Find research datasets worth reusing

opencc-by-4.0Oct 2023View details →

Data for : Ecological associations distribution modelling of marine plankton at global scale

Git repository : https://gitlab.univ-nantes.fr/combi-ls2n/adm

opencc-by-4.0Dec 2022View details →

Upscaling Tower-Based Net Ecosystem Productivity to global 250m using the Data Augmentation Method by Considering their Spatial Distribution

Terrestrial ecosystems have emerged as critical carbon sinks, holding a crucial role in the carbon cycle. Net ecosystem productivity (NEP) is a highly significant parameter in terrestrial ecosystems, representing the net ecosystem exchange (NEE) between ecosystems and the atmosphere, without considering other carbon fluxes from disturbances. In this NEP product, we harmonized various sets of tower-based NEP from flux sites as target variable, remote sensing product and meteorological data as traning variables. We further optimizied these smaple sets to address the problems in spatial distribution, culminating in a global NEP product spanning the years 2001-2022, achieved through the application of the random forest method. This dataset contains NEP data for global terrestrial ecosystems for the period 2001-2022 in MgC with a temporal resolution of 1 year. The spatial resolution of the product is 250m and the data format is TIFF. For detailed instructions on how to use the dataset, see User Guides.doc!

openNov 2024View details →

Global Landside Clustering of Aquaculture Ponds Distribution Acquired from Dense Time-Series Sentinel-2 Images by Google Earth Engine

This dataset reveals the global distribution pattern of landside clustering aquaculture ponds (LCAP) from a spatial perspective for the first time. It was derived from 4,015,054 tiles of the 10-m Sentinel-2 time-series images collected throughout 2020. The total area of global LCAP was estimated at 55,337.03 km2. Accuracy verification revealed that the Omission Error and Commission Error of the data is 7.51% and 16.69% respectively. We provide this dataset in ESRI shapefile format (.zip), which can be opened by ArcGIS. We invite you to download and utilize this dataset and recommend citing the following two references.

opencc-zeroSep 2022View details →

Investigating the utility of Anchored Hybrid Enrichment data to resolve the relationships among the Killifishes (Actinopterygii: Cyprinodontiformes), a globally distributed group of fishes

The Killifishes (Blenniiformes: Cyprinodontoidea) are a diverse and well-known group of fishes that contains sixteen families inclusive of Anablepidae, Aphaniidae Aplocheilidae, Cubanichthyidae, Cyprinodontidae, Fluviphylacidae, Fundulidae, Goodeidae, Nothobranchiidae, Orestiidae, Pantanodontidae, Poeciliidae, Procatopodidae, Profundulidae, Rivulidae, and Valenciidae and more than 1,200 species that are globally distributed in tropical and temperate, freshwater and estuarine habitats. The evolutionary relationships among the families within the group, based on different molecular and morphological data sets, have remained uncertain. Therefore, the objective of this study was to use a targeted approach, anchored hybrid enrichment, to resolve the phylogenetic relationships among the families within the Superfamily Cyprinodontoidea (formerly the Cyprindontiformes). This study included more than 100 individuals, representing all sixteen families within Cyprinodontoidea, including many recently diagnosed families. We recovered an average of 244 loci per individual. These data were submitted to phylogenetic analyses (RaxML and ASTRAL) and although we recovered many of the same relationships as in previous studies of the group, several novel sets of relationships for other families also were recovered. In addition, two well-established clades were recovered as monophyletic and are in agreement with most previous studies. We also assessed the degree of gene tree discordance in our dataset to evaluate support for alternative topological hypotheses for interfamilial relationships within the Cyprinodontoidea using a variety of different analyses. The results from this study will provide a robust, historical framework needed to investigate a plethora of biogeographic, taxonomic, ecological, and physiological questions for this group of fishes.

opennotspecifiedFeb 2021View details →

Fig. 1. Community divergence from global distributions. Distributions comparing 1303 in The influence of juvenile dinosaurs on community structure and diversity

