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30 results for “Community phylogeny”
Taxon sampling and inferred community phylogenies: R replication code and data.
<p>1 ) Code for simulating community phylogenies:</p> <p>community_simulations_creation.R</p> <p>[taxon].gene</p> <p>[taxon].phy</p> <p>[taxon].RAxML_bestTree.tre</p> <p>[taxon].Simulate.A.Community.pl</p> <p>[taxon].Simulate.B.Community.pl</p> <p>[taxon].Simulate.C.Community.pl</p> <p>[taxon].Simulate.D.Community.pl</p> <p> </p> <p>2) R code for creating and comparing phylogenetic diversity metrics:</p> <p>simulated_metric_calculation_and_comparison.R</p> <p>empirical_metric_calculation_and_comparison.R</p> <p> </p> <p>3) R code and data for statistical analyses:</p> <p>simulated_data_analysis.R</p> <p>empirical_data_analysis.R</p> <p>simulated_interval_individual_lme_data.csv</p> <p>simulated_summary_interval_individual_lme_data.csv</p> <p>empirical_interval_individual_lme_data.csv</p> <p>empirical_summary_interval_lme_data.csv</p> <p> </p>
Data and code from: Traits and phylogenies modulate the environmental responses of wood-inhabiting fungal communities across spatial scales
<p>Identifying the spatial scales at which community assembly processes operate is fundamental for gaining a mechanistic understanding of the drivers shaping ecological communities. In this study, we examined whether and how traits and phylogenetic relationships structure fungal community assembly across spatial scales.</p> <p>We applied joint species distribution modelling to a European-scale dataset on 215 wood-inhabiting fungal species, which includes data on traits, phylogeny and environmental variables measured at the local (log-level) and regional (site-level) scales.</p> <p>At the local scale, wood-inhabiting fungal communities were mostly structured by deadwood decay stage, and the trait and phylogenetic patterns along this environmental gradient suggested the lack of diversifying selection.</p> <p>At regional scales, fungal communities and their trait distributions were influenced by climatic and connectivity-related variables. The fungal climatic niches were not phylogenetically structured, suggesting that diversifying selection or stabilizing selection for climatic niches has played a strong role in wood-inhabiting communities. In contrast, we found a strong phylogenetic signal in the responses to connectivity-related variables, revealing phylogenetic homogenization in small and isolated forests.</p> <p>Altogether, our results show that species-level traits and phylogenies modulate the responses of wood-inhabiting fungi to environmental processes acting at different scales. This result suggests that the evolutionary histories of fungal traits diverge along different environmental axes.</p>
Host phylogeny and elevation predict infection by avian haemosporidians in a diverse New Guinean bird community (R script for analyses, figures, and supplemental figures )
<p>This script performs the glmm analysis of the elevation and infection prevalence data as well as the script required to generate the figures in the article.</p>
Data from: Host phylogeny and functional traits differentiate gut microbiomes in a diverse natural community of small mammals
<p>Differences in the bacteria inhabiting mammalian gut microbiomes tend to reflect the phylogenetic relatedness of their hosts, a pattern dubbed phylosymbiosis. Although most research on this pattern has compared the gut microbiomes of host species across biomes, understanding the evolutionary and ecological processes that generate phylosymbiosis requires comparisons across phylogenetic scales and under similar ecological conditions. We analyzed the gut microbiomes of 14 sympatric small-mammal species in a semi-arid African savanna, hypothesizing that there would be a strong phylosymbiosis pattern associated with the different body sizes and diets of the mammalian lineages present. Consistent with phylosymbiosis, microbiome dissimilarity increased with phylogenetic distance among hosts, ranging from congeneric sets of mice and hares that did not differ significantly in microbiome composition to species from different taxonomic orders that had almost no gut bacteria in common. While phylosymbiosis was detected among just the 11 species of rodents, it was substantially weaker than comparisons involving all 14 species together. In contrast, microbiome diversity and composition were generally more strongly correlated with body size, dietary breadth, and dietary overlap in comparisons restricted to rodents than in those including all lineages. The starkest divides in microbiome composition thus reflected the broad evolutionary divergence of hosts, regardless of body size or dietary composition, while subtler microbiome differences reflected variation in ecologically important traits between closely related hosts. Strong phylosymbiotic patterns arose deep in the phylogeny, and ecological filters that promote functional differentiation of cooccurring host species may disrupt or obscure this pattern near the tips.</p>
Data and code from: Effects of phylogeny on coexistence in model communities
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Data from: Phylogeny does not predict the outcome of heterospecific pollen-pistil interactions in a species-rich alpine plant community
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Data and code from: Traits and phylogenies modulate the environmental responses of wood-inhabiting fungal communities across spatial scales
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Data from: Host phylogeny and functional traits differentiate gut microbiomes in a diverse natural community of small mammals
