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opencc-by-4.0Sep 2024View details →

Butuan City, Philippines Population Grids for the Year 2020 with DEGURBA Classification

Population grids of Butuan City, Philippines for the year 2020, in Esri Shapefile and TIFF (raster) formats. The population grids were generated through disaggregation of barangay-level population data to square grid cells (e.g., 1km x 1km), following the method presented in [1], using building footprints data (Google Open Buildings) as a covariate. In detail, the total population of each census unit (barangay) is proportionally distributed across its building footprints, based on the assumption that the presence of building footprints correlates with population distribution. The population within each grid cell is then calculated by summing the proportionally distributed population from the building footprints within that cell. Before implementing the disaggregation procedure, minor cleaning of the building footprint data was conducted. This involved removing building polygons with an area of less than 6 m², as buildings below this size are assumed to be uninhabitable. This assumption is based on the minimum room size requirements outlined in the National Building Code of the Philippines (PD 1096). The 1km x 1km Shapefile contains two main attributes ('pop2020' and 'degurba'): 'pop2020' is the estimated population at each 1km x 1km grid cell for the year 2020; 'degurba' corresponds to the classification of each grid cell based on the DEGURBA (Degree of Urbanisation) classification methodology [1]. For the raster version of the data, the pixel values correspond to the total population in that pixel. Data sources: <ul> <li>Building footprints © 2021 Google Open Buildings dataset, licensed under ODbL 1.0, <a href="https://sites.research.google/open-buildings/" target="_blank" rel="noopener">https://sites.research.google/open-buildings/</a></li> <li>Population Data © 2020 Philippine Statistics Authority (PSA), <a href="https://psa.gov.ph/content/2020-census-population-and-housing-2020-cph-population-counts-declared-official-president" target="_blank" rel="noopener">https://psa.gov.ph/content/2020-census-population-and-housing-2020-cph-population-counts-declared-official-president </a></li> <li>Barangay Boundaries © 2023 PSA and NAMRIA via OCHA Centre for Humanitarian Data - HDX, <a href="https://data.humdata.org/dataset/cod-ab-phl" target="_blank" rel="noopener">https://data.humdata.org/dataset/cod-ab-phl?</a></li> </ul> Reference [1] Applying the Degree of Urbanisation A METHODOLOGICAL MANUAL TO DEFINE CITIES, TOWNS AND RURAL AREAS FOR INTERNATIONAL COMPARISONS 2021 Edition, <a href="https://dx.doi.org/10.2785/706535" target="_blank" rel="noopener">https://dx.doi.org/10.2785/706535</a>

opencc-by-4.0Mar 2024View details →

Dataset for Rapid polygenic adaptation in a wild population of ash trees under a novel fungal epidemic

Dataset for Rapid polygenic adaptation in a wild population of ash trees under a novel fungal epidemic Code used for plotting of main figures and quantifying allelic shifts attached in the GitHub repository CareyMetheringham/MardenPark. Additional files for analysis of GEBV shifts between adults and juveniles, estimation of heritability, trends in green up and simulations of allelic shifts included as: <ul> <li>GEBV-regression.Rmd</li> <li>heritabilityEst.R</li> <li>GreeningAnalysis.R</li> <li>Simulated_selection_analysis.Rmd</li> <li>Distinguishing the effects of selection from genetic drift.pdf</li> </ul> Data files: <ul> <li>S1 - phenotypic measurements for adult and juvenile trees</li> <li>S2 - Effect sizes for SNPs used to calculate GEBV</li> <li>S3 - Allelic frequencies of sites used to calculate GEBV</li> <li>related_trees.csv - Predicted parentage of trees</li> <li>gebv_model_df.csv - Data used for greenup calculations in GreeningAnalysis.R</li> <li>maf1.pass2.miss25.snps.only.LD.vcf - Filtered file of high MAF SNPs used for parentage estimation</li> <li>unlinked_sites.csv - unlinked sites used in GEBV-regression.Rmd</li> <li>ebv_table_10000_250 - table of estimated breeding values in field trial populatio, used for heritability estimation</li> <li>MP_eefects_MIA_and_MAA.csv - Data for plotting Figure 3 - Estimated effect size of the major and minor allele, plus standard error on the estimate</li> </ul>

opencc-by-4.0Sep 2024View details →

Wolf population size and composition in one of Europe's strongholds, the Romanian Carpathians

