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Calling structural variants with confidence from short-read data in wild bird populations

Comprehensive characterisation of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation (SV), reproducible and high-confidence SV callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus) individuals. To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of SVs is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analysing short-read discovered SV datasets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality-filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence SV callsets.

Data from: To lose is to win: long-term co-occurrence of two asexual populations realized by a dormant strategy of the inferior competitor

Asexual organisms are ubiquitous. While they are the same single species with the same ecological requirements, multiple asexual genotypes within a species are often found in a single habitat. Niche partitioning in time and space among genotypes has been proposed to explain this phenomenon. However, it is not clear whether these different genotypes co-occur in the long term. Therefore, we examined the population dynamics of two asexual Daphnia cf. pulex genotypes (JPN1 and JPN2) over nine years in a small mountain lake. These two genotypes consistently occurred in the same seasons and layers, suggesting that niche partitioning cannot explain their long-term co-occurrence. The abundance of JPN1 was typically higher in most years. However, the abundance of dormant eggs in lake sediments was at the same level between the genotypes. The laboratory experiment showed that JPN1 excluded JPN2. However, many JPN2 individuals produced the dormant eggs before JPN1 competitively excluded them from the experiment. Furthermore, the competitively inferior JPN2 produced the dormant eggs abundantly in the medium containing a crowding cue from JPN1. However, no such trend was observed for JPN1. These results showed that the competitively inferior asexual genotype could maintain the population with the competitively superior genotype for a long period of time because it had the ability to detect the increase in competitors and produce the dormant eggs each year before being competitively eliminated. Based on these results, we suggest that the variation in the genotype-specific response in dormant egg production to environmental change plays a key role in the long-term co-occurrence of different asexual genotypes in single habitats.

Data from: using camera traps and N-mixture models to estimate population abundance: model selection really matters

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.

Data for: Shifts in plant-invertebrate interactions between wild and ex-situ conservation populations of a critically endangered tree

Ex-situ conservation is an effective approach to prevent the extinction of endangered species. Biotic interactions (eg herbivory and pollination) are critical to ex-situ conservation success, including plant establishment, survival, and reproduction. However, shifts in biotic interactions between wild and ex-situ populations are still poorly understood. We compared herbivory and pollination characteristics between the only wild population (WP) and three ex-situ populations (LP, local population, nearby WP; NP, north population, ca. 850 km; and SP, south population, ca. 750 km) of a critically endangered tree species (Sinojackia huangmeiensis) to explore the latitudinal changes in plant-invertebrate interactions. Larvae of the Limacodidae family were the dominant herbivores in WP, LP, and NP, while the only herbivore observed in SP was a snail. Compared to WP, the leaf herbivory rate was unchanged in LP but decreased in NP and SP. Leaf defense traits (total phenols, tannins, leaf thickness, and leaf dry matter content) increased or remained unchanged in the three ex-situ populations. A pollinator (Apis cerana) of S. huangmeiensis was present in the four populations. NP and SP lacked some pollinators that were found in both WP and LP, but they shared one pollinator that was not observed in WP and LP. The pollinator visiting frequency increased in SP, while it did not change significantly in LP and NP. Synthesis and applications: Our results suggested that both herbivory and pollination of S. huangmeiensis changed in ex-situ populations, with complete or partial changes in herbivores, leaf herbivory rate, pollinators, pollinator visiting frequency, and fruit set in the two distant ex-situ populations. This work provides a unique empirical study of shifts in both antagonistic and mutualistic biotic interactions between wild and ex-situ populations. We emphasized that it is essential to integrate herbivore and pollinator management in future ex-situ conservation of plant species.

Data from: Pace and parity predict short-term persistence of small plant populations

Life history traits are used to predict asymptotic odds of extinction from dynamic conditions. Less is known about how life history traits interact with stochasticity and population structure of finite populations to predict near-term odds of extinction. Through empirically parameterized matrix population models, we study the impact of life history (reproduction, pace), stochasticity (environmental, demographic), and population history (existing, novel) on the transient population dynamics of finite populations of plant species. Among fast and slow pace and either uniform or increasing reproductive intensity or short or long reproductive lifespan, slow, semelparous species are at the greatest risk of extinction. Long reproductive lifespans buffer existing populations from extinction while the odds of extinction of novel populations decreases when reproductive effort is uniformly spread across the reproductive lifespan. Our study highlights the importance of population structure, pace, and two distinct aspects of parity for predicting near-term odds of extinction.