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Community composition of arctic root-associated fungi mirrors host plant phylogeny
<p></p><p>The number of plant species regarded as non-mycorrhizal increases at higher latitudes, and several plant species in the High-Arctic Archipelago Svalbard have been reported as non-mycorrhizal. We used the rRNA ITS2 and 18S gene markers to survey which fungi, as well as other micro-eukaryotes, were associated with roots of 31 arctic plant species not usually regarded as mycorrhizal in Svalbard. We assessed to what degree the root-associated fungi showed any host preference and whether the phylogeny of the plant hosts may mirror the composition of root-associated fungi. Fungal communities were largely structured according to host plant identity and to a less extent by environmental factors. We observed a positive relationship between the phylogenetic distance of host plants and the distance of fungal community composition between samples, indicating that the evolutionary history of the host plants plays a major role for which fungi colonize the plant roots. In contrast to the ITS2 marker, the 18S rRNA gene marker showed that chytrid fungi were prevalently associated with plant roots, together with a wide spectrum of amoeba-like protists and nematodes. Our study confirms that arbuscular mycorrhizal (AM) fungi are present also in arctic environments in low abundance.</p><p></p>
Data from: The interaction of phylogeny and community structure: linking the community composition and trait evolution of clades
Aim. Community phylogenetic studies use information about species' evolutionary relationships to understand the ecological processes of community assembly. A central premise of the field is that species' evolution maps onto ecological patterns, and phylogeny reveals something more than species' traits alone about ecological mechanisms structuring communities such as environmental filtering, competition, and facilitation. We argue, therefore, that there is a need to better understand and model the interaction of phylogeny with species' traits and community composition. Innovation. We outline a new approach that identifies clades that are eco-phylogenetically clustered or overdispersed, and then assesses whether those clades have different rates of trait evolution. Eco-phylogenetic theory would predict that the traits of clustered or overdispersed clades might have evolved differently, either in terms of tempo (fast or slow) or mode (e.g., under constraint or neutrally). We suggest that modelling the evolution of independent trait data in these clades represents a strong test of whether there is an association between species' ecological co-occurrence patterns and evolutionary history. Main conclusions. Using an empirical dataset of mammals from around the world, we identify two clades of rodents whose species tend not to co-occur in the same local assemblages (are phylogenetically overdispersed), and then find independent evidence of slower rates of body mass evolution in these clades. Our approach, which assumes nothing about the mode of species' trait evolution but rather seeks to explain it using ecological information, presents a new way to examine eco-phylogenetic structure.
Flower traits, habitat and phylogeny as predictors of pollinator service: a plant community perspective
<p>Pollinator service is essential for successful sexual reproduction and long-term population persistence of animal-pollinated plants, and innumerable studies have shown that insufficient service by pollinators results in impaired sexual reproduction ("pollen limitation"). Studies directly addressing the predictors of variation in pollinator service across species or habitats remain comparatively scarce, which limits our understanding of the primary causes of natural variation in pollen limitation. This paper evaluates the importance of pollination-related features, evolutionary history and environment as predictors of pollinator service in a large sample of plant species from undisturbed montane habitats in southeastern Spain. Quantitative data on pollinator visitation were obtained for 191 insect-pollinated species belonging to 142 genera in 43 families, and the predictive values of simple floral traits (perianth type, class of pollinator visitation unit, and visitation unit dry mass), phylogeny, and habitat type were assessed. A total of 24,866 pollinator censuses accounting for 5,414,856 flower-min of observation were conducted on 510 different dates. Flowering patch and single flower visitation probabilities by all pollinators combined were significantly predicted by the combined effects of perianth type (open vs. restricted), class of visitation unit (single flower vs. flower packet), mass of visitation unit, phylogenetic relationships, and habitat type. Pollinator composition at insect order level varied extensively among plant species, largely reflecting the contrasting visitation responses of Coleoptera, Diptera, Hymenoptera and Lepidoptera to variation in floral traits. Pollinator composition had a strong phylogenetic component, and the distribution of phylogenetic autocorrelation hotspots of visitation rates across the plant phylogeny differed widely among insect orders. Habitat type was a key predictor of pollinator composition, as major insect orders exhibited decoupled variation across habitat types in visitation rates. Comprehensive pollinator sampling of a regional plant community has shown that pollinator visitation and composition can be parsimoniously predicted by a combination of simple floral features, habitat type and evolutionary history. Ambitious community-level studies can help to formulate novel hypotheses and questions, shed fresh light on long-standing controversies in pollination research (e.g., "pollination syndromes"), and identify methodological cautions that should be considered in pollination community studies dealing with small, phylogenetically-biased plant species samples.</p>
