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opencc-by-4.0Apr 2024View details →

Data from: Interannual radial growth response of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) to severe droughts: an analysis along a gradient of soil properties and rooting characteristics

Dataset related to the publication: &bdquo;Interannual radial growth response of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) to severe droughts: an analysis along a gradient of soil properties and rooting characteristics” Information on the data and the tree species_site_key used can be found in the attached Read me file.

Fig. 4 in Fish assemblage in a dammed tropical river: an analysis along the longitudinal and temporal gradients from river to reservoir

Fig. 4. Ordination diagram from Canonical Correspondence Analysis of the abundance of the 14 most numerous species with abiotic variables. Zone codes: 1 = Zone 1; 2 = Zone 2; 3 = Zone 3; and 4 = Zone 4. Species codes: Aspar = Astyanax parahybae; Astbim = Astyanax cf. bimaculatus; Cickel = Cichla kelberi; Geobra = Geophagus brasiliensis; Hopmal = Hoplias malabaricus; Hypaur = Hypostomus auroguttatus; Hoplit = Hoplosternum littorale; Hypaff = Hypostomus affinis; Lepcop = Leporinus copelandii; Lepcon = Leporinus conirostris; Metmac = Metynnis maculatus; Olihep = Oligosarcus hepsetus; Pimmac = Pimelodus maculatus; Plasqu = Plagioscion squamosissimus.

Fig. 3 in Fish assemblage in a dammed tropical river: an analysis along the longitudinal and temporal gradients from river to reservoir

Fig. 3. Spatial variation in species number and biomass by zone (1, 2, 3, 4) in Paraíba do Sul River and Funil Reservoir.

Fig. 1 in Fish assemblage in a dammed tropical river: an analysis along the longitudinal and temporal gradients from river to reservoir

Fig. 1. Paraíba do Sul River - Funil Reservoir system. The four sampled zones are shown (1 = Zone 1; 2 = Zone 2; 3 = Zone 3, and 4 = Zone 4).

Fig. 2 in Fish assemblage in a dammed tropical river: an analysis along the longitudinal and temporal gradients from river to reservoir

Fig. 2. Individual-based rarefaction curves by zone (1, 2, 3, 4) for species richness in the Paraíba do Sul River and Funil Reservoir.

Fig. 6 in Ground beetles (Coleoptera: Carabidae) from the region of Cape Emine (central Bulgarian Black sea coast). Part III. Spatial distribution and gradient analysis

Fig. 6. PCA distribution of the sampling sites and the subclasses of life forms (according to Sharova 1981): Z_Phytob – Zoophagous phytobionts; Z_Strat – Zoophagous stratobionts; M_Strat – Mixophytophagous stratobionts; M_Short – Mixophytophagous stratohortobionts; M_Geoh – Mixophytophagous geobionts.

Fig. 7 in Ground beetles (Coleoptera: Carabidae) from the region of Cape Emine (central Bulgarian Black sea coast). Part III. Spatial distribution and gradient analysis

Fig. 7. PCA distribution of the sampling sites and categories of life forms (according to SHAROVA 1981): Life form class 1. Zoophagous. Life form subclass: 1.1 – Phytobios; 1.2 – Epigeobios; 1.3 – Stratobios; 1.4 – Geobios. Life form groups: 1.1.2 – stemdwelling hortobionts; 1.1.3 – leaf-dwelling dendrohortobionts; 1.2.2 – large walking epigeobionts; 1.2.2(1) – large walking dendroepigeobionts; 1.2.3 – running epigeobionts; 1.2.4 – flying epigeobionts; 1.3(1) – series crevice-dwelling stratobionts; 1.3(1).1 – surface & litter-dwelling; 1.3(1).2 – litter-dwelling; 1.3(1).3 – litter & crevice-dwelling; 1.3(1).4 – endogeobionts; 1.3(1).5 – litter & bark-dwelling; 1.3(1).6 – bothrobionts; 1.3(2).1 – litter & soil-dwelling; 1.4.2(1) – large digging geobionts. Life form class 2. Mixophytophagous. Life form subclass: 2.1 – Stratobios; 2.2 – Stratohortobios; 2.3 – Geohortobios. Life form groups: 2.1.1 – crevice-dwelling stratobionts; 2.2.1 – stratohortobionts; 2.3.1 – harpaloid geohortobionts; 2.3.1(1) – crevice-dwelling harpaloid geohortobionts; 2.3.2 – zabroid geohortobionts; 2.3.3 – dytomeoid geohortobionts.

Fig. 4 in Ground beetles (Coleoptera: Carabidae) from the region of Cape Emine (central Bulgarian Black sea coast). Part III. Spatial distribution and gradient analysis

Fig. 4. Ordination of the sampling sites in relation to the humidity and vegetation. The calculations were performed by the use of the results from all of the sampling sites and all of the catches, standardized through the recalculation of the data as number of specimens per 100 trapdays.

Fig. 3 in Ground beetles (Coleoptera: Carabidae) from the region of Cape Emine (central Bulgarian Black sea coast). Part III. Spatial distribution and gradient analysis

Fig. 3. Distribution of the permanent species in relation to the humidity and vegetation. The analysis included only the permanent species – those with a frequency above 50% (see TEOFILOVA 2015): A aenea – Amara aenea; A anth – Amara anthobia; A famil – Amara familiaris; Ac megac – Acinopus megacephalus; Agon sp – Agonum (Europhilus) sp.; Br crep – Brachinus crepitans; Br expl – Brachinus explodens; C ambig – Calathus ambiguus; C cinct – Calathus cinctus; C fuscip – Calathus fuscipes; Car conv – Carabus convexus; Car cor – Carabus coriaceus; Car ullr – Carabus ullrichi; Chl nit – Chlaenius nitidulus; H dimid – Harpalus dimidiatus; H dist – Harpalus distinguendus; H flavic – Harpalus flavicornis; H rubrip – Harpalus rubripes; H tardus – Harpalus tardus; Laem ter – Laemostenus terricola; Lei ruf – Leistus rufomarginatus; M maurus – Microlestes maurus; M minut – Microlestes minutulus; Myas ch – Myas chalybaeus; N brevic – Nebria brevicollis; O azur – Ophonus azureus; Par mend – Parophonus mendax; Ps rufip – Pseudoophonus rufipes; Pt melas – Pterostichus melas; Tr q – Trechus quadristriatus.

openCC (other)Jun 2020View details →

edi40/100

Explaining global variation in the latitudinal diversity gradient: Meta-analysis confirms known patterns and uncovers new one

This dataset is also available on the Dryad Digital Repository (link: https://doi.org/10.5061/dryad.rg5rd). The code is also available on GitHub (link: https://github.com/nlkinlock/LDGmeta-analysis). This dataset was created to explore patterns in biodiversity across latitude. The pattern of increasing biological diversity from high latitudes to the equator [latitudinal diversity gradient (LDG)] has been recognized for greater than 200 years. Empirical studies have documented this pattern across many different organisms and locations. In order to quantify the evidence for the global LDG and the associated spatial, taxonomic and environmental factors, a systematic review, followed by a meta-analysis of the resulting dataset, were carried out. This dataset contains a large number of individual LDGs that have been published in the 14 years since Hillebrand's ground‐breaking meta‐analysis of the LDG.

opencc-by-4.0Sep 2020View details →

Sample data for analysis of period/frequency gradient and phase gradient in spreadouts, ex vivo models of somitogenesis

Here are timelapse imaging (as .tif) of a dynamic Notch signaling reporter (i.e. LuVeLu) in spreadouts, ex vivo models of somitogenesis. Also here are the corresponding period and phase wavelet movies, generated using a wavelet analysis workflow developed by Gregor Mönke. These sample data are used to run an accompanying Python script, available at: <a href="https://github.com/PGLSanchez/EMBL_OscillationsAnalysis/tree/master/FrequencyPhase_GradientSlopeAnalysis">https://github.com/PGLSanchez/EMBL_OscillationsAnalysis/tree/master/FrequencyPhase_GradientSlopeAnalysis</a>

opencc-zeroJun 2021View details →

Latitudinal gradient in the intensity of biotic interactions in terrestrial ecosystems: Sources of variation and differences from the diversity gradient revealed by meta-analysis

The Latitudinal Biotic Interaction Hypothesis (LBIH) states that the intensity of biotic interactions increases from high to low latitudes. This hypothesis, which may partly explain latitudinal gradients in biodiversity, remains hotly debated, largely due to variable outcomes of published studies. We used meta-analysis to identify the scope of the LBIH in terrestrial ecosystems. For this purpose, we explored the sources of variation in the strength of latitudinal changes in herbivory, carnivory, and parasitism (119 publications) and compared these gradients with gradients in the diversity of the respective groups of animals (102 publications). Overall, both herbivory and carnivory decreased towards the poles, while parasitism increased. The latitudinal gradient in herbivory and carnivory was threefold stronger above 50–60º than at lower latitudes and was significant due to interactions involving ectothermic consumers, studies using standardized prey (i.e. prey lacking local anti-predator adaptations) and studies aimed at testing LBIH. The poleward decrease in biodiversity did not differ between ectothermic and endothermic animals or among climate zones and was four-fold stronger than decrease in herbivory and carnivory. The discovered differences between the gradients in biotic interactions and biodiversity suggest that these two global macroecological patterns are likely shaped by different factors.

opencc-zeroDec 2016View details →

Data from: Explaining global variation in the latitudinal diversity gradient: meta-analysis confirms known patterns and uncovers new ones

