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248 results for “Plant phylogenetics”
Evolutionary dynamics of mycorrhizal symbiosis in land plant diversification - phylogenetic data
<p>This submission supplements the manuscript entitled <em>Evolutionary dynamics of mycorrhizal symbiosis in land plant diversification</em> by <strong>Frida A.A. Feijen, Rutger A. Vos, Jorinde Nuytinck & Vincent S.F.T. Merckx.</strong></p> <p>The contents of this submission are dating analysis results for rootings of the land plant topology. Contains the following files:</p> <ul> <li>*.log.gz BEAST logs</li> <li>*.trees.gz BEAST trees</li> <li>*.tiff screen dumps of tracer, showing the burn-in</li> <li>*.consensus.trees produced with treeannotator</li> </ul> <p><strong>For more information</strong>: https://github.com/naturalis/mycorrhiza/tree/v1.0.0</p>
Phylogenetic analyses of hub genes accompanying the study "Environmental gradients reveal stress hubs predating plant terrestrialization"
<p>135 ML phylogenies of hub genes identified in the study "Environmental gradients reveal stress hubs predating plant terrestrialization"</p>
Data from: Resource addition drives taxonomic divergence and phylogenetic convergence of plant communities
1. Anthropogenic environmental changes are known to affect the Earth's ecosystems. However, how these changes influence assembly trajectories of the impacted communities remains a largely open question. 2. In this study, we investigated the effect of elevated nitrogen (N) deposition and increased precipitation on plant taxonomic and phylogenetic β-diversity in a 9-year field experiment in the temperate semi-arid steppe of Inner Mongolia, China. 3. We found that both N and water addition significantly increased taxonomic β-diversity, whereas N, not water, addition significantly increased phylogenetic β-diversity. After the differences in local species diversity were controlled using null models, the standard effect size of taxonomic β-diversity still increased with both N and water addition, while water, not N, addition, significantly reduced the standard effect size of phylogenetic β-diversity. The increased phylogenetic convergence observed in the water addition treatment was associated with the colonization of different, but phylogenetically closely related, species into different replicate plots of the treatment. Species colonization in this treatment was found to be trait-based, with leaf nitrogen concentration being the key functional trait. 4. Synthesis. Our analyses demonstrate that anthropogenic environmental changes may affect the assembly trajectories of plant communities at both taxonomic and phylogenetic scales. Our results also suggest that while stochastic processes may cause communities to diverge in species composition, deterministic process could still drive communities to converge in phylogenetic community structure.
Dataset of Rainy years counteract negative effects of drought on taxonomic, functional, and phylogenetic diversity: resilience in annual plant communities
<p>Data used in the article: </p> <p><strong>Rainy years counteract negative effects of drought on taxonomic, functional, and phylogenetic diversity: resilience in annual plant communities</strong></p> <p><strong>Abstract</strong></p> <p>1- Climate models forecast changes in the amounts and distribution of rain, which may affect ecosystems worldwide, especially in drylands where water is already the limiting factor for plant life. Annual plant communities are common in drylands where they can complete their entire life cycle during the rainy period while avoiding the dry season. Moreover, seed dormancy allows them to disperse over time by remaining in the seed bank for long periods. However, the extent to which these communities will be able to tolerate increasing drought is uncertain.</p> <p>2- We performed a five-year rainfall reduction treatment under field conditions and determined its effects on annual plant communities in a Mediterranean gypsum ecosystem. We assessed the taxonomic, functional, and phylogenetic diversity of these communities each year for five years.</p> <p>3-The taxonomic and functional diversity decreased under the rainfall reduction treatment whereas the phylogenetic diversity increased. Moreover, the relative importance of species with drought-resistant functional designs increased in the community assemblages. However, after a rainy season with above average rainfall, all of the diversity values recovered completely even under the rainfall reduction treatment.</p> <p>4- Our results provide important insights into the responses of these plant communities under a climate change scenario, where they indicate high losses of diversity during drought events but rapid recovery in milder years.</p> <p><em>Synthesis</em> Our findings highlight the great resilience of annual plant communities in drylands, which may allow them to tolerate increased drought under the present climate change scenario.</p>