Strategies of coexistence with large carnivores should integrate scientific evidence, population monitoring and estimates providing an opportunity for advancing outdated management paradigms. We estimated wolf population density and social dynamics across a 1,400 km2 area in a data-poor region of Romanian Carpathians. Across three consecutive years (2017-2018 until 2019-2020), we collected and genotyped 505 noninvasive DNA wolf samples (scat, hair and urine) to identify individuals, reconstruct pedigrees and check for presence of hybridization with domestic dogs. We identified 27 males, 20 females, and one F1 wolf-dog hybrid male. We delineated six wolf packs, with pack size varying between two and seven individuals, and documented yearly changes in pack composition. Using a spatial capture recapture approach, we estimated population density at 2.35 wolves/100 km2 (95% BCI = 1.68–3.03) and population abundance at 70 individuals (95% BCI = 49–89). Noninvasive DNA data collection coupled with spatial capture-recapture has the potential to inform on wolf population size and dynamics at broader spatial scales, across different sampling areas representative for the diverse Carpathian landscapes, and across different levels of human impact, supporting wildlife decision making in one of Europe's main strongholds for large carnivores.

opencc-by-4.0Oct 2024View details →

Role of individual and population heterogeneity in shaping dynamics of multi-pathogen shedding in an island endemic bat

Dataset for the manuscript "Role of individual and population heterogeneity in shaping dynamics of multi-pathogen shedding in an island endemic bat", including information of the bat samples and infection data.

opencc-by-4.0Jun 2024View details →

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-4.0Nov 2024View details →

Adaptive genomic signatures of globally invasive populations of the yellow fever mosquito Aedes aegypti

*  These authors contributed equally: Alejandro N. Lozada-Chávez, Irma Lozada-Chávez. <h3> </h3> <h1>Supplementary Dataset</h1>   This repository contains the  Supplementary Data (from 1 to 12) cited in our paper "Adaptive genomic signatures of globally invasive populations of the yellow fever mosquito Aedes aegypti" in Nature Ecology and Evolution: <a title="Aedes aegypti domestication." href="https://doi.org/10.1038/s41559-025-02643-5">https://doi.org/10.1038/s41559-025-02643-5</a> These datasets are available in the section "Supplementary Information" of our paper, but with the absence of the SD-9 due its large big size (~3Gb after decompressed). Here you can find the complete set of datasets in a single ZIP file: 41559_2025_2643_MOESM5_ESM_Supplementary_Data.zip   LIST OF DATASETS: 1) Supplementary Data 1. SNP statistics for populations through genomic regions (TXT).  2) Supplementary Data 2. Sequences of new detected nrEVEs (FASTA).  3) Supplementary Data 3. Phylogenetic trees for populations and individuals (NEWICK).  4) Supplementary Data 4. Information for 8,120 hard selective sweeps detected with RAiSD in out-of-Africa populations (TXT).  5) Supplementary Data 5. Information for 1,030 SNP outliers detected with PCAdapt within 2,266 genes (VCF format).  6) Supplementary Data 6. Matrix with DoS scores for 11,651 orthologous protein-coding genes in AaegL5 and each Ae. aegypti population (TXT).  7) Supplementary Data 7. Matrix with MKT scores for 11,651 orthologous protein-coding genes in AaegL5 and each Ae. aegypti population (TXT).  8) Supplementary Data 8. Matrix with DoS scores used to estimate relaxed selection (TXT).  9) Supplementary Data 9. Matrix with SNPs and genomic coordinates within adaptive protein-coding genes and ncRNAs that are shared or private for out-of-Africa populations against African populations (TXT).  10) Supplementary Data 10. Matrix with 483 nonsynonymous SNPs and their allele frequencies for our 40 populations Florida and Colombia (TXT). 11) Supplementary Data 11. Genomic coordinates of SNPs in AaegL5 obtained from the literature and VectorBase (TXT).  12) Supplementary Data 12. Source data of metrics used to plot Figure 4b (TXT).   UPDATES NOTE: <ul> <li>Repository version 3. Final version of datasets for the accepted manuscript.</li> <li>Repository version 2. Incomplete datasets: Files as prelimary versions and their content may vary. The SD-10 is not present (matrix with 483 SNPs) was added. The SD-7 is a broken file (cannot be opened).</li> <li>Repository version 1.  Incomplete datasets: Files as prelimary versions and their content may vary. Two final SD files are not present.</li> </ul>   CITATION OF THIS REPOSITORY: Lozada-Chávez, A. N., Lozada-Chávez, I., Alfano, N., Palatini, U., Sogliani, D., Elfekih, S., Degefa, T., Sharakhova, M. V., Badolo, A., Patchara, S., Casas-Martinez, M., Carlos, B. C., Carballar-Lejarazú, R., Lambrechts, L., Souza-Neto, J. A., & Bonizzoni, M. (2024). Adaptive genomic signatures of globally invasive populations of the yellow fever mosquito Aedes aegypti [Data set]. Zenodo. https://doi.org/10.5281/zenodo.14948092

