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opencc-zeroDec 2016View details →

FIGURE 41 – 48 in A new widespread European bee species of the genus Dasypoda Latreille (Hymenoptera, Apoidea)

FIGURE 41 – 48. Structure of male sterna and genitalia: 41 – 42. Sternum 8 (ventral view; scale = 0.5 mm); 43 – 44. Apex of sternum 8 (ventral view; scale = 0.1 mm); 45 – 48. Genitalia (45 – 46 — dorsal, 47 – 48 — ventral view; scale = 0.5 mm);. (41, 43, 45, 47 — Dasypoda morawitzi sp. nov.; 42, 44, 46, 48 — D. hirtipes).

opencc-zeroOct 2023View details →

Data and code: Microgeographic variation in demography and thermal regimes stabilize regional abundance of a widespread freshwater fish

Predicting the persistence of species under climate change is an increasingly important objective in ecological research and management. However, biotic and abiotic heterogeneity can drive asynchrony in population responses at small spatial scales, complicating species-level assessments. For widely distributed species consisting of many fragmented populations, such as brook trout (Salvelinus fontinalis), understanding drivers of asynchrony in population dynamics can improve predictions of range-wide climate impacts. We analyzed demographic time-series from mark-recapture surveys of eleven natural brook trout populations in eastern Canada over 13 years to examine the extent, drivers, and consequences of fine-scale population variation. The focal populations were genetically differentiated, occupied a small area (~25 km2) with few human impacts, and experienced similar climate conditions. Recruitment was highly asynchronous, weakly related to climate variables, and showed population-specific relationships with other demographic processes, generating diverse population dynamics. In contrast, individual growth was mostly synchronized among populations and driven by a shared positive relationship with stream temperature. Outputs from population-specific models were unrelated to four of five hypothesized drivers (recruitment, growth, reproductive success, phylogenetic distance), but variation in groundwater inputs strongly influenced stream temperature regimes and stock-recruitment relationships. Finally, population asynchrony generated a portfolio effect that stabilized regional species abundance. Our results demonstrate that population demographic and habitat diversity at microgeographic scales can play a significant role in moderating species responses to climate change. Moreover, we suggest that the absence of human activities within study streams preserved natural habitat variation and contributed to asynchrony in brook trout abundance, while the small study area eased monitoring and increased the likelihood of detecting asynchrony. Therefore, anthropogenic habitat degradation, landscape context, and spatial scale must be considered when developing management strategies to monitor and maintain populations that are diverse, stable, and resilient to climate change.

Figure 7 in Revalidation of Leucetta floridana (Haeckel, 1872) (Porifera, Calcarea): a widespread species in the tropical western Atlantic

Figure 7. Box-and-whisker plot (maximum and minimum size; upper and lower quartiles and median) of spicule size of Leucetta spp. A, triactine I length; B, triactine I width; C, triactine II length; D, triactine II width; E, tetractine I length; F, tetractine I width; G, tetractine II length; H, tetractine II width. Leucetta floridana (Caribbean), Z Leucetta floridana (Brazil), Leucetta sp., Leucetta microraphis.

Figure 5 in Revalidation of Leucetta floridana (Haeckel, 1872) (Porifera, Calcarea): a widespread species in the tropical western Atlantic

Figure 5. Leucetta floridana from the Caribbean (UFRJPOR 5360). A, L. floridana in situ (photo: S. Zea). B, transversal section of the cortex and choanosome; C, transversal section of the choanosome and atrium; D, triactine I; E, triactine II and the small triactines I; F, tetractine I; G, detail of the apical actine of tetractines I protruding into the atrium; H, tetractine II and several triactines I and tetractines I. Scale bars: A = 1 cm; B–H = 100 Mm.

