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248 results for “Plant phylogenetics”
Figure S25 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S25. Tanglegram comparing the ASTRAL single-copy genes phylogeny (Figure S14) with the RAxML amino acid single-copy genes phylogeny (Figure S20).
Figure S28 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S28. Levels of topological congruence between phylogenies generated in different ways, estimated as Robinson-Foulds (RF) distances between species trees. Exact values are in Table S17. Thickness of the connecting lines reflects RF distance. Abbreviations are as follows 'AS' = ASTRAL-3; 'RA' = RAxML; '997' = all genes without paralogs, '997p'= all genes with paralogs, 'SC' = single-copy genes; 'NT' = nucleotide alignment; 'AA' = amino acid alignment; 'PB' = PhyloBayes phylogeny; 'CP' = chloroplast phylogeny.
Figure S40 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S40. Phyloregionalization of Australia using the metachronogram. Subfigures show clustering results with two to eight phyloregions, as well as the results of phyloregionalization analyses using the geographic residuals of phylogenetic turnover, and ancient phylogenetic turnover with a cut-off of 5, 10, and 20 million years.
Figure S44 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S44. Phyloregionalization per continent using the genus-level Mimosoid phylogeny (rather than the metachronogram). Caption otherwise as for Figure 3.
Figure S41 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S41. Phyloregionalization of the global tropics using the metachronogram. Subfigures show clustering results with two to eight phyloregions, as well as the results of phyloregionalization analyses using the geographic residuals of phylogenetic turnover, and ancient phylogenetic turnover with a cut-off of 5, 10, and 20 million years.
Figure S39 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S39. Phyloregionalization of Asia using the metachronogram. Subfigures show clustering results with two to eight phyloregions, as well as the results of phyloregionalization analyses using the geographic residuals of phylogenetic turnover, and ancient phylogenetic turnover with a cut-off of 5, 10, and 20 million years.
Figure S32 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S32 (lef). Internode certainty values based on the 821 single-copy gene trees mapped onto the single-copy genes ASTRAL species tree (Figure S14). For each node, the upper number shows the quartet-based Extended Quadripartition Internode Certainty (EQP-IC) score calculated with QuartetScores, and the lower number shows the bipartition-based Internode Certainty All score calculated with PhyParts, both rounded down to two digits. Boxes are coloured based on unrounded values: green for values ≥ 0.5, yellow for values ≥ 0 and <0.5, and red for values <0. Branch lengths are set equal for easier visualisation. Inset depicts a correlation plot between the two measures.
Figure S33 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S33 (right).'esults of ASTRAL's polytomy test based on the 821 single-copy gene trees mapped onto the single-copy genes ASTRAL species tree (Figure S14). Node numbers are tests of the null hypothesis that a branch should be replaced by a polytomy. Only node numbers> 0.05 are shown. Branch lengths are set equal for easier visualisation.
Figure S31 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S31. Gene tree incongruence mapped onto the time-calibrated version of the phylogenomic backbone of Caesalpinioideae. Each branch is coloured to reflect the ratio of total supporting versus total conflicting gene trees as determined by PhyParts. Clades named by Koenen et al. (24) are labelled. Two recent radiations in Madagascar, one in the Dichrostachys clade and one in Albizia, are highlighted.
Figure S36 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S36. Phyloregionalization of North America using the metachronogram. Subfigures show clustering results with two to eight phyloregions, as well as the results of phyloregionalization analyses using the geographic residuals of phylogenetic turnover, and ancient phylogenetic turnover with a cut-off of 5, 10, and 20 million years.
Figure S14 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S14. Phylogeny of Caesalpinioideae. ASTRAL species tree based on the 821 single-copy gene trees. Local posterior probability support values are only shown for nodes with a local posterior probability <1. Branch lengths are expressed in coalescent units. Terminal branches were assigned an arbitrary uniform length for visual clarity.