opencc-by-4.0Mar 2024View details →

SINGER-inferred targets for exceptional population differentiation in coalescence times in African populations in 1000 Genomes Project

This repo saves the gene targets which shows the signal of population differentiation in coalescence times in African populations in 1000 Genomes Project.  Here are the detailed explanations for the header of the files: chrom               The chromosome where the genomic window is located (e.g., chr1, chrX). window_start        The 0-based start position of the genomic window being analyzed. window_end          The 1-based end position of the genomic window (exclusive). score               Ratio between the overall diversity and the population specific diversity, in the genomic window. transcript_chrom    The chromosome where the transcript is located. transcript_start    The 0-based start position of the transcript. transcript_end      The 1-based end position of the transcript (exclusive). transcript_id       The unique identifier for the transcript (e.g., Ensembl or RefSeq ID). strand              The strand of the transcript: "+" for forward, "-" for reverse. coding_start        The start position of the coding region of the transcript (if applicable). coding_end          The end position of the coding region of the transcript (if applicable). RGB                 The RGB color used for visualization in genome browsers (format: R,G,B). block_count         The number of exons in the transcript. block_sizes         Comma-separated list of exon lengths (in base pairs). block_starts        Comma-separated list of exon start positions relative to transcript_start.

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.

Inter- and intraspecific selection in alien plants: how population growth, functional traits and climate responses change with residence time

Aim: When alien species are introduced to new ranges, climate or trait mismatches may initially constrain their population growth. However, inter- and intraspecific selection in the new environment should cause population growth rates to increase with residence time. Using a species-for-time approach, we test whether with increasing residence time (a) negative effects of climatic mismatches between the species' new and native range on population growth weaken, and (b) functional traits converge towards values that maximize population growth in the new range. Location: Germany. Time period: 12,000 years BP to present. Major taxa studied: 46 plant species of the Asteraceae family. Methods: We set up a common-garden mesocosm-experiment using annual plant species with a wide range of residence times (7-12,000 years) and followed their population dynamics over two years. We calculated climatic distance between the common garden and the species' native range. We also measured key functional traits of each species to analyse trait-demography relationships and test trait convergence with increasing residence time. Results: We found no support for the hypothesis that negative effects of climatic mismatches on population growth weaken with residence time. However, seed mass had a clear negative effect on population growth. As expected under such strong directional selection between or within species, increasing residence time led seed mass to converge to low values that increase population growth. Accordingly, population growth tended to increase with residence time. Main conclusions: We identify trait but not climatic mismatches as important constraints on population growth of invaders. Understanding how inter- and intraspecific selection shapes functional traits of alien species should improve the predictability of future invasions and help understanding limits to the population growth and spread of invaders already present. In a broader context, this study contributes to the conceptual integration of invasion biology with community, functional, and population ecology.