Data from: Population structure and species delimitation in the Wehrle's salamander complex

Species are the fundamental unit of biodiversity studies. However, many species complexes are difficult to delimit, especially those characterized by complicated patterns of population structure. Salamanders in the family Plethodontidae often form species by slowly fragmenting across a landscape over space and time. They thus provide many examples of species complexes in which gradual Darwinian evolution has resulted in multiple units of varying degrees of differentiation, including incompletely separated lineages. Here we report on a molecular systematic investigation of woodland salamanders in the Plethodon wehrlei group, which has recently been split from two species into five. To quantify patterns of genetic variation, we collected genetic samples from 24 individuals from 20 populations, including all species and representing a carefully selected subset of previous work. From these samples, we obtained genomic data using anchored hybrid enrichment, which resulted in 319 loci averaging 1300 base pairs in length. Biallelic single nucleotide polymorphisms (SNPs) were randomly selected from 316 of these loci for some analyses. We examined patterns of genetic structure using PCA, DAPC, FEEMS, and STRUCTURE, and found that all of the recognized species formed genetic clusters; however, P. wehrlei and P. punctatus were relatively weakly differentiated, and STRUCTURE identified three separate clusters within P. jacksoni. Species trees inferred using wASTRAL, BPP, and TreeMix all recovered the same topology, with P. dixi sister to the other taxa, which included a northern clade (P. wehrlei, P. punctatus, P. pauleyi) and a southern clade (P. jacksoni, with three separate groups). TreeMix only inferred one gene flow event. We evaluated the candidate species using BPP and the genealogical divergence index (gdi). While BPP delimited all candidate species with strong support (all posterior probabilities = 1.0), the gdi only strongly supported P. dixi and P. pauleyi, both of which have only been recently described. We discuss the difficult problem of species delimitation in groups that form species via range fragmentation. We also provide a vision for future research with the aim of better testing and diagnosing the species diversity within the P. wehrlei group.

Data from: Range-wide genetic analysis of an endangered bumble bee (Bombus affinis) reveals population structure, isolation by distance, and low colony abundance

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 (Bombus affinis) is the first federally-listed bumblebee species in North America. We conducted a range-wide population genetics study of B. affinis 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 B. affinis 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 B. affinis 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.

Data from: Landscape heterogeneity drives population structure in four western bumble bee species

Bumble bees are critical pollinators in wild, agricultural, and urban ecosystems—providing the necessary ecological services for food and crop production. In western North America, mountain ranges have high bumble bee species richness. However, as climate change increases temperatures and restricts montane populations to higher elevational spaces, their ability to disperse and maintain genetic diversity decreases. This genetic isolation could lead to the extirpation of local pollinator communities and an overall loss of pollinators. We analyzed the genetic diversity of four broadly sympatric species of bumble bees across the Rocky and Cascade Mountains of western North America to assess habitat isolation's impact on population genetic structure. We expected species restricted to higher elevation habitats to display higher population structure and less genetic diversity across the landscape. We sampled approximately 150 bees per species from seven to eight sites across each species' range. We genotyped bees with an average of 10 loci and used FST and Bayesian Structure analysis to quantify population differentiation. Using isolation by distance and isolation by resistance analyses, species with both narrow and broad habitat suitability requirements showed evidence of habitat suitability restricting gene flow. Although each species showed varying degrees of genetic structure and gene flow, knowing how habitat heterogeneity drives genetic structure and isolation can help guide conservation efforts and determine focal regions for bumble bee conservation in the face of climate change.

COI and Cytb data of Lagocephalus spadiceus in eight populations

The Late Pleistocene-Holocene climate fluctuations have had a major impact on phylogeographic structure and historical dynamics of marine fishes in the marginal seas of the western Pacific Ocean. Lagocephalus spadiceus is a high-nutritional and economic-value species in the Southeast China Sea. The study was to assess the population genetic diversity and demography of L. spadiceus in the South China Sea (SCS). A sample of 300 specimens from eight geographic locations along the coast of mainland China and Hainan Island were obtained for this study. The mitochondrial cytochrome oxidase I (COI) and cytochrome b (Cyt b) gene datasets had high haplotype diversity but low nucleotide diversity. The genetic structure and phylogenetic analyses indicated that there was no significant population structure among the eight geographic locations. The low genetic diversity of L. spadiceus was associated with population expansion in the Late Pleistocene-Holocene period. This was supported by star haplotype networks, neutrality tests, unimodal mismatch distributions and Bayesian skyline plots. These findings have important reference value for the protection of genetic resources. Furthermore, the study illuminates the complex relationship between Pleistocene-Holocene temperature variability and phylogeography.

