treatments. Plastic mulches can reduce populations of pests such as <em>D. suzukii</em> and overall have no severe non-target effects on other arthropods in Wisconsin raspberry.</p>
Data from: Friction and instability of glaucophane gouges at blueschist temperatures support abundance of intermediate-depth earthquakes
<p>Fluid release from the hydraulically-confined dehydration of blueschist minerals may significantly elevate fluid pressures and concomitantly reduce effective stresses. This is a viable mechanism to explain brittle failure and frictional instability, and it is a possible explanation for intermediate-depth earthquakes in cold subduction zones. We examine this hypothesis for glaucophane – a key index mineral for blueschist facies – at lower confining stresses where behavior is poorly understood. We conduct laboratory shear tests on glaucophane gouge at temperatures of 100–500<em>℃</em> and effective normal stresses of 50–200 <em>MPa</em>, to explore the controls of temperature, stresses and excess pore fluid pressures on fault friction. Frictional strength of glaucophane gouge at representative temperatures and stresses is ~0.70 and insensitive to temperature with a slight increase in friction coefficient at lower effective stresses. Elevating temperature promotes a transition from velocity-strengthening to mild velocity-weakening behavior, indicating the destabilizing effect of high-temperature downdip in subduction zones. Reducing effective normal stress or concomitantly elevating pore fluid pressure, potentially sourced from dehydration reactions, further strengthens the velocity-weakening response and would be manifest as moderate-sized earthquakes. This observed instability at higher temperatures or lower stresses is indexed with and accompanied by denser distributions of strongly- to moderately-localized shears in the microstructures – congruent with the observed mechanical response. Our results support the potential for enhanced unstable sliding of glaucophane gouges at lower effective stresses and at blueschist facies temperatures - and have significant implications for understanding the abundance of intermediate-depth earthquakes apparent in cold subduction zones.</p>
Data from: Abundance models of endemic birds of the Sierra Nevada de Santa Marta, northern South America, suggest small population sizes and dependence on montane elevations
<p>Abundance measures are almost non-existent for several bird species threatened with extinction, particularly range-restricted Neotropical taxa, for which estimating population sizes can be challenging. Here we use data collected over nine years to explore the abundance of 11 endemic birds from the Sierra Nevada de Santa Marta (SNSM), one of Earth's most irreplaceable ecosystems. We established 99 transects in the "Cuchilla de San Lorenzo" Important Bird Area within native forest, early successional vegetation, and areas of transformed vegetation by human activities. A total of 763 bird counts were carried out covering the entire elevation range in the study area (~175–2650 m). We applied hierarchical distance-sampling models to assess elevation- and habitat-related variation in local abundance and obtain values of population density and total and effective population size. Most species were more abundant in the montane elevational range (1800–2650 m). Habitat-related differences in abundance were only detected for five species, which were more numerous in either early succession, secondary forest, or transformed areas. Inferences of effective population size indicated that at least four endemics likely maintain populations no larger than 15,000–20,000 mature individuals. Estimates of species' area of occupancy and effective population size were lower than most values previously described, a possible consequence of increasing anthropogenic threats. At least four of the endemics exceeded criteria for threatened species listing and a thorough evaluation of their extinction risk should be conducted. Population strongholds for most of the study species were located on the northern and western slopes of the SNSM between 1500–2700 m. We highlight the urgent need for facilitating effective protection of native vegetation in premontane and montane ecosystems to safeguard critical habitats for the SNSM's endemic avifauna. Follow-up studies collecting abundance data across the SNSM are needed to obtain precise range-wide density estimations for all species.</p>
Data on arthropod abundance in tropical forest restoration plots with high or low plant phylogenetic diversity
<p>Consideration of plant phylogenetic diversity in ecological restoration carries substantial potential, as communities with a greater diversity of lineages with older evolutionary histories can increase the diversity of niches and thus are likely to recover larger species networks than communities clustered in specific clades with reduced variation in functional traits. In this study, we experimentally assessed how arthropod communities were affected by the phylogenetic diversity of a set of tropical tree species. We established 12 experimental restoration plots with either high or low plant phylogenetic diversity, while maintaining constant the number of plant species. After one and three years, arthropods with different feeding habits (herbivores, predators, pollinators, and detritivores) were collected and identified as morphospecies or operational taxonomic units using metabarcoding techniques. We provide insights on the influence of plant phylogenetic diversity on arthropod abundance and species diversity, particularly among predator, pollinator, and detritivore common and dominant species, which increased with plant phylogenetic diversity. The trend, however, was the opposite for the diversity of herbivore common and dominant species, which decreased as plant phylogenetic diversity increased. These findings highlight the importance of considering plant species richness when designing restoration strategies, but also their evolutionary histories, as the same number of plant species can produce different outcomes for higher trophic levels, as a function of their phylogenetic relationships. </p>
