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193 results for “diversity dynamics”
Figure 2. from: Tree Diversity and Dynamics of the Forest of Seu Nico, Viçosa, Minas Gerais, Brazil - Biodiversity Data Journal 3: e5425 (31 July 2015) https://doi.org/10.3897/BDJ.3.e5425
Figure 2. - Croqui of the 100 x 100 m FSN Dynamics Plot (Suppl. material 1).
A comparative study of the dynamics and diversity of Bdel-lovibrio and like organisms in Lakes Annecy and Geneva
<p>Specific run :</p> <p>Raw files R1 and R2</p> <p>Tags lists</p> <p>OTUs tables filtered and unfiltered</p>
Genetic diversity and spread dynamics of SARS-CoV-2 variants present in African populations
<p>The dynamics of coronavirus disease-19 (COVID-19) have been extensively researched in many settings around the world, but little is known about these patterns in Africa. 7540 complete nucleotide genomes from 51 African nations were obtained and analysed from the National Center for Biotechnology Information (NCBI) and Global Initiative on Sharing Influenza Data (GISAID) databases to examine genetic diversity and spread dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) lineages circulating in Africa. Utilising a variety of clade and lineage nomenclature schemes, we looked at their diversity, and used maximum parsimony inference methods to recreate their evolutionary divergence and history. According to this study, only 465 of the 2610 Pango lineages found to have existed in the world circulated in Africa after three years of the COVID-19 pandemic outbreak, with five different lineages dominating at various points during the outbreak. We identified South Africa, Kenya, and Nigeria as key sources of viral transmissions between Sub-Saharan African nations. These findings provide insight into the viral strains that are circulating in Africa and their evolutionary patterns.</p>
Data from: Dispersal versus environmental filtering in a dynamic system: drivers of vegetation patterns and diversity along stream riparian gradients
1. Both environmental filtering and dispersal filtering are known to influence plant species distribution patterns and biodiversity. Particularly in dynamic habitats, however, it remains unclear whether environmental filtering (stimulated by stressful conditions) or dispersal filtering (during re-colonization events) dominates in community assembly, or how they interact. Such a fundamental understanding of community assembly is critical to the design of biodiversity conservation and restoration strategies. 2. Stream riparian zones are species-rich dynamic habitats. They are characterized by steep hydrological gradients likely to promote environmental filtering, and by spatiotemporal variation in the arrival of propagules likely to promote dispersal filtering. We quantified the contributions of both filters by monitoring natural seed arrival (dispersal filter) and experimentally assessing germination, seedling survival and growth of 17 riparian plant species (environmental filter) along riparian gradients of three lowland streams that were excavated to bare substrate for restoration. Subsequently, we related spatial patterns in each process to species distribution and diversity patterns after 1 and 2 years of succession. 3. Patterns in initial seed arrival were very clearly reflected in species distribution patterns in the developing vegetation and were more significant than environmental filtering. However, environmental filtering intensified towards the wet end of the riparian gradient, particularly through effects of flooding on survival and growth, which strongly affected community diversity and generated a gradient in the vegetation. Strikingly, patterns in seed arrival foreshadowed the gradient that developed in the vegetation; seeds of species with adult optima at wetter conditions dominated seed arrival at low elevations along the riparian gradient while seeds of species with drier optima arrived higher up. Despite previous assertions suggesting a dominance of environmental filtering, our results demonstrate that nonrandom dispersal may be an important driver of early successional riparian vegetation zonation and biodiversity patterns as well. 4. Synthesis: Our results demonstrate (and quantify) the strong roles of both environmental and dispersal filtering in determining plant community assemblies in early successional dynamic habitats. Furthermore, we demonstrate that dispersal filtering can already initiate vegetation gradients, a mechanism that may have been overlooked along many environmental gradients where interspecific interactions are (temporarily) reduced.