Data from: strawberry guava invasion of a Hawaiian rainforest: changing population pattern

Strawberry guava (waiawī, Psidium cattleyanum O. Deg., Myrtaceae) is a small tree invasive on oceanic islands where it may alter forest ecosystem processes and community structure. To better understand the dynamics of its invasion in Hawaiian rainforests in anticipation of the release of a biocontrol agent, we measured growth and abundance of vertical stems >= 0.5 cm DBH for 16 years (2005-2020) in an intact Metrosideros-Cibotium rainforest on windward Hawai'i Island. Specifically, we compared the growth and abundance of both shoots (originating from seed or from the root mat) and sprouts (originating above ground from established stems) in four replicate study sites. Mean stem density increased from 9562 stems/ha in 2005 to 26,595 stems/ha in 2020, the majority of which were stems < 2 cm DBH. Mean annual rates of population growth (lambda) varied between 1.03 and 1.17. Early in the invasion, both density and per capita recruitment of shoots was greater than that of sprouts, but as overall stem density increased over time, sprout abundance and recruitment came to surpass that of shoots. Relative growth rates among small stems < 2 cm DBH declined over time for both shoots and sprouts, but relative growth rates of sprouts were consistently greater than that of shoots after the first 3 years. The capacity of strawberry guava to recruit from both rooted shoots and vegetative sprouts contributes to the facility with which it can invade intact rainforest, persist in the forest understory, and respond to canopy opening. Strawberry guava thus poses a considerable risk of stand replacement for Hawaiian rainforests. Stand management will require perpetual efforts of guava control at high priority sites as extreme weather events associated with climate change bring canopy-opening events due to storms, drought and pathogens.

Data from: Vocal signatures affected by population identity and environmental sound levels

Passive acoustic monitoring has improved our understanding of vocalizing organisms in remote habitats and during all weather conditions. Many vocally active species are highly mobile, and their populations overlap. However, distinct vocalizations allow the tracking and discrimination of individuals or populations. Using signature whistles, the individually distinct calls of bottlenose dolphins, we calculated a minimum abundance of individuals, characterized and compared signature whistles from five locations, and determined reoccurrences of individuals throughout the Mid-Atlantic Bight and Chesapeake Bay, USA. We identified 1,888 signature whistles in which the duration, number of extrema, start, end, and minimum frequencies of signature whistles varied significantly by site. All characteristics of signature whistles were deemed important for determining from which site the whistle originated and due to the distinct signature whistle characteristics and lack of spatial mixing of the dolphins detected at the Offshore site, we suspect that these dolphins are of a different population than those at the Coastal and Bay sites. Signature whistles were also found to be shorter when sound levels were higher. Using only the passively recorded vocalizations of this marine top predator, we obtained information about its population and how it is affected by ambient sound levels, which will increase as offshore wind energy is developed. In this rapidly developing area, these calls offer critical management insights for this protected species.

Data and code for: Sea level rise causes shorebird population collapse before habitat drowns

Sea level rise causes habitat loss and is considered to be a key threat to coastal species globally. Sea level rise also reduces habitat quality, potentially threatening populations already before habitat drowns and is lost. The extent and timing of changes in habitat quality for wildlife actively adapting to sea level rise, and how this affects population numbers under different emission scenarios, is unknown. Here, we combine long-term field data with models of sea level rise, marsh geomorphology, adaptive behaviour, and population dynamics to show that habitat quality is already declining on three islands due to increased flooding of shorebird nests. Also, population collapses are projected well before habitat drowns. Habitat loss, a widely used proxy, thus severely underestimates population impacts of sea level rise and coastal species will suffer much sooner than previously thought. Despite shorebirds adapting by moving to higher grounds, sea level rise will result in up to 79% fewer birds in a century, eventually leading to extinction in their prime habitat. Local gas mining exacerbates matters, as deep soil subsidence makes habitat even more vulnerable to sea level rise, effectively halving the window of opportunity for conservation action. Climate change ultimately jeopardizes the biodiversity value of this UNESCO World Heritage Area, and nature management needs to take this long-term perspective on board by in the short-term, boosting the accretion of tidal marshes or developing flood-safe alternative habitat elsewhere.