Figure 1 in Revalidation of Leucetta floridana (Haeckel, 1872) (Porifera, Calcarea): a widespread species in the tropical western Atlantic

Figure 1. Sampling sites. Caribbean: 1 – Bocas del Toro (BDT), 2 – San Andrés Island (SAN), 3 – Urabá (URA); Brazil: 4 – Ceará (CEA), 5 – Rio Grande do Norte (RGN), 6 – Rocas Atoll (RAT), 7 – Fernando de Noronha Archipelago (FNO), 8 – Abrolhos Archipelago (ABR); Pacific: 9 – Australia (GBR), 10 – New Caledonia (NCA).

Figure 6 in Revalidation of Leucetta floridana (Haeckel, 1872) (Porifera, Calcarea): a widespread species in the tropical western Atlantic

Figure 6. Leucetta sp. from Brazil. A, live specimen (photo: G. Muricy); B, triactine I; C, tetractines I; D, triactine II and tetractine II. Scale bars: A = 1 cm, B–D = 100 Mm.

Figure 3. Leucetta microraphis from New Caledonia. A in Revalidation of Leucetta floridana (Haeckel, 1872) (Porifera, Calcarea): a widespread species in the tropical western Atlantic

Figure 3. Leucetta microraphis from New Caledonia. A, preserved specimen; B, triactine I; C, triactine II and several triactines I and tetractines I; D, tetractine I. Scale bars: A = 1 cm; B–D = 100 Mm.

opencc-zeroNov 2023View details →

Interspecific introgression and widespread intraspecific gene flow in a clade of tropical and subtropical seabirds

The mechanisms that restrict gene flow between populations and facilitate population differentiation and speciation vary across the tree of life. In systems where physical barriers to gene flow are dynamic over time and space, such as many marine species, genetic introgression may be a major factor in the speciation process. In sympatric species of seabirds, hybridization has been frequently observed but few studies have investigated patterns of introgression. We used whole-genome sequence data to test for interspecific introgression between five pairs of tropical and subtropical seabird species and to test for gene flow within species across major land mass barriers and ocean basins. We found evidence for introgression between: blue-footed (Sula nebouxii) and Peruvian boobies (S. variegata); masked (S. dactylatra) and Nazca boobies (S. granti); and blue-footed and Nazca boobies. We found no evidence of introgression between blue-footed and brown boobies (S. leucogaster), or masked and brown boobies, despite observed hybridization between these species. We also found evidence for gene flow across several major land masses in three pantropical species: red-footed (S. sula), brown, and masked boobies. Finally, we report mixed evidence for ancient introgression between brown boobies and the ancestor of blue-footed, Peruvian, masked, and Nazca boobies. Our work indicates (1) that interspecific introgression has shaped contemporary booby diversity in the eastern Pacific, and (2) that contemporary physical barriers to gene flow between booby colonies are not absolute. Our findings contribute novel insights to the growing body of evidence that introgression is a widespread evolutionary process.

opencc-by-4.0Dec 2023View details →

Supporting data sets for "Evolutionary analyses of IDRs reveal widespread signals of conservation"

S1: Disorder and order regions of alignments computed from AUCPreD scores which passed the 30 residue minimum length and phylogenetic diversity filters. The "ppids" column indicates the sequences in each alignment which were not excluded due these and other filtering criteria. See the main text methods for more details. S2: Substitution model parameters fit to meta-alignments derived from disorder and order filtered regions. S3: Features of segments in all regions. S4: Contrasts and root estimates of disorder scores in filtered regions computed with Felsenstein's contrasts algorithm. S5: Contrasts and root estimates of features in filtered regions computed with Felsenstein's contrasts algorithm. S6: Estimated BM and OU model parameters of simulated data. S7: Estimated BM and OU model parameters of features in filtered regions computed with maximum likelihood.

opencc-by-4.0Dec 2022View details →

Data from "Stability of genome-wide methylation patterns and parental environmental effects in the widespread, long-lived Lombardy poplar"