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).

Selection against individuals from genetic introgression of escaped farmed salmon in a natural population of Atlantic salmon

The viability of wild Atlantic salmon populations is threatened by genetic introgression from escaped farmed salmon. Farmed Atlantic salmon are genetically improved for important commercial traits and a life in captivity but are poorly adapted to the natural environment. The rate of geneflow from escaped farmed to wild salmon depends on their spawning success and on offspring survival at various life-stages. We here investigate relative survival of introgressed juvenile Atlantic salmon (parr) in a river in northern Norway. The studied population has experienced genetic introgression from farmed salmon for about four generations (20 years). We followed two cohorts of parr from the year of hatching (0+) to the age of two years (2+). Farmed genetic introgression was quantified at the individual level and on a continuous scale using diagnostic SNPs. Population-level genetic introgression decreased from 0+ to 2+ by 64% (2011 cohort) and 37% (2013 cohort) . This change was driven by a 70% (2011 cohort) and 49% (2013 cohort) lower survival from age 0+ to 2+ in introgressed parr compared to parr of wild origin. Our observations show that there is natural selection against genetic introgression with a potential cost of lower productivity.The viability of wild Atlantic salmon populations is threatened by genetic introgression from escaped farmed salmon. Farmed Atlantic salmon are genetically improved for important commercial traits and a life in captivity but are poorly adapted to the natural environment. The rate of geneflow from escaped farmed to wild salmon depends on their spawning success and on offspring survival at various life-stages. We here investigate relative survival of introgressed juvenile Atlantic salmon (parr) in a river in northern Norway. The studied population has experienced genetic introgression from farmed salmon for about four generations (20 years). We followed two cohorts of parr from the year of hatching (0+) to the age of two years (2+). Farmed genetic introgression was quantified at the individual level and on a continuous scale using diagnostic SNPs. Population-level genetic introgression decreased from 0+ to 2+ by 64% (2011 cohort) and 37% (2013 cohort) . This change was driven by a 70% (2011 cohort) and 49% (2013 cohort) lower survival from age 0+ to 2+ in introgressed parr compared to parr of wild origin. Our observations show that there is natural selection against genetic introgression with a potential cost of lower productivity.

Major population splits coincide with episodes of rapid climate change in a forest-dependent bird

Climate change influences population demography by altering patterns of gene flow and reproductive isolation. Direct mutation rates offer the possibility for accurate dating on the within-species level but are currently only available for a handful of vertebrate species. Here, we use the first directly estimated mutation rate in birds to study the evolutionary history of pied flycatchers (Ficedula hypoleuca). Using a combination of demographic inference and environmental niche modelling, we show that all major population splits in this forest-dependent system occurred during periods of increased climate instability and rapid global temperature change. We show that the divergent Spanish subspecies originated during the Eemian-Weichselian transition 115 – 104 thousand years ago (kya), and not during the last glacial maximum (26.5 - 19 kya), as previously suggested. The magnitude and rates of climate change during the glacial-interglacial transitions that preceded population splits in pied flycatchers were similar to, or exceeded, those predicted to occur in the course of the current, human-induced climate crisis. As such, our results provide a timely reminder of the strong impact that episodes of climate instability and rapid temperature changes can have on species' evolutionary trajectories, with important implications for the natural world in the Anthropocene.