Fig. 1. Community divergence from global distributions. Distributions comparing 1303 global taxa with local community taxa (median). Overall, global taxa are more left skewed and communities are more bimodal. "A" indicates the largest deviation from the global distribution; the same deviation is clearly shown in the carnivore distribution.

opencc-by-4.0May 2022View details →

Dataset for "Sensitivity of subregional distribution of socioeconomic conditions to the global assessment of water scarcity"

This dataset contains the data related to the final analysis for "Sensitivity of subregional distribution of socioeconomic conditions to the global assessment of water scarcity".

opennotspecifiedMay 2022View details →

FIG. 2 in Analysis of the diversity and distributional patterns of coleopteran families on a global scale

FIG. 2. Cluster analyses and corresponding regionalisation schemata based on (a) a streamlined but nevertheless fairly comprehensive dataset excluding very widespread families and family-poor ecoregions; (b) endemic-rich ecoregions only.

opennotspecifiedMay 2022View details →

FIG. 1 in Analysis of the diversity and distributional patterns of coleopteran families on a global scale

FIG. 1. Global patterns of coleopteran family diversity and endemism. (a) family richness; (b) weighted endemism.

opencc-zeroJul 2022View details →

Vascular epiphyte global distributions

<div> Aim: Vascular epiphytes are ubiquitous components of wet tropical forests where they contribute substantially to local and regional plant diversity. While some basic epiphyte distribution patterns are relatively well studied, little effort has been made to understand the drivers responsible for constraining their global distribution. This study quantifies the substantial contribution of epiphytes to global gradients and centres of vascular plant diversity and explores whether epiphytes vary from terrestrial plants in relation to contemporary and historical environmental variables. Location: Global. Time period: Present. Major taxa studied: Tracheophyta. Methods: Using a comprehensive epiphyte species list (EpiList 1.0), and distribution information for 27,850 epiphyte species derived from numerous literature sources, we describe the global biogeography of epiphytes. We used generalized linear mixed effects models to assess the relationship between epiphytic and terrestrial plant diversity, and contemporary and historical environmental predictors. Results: We find that epiphytes substantially contribute to global centres of vascular plant diversity, accounting for up to 39% of the vascular flora in Neotropical regions. Epiphytes decrease in species numbers with increasing latitude at a rate three times faster than terrestrial plants, a trend that is driven mainly by the distribution of tropical forests and precipitation. Further, large regional differences emerge that are explained by several large endemic angiosperm families (e.g., Neotropical Bromeliaceae) that are absent in other tropical regions. Main conclusions: Our results show that epiphytes are disproportionately diverse in most global centres of plant diversity and play an important role in driving the global latitudinal diversity gradient for plants. The distribution of precipitation and tropical forests emerge as major drivers of the latitudinal diversity gradient in epiphyte species richness. Finally, our findings demonstrate how epiphyte floras in different biogeographical realms are composed of different families and higher taxa revealing an important signature of historical biogeography. </div>

opencc-zeroJun 2022View details →

Datasets from: The distribution of covert natural enemies of a globally invasive crop pest, the fall armyworm, in Africa; enemy-release and spillover events