Data from: Genetic analysis of red deer (Cervus elaphus) administrative management units in a human-dominated landscape - patterns of genetic diversity, population structure and gene flow

Red deer (Cervus elaphus) throughout central Europe are impacted by different anthropogenic activities including habitat fragmentation, selective hunting, and translocations. This has substantial influences on genetic diversity and the long-term conservation of local populations of this species. Here we use genetic samples from 480 red deer individuals to assess the genetic diversity and differentiation of the 12 administrative management units located in Schleswig Holstein, the northernmost federal state in Germany. We applied multiple analytical approaches and show that the history of local populations (i.e., translocations, culling of individuals outside of designated red deer zones, and anthropogenic infrastructures) has led to comparably low levels of genetic diversity. The mean expected heterozygosity was below 0.6 and we observed on average 4.2 alleles across 12 microsatellite loci. Effective population sizes below the recommended level of 50 were estimated for multiple local populations. Our estimates of genetic structure and gene flow show that red deer in northern Germany are best described as a complex network of asymmetrically connected subpopulations, with high genetic exchange among some local populations and reduced connectivity of others. Genetic diversity was also correlated with population densities of neighboring management units. Based on these findings, we suggest that connectivity among existing management units needs to be considered in the practical management of the species, which means that some administrative management units should be managed together, while the effective isolation of other units needs to be mitigated.

Data from: genetic evidence of differential dispersal pattern in Asiatic wild dog: comparing populations with different pack size and tiger densities

Dispersal is a multi-causal, crucial life-history event in shaping the genetic and behavioral structure of mammals. We assessed the dispersal pattern of dholes aka Asiatic wild dog (Cuon alpinus), a social monogamous mammal at two tiger reserves of Maharashtra with different degrees of pack size and competition with tigers i.e. Tadoba-Andhari (TATR, smaller pack size, higher tiger density) and Nawegaon-Nagzira (NNTR, larger pack size, lower tiger density). We used the microsatellite data of 174 individual genotypes (98 males and 67 females) to assess the dispersal pattern of dholes from two populations with varying pack size, tiger density, and landscape connectivity using gene flow as a proxy. We compared the population structure, pairwise F statistics, assignment index, and relatedness across a spatial scale. Overall, the results suggested a difference in sex-bias dispersal pattern for the two sub-populations, exhibiting significant results for female-biased dispersal in the TATR population with a smaller pack size and higher tiger density. Our study highlights the variability in sex-biased dispersal patterns in two different populations which could be the consequence of different variables such as pack size, tiger density, and geographical scale. The study warrants further quantitative investigation including several factors including individual behavior, pack composition, pack size, tiger density, etc. In the present Anthropocene era, determining the sex bias in dispersal patterns for a short-range, pack-living carnivore will help in devising an effective conservation management plan for their long-term survival.

Data from: Major group-B enterovirus populations deleted in the noncoding 5' region of genomic RNA modulate activation of the type I interferon pathway in cardiomyocytes and induce myocarditis

Major 5'-terminally deleted (5'TD) RNA forms of group-B coxsackievirus (CVB-5'TD) has been associated with myocarditis in both mice and humans. Although it is known that interferon-β (IFN-β) signaling is critical for an efficient innate immune response against CVB-induced myocarditis, the link between CVB-5'TD RNA forms and type I IFN signaling in cardiomyocytes remains to be explored. In a mouse model of CVB3/28-induced myocarditis, major early-emerging forms of CVB-5'TD RNA have been characterized as replicative viral populations that impair IFN-β production in the heart. Synthetic CVB3/28 RNA forms mimicking each of these major 5'TD virus populations were transfected in mice and have been shown to modulate innate immune responses in the heart and to induce myocarditis in mice. Remarkably, transfection of synthetic viral RNA with deletions in the secondary structures of the 5'-terminal CVB3 RNA domain I, modifying stem-loops "b", "c" or "d", were found to impair IFN-β production in human cardiomyocytes. In addition, the activation of innate immune response by Poly(I:C), was found to restore IFN-β production and to reduce the burden of CVB-5'TD RNA-forms in cardiac tissues, thereby reducing the mortality rate of infected mice. Overall, our results indicate that major early-emerging CVB3 populations deleted in the domain I of genomic RNA, in the 5' noncoding region, modulate the activation of the type I IFN pathway in cardiomyocytes and induce myocarditis in mice. These findings shed new light on the role of replicative CVB-5'TD RNA forms as key pathophysiological factors in CVB-induced human myocarditis.