Data from: Post-fire response and genetic diversity in Erica coccinea: connecting population dynamics and diversification in a biodiversity hotspot
Understanding the proceses of biological diversification is a central topic in evolutionary biology. The South African Cape fynbos, one of the major plant biodiversity hotspots out of the tropics, has prompted several hypotheses about the causes of generation and maintenance of biodiversity. Fire has been traditionally invoked as a key element to explain high levels of biodiversity in highly speciose fynbos taxa, such as the genus Erica. In this study, we have implemented a microevolutionary approach to elucidate how plant-response to fire may contribute to explain high levels of diversification in Erica. By using microsatellite markers, we investigated the genetic background of seeder (fire-sensitive) and resprouter (fire-resistant) populations of the fynbos species Erica coccinea. We found higher within-population genetic diversity and higher among-population differentiation in seeder populations and interpreted these higher levels of genetic diversification as a consequence of the comparatively shorter generation times and faster population turnover in the seeder form of this species. Considering that genetic divergence among populations may be seen as the initial step to speciation, the parallelism between these results and the pattern of biodiversity at the genus level offers stimulating insights into understanding causes of speciation of the genus Erica in the Cape fynbos.
Explosive Cenozoic origin and diversity-dependent diversification dynamics shaped the evolution of Australian skipper butterflies
<p><span>Australia was predominantly tropical for most of the early Cenozoic, then transitioned to a cooler and drier climate in the Oligocene. In response to this increasing aridity, some lineages adapted to more xeric ecosystems, contracted, or became restricted to increasingly fragmented mesic refugia, or went extinct. Yet, the lack of macroevolutionary studies at a continental scale precludes a better understanding of Australian biodiversity patterns and processes during the Cenozoic. Here, we infer a robust dated phylogenomic tree for a radiation of Australian endemic butterflies, the Trapezitinae skippers, to test the impact of biotic and abiotic drivers on Cenozoic diversification dynamics in Australia. These butterflies originated during the Eocene (<em>ca</em>. 42 Ma) in the mesic biome of Australia. Trapezitinae exploded in diversity during a cool, dry period in the late Oligocene and early Miocene, then experienced a sharp deceleration in speciation. Xeric ecosystems appear to have been colonized more recently, supporting the hypothesis of arid and semi-arid biomes as evolutionary sinks. Temperature-dependent and phytophagy-dependent diversification models received little support. Instead, we find evidence for diversity-dependent processes with a declining diversification in Trapezitinae likely linked to limited ecological opportunities following a rapid initial burst of diversification.</span></p>
Data from: Observed and dark diversity dynamics over millennial time scales: Fast-life history traits linked to expansion lags of plants in northern Europe
<p>Global change drivers (e.g. climate and land use) affect the species and functional traits observed in a local site but also its dark diversity—the set of species and traits locally suitable but absent. Dark diversity links regional and local scales and, over time, reveals taxa under expansion lags by depicting the potential biodiversity that remains suitable but is absent locally. Since global change effects on biodiversity are both spatially and temporally scale dependent, examining long-term temporal dynamics in observed and dark diversity would be relevant to assessing and foreseeing biodiversity change. Here, we used sedimentary pollen data to examine how both taxonomic and functional observed and dark diversity changed over the past 14500 years in northern Europe. We found that taxonomic and functional observed and dark diversity increased over time, especially after the Late Glacial and during the Late Holocene. However, dark diversity dynamics revealed expansion lags related to species' functional characteristics (dispersal limitation and stress intolerance) and an extensive functional redundancy when compared to taxa in observed diversity. We highlight that assessing observed and dark diversity dynamics is a promising tool to examine biodiversity change across spatial scales, its possible causes, and functional consequences.</p>