Populations restored using regional seed are genetically diverse and similar to natural populations in the region

Ecological restoration and plant re-introductions aim to create plant populations that are genetically similar to natural populations to preserve the regional gene pool, yet genetically diverse to allow adaptation to a changing environment. For this purpose, seeds for restoration are increasingly sourced from multiple populations in the target region. However, it has only rarely been tested whether using regional seed indeed leads to genetically diverse restored populations which are genetically similar to natural populations. We used single nucleotide polymorphism (SNP) markers to investigate genetic diversity within and differentiation among populations of Centaurea jacea and Betonica officinalis on restored and natural meadows in the White Carpathians, Czech Republic. The restoration took place 20 years ago using regional seeds propagated from a mix of multiple regional source populations. We included original regional seeds in our analysis to compare the restored populations with their origin (only in C. jacea). Additionally, we analysed conventional seeds without certified origin because these would have constituted a common alternative for restoration seeding in the absence of regional seeds. The differentiation between restored and natural populations (mean pairwise FST = 0.018 in Centaurea and 0.021 in Betonica) was similar to the differentiation among natural populations (FST = 0.023 and 0.021), and the restored populations were slightly more genetically diverse than the natural populations. In addition, restored populations were relatively similar to their origin, the regional seeds (FST = 0.015). In contrast, conventional seeds were strongly differentiated from all regional populations (FST = 0.100 and 0.059, in Centaurea and Betonica, respectively) and harboured substantially lower genetic diversity. We also found signs of gene flow via pollen or seed dispersal from natural to restored populations but not vice versa. Policy implications. Regionally sourced seeds can produce genetically diverse populations at natural levels of genetic differentiation.

opencc-by-4.0Nov 2021View details →

Population-based age-stratified seroepidemiological investigation protocol for coronavirus 2019 (COVID-19) infection in the Federation of Bosnia and Herzegovina

Results of population-based age stratified seroepidemiological investigation in the Federation of Bosnia and Herzegovina

opencc-by-4.0Nov 2021View details →

A NATIONAL STUDY OF SEROPREVALENCE OF COVID-19 INFECTION IN THE POPULATION OF THE REPUBLIKA SRPSKA

Results of population-based age stratified seroepidemiological investigation in the Republika Srpska.

Playa-Montmany, et al.: The thermoregulatory role of relative bill and leg surface areas in a Mediterranean population of Great tit

There is growing evidence on the role of legs and bill as 'thermal windows' in birds coping with heat stress. However, there is a lack of empirical work examining the relationship between the relative bill and/or leg surface areas and key thermoregulatory traits such as the limits of the thermoneutral zone (TNZ) or the cooling efficiency at high temperatures. Here, we explored this relationship in a Mediterranean population of Great tit (Parus major) facing increasing thermal stress in its environment. The lower and upper critical limits of the TNZ were found to be 17.7 ± 1.6°C and 34.5 ± 0.7°C, respectively, and the basal metabolic rate was 0.96 ± 0.12 ml O2 min-1 on average. The evaporative water loss (EWL) inflection point was established at 31.85 ± 0.27°C and was not significantly different from the value of the upper critical limit. No significant relationship was observed between the relative bill or tarsi size and TNZ critical limits, breadth, mass-independent VO2 or mass-independent EWL at any environmental temperature (from 10°C to 40°C). However, Great tit males (but not females) with larger tarsi areas (a proxy of leg surface area) showed higher cooling efficiencies at 40°C. We found no support for the hypothesis that the bill surface area plays a significant role as a thermal window in Great tits, but the leg surface areas may play a role in males' physiological responses to high temperatures. On the one hand, we argue that the studied population occupies habitats with available microclimates and fresh water for drinking during summer, so active heat dissipation by EWL might be favored instead of dry heat loss through the bill surface. Conversely, male dominance behaviors could imply a greater dependence on cutaneous evaporative water loss through the upper leg surfaces as a consequence of higher exposure to harsh environmental conditions than faced by females.