Data from: Mycorrhizal symbiosis increases plant phylogenetic diversity and regulate community assembly
<p>The intricate mechanisms shaping plant diversity and community composition are the cornerstone of ecological understanding. Yet, the role of mycorrhizal symbiosis, the fundamental partnership between fungi and plant roots, in influencing community composition has often been underestimated. Here, we use extensive species survey data from 1,315 terrestrial ecosystem sites to elucidate the influence of mycorrhizal symbiosis on plant phylogenetic diversity and its implications for community assembly processes. Our findings demonstrate that increasing mycorrhizal symbiotic potential leads to greater phylogenetic dispersion within plant communities. Furthermore, we unveil a distinct dichotomy in the assembly processes governed by mycorrhizal status. Mycorrhizal species predominantly influence deterministic processes, suggesting a role in niche-based community assembly. Conversely, non-mycorrhizal species exert a stronger influence on stochastic processes, highlighting the importance of random events in shaping community structure. These results underscore the crucial but often hidden role of mycorrhizal symbiosis in driving plant community diversity and assembly. This study provides valuable insights into the complex mechanisms shaping ecological communities and the way for more informed conservation and management practices that acknowledge the complex interplay between symbiosis and ecological community dynamics.</p>
Figure 5. A phylogenetic tree was generated using the neighbor-joining method which shows the genetic relationship between C. sphaerospermum 2 in Morphological and molecular identification of Cladosporium sphaerospermum isolates collected from tomato plant residues
Figure 5. A phylogenetic tree was generated using the neighbor-joining method which shows the genetic relationship between C. sphaerospermum 2 (as indicated in red circle) and the other C. sphaerospermum isolates deposited in GenBank (NCBI)
Text-fig. 5. Most parsimonious trees obtained after addition of the Pennipollis plant to the (A) D&E and (B) J/M trees. Relative parsimony of alternative positions of the Pennipollis plant is indicated as in Text-fig. 2; abbreviations as in Text-fig. 1. in Early Cretaceous Monocots: A Phylogenetic Evaluation
Text-fig. 5. Most parsimonious trees obtained after addition of the Pennipollis plant to the (A) D&E and (B) J/M trees. Relative parsimony of alternative positions of the Pennipollis plant is indicated as in Text-fig. 2; abbreviations as in Text-fig. 1.
Figure 6 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)
Figure 6. Secondary structure models of the highly variable proximal part of helix 43 (S6, Fig. 1) in Zygaeninae. All structures are based on thermodynamic folding by minimizing the free energy and have been calculated considering the entire nucleotide sequence of helix 43. The change in the Gibb's free energy (dG) refers to the S6 structure only. Applied ambiguity code: G/A = R, C/U = Y.
Figure 3 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)
Figure 3. Consensus structure and base pair probability matrix of helix E23-5 (S3, Fig. 1) in Lepidoptera. Nucleotides in circles indicate consistent and/or compensatory substitutions. The size of squares in the grid is proportional to the probability of a base pairing. Note that the species Z. centaureae, Z. laeta and Z. huguenini have been omitted from this analysis because of their deviating secondary structure (compare with Fig. 4).
Figure 2 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)
Figure 2. Distribution of pairwise tree edit distances between highly variable SSU rRNA secondary structure areas (S1–S6, Fig. 1) of Zygaenoidea excluding taxa of the subgenus Mesembrynus (top) and of Zygaena species belonging to the subgenus Mesembrynus only (bottom). The extreme values in the Zygaenoidea tree edit distance distribution on the right all involve Z. excelsa, a species showing a highly derived secondary structure in the area S6 (compare with Fig. 6).
Figure 1 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)
Figure 1. Secondary structure model of the SSU (18S) rRNA gene sequence of Zygaena (Mesembrynus) sarpedon lusitanica Reiss, 1936 (Lepidoptera: Zygaenidae; accession no. AJ830858) and structure variation in the helices E10-1 and E23-12 among species of the subfamily Zygaeninae. Nucleotides in the model are continuously numbered beginning at the 5′-end of the molecule; tick marks identify every tenth base. Light shading indicate helices numbered according to Wuyts et al. (2002). S1–S6 (dark shades) denote areas with variable secondary structure in the subfamily Zygaeninae. Roman numerals specify the domains I, II