Quaternary diversity dynamics of Australian reptiles - Electronic supplement
<p>Supplement paper 2</p> <p><em>Electronic data files</em></p> <p>File ES2.1 - Metadata for the included specimens (.xlsx)</p> <p>File ES2.2 – Folder containing surface models (.ply) of the crania of the included specimens, landmark pairs, and sliding landmark data</p> <p>File ES2.3a – 3D landmark coordinates of maxillae (.tps)</p> <p>File ES2.3b – 3D landmark coordinates of maxillae (missing data estimated, curves equidistant) (.tps)</p> <p>File ES2.4a – 3D landmark coordinates of frontals (.tps)</p> <p>File ES2.4b – 3D landmark coordinates of frontals (missing data estimated, curves equidistant) (.tps)</p> <p>File ES2.5 – R code for evaluating landmark estimation (.R)</p> <p>File ES2.6 – R code for estimating effects of sample size (.R)</p> <p>File ES2.7 – R code for estimating effects of missing landmarks (.R)</p> <p>File ES2.8 – Results of landmark estimation performance analyses (.csv)</p> <p>File ES2.9 – Pairwise Procrustes distances of different groupings and CVA results (maxillae; .xlsx)</p> <p>File ES2.10 - Pairwise Procrustes distances of different groupings and CVA results (frontals; .xlsx)</p> <p>File ES2.11 - Pairwise Procrustes variances of different groupings (maxillae; .xlsx)</p> <p>File ES2.12 - Pairwise Procrustes variances of different groupings (frontals; .xlsx)</p> <p>File ES2.13 – Results of sample size analyses (.csv)</p> <p>File ES2.14 – Results of missing landmarks analyses (.csv)</p> <p>File ES2.15 – Results of estimation vs. deletion analyses (.xlsx)</p> <p> </p> <p>Supplement paper 3</p> <p><em>Electronic data files</em></p> <p>File ES3.1 – Metadata for the included specimens (.csv)</p> <p>File ES3.2 – Folder containing landmark file (.tps) and bilateral landmark pairs (.txt)</p> <p>File ES3.3 – Metadata for the specimens included in compactness analyses and results of the compactness measurements (.csv)</p> <p>File ES3.4 – ImageJ Macro for measuring vertebral compactness (.ijm)</p> <p>File ES3.5 – Accuracy of classifications using CVA (.xlsx)</p> <p>File ES3.6 – Results of Procrustes ANOVAs testing for influences of taxonomic groupings, size, and the interaction of grouping and size on vertebral shape (.txt)</p> <p>File ES3.7– Typicality probabilities of fossils belonging to extant species (.xlsx)</p> <p>File ES3.8 – Procrustes distances between fossils of different sites / groupings and extant species (.xlsx)</p> <p>File ES3.9 – Procrustes variance in juvenile versus adult specimens (.xlsx)</p> <p>File ES3.10 – Phylogenetic signal of shape results (.txt)</p> <p>File ES3.11 – Results of the trajectory analyses (.xlsx)</p> <p> </p> <p>Supplement paper 4</p> <p><em>Electronic data files</em></p> <p>File ES4.1 – Metadata for tissue specimens and data for correlation analyses (.csv)</p> <p>File ES4.2 – Folder containing surface models (.ply) of the included crania</p> <p>File ES4.3 – Metadata for alcohol specimens (maxillae) (.csv)</p> <p>File ES4.4 – Metadata for alcohol specimens (<em>Rankinia</em> maxillae) (.csv)</p> <p>File ES4.5 – Metadata for alcohol specimens (<em>Rankinia</em> crania) (.csv)</p> <p>File ES4.6 – 3D landmark coordinates of maxillae (.tps)</p> <p>File ES4.7 – Folder containing 3D landmark files and landmark pairs of population cluster analyses</p> <p>File ES4.8 – Procrustes distances between genera means, plus statistics (.xlsx)</p> <p>File ES4.9 – R code for evaluating landmark estimation (.R)</p> <p>File ES4.10 – Occurrence points used for creating the niche models (.csv)</p> <p>File ES4.11 – Folder containing SNAPP tree files (.trees) and log files (.log) of the 4 SNAPP runs</p> <p>File ES4.12 – Model outputs of SSDM ensemble models using different GCMs (.xlsx)</p> <p> </p> <p>Supplement paper 5</p> <p><em>Electronic data files</em></p> <p>File ES5.1 – Supplementary references (.docx)</p> <p>File ES5.2 – Body size, microhabitat and spiny tail data of the 2877 squamate species used in the study (.csv)</p> <p>File ES5.3 – Tree file (.tre)</p> <p>File ES5.4 – Results of the D statistic (.csv)</p> <p>File ES5.5 – Results of the fitPagel funtion (.csv)</p> <p>File ES5.6 – Phylogenetic ANOVA results (spiny tails vs microhabitat) (.csv)</p> <p>File ES5.7 – Phylogenetic ANOVA results (spiny tails vs. body size) (.csv)</p> <p>File ES5.8 – Phylogenetic logistic regression results (.csv)</p> <p>File ES5.9 – Phylogenetic ANOVA results (microhabitat vs body size) (.csv)</p> <p>File ES5.10 – Results of the HiSSE models (.csv)</p>