Fig. 2 in Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Fig. 2. Drivers of phylogenetic turnover of Mimosoid legumes across the global lowland tropics. Bars show relative fractions of phylogenetic turnover explained by predictors (rescaled to add up to one). Numbers above bars are absolute explained percentages of turnover (tables S12 and S20). (A) Phylogenetic turnover explained by climatic distance (maroon), geographic distance (blue), or their interaction (cream). Turnover is assessed across four depths in the phylogeny: with the full metachronogram (age cutoff of 0) and with all clades younger than 5, 10, and 20 Ma collapsed. Note that it was not possible to fit a model to the phylogeny collapsed at 20 Ma for the pantropical and Australian models. (B) Phylogenetic turnover explained by MAP (green) and/or annual mean temperature (orange). Turnover is expressed as phylogenetic turnover not explained by geographic distance ("geographic residuals"). (C) Geographic residuals of phylogenetic turnover explained by MAP (green) and/or precipitation seasonality (gray; left) or dry season length (DSL) (i.e., the number of consecutive months with precipitation <100 mm/month; yellow; right). See fig. S45 for results obtained with an alternative, genus-level Mimosoid phylogeny. P, MAP; T, annual mean temperature; Pseas, precipitation seasonality.
Fig. 1 in Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Fig. 1. Mimosoid evolution and diversity across precipitation gradients. (A) Phylogeny of Mimosoid legumes showing the evolution of precipitation niches and transcontinental dispersal events through time. Branch colors correspond to mean annual precipitation (MAP) estimates [see (C) for scale]. Pie charts at tips and nodes of named clades [sensu (24)] represent observed and estimated spatial distributions [based on area definitions in (D)]. Ancestral niches and areas were estimated using a complete metachronogram for Caesalpinioideae, including non-Mimosoid Caesalpinioideae taxa, but only the Mimosoid clade is shown here. Green circles on branches indicate shifts between precipitation categories [following (17)] that encompass a difference of at least 250-mm MAP; red triangles indicate postulated transcontinental dispersals according to the best-supported model. The six most species-rich genera are labeled. (B) Fractions of niche shifts and transcontinental dispersal events, averaged across multiple optimizations, relative to total phylogenetic splits plotted through time for 5-Ma bins. (E) Mimosoid growth form diversity across the tropical precipitation gradient, from deserts with <50-mm MAP (left) through savannas to rain forests with>5000-mm MAP (right). See the Supplementary Results for species names and photographers. See fig. S51 for more information.
Data from: Resource addition drives taxonomic divergence and phylogenetic convergence of plant communities
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Data from: Mycorrhizal symbiosis increases plant phylogenetic diversity and regulate community assembly
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Data from: Avoiding impacts of phylogenetic tip-state-errors on dispersal and extirpation rates in alpine plant biogeography
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Replication code and data for: "Machine Learning Predicts Large Scale Declines in Native Plant Phylogenetic Diversity."
<p>Replication code and data for the paper: "Machine Learning Predicts Large Scale Declines in Native Plant Phylogenetic Diversity." The following files are included in this repository:</p> <p>1) R scripts (numbered 0 through 9) include replication code for data analysis</p> <p>2) Datasets (6 zip folders) contain the data analyzed in the R scripts</p> <p> </p> <p> </p>
Data from: Introduced bees (Osmia cornifrons) collect pollen from both coevolved and novel host-plant species within their family-level phylogenetic preferences
<p><span><span><span><span><span><span><span><span><span><span><span>Studying the pollen preferences of introduced bees allows us to investigate how species utilize host-plants when establishing in new environments. <i>Osmia cornifrons</i> is a solitary bee introduced into North America from East-Asia for pollination of crops in the Rosaceae. We investigated whether <i>O. cornifrons</i> 1) more frequently collected pollen from host-plant species they coevolved with from their geographic origin, or 2) prefer hosts-plant species of specific plant taxa independent of origin. To address this question, using pollen metabarcoding we examined the identity and relative abundance of pollen in larval provisions from nests located in different habitats with varying abundance of East-Asian and non-Asian plant species. Our results show that <i>O. cornifrons</i> disproportionately, yet not exclusively, collected pollen from their native range. Plants in the family Rosaceae were their most preferred pollen hosts, where they differentially collected species native to East-Asia, Europe, or North America depending on the landscape. Our results suggest that while <i>O. cornifrons</i> more frequently collect pollen of East-Asian origin, the collection of pollen from novel species within their phylogenetic familial affinities can facilitate pollinator establishment. This phylogenetic preference highlights the effectiveness of <i>O. cornifrons</i> as crop pollinators of a variety of Rosaceae crops from different geographic origins. Ourresults imply that globalization of non-native plant species may ease the naturalization of their coevolved pollinators outside of their native range. </span></span></span></span></span></span></span></span></span></span></span></p>