Data from : 'Stability of genome-wide methylation patterns and parental environmental effects in the widespread, long-lived Lombardy poplar' An Vanden Broeck*, Tim Meese*, Pieter Verschelde, Karen Cox, Berthold Heinze, Dieter Deforce, Ellen De Meester and Filip Van Nieuwerburgh   Related publication: Vanden Broeck, A.*, Meese, T.*, Verschelde, P. et al. Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar. BMC Biol 22, 30 (2024). https://doi.org/10.1186/s12915-024-01816-1 <ul> <li>* These authors contributed equally.</li> </ul> -------------------------------------------------- Background: Despite the increasing number of epigenomic studies in plants, little is known about the forces that shape the methylome in long-lived woody perennials. The Lombardy poplar (Populus nigra cv. 'Italica' Duroi) offers an ideal opportunity to investigate the impact of the individual environmental history of trees on the methylome. Results: We present the results of three interconnected experiments on Lombardy poplar. In the first experiment, we investigated methylome variability during a growing season and across vegetatively reproduced generations. We found that ramets collected over Europe and raised in common conditions have stable methylomes in symmetrical CG-contexts. In contrast, seasonal dynamics occurred in methylation patterns in CHH-context. In the second experiment, we investigated whether methylome patterns of plants grown in a non-parental environment correlate with the parental climate. We did not observe any biological relevant pattern that significantly correlates with the parental climate. Finally, we investigated whether the parental environment has persistent carry-over effects on the vegetative offspring's' phenotype. We combined new bud set observations of three consecutive growing seasons with former published bud set data. Using a linear mixed effects analysis, we found a statistically significant but weak short-term, parental carry-over effect on the timing of bud set. However, this effect was negligible compared to the direct effects of the offspring environment. Conclusions: Genome-wide cytosine methylation patterns in symmetrical GC-context are stable in Lombardy poplar and appear to be mainly the result of random processes. In this widespread poplar clone, methylation patterns in GC-context can be used as bio-markers to infer a common ancestor and thus to investigate the environmental history of a specific Lombardy poplar on short time-scales. The Lombardy poplar shows high phenotypic plasticity in a novel environment which enabled this clonal tree to adapt and survive all over the temperate regions of the world.   ADDITIONAL FILES Additional file 1. CSV-file with information on the Lombardy poplar trees samples used for whole genome bisulfite sequencing (WGBS) in the two methylome experiments (metadata). The raw fastq datafiles obtained by whole genome bisulfite sequencing (WGBS) are available at the <a href="https://www.ncbi.nlm.nih.gov/geo/">Gene Expression Omnibus (GEO) database</a> (submission  GSE225596). Additional file 2. CSV-file with mapping statistics, bisulfite conversion rates and percentages of cytosine methylation for each DNA-sample analyzed by whole genome bisulfite sequencing (WGBS). (processed data). Additional file 3. CSV-file with the total list of GO terms that were enriched in DMRs. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively) (processed data). Additional file 4. POWERPOINT-file. Heatmaps with GO terms over-represented in promoters containing DMRs in CpG-context per between-group pairwise comparison. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively). A. HUN4 versus ITS3; B. HUN4 versus UKD2, C; ITS3 versus SPC1; D. HUN4 versus SCP1,  E. SPC1 versus UKD2 Additional file 5. CSV-file with the raw data of the bud set observations in the common garden experiment (raw data). Additional file 6. HTML-file with the R source codes to reproduce the results of the bud set analysis (code, R script). Additional file 7. A text-file representing the Snakefile (i.e. a readable Python-based workflow) including the different steps and rules of the bioinformatics of the WGBS data analyses (code, Snakefile). Additional file 8. RMD-file with the code to reproduce the analyses to identify differential methylated predefined regions (code, R script). Additional file 9. R-script with the code to reproduce the clustering and visualizing of the GO enrichment results (code, R script). Supporting files 1. Zip-folder with: i) excel-files listing the genes in DMRs, and ii) PNG-files with the ‘Biological Coefficient of Variation (BCV)’-plots between any of the six pairwise comparisons of Lombardy poplars grouped per ortet and identified with Bioconductor package edgeR. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively) (processed data). Supporting files 2. Zip-folder with PNG-files representing heatmaps and excel-files with clustered GO terms significant over-represented in promoters and gene regions located in DMRs. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively. The files were obtained with the Bioconductor package simplifyEnrichment (processed data). --------------------------------------------------------- Version 3: <ul> <li>Renaming of file names according to the publisher's guidelines</li> <li>Additional file 2 includes also bisulfite conversion rates per sample</li> </ul>

opencc-by-4.0Dec 2023View details →

Maternal body condition affects the response of the gut microbiome to a widespread contaminant in larval spined toads

Datasets (metadata and phyloseq object)  Scripts used for the statistical analyses

opencc-zeroMar 2024View details →

Contrasting effects of host or local specialization: widespread haemosporidians are host generalist whereas local specialists are locally abundant

Aim: Despite the wide distribution of many parasites around the globe, the range of individual species varies significantly even among phylogenetically related taxa. Since parasites need suitable hosts to complete their development, parasite geographical and environmental ranges should be limited to communities where their hosts are found. Parasites may also suffer from a trade-off between being locally abundant or widely dispersed. We hypothesize that the geographical and environmental ranges of parasites are negatively associated to their host specificity and their local abundance. Location: Worldwide Time period: 2009 to 2021 Major taxa studied: Avian haemosporidian parasites Methods: We tested these hypotheses using a global database which comprises data on avian haemosporidian parasites from across the world. For each parasite lineage, we computed five metrics: phylogenetic host-range, environmental range, geographical range, and their mean local and total number of observations in the database. Phylogenetic generalized least squares models were ran to evaluate the influence of phylogenetic host-range and total and local abundances on geographical and environmental range. In addition, we analysed separately the two regions with the largest amount of available data: Europe and South America. Results: We evaluated 401 lineages from 757 localities and observed that generalism (i.e. phylogenetic host range) associates positively to both the parasites' geographical and environmental ranges at global and Europe scales. For South America, generalism only associates with geographical range. Finally, mean local abundance (mean local number of parasite occurrences) was negatively related to geographical and environmental range. This pattern was detected worldwide and in South America, but not in Europe. Main Conclusions: We demonstrate that parasite specificity is linked to both their geographical and environmental ranges. The fact that locally abundant parasites present restricted ranges, indicates a trade-off between these two traits. This trade-off, however, only becomes evident when sufficient heterogeneous host communities are considered.

opencc-zeroMar 2024View details →

Data from: Testing metabolic cold adaptation and the climatic variability hypotheses across the latitudinal range of a widespread, supratidal water beetle

Temperature significantly impacts ectotherm physiology, with thermal and metabolic traits varying with latitude but the drivers of this variation remain unclear, despite obvious consequences in the face of ongoing global change. This study explores metabolic cold adaptation (MCA) and the climatic variability hypothesis (CVH) to evaluate local adaptation and phenotypic plasticity of metabolic rates and thermal limits in two populations of the supratidal rockpool beetle Ochthebius lejolisii from localities experiencing contrasting thermal variability. Reciprocal acclimation was conducted under spring temperature regimes of both localities, incorporating local diurnal variation. Metabolic rates were measured by closed respirometry, and thermal tolerance limits estimated through thermography. In line with MCA, the northern population (colder climate) showed higher metabolic rates and Q10s at lower temperatures than the southern population. As predicted by the CVH, the southern population (more variable climate) showed higher upper thermal tolerance but only the northern population was able to acclimate upper thermal limits. This pattern suggests the existence of trade-offs in thermal adaptation in this species, likely increasing the vulnerability of populations on Mediterranean coasts to the projected increases in extreme temperatures under ongoing climate change.

opencc-by-4.0Jan 2022View details →

Data for Ecology Letters paper: Jack-of-all-trades paradigm meets long-term data: generalist herbivores are more widespread and locally less abundant.

Data, R-code, and meta-data document for a 2022 paper in Ecology Letters that examines assumptions about associations between local abundance and dietary specialization using an 18-year dataset of caterpillar-plant interactions in Ecuador.

opencc-by-4.0Feb 2022View details →

Widespread ripples synchronize human cortical activity during sleep, waking, and memory recall

These are the data and code for the article 'Widespread ripples synchronize human cortical activity during sleep, waking, and memory recall.' Please cite this article when using these data or code.

opencc-by-4.0Feb 2022View details →

Genetic basis of growth reaction to drought stress differs in contrasting high-latitude treeline ecotones of a widespread conifer

Raw and filtered SNP data and raw tree ring data of the analysed trees. R scripts for SNP filtering, phenotypic data and genotype-phenotype association analysis.

opencc-zeroJun 2022View details →

Interspecific coprophagia by wild red foxes: DNA metabarcoding reveals a potentially widespread form of commensalism among animals

Vertebrate animals are known to consume other species' faeces, yet the role of such coprophagy in species dynamics remains unknown, not least due to the methodological challenges of documenting it. In a large-scale metabarcoding study of red fox and pine marten scats, we document a high occurrence of domestic dog DNA in red fox scats and investigate if it can be attributed to interspecific coprophagia. We tested whether experimental artifacts or other sources of DNA could account for dog DNA, regressed dog occurrence in the diet of fox against that of the fox' main prey, short-tailed field voles, and consider whether predation or scavenging could explain the presence of dog DNA. Additionally, we determined the calorific value of dog faeces through calorimetric explosion. The high occurrence of dog DNA in the diet of fox, the timing of its increase, and the negative relationship between dog and the fox's main prey, point to dog faeces as the source of DNA in fox scats. Dog faeces being highly calorific, we found that foxes, but not pine martens, regularly exploit them, seemingly as an alternative resource to fluctuating prey. Scattered accounts from the literature may suggest that interspecific coprophagia is a potentially frequent and widespread form of interaction among vertebrates. However, further work should address its prevalence in other systems as well as the implications for ecological communities. Tools such as metabarcoding offer a way forward.

opencc-zeroJul 2022View details →

Low winter temperatures and divergent freezing resistance set the cold range limit of widespread alpine graminoids

Aim: "Where and why does a species exist" is a fundamental question in ecology. However, the actual range limits of alpine plant species are largely unexplored and unexplained. We aim at identifying the low temperature range limits of the two most abundant alpine graminoid species on acidic soils that intermingle in mosaics of high-elevation habitats across the European Alps. Location: Alpine grasslands in the Swiss Alps. Taxon: Carex curvula (Cyperaceae) and Nardus stricta (Poaceae), named by the genus name hereafter. Results: Carex and Nardus clearly segregated across different microsites. Season length, growing degree hours and soil chemistry (pH, C/N-ratio, phosphorus) did not demarcate the two species' ranges, while their distribution was strongly affected by soil minimum temperature in winter. Carex occurred at sites with and without protecting snow cover and resisted low soil temperatures (-13 °C). Nardus was absent at microsites with snow cover duration less than 5 months and soil minimum temperatures below -5 °C. During the growing season, leaves of Carex had a higher freezing resistance with LT50 of -16.1 °C than those of Nardus with LT50 of -13.3 °C (LT50: lethal temperature for 50% of the tissue). Tetrazolium staining in shoots also revealed a higher freezing resistance in Carex compared to Nardus, and shoot apices tolerated lowest temperatures: Carex -30 °C, Nardus -24 °C. Though, a vital shoot apex alone did not ensure regrowth after winter. Regrowth after severe frost events requires intact vessels and roots, all less freezing tolerant than apical meristems and young leaves. Main conclusions: The cold range limits of these widespread alpine graminoid species are evidently set by thermal extremes in winter. Microtopography, thus snow distribution pattern, in concert with the species' freezing resistance explains the cold edge of the fundamental niche of these two species.

opencc-by-4.0Mar 2019View details →

Fig. 2 in . Study of Nosema spp. in the Tomsk region, Siberia: co-infection is widespread in honeybee colonies

Fig. 2. Distribution of Nosema species in bee colonies (Apis mellifera) throughout the Tomsk region (dots A–I). Bee colonies not infected by Nosema are indicated in yellow; bee