Discordant spatio-temporal dynamics of functional and phylogenetic diversity of rotiferan communities exposed to aquaculture effluent
<p>The growth of the human population brought about the global intensification of aquacultural production, and aquaculture became the fastest growing animal husbandry sector. Effluent from aquaculture is an anthropogenic environmental burden, containing organic matter, nutrients, and suspended solids that affect water quality, especially in water bodies of high biodiversity and conservation value. Water quality assessment often relies on bioindicators, analysing changes in taxonomic diversity of various freshwater organismal groups. Stepping beyond taxon diversity, we used functional and phylogenetic diversities of rotifers to identify factors affecting their community organization in response to an aquaculture effluent gradient in the largest oxbow lake in the Carpathian Basin, Hungary. Sampling was carried out three times per season at five points along a 3.5 km section of the oxbow lake, including the point of effluent inflow. We used eight traits to evaluate functional diversity: body size, trophi type, feeding mode, protection type, body wall type, corona type, habitat preference, and tolerance level. Functional and phylogenetic distances among the 24 species identified indicated trait conservatism. Rotiferan diversity increased with increasing distance from the point of influx in spring and summer. Among the factors affecting community organization in spring and summer, we find examples of environmental filtering, while in autumn the role of biotic interaction is more frequent. Under nutrient-rich conditions in spring and summer, organisms belonging to the same functional group were dominant, while under oligotrophic conditions more diverse but less abundant groups were present. Considering functional and phylogenetic traits allowed us to identify organising forces of rotifer communities in the largest oxbow lake of the Hungarian Lowland.</p>
Data from: Post-fire response and genetic diversity in Erica coccinea: connecting population dynamics and diversification in a biodiversity hotspot
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Data from: Seasonal dynamics of waterbird assembly mechanisms revealed by phylogenetic and functional diversity in a subtropical wetland
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Genetic diversity and spread dynamics of SARS-CoV-2 variants present in African populations
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Data from: Dendritic network structure and dispersal affect temporal dynamics of diversity and species persistence
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Data from: On-farm dynamic management of genetic diversity: the impact of seed diffusions and seed saving practices on a population-variety of bread wheat
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Data from: Diversity dynamics of Phanerozoic terrestrial tetrapods at the local-community scale
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Data from: Global gradients in vertebrate diversity predicted by historical area-productivity dynamics and contemporary environment
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Data from: Diversity dynamics of mammals in relation to tectonic and climatic history: comparison of three Neogene records from North America
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Data from: Past and present dynamics of sorghum and pearl millet diversity in Mount Kenya region
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Data from: An analysis of the impacts of Cretaceous Oceanic Anoxic Events on global molluscan diversity dynamics
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Explosive Cenozoic origin and diversity-dependent diversification dynamics shaped the evolution of Australian skipper butterflies
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.