Phylogenetic restriction of plant invasion in drought-stressed environments: implications for insect-pollinated plant communities in water-limited ecosystems
<p><span><strong>Background</strong>: Plant-pollinator community diversity has been found to decrease under conditions of drought stress, however research into the temporal dimensions of this phenomenon remains limited. In this study, we investigated the effect of seasonal drought on the temporal niche dynamics of entomophilous flowering plants in a water-limited ecosystem. We hypothesized that closely related native and exotic plants would tend to share similar life history, and that peak flowering events would therefore coincide with phylogenetic clustering in plant communities based on expected phenological responses of plant functional types to limitations in soil moisture availability.</span></p> <p><span><strong>Location</strong>:<b> </b>Galiano Island, British Columbia, Canada</span></p> <p><span><strong>Methods</strong>:<b> </b>Combining methods from pollinator research and phylogenetic community ecology, we tested the influence of environmental filtering over plant community phenology across gradients of landscape disturbance and soil moisture. Floral resource availability and community structure were quantified by counts of flowering shoots. We constructed a robust phylogeny to analyze spatial and temporal variation in phylogenetic patterns across the landscape, testing the significance of the observed patterns against a randomly generated community phylogeny. Phylogenetic metrics were then regressed against factors of disturbance and soil moisture availability. </span></p> <p><span><strong>Results</strong>:<b> </b>Critical seasonal fluctuations in floral resources coincided with significant phylogenetic clustering in plant communities, with decreasing plant diversity observed under conditions of increasing drought stress. Exotic plant species in the Asteraceae became increasingly pervasive across the landscape, occupying a late season temporal niche in drought-stressed environments.</span></p> <p><span><strong>Main conclusion</strong>:<b> </b>Results suggest that environmental filtering is the dominant assembly process structuring the temporal niche of plant communities in this water-limited ecosystem. Based on these results, and trends seen elsewhere, the overall diversity of plant-pollinator communities may be expected to decline with the increasing drought stress predicted under future climate scenarios.</span></p>
Data from: Phylogenetic conservatism and biogeographic affinity influence woody plant species richness-climate relationships in eastern Eurasia
<p>Mechanisms underlying species richness patterns remain a central yet controversial issue in biology. Climate has been regarded as a major determinant of species richness. However, the relative influences of different evolutionary processes, (i.e. niche conservatism, diversification rate, and time for speciation) on species richness-climate relationships remain to be tested. Here, using newly compiled distribution maps for 11,422 woody plant species in eastern Eurasia, we estimated species richness patterns for all species and for families with tropical and temperate affinities separately, and explored the phylogenetic signals in species richness patterns of different families and their relationships with contemporary climate and climate change since the Last Glacial Maximum (LGM). We further compared the effects of niche conservatism (represented by contemporary-ancestral climate niches differences), diversification rate and time for speciation (represented by family age) on variation in the slopes of species richness-climate relationships. We found that winter coldness was the best predictor for species richness patterns of most tropical families while Quaternary climate change was the best predictor for those of most temperate families. Species richness patterns of closely-related families were more similar than those of distantly-related families within eudicots, and significant phylogenetic signals characterized the slopes of species richness-climate relationships across all angiosperm families. Contemporary-ancestral climate niche differences dominated variation in the relationships between family-level species richness and most climate variables. Our results indicate significant phylogenetic conservatism in family-level species richness patterns and their relationships with contemporary climate within eudicots. These findings shed light on the mechanisms underlying large-scale species richness patterns and suggest that ancestral climatic niche may influence the evolution of species richness-climate relationships in plants through niche conservatism.</p>
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Allen Brain Atlas
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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.