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Data from: Planktonic protistan communities in lakes along a large-scale environmental gradient
- 负责人：
- DOI：
- doi:10.5061/dryad.7s6s8
- 摘要：
- operational taxonomic units (OTUs). The highest OTU richness was found in traditional phytoplankton groups like Dinoflagellata, Chrysophyceae, Chlorophyta and Cryptophyta
Data from: Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data
- 负责人：
- DOI：
- doi:10.5061/dryad.8rv46
- 摘要：
- 1. Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The Generalized Mixed Yule Coalescent (GMYC) and the Poisson Tree Process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. 2. Here we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2,000 separate species delimitation analyses across 16 empirical datasets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. 3. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. 4. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses.
Data from: High throughput sequencing combined with null model tests reveals specific plant-fungi associations linked to seedling establishment and survival
- 负责人：
- DOI：
- doi:10.5061/dryad.qh5js47
- 摘要：
- 1. Plant-fungal interactions are important for plant community assembly, but quantifying these relationships remains challenging. High throughput sequencing of fungal communities allows us to identify plant-fungal associations at a high level of resolution, but often fails to provide information on taxonomic and functional assignment of fungi. 2. We transplanted seeds of Pinus cembra across an elevational gradient (1850-2250 m a.s.l.) and identified environmental factors and known fungal associates important for seedling establishment and survival. We then applied null model tests to identify taxonomically unassigned fungi associated with pine recruitment. 3. Early seedling establishment was positively associated with multiple abiotic factors, while seedling survival was positively associated with the absence of a known pathogenic fungus and other biotic factors. Null model tests identified known mycorrhizal partners and a large number of unassigned operational taxonomic units (OTUs) associated with seedling survival, including mycorrhizal, saprotrophic and pathogenic species. 4. Synthesis: We conclude that high throughput metabarcoding paired with null model tests, is a valuable approach for identifying hidden plant-fungal associations within large and complex DNA metabarcoding datasets. Such an approach can be an important tool in illuminating the black box of plant-microbe interactions, and thus understanding ecosystem dynamics.
Data from: Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida (Agassiz in Verrill, 1864) indicates a lack of bacterial association specificity at a lower taxonomic rank
- 负责人：
- DOI：
- doi:10.5061/dryad.05st3
- 摘要：
- a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We als
Data from: Microbe biogeography tracks water masses in a dynamic oceanic frontal system
- 负责人：
- DOI：
- doi:10.5061/dryad.qh767
- 摘要：
- g to the spread of Antarctic intermediate water. However, within both the sub-surface layer and the intermediate depth stratum there was evidence for OTU turnover
Data from: Linking social and spatial networks to viral community phylogenetics reveals subtype-specific transmission dynamics in African lions
- 负责人：
- Fountain-Jones, Nicholas M.
- 关键词：
- feline immunodeficiency virus generalized dissimilarity modelling landscape ecology OTU networks transmission mode wildlife disease community ecology
- DOI：
- doi:10.5061/dryad.8j3s3
- 摘要：
- 1.Heterogeneity within pathogen species can have important consequences for how pathogens transmit across landscapes; however, discerning different transmission routes is challenging. 2.Here we apply both phylodynamic and phylogenetic community ecology techniques to examine the consequences of pathogen heterogeneity on transmission by assessing subtype specific transmission pathways in a social carnivore. 3.We use comprehensive social and spatial network data to examine transmission pathways for three subtypes of feline immunodeficiency virus (FIVPle) in African lions (Panthera leo) at multiple scales in the Serengeti National Park, Tanzania. We used FIVPle molecular data to examine the role of social organization and lion density in shaping transmission pathways and tested to what extent vertical (i.e., father and/or mother offspring relationships) or horizontal (between unrelated individuals) transmission underpinned these patterns for each subtype. Using the same data, we constructed subtype specific FIVPle co-occurrence networks and assessed what combination of social networks, spatial networks, or co-infection best structured the FIVPle network. 4.While social organization (i.e., pride) was an important component of FIVPle transmission pathways at all scales, we find that FIVPle subtypes exhibited different transmission pathways at within- and between-pride scales. A combination of social and spatial networks, coupled with consideration of subtype co-infection, was likely to be important for FIVPle transmission for the two major subtypes, but the relative contribution of each factor was strongly subtype specific. 5.Our study provides evidence that pathogen heterogeneity is important in understanding pathogen transmission, which could have consequences for how endemic pathogens are managed. Furthermore, we demonstrate that community phylogenetic ecology coupled with phylodynamic techniques can reveal insights into the differential evolutionary pressures acting on virus subtypes, which can manifest into landscape-level effects.
Data from: Soil fungal communities of grasslands are environmentally structured at a regional scale in the Alps
- 负责人：
- DOI：
- doi:10.5061/dryad.88fm3
- 摘要：
- sequences that were clustered into operational taxonomic units (OTUs). The OTU diversity-area relationship revealed uneven distribution of fungal taxa ac
Data from: Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet
- 负责人：
- DOI：
- doi:10.5061/dryad.v0p71
- 摘要：
- data revealed a total of 292 Operational Taxonomic Units (OTU) in the gut contents of the arc-eye hawkfish (Paracirrhites arcatus), the flame hawkfish