These datasets are for the analyses carried out in paper in Journal of Animal Ecology titled 'The distribution of covert natural enemies of a globally invasive crop pest, the fall armyworm, in Africa; enemy-release and spillover events.' The authors of the paper are Amy J. Withers, Annabel Rice, Jolanda de Boer, Philip Donkersley, Aislinn J. Pearson, Gilson Chipabika, Patrick Karangwa, Bellancile Uzayisenga, Benjamin A. Mensah, Samuel Adjei Mensah, Phillip Obed Yobe Nkunika, Donald Kachigamba, Judith A. Smith, Christopher M. Jones and Kenneth Wilson. Invasive species pose a significant threat to biodiversity and agriculture worldwide, and here we investigated the prevalence of natural enemies in fall armyworm (Spodoptera frugiperda) in Africa. This study aimed to identify which microbial pathogens are present in invasive fall armyworm, and determine the geographical, meteorological, and temporal variables that influence prevalence. Larval samples were screened from Malawi, Rwanda, Kenya, Zambia, Sudan, and Ghana for the presence of four different microbial natural enemies; two nucleopolyhedroviruses, Spodoptera frugiperda NPV (SfMNPV) and Spodoptera exempta NPV (SpexNPV); the fungal pathogen Metarhizium rileyi; and the bacterium Wolbachia. One dataset (ALL_diseaseprevalence_year_season) includes the results of this screening for all four microbial nartural enemies and sampling information, the other dataset (SfMNPVprevalence_weather_topographic_temporal_variables) includes the results for SfMNPV and sampling information alongside variables relating to temperature, rainfall, elevation, growing season and time since the fall armyworm first arrived in each country. These variables were used to investigate whether SfMNPV prevalence was affected by geographical, meteorological or temporal variables.

opencc-zeroOct 2022View details →

Deep vicariance and frequent transoceanic dispersal shape the evolutionary history of a globally distributed fern family

Premise Historical biogeography of ferns is typically expected to be dominated by long-distance dispersal, due to their minuscule spores. However, few studies have inferred the historical biogeography of a large and widely distributed group of ferns to test this hypothesis. Our aims are to determine the extent to which long-distance dispersal vs. vicariance have shaped the history of the fern family Blechnaceae, to explore ecological correlates of dispersal and diversification, and to determine whether these patterns differ between the northern and southern hemispheres. Methods We used sequence data for three chloroplast loci to infer a time-calibrated phylogeny for 154 out of 265 species of Blechnaceae, including representatives of all genera in the family. This tree was used to conduct ancestral range reconstruction and stochastic character mapping, estimate diversification rates, and identify ecological correlates of diversification. Key results Blechnaceae originated in Eurasia and began diversifying in the late Cretaceous. A lineage comprising most extant diversity diversified principally in the austral Pacific region around the Paleocene-Eocene Thermal Maximum. Land connections that existed near the poles during periods of warm climates likely facilitated migration of several lineages, with subsequent climate-mediated vicariance shaping current distributions. Long-distance dispersal is frequent and asymmetrical, with New Zealand/Pacific Islands, Australia, and tropical America being major source areas. Conclusions Ancient vicariance and extensive long-distance dispersal have shaped the history of Blechnaceae in both the northern and southern hemispheres. The exceptional diversity in austral regions appears to reflect rapid speciation in these areas; mechanisms underlying this evolutionary success remain uncertain.

opencc-by-4.0Apr 2024View details →

Global distribution and environmental correlates of marine bioturbation

This repository contains the R scripts necessary for conducting the data analysis for the paper titled 'Global distribution and environmental correlates of marine bioturbation', authored by Shuang Zhang, Martin Solan, and Lidya Tarhan. It includes five R files, which should be executed in the following order: 01-Db_L_data_compilation: Initial data exploration and compilation (calculating average Db and L over time) 02-Db_L_data_explore: Further data exploration and analysis 03-Machine_learning_train: Building the machine learning framework 04-Machine_learning_predict: Using the trained machine learning framework to predict global Db and L values 05-MPA_analysis: Marine Protected Area (MPA) analysis The repository also contains all necessary data to run these scripts. In addition, this repository also contains the appendix figures for the bioturbation paper.

Fig 20 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters

Fig 20. The original drawings of species of the C. lorenzianus complex. A: Resting spore of C. mitra by Bailey [17]. B and C: C. mitra by Cleve [18]. Vegetative chain, intercalary valve, terminal seta and apical view of seta positions (C), and chain with resting spores (B, lectotype). D: Vegetative chain of C. lorenzianus by Grunow [8]. E and F: Chaetoceros decipiens by Cleve [7]. G and H: Resting spores of C. lorenzianus by Okamura [39]. doi:10.1371/journal.pone.0168887.g020