Population genetics as a tool to elucidate pathogen reservoirs: Lessons from Pseudogymnoascus destructans, the causative agent of White-Nose disease in bats

Emerging infectious diseases pose a major threat to human, animal, and plant health. The risk of species-extinctions increases when pathogens can survive in the absence of the host. Environmental reservoirs can facilitate this. However, identifying such reservoirs and modes of infection is often highly challenging. In this study, we investigated the presence and nature of an environmental reservoir for the ascomycete fungus Pseudogymnoascus destructans, the causative agent of White-Nose disease. Using 18 microsatellite markers, we determined the genotypic differentiation between 1,497 P. destructans isolates collected from nine closely situated underground sites where bats hibernate (i.e., hibernacula) in Northeastern Germany. This approach was unique in that it ensured that every isolate and resulting multi-locus genotype was not only present, but also viable and therefore theoretically capable of infecting a bat. The distinct distribution of multi-locus genotypes across hibernacula demonstrates that each hibernaculum has an essentially unique fungal population. This would be expected if bats become infected in their hibernaculum (i.e., the site they spend winter in to hibernate) rather than in other sites visited before they start hibernating. In one hibernaculum where both the walls and the hibernating bats were sampled at regular intervals over five consecutive winter seasons (1,062 isolates), higher genotypic richness was found on walls compared to bats and multi-locus genotypes showed a stable frequency over multiple winters. This clearly implicates hibernacula walls as the main environmental reservoir of the pathogen, from which bats become re-infected annually during hibernation.

Population connectivity across a highly fragmented distribution: Phylogeography of the Chalcophaps doves

Chalcophaps is a morphologically conserved genus of ground-walking doves distributed from India to mainland China, south to Australia, and across the western Pacific to Vanuatu. Here, we reconstruct the evolutionary history of this genus using DNA sequence data from two nuclear genes and one mitochondrial gene, sampled from throughout the geographic range of Chalcophaps. We find support for three major evolutionary lineages in our phylogenetic reconstruction, each corresponding to the three currently recognized Chalcophaps species. Despite this general concordance, we identify discordant mitochondrial and nuclear ancestries in the subspecies C. longirostris timorensis, raising further questions about the evolutionary history of this Timor endemic population. Within each of the three species, we find evidence for isolation by distance or hierarchical population structure, indicating an important role for geography in the diversification of this genus. Despite being distributed broadly across a highly fragmented geographic region known as a hotspot for avian diversification, the Chalcophaps doves show modest levels of phenotypic and genetic diversity, a pattern potentially explained by strong population connectivity owing to high overwater dispersal capability.

opencc-zeroDec 2019View details →

Microsatellite data from various African buffalo (Syncerus caffer) populations throughout Africa

1280 African buffalo (Syncerus caffer) samples genotyped with up to 19 microsatellites. 1275 samples are from East (12 populations) and southern Africa (4 populations). 5 samples are from central Africa (2 populations).

Episodes of high recruitment buffer against climate-driven mass mortality events in a North Pacific seabird population

Longitudinal studies of marked animals provide an opportunity to assess the relative contributions of survival and reproductive output to population dynamics and change. Cassin's auklets are a long-lived seabird that maximizes annual reproductive effort in resource-rich years through a behavior called double brooding, the initiation of a second breeding attempt following the success of the first during the same season. Our objective was to explore whether double brooding influenced population change by contributing a greater number of future recruits. We fit temporal symmetry models to 32-years of mark-recapture data of Cassin's auklets to infer the mechanisms underlying the observed variability in per capita recruitment rates. We found that periodic peaks in recruitment were explained by an increase in available nest sites, the proportion of the population double brooding 4 years prior, and spring upwelling conditions. Estimates of population change suggests a relatively stable population throughout the time series, attributable to a "floating" demographic class of sexually mature individuals excluded from breeding by competition which quickly fill vacant sites following periods of low adult survival. Our results highlight the importance of recruitment in maintaining the population of a long-lived seabird periodically impacted by adverse environmental conditions.