Data for: Preening correlates with lower feather bacteria abundance but not feather coloration in a lek-breeding bird
<p>Feathers are structures unique to birds that serve important functions such as flight, thermoregulation, and communication. Bacteria that live on the feathers, particularly ones that can break down keratin, have the potential to damage feathers and disrupt their use in communication. We predicted that birds could behaviorally manage their feather bacterial abundances by preening their feathers. We also predicted that individuals with lower feather bacterial abundances would have brighter and more colorful feathers. To test these predictions, we measured the amount of time individuals in a colony of captive Indian peafowl (<em>Pavo cristatus</em>) spent preening their feathers. We also collected feathers to determine bacteria abundance on the feather surface and to measure feather coloration. We found that birds had lower feather bacteria levels when they spent more time preening their own feathers, but only in female birds. We also found that bacteria abundances were not correlated with any feather color variables we measured. These results suggest that birds can manage feather bacterial abundances by preening but feather bacteria may not influence feather coloration in this species.</p>
Data from: using camera traps and N-mixture models to estimate population abundance: model selection really matters
<p>Estimating the abundance or density of wildlife populations is a critical part of species conservation and management, but estimates can vary greatly in precision and accuracy according to the data collection and statistical methods, sampling and ecological variation, and sample size. N-mixture models are a common method which has been applied to a wide range of taxa for estimating population abundance from non-invasive data representing the distribution of the species. We used population estimates from an aerial survey of moose and videos from camera traps to assess the sensitivity of N-mixture models to ecological conditions, the spatial scale at which they were measured, the criteria used to define independent detections, and model choice based on the common statistical criterion of parsimony. The most parsimonious N-mixture models were considerably biased, producing implausibly large and considerably imprecise estimates of the abundance of moose. Most of the other models produced estimates of abundance that were ecologically realistic and relatively accurate. The accuracy of population estimates produced by N-mixture models were not overly sensitive to the formulation of models, the scale at which ecological conditions were measured, or the criteria used to define independent detection and by extension sample size. Our results suggest that parsimony was a poor measure of the predictive accuracy of the population estimates produced with the N-mixture model. Collecting and processing data from the aerial survey was less expensive and took less time, but data from camera traps can provide valuable information on behavior of the target species as well as insights into multiple species in the community.</p>
Data from: Range-wide genetic analysis of an endangered bumble bee (Bombus affinis) reveals population structure, isolation by distance, and low colony abundance
<p>Declines in bumblebee species ranges and abundances are documented across multiple continents and have prompted the need for research to aid species recovery and conservation. The rusty patched bumblebee (<em>Bombus affinis</em>) is the first federally-listed bumblebee species in North America. We conducted a range-wide population genetics study of <em>B. affinis</em> from across all extant conservation units to inform conservation efforts. To understand the species' vulnerability and help establish recovery targets, we examined population structure, patterns of genetic diversity, and population differentiation. Additionally, we conducted site-level analysis of colony abundance to inform prioritizing areas for conservation, translocation, and other recovery actions. We find substantial evidence of population structuring along an east-to-west gradient. Putative populations show evidence of isolation by distance, high inbreeding coefficients, and a range wide male diploidy rate of ~15%. Our results suggest the Appalachians represents a genetically distinct cluster with high levels of private alleles and substantial differentiation from the rest of the extant range. Site-level analyses suggest low colony abundance estimates for <em>B. affinis</em> compared to similar datasets of stable, co-occurring species. These results lend genetic support to trends from observational studies suggesting B. affinis has undergone a recent decline and exhibits substantial spatial structure. The low colony abundances observed here suggest caution in overinterpreting the stability of populations even where <em>B. affinis</em> is reliably detected interannually. These results help delineate informed management units, provide context for the potential risks of translocation programs, and can help set clear recovery targets for this and other threatened bumblebee species.</p>
Data from: Phylogenomic position of eupelagonemids, abundant and diverse deep-ocean heterotrophs