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zenodo36/100

CMIP6 tmax and tmin data for 50 most populous cities in USA

These data were downloaded from Google Earth Engine. Each csv includes Year Month Day CM Scenario and other columns. CM includes three scenario (historical, ssp245 and ssp585). The scenario involves the parameter (tasmax or tasmin). Other columns means the city ID. The city ID and corresponding city name can be seen in the csv file named UID Abbreviation.csv above and the shapefile of cities were used from the open repository (Chen et al. 2022). This global inventory includes 247 cities within the contiguous US. This can be found at: Chen, B., Wu, S., Song, Y. et al. Contrasting inequality in human exposure to greenspace between cities of Global North and Global South. Nat Commun 13, 4636 (2022). https://doi.org/10.1038/s41467-022-32258-4. And to select the 50 populous cities, 1 km X 1 km resolution imagery of population by Wang et. al (2022) was used.[Wang, X., Meng, X. & Long, Y. Projecting 1 km-grid population distributions from 2020 to 2100 globally under shared socioeconomic pathways. Sci Data 9, 563 (2022). https://doi.org/10.1038/s41597-022-01675-x]. Based on this, we ranked 50 cities from those 247 US cities found in Chen et al. 2022. Those data and real names of the cities can be studied from these papers.

zenodo36/100

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> 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. <h1>2.    Changes in abundance and distribution of European forest bird species</h1> 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). 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). 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). <h1>3.    Trait and specialisation data for European forest bird species</h1> 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). 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). 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. <h1>4.    Data analysis</h1> 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). 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). 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.

opencc-by-4.0Jun 2024View details →

opencc-zeroOct 2021View details →

Supplementary material and data from: Cranial volume and palate length of cats, Felis spp., under domestication, hybridisation and in wild populations

Reduced brain size, compared with wild individuals, is argued to be a key characteristic among domestic mammal species, and is often thought to be a component of the "domestication syndrome". However, brain size comparisons are often based on old, inaccessible literature and in some cases drew comparisons between domestic animals and wild species that are no longer thought to represent the true progenitor species of the domesticated variant in question. Here we set out to replicate results concerning cranial volumes in domestic cats that were published in the 1960s and 1970s and compared wildcats, domestic cats and their hybrids. In light of new research and ideas surrounding domestication and its effects on domestic animals a replication of these studies is highly relevant. Apart from replicating these studies we also present new data on palate length in Felis cat skulls. Here we provide all data (both new and old digitzed data) upon which we based the analysis discussed in this manuscript. We further provide a link to the code used in the analysis.

opencc-zeroOct 2021View details →

Data from: Invasive hybridization has variable effects on survival among salmonid populations

Human-mediated hybridization threatens global biodiversity, but the fitness consequences of hybridization are poorly understood, especially in vertebrates. We used capture-recapture data from 5,249 individuals in three hybridizing populations of invasive rainbow trout (Oncorhynchus mykiss) and native cutthroat trout (O. clarkii) to quantify the effects of rainbow trout genetic admixture and environmental conditions on survival. Seasonal variation in environmental conditions interacted with individual admixture to influence seasonal survival. Overall, annual survival declined with admixture at the warmest site (juvenile hybrids with 25% non-native ancestry had 20.7% lower annual survival than non-hybridized cutthroat trout) but increased with admixture at the coldest site (juvenile hybrids with 25% non-native ancestry had 19.7% higher survival than non-hybridized cutthroat trout), providing evidence that fitness effects of hybridization vary in a context-dependent manner. Furthermore, higher survival for hybrids in cold streams and lower survival in warm streams is opposite of admixture-environment correlations, demonstrating that environmental gradients often used to infer patterns of hybridization may poorly predict variation in fitness across the landscape. Individual-based studies measuring fitness-related traits in vertebrate taxon are rare. Most studies of human-mediated hybridization in wild populations quantify the spatial extent of non-native admixture or test for admixture-environment associations to infer factors affecting fitness in hybridizing populations. We used an extensive capture-recapture dataset to measure seasonal survival in hybridized populations that experience different environmental conditions. Our work shows that non-native admixture can affect survival differently among seasons and populations, and that inferences from individual-based studies can conflict with those from admixture-environment associations. For studies of non-native hybridization, this work highlights the importance of directly measuring fitness (survival and reproductive success), and at appropriate spatial and temporal scales to elucidate the variation in fitness differences (i.e., among populations and seasons).