Data from: Soil abiotic variables are more important than Salicaceae phylogeny or habitat specialization in determining soil microbial community structure
Predicting the outcome of interspecific interactions is a central goal in ecology. The diverse soil microbes that interact with plants are shaped by different aspects of plant identity, such as phylogenetic history and functional group. Species interactions may also be strongly shaped by abiotic environment, but there is mixed evidence on the relative importance of environment, plant identity, and their interactions in shaping soil microbial communities. Using a multi-factor, split-plot field experiment, we tested how hydrologic context, and three facets of Salicaceae plant identity - habitat specialization, phylogenetic distance, and species identity - influence soil microbial community structure. Analysis of microbial community sequencing data with generalized dissimilarity models showed that abiotic environment explained up to 25% of variation in community composition of soil bacteria, fungi, and archaea, while Salicaceae identity influenced less than 1% of the variation in community composition of soil microbial taxa. Multivariate linear models indicated that the influence of Salicaceae identity was small, but did contribute to differentiation of soil microbes within treatments. Moreover, results from a microbial niche breadth analysis show that soil microbes in wetlands have more specialized host associations than soil microbes in drier environments - showing that abiotic environment changed how plant identity correlated with soil microbial communities. This study demonstrates the predominance of major abiotic factors in shaping soil microbial community structure; the significance of abiotic context to biotic influence on soil microbes; and the utility of field experiments to disentangling the abiotic and biotic factors that are thought to be most essential for soil microbial communities.
Data from: Plant geographic origin and phylogeny as potential drivers of community structure in root-inhabiting fungi
1. Root-inhabiting fungal communities, including mutualists and antagonists, influence host plant performance, and can potentially shape plant community composition. However, there is uncertainty about how root-inhabiting fungal communities are structured, and if fungal community characteristics are significant predictors of host plant abundance. 2. In this study, we first assessed how root-inhabiting fungal communities were structured in relation to the phylogeny and geographic origins (native vs exotic) of their host plants in an old-field community. In addition, we took into consideration the spatial arrangements (i.e. physical locations) of the individual host plants. We then tested if the relative abundances of pathogenic and beneficial arbuscular mycorrhizal (AM) fungi could predict host plant abundances. 3. We found that host plant phylogeny was an important factor in structuring the whole fungal community, irrespective of host plant origin. Furthermore, the spatial arrangements of individual host plants were a strong predictor of AM fungal community structure. Host plant phylogeny and spatial arrangements appeared to similarly affect the structure of pathogenic fungal communities. No distinct differences were observed between native and exotic plant species in fungal community characteristics. The relative abundances of AM and pathogenic fungi were not significant predictors for observed abundances of their host plants. 4. Synthesis. Host plant phylogeny and spatial arrangements can structure naturally occurring root-inhabiting fungal communities. The absence of distinct differences in fungal community composition, including pathogens, in exotic and native plants suggests long residence times and the consequent naturalization of exotic species in the region, allowing for the establishment of similar plant-microbial interactions between native and exotic species.
Data from: Ecological mechanisms and phylogeny shape invertebrate stoichiometry: a test using detritus-based communities across Central and South America
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Data from: Plant geographic origin and phylogeny as potential drivers of community structure in root-inhabiting fungi
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Data from: Soil abiotic variables are more important than Salicaceae phylogeny or habitat specialization in determining soil microbial community structure
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Community composition of arctic root-associated fungi mirrors host plant phylogeny
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Data from: Community phylogeny of the globally critically imperiled pine rockland ecosystem
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Data from: Plant DNA-barcode library and community phylogeny for a semi-arid East African savanna
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Data from: The interaction of phylogeny and community structure: linking the community composition and trait evolution of clades
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