<p>Eupelagonemids, formerly known as Deep Sea Pelagic Diplonemids I (DSPD I), are among the most abundant and diverse heterotrophic protists in the deep ocean, but little else is known about their ecology, evolution, or biology in general. Originally recognized solely as a large clade of environmental ribosomal subunit RNA gene sequences (SSU rRNA), branching with a smaller sister group DSPD II, they were postulated to be diplonemids, a poorly-studied branch of Euglenozoa. Although new diplonemids have been cultivated and studied in depth in recent years, the lack of cultured eupelagonemids has limited data to a handful of light micrographs, partial SSU rRNA gene sequences, a small number of genes from single amplified genomes (SAGs), and only a single formal described species, <em>Eupelagonema oceanica</em>. To determine exactly where this clade goes in the tree of eukaryotes and begin to address the overall absence of biological information about this apparently ecologically important group, we conducted single-cell transcriptomics from two eupelagonemid cells. A SSU rRNA gene phylogeny shows these two cells represent distinct subclades within eupelagonemids, each different from <em>E. oceanica</em>. Phylogenomic analysis based on a 125-gene matrix contrasts with the findings based on ecological survey data, and shows eupelagonemids branch sister to the diplonemid subgroup Hemistasiidae.</p>
Data from 'Exploring Depth-Related Patterns of Sponge Diversity and Abundance in Marginal Reefs'
<p>Datasets species ID generated during and/or analysed in the paper 'Exploring Depth-Related Patterns of Sponge Diversity and Abundance in Marginal Reefs’, published in <em>Ecology and Evolution.</em></p>
Data from: Shooting area of infrared camera traps affects recorded taxonomic richness and abundance of ground-dwelling invertebrates
<p>Ground-dwelling invertebrates are vital for soil biodiversity and function maintenance. Contemporary biodiversity assessment necessitates novel and automatic monitoring methods because of the threat of sharp reductions in soil biodiversity in farmlands worldwide. Using infrared camera traps (ICTs) is an effective method for assessing richness and abundance of ground-dwelling invertebrates. However, the influence that the shooting area of ICTs has on the diversity of ground-dwelling invertebrates has not been strongly considered during survey design. In this study, data from 6 ICTs with two shooting areas (A1, 38.48 cm<sup>2</sup>; A2, 400 cm<sup>2</sup>) were used to investigate ground-dwelling invertebrates in a farm in a city on the Eastern Coast of China from 20:00 on July 31 to 00:00 on September 29, 2022. Over the course of 59 days and 1,420 h, invertebrates within 9 taxa, 2,447 individuals, and 112,909 ind./m<sup>2</sup> were observed from 222,912 images. Our results show that ICTs with relatively large shooting areas recorded relatively high taxonomic richness and abundance of total ground-dwelling invertebrates, relatively high abundance of the dominant taxon, and relatively high daily and hourly abundance of most taxa. The shooting areas of ICTs significantly affected the recorded taxonomic richness and abundance of ground-dwelling invertebrates throughout the experimental period and at fine temporal resolutions. Overall, these results suggest that the shooting areas of ICTs should be considered when designing experiments, and ICTs with relatively large shooting areas are more favorable for monitoring the diversity of ground-dwelling invertebrates. This study further provides an automatic tool and high-quality data for biodiversity monitoring and protection in farmlands.</p>
Data from: Land consolidation impacts the abundance and richness of natural enemies but not pests in small-holder rice systems
<p>Traditional small-holder agricultural landscapes in southern China are being consolidated to increase mechanization levels in agriculture, but it is unclear how this influences rice arthropod communities in these landscapes. Here, based on a six-year study in 20 rice fields, we evaluated the impact of land consolidation on arthropod communities, crop damage, and rice yield. We also analyzed how effects of land consolidation were moderated by the proportion of large semi-natural habitat patches and insecticide use. We found that, compared to consolidated fields, rice fields in traditional farmlands had a higher abundance and family richness of natural enemies, but a similar abundance of rice pests. Land consolidation did not significantly interact with the proportion of large semi-natural habitat patches or insecticide application, in terms of affecting arthropods. The proportion of semi-natural habitat reduced the negative effect of insecticide application on key rice pests, but no equivalent interaction occurred for natural enemies.</p> <p><em>Syntheses and Applications:</em> Land consolidation can have negative impacts on the abundance and richness of natural enemies, but not pests in small-holder rice systems, and these impacts are independent from insecticide application and proportion of semi-natural habitat in the landscape. We recommend the implementation of agri-environmental measures or re-establishing field margin vegetation during the consolidation process to mitigate these potential negative effects, although trade-off between enhancing crop yields and preserving rice arthropod biodiversity should be considered. We encourage future research to focus on the detailed assessment of the function of linear habitats for a better understanding of the impact of land consolidation.</p>
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>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.