Fig 5 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters

Fig 5. Chaetoceros elegans sp. nov. SEM (A–E) and TEM (F and G). A: Terminal valve view with external process of rimoportula and poroids on valve face; strain MC1048. B and C: Intercalary cells demonstrating large apertures and valve faces; strain M1 (B), strain MC1048 (C). D and E: Terminal valves with central processes (arrowheads) and silica ear-like structures (arrows in D) in strain YL7. F: Annulus, costae and poroid pattern near intercalary valve centre; strain YL7. G: Parallel rows of poroids on the mantle; arrowhead indicates ring-shaped constriction; strain YL7. A–E scale bars, 5 μm. F and G scale bars, 2 μm. doi:10.1371/journal.pone.0168887.g005

Fig 19 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters

Fig 19. Molecular phylogenetic tree. Based on analyses of the D1-D3 region of the LSU rDNA sequences. Numbers indicated on the branches are posterior probability of Bayesian analyses (MrB) and boot strap support of neighbor joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) analyses. doi:10.1371/journal.pone.0168887.g019

Fig 1 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters

Fig 1. LM of Chaetoceros decipiens. A, C, E, F: Chain views of lectotype material MIC5366 (A) and strains P10E5 (C), P14B3B (E), D12 (F). B and D: Detail of chains showing constrictions (arrows) between the mantle and the girdle bands, and the fused extensions of sibling setae, which are short, longer or even absent (arrowheads); lectotype material MIC5366 (B) and strain P10E5 (D). G: Chain view of strain D10, note the V-shaped protrusion located centrally on the terminal valve (arrowhead). A and C: scale bars, 50 μm. B, D, E, F: scale bars, 20 μm. G: scale bar, 10 μm. doi:10.1371/journal.pone.0168887.g001

Fig 4 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters

Fig 4. LM of Chaetoceros elegans sp. nov. Strain YL7. A: Chain view displaying seta divergence in the apical plane. B: Solitary cell. C: Chain view demonstrating large apertures and chloroplasts. D: End of chain showing constrictions (arrows) between the mantle and the girdle, and V-shaped protrusion (arrowhead) located centrally on terminal valve. A and B scale bars, 50 μm. C and D scale bars, 20 μm. doi:10.1371/journal.pone.0168887.g004

Fig 13 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters

Fig 13. LM of Chaetoceros mitra. Strain P10A1. A: Straight chain showing seta divergence and apertures. B: Detail of chain showing constrictions (arrows) between mantle and girdle. C: Valve structure of terminal valve. A and B scale bars, 20 μm. C scale bar, 10 μm. doi:10.1371/journal.pone.0168887.g013

Fig 12 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters

Fig 12. Chaetoceros mannaii sp. nov. LM (A), SEM (B) and TEM (C–F); strain N1. A and B: Setae with oval poroids. C: Terminal valve showing valve structure and rimoportula with external projection. D: Poroids and costae on the mantle. E and F: Girdle bands with poroids. A scale bar, 10 μm. B scale bar, 5 μm. C–F scale bars, 2 μm. doi:10.1371/journal.pone.0168887.g012

Fig 8 in Diversity in the Globally Distributed Diatom Genus Chaetoceros (Bacillariophyceae): Three New Species from Warm-Temperate Waters

Fig 8. Chaetoceros laevisporus sp. nov. LM (A–C), SEM (D and E) and TEM (F). Fig A: Part of a chain showing constrictions (arrows) between mantle and girdle, and V- shaped protrusion (arrowhead) located centrally on the terminal valve; strain N7. B: Dividing chain showing seta divergence; strain DY1. C: Structure of terminal seta; strain DY1. D: Chain in girdle view showing cells and apertures; strain N7. E: Terminal valve with rimoportula without external process (arrowhead); strain N7. F: Valve views of intercalary (upper) and terminal valves (below); strain N7. A, C, D scale bars, 20 μm. B scale bar, 100 μm. E and F scale bars, 5 μm. doi:10.1371/journal.pone.0168887.g008