Aim: The pattern of increasing biological diversity from high latitudes to the equator [latitudinal diversity gradient (LDG)] has been recognized for > 200 years. Empirical studies have documented this pattern across many different organisms and locations. Our goal was to quantify the evidence for the global LDG and the associated spatial, taxonomic and environmental factors. We performed a meta-analysis on a large number of individual LDGs that have been published in the 14 years since Hillebrand's ground-breaking meta-analysis of the LDG, using meta-analysis and meta-regression approaches largely new to the fields of ecology and biogeography. Location: Global. Time period: January 2003–September 2015. Major taxa studied: Bacteria, protists, plants, fungi and animals. Methods: We synthesized the outcomes of 389 individual cases of LDGs from 199 papers published since 2003, using hierarchical mixed-effects meta-analysis and multiple meta-regression. Additionally, we re-analysed Hillebrand's original dataset using modern methods. Results: We confirmed the generality of the LDG, but found the pattern to be weaker than was found in Hillebrand's study. We identified previously unreported variation in LDG strength and slope across longitude, with evidence that the LDG is strongest in the Western Hemisphere. Locational characteristics, such as habitat and latitude range, contributed significantly to LDG strength, whereas organismal characteristics, including taxonomic group and trophic level, did not. Modern meta-analytical models that incorporate hierarchical structure led to more conservative and sometimes contrasting effect size estimates relative to Hillebrand's initial analysis, whereas meta-regression revealed underlying patterns in Hillebrand's dataset that were not apparent with a traditional analysis. Main conclusions: We present evidence of global latitudinal, longitudinal and habitat-based patterns in the LDG, which are apparent across both marine and terrestrial realms and over a broad taxonomic range of organisms, from bacteria to plants and vertebrates.

opencc-zeroApr 2022View details →

Data from: Experimental analysis of organ decay and pH gradients within a carcass and the implications for phosphatization of soft tissues

Replacement of soft-tissues by calcium phosphate yields spectacular fossils. Decay experiments have shown that pH is a major control on the precipitation of calcium phosphate and tissue replication: for this to occur pH must fall below the carbonic acid dissociation constant (pH 6.38). However, in the fossil record, phosphatisation is highly selective - some internal organs, such as muscles, stomachs, and intestines, appear to preferentially phosphatise while other organs seldomly phosphatise. The reasons for this are unclear but one hypothesis is that, during decay, organs create distinct chemical microenvironments and only some fall below the critical pH threshold for mineralization to occur. Here, we present a novel investigation using microelectrodes that records fluctuating dynamic spatial and temporal pH gradients inside of organs within a carcass in real time. Our experiments demonstrate that within a decaying carcass, organ-specific microenvironments are not generated. Rather, a pervasive pH environment forms within the body cavity (i.e. the coelom) which persists until integumentary failure. With no evidence to support the development of organ-specific microenvironments during decay other factors must control organ phosphatisation. We propose it is tissue histology that plays an important role in selective phosphatisation. Tissues with high phosphate content (and those rich in collagen) are most likely to phosphatise. Internal organs that have low tissue-bound phosphate, including the integuments of the stomach and intestine, only phosphatise when associated with ingested phosphate-rich organic matter. Identifying the driver behind selective phosphatisation may provide insights into other highly selective modes of soft-tissue preservation i.e. pyritization.

opencc-zeroJul 2022View details →

Assessment of the stream invertebrate β-diversity along an elevation gradient using a bidimensional null model analysis

Aim: β-Diversity, commonly defined as the compositional variation among localities that links local diversity (α‐diversity) and regional diversity (γ‐diversity), can arise from two different ecological phenomena, namely the spatial species turnover (i.e. species replacement) and the nestedness of assemblages (i.e. species loss). However, any assessment that does not account for stochasticity in community assembly could be biased and misinform conservation management. In this study, we aimed to provide a better understanding of the overall ecological phenomena underlying stream β-diversity along elevation gradients, and at contributing to the rich debate on null model approaches to identify non-random patterns in the distribution of taxa. Location: Swiss Alpine region. Methods: Based on presence-absence data of 78 stream invertebrate families from 309 sites, we analyzed the effect size of non-random spatial distribution of stream invertebrates on the β-diversity and its two components (i.e. turnover and nestedness). We used a modelling framework that allows exploring the complete range of existing algorithm sused in null model analysis, and to assess how distribution patterns vary according to an array of possible ecological assumptions. Results: Overall, the turnover of stream invertebrates and the nestedness of assemblages were significantly lower and higher, respectively, than the ones expected by chance. This pattern increased with elevation, and the consistent trend observed along the altitudinal gradient, even in the most conservative analysis, strengthened our findings. Main conclusions: Our study suggests that deterministic distribution of stream invertebrates in the Swiss Alpine region is significantly driven by differential dispersal capacity and environmental stress gradients. As long as the ecological assumptions for constructing the null models and their implications are acknowledged, we believe that they still represent useful tools to measure the effect size of non-random spatial distribution of taxa on β-diversity.

opencc-by-4.0Jul 2023View details →

Contents of Supplemental Table S15 of the gradient analysis of Mesotaenium endlicherianum

Contents of the large Supplemental Table S15 of the study "Environmental gradients reveal stress hubs predating plant terrestrialization"

Fig. 2 in Ground beetles (Coleoptera: Carabidae) from the region of Cape Emine (central Bulgarian Black sea coast). Part III. Spatial distribution and gradient analysis

Fig. 2. DCA analysis of the trapdays data for all of the sampling sites.

Fig. 1 in Ground beetles (Coleoptera: Carabidae) from the region of Cape Emine (central Bulgarian Black sea coast). Part III. Spatial distribution and gradient analysis

Fig. 1. PCA distribution of the sampling sites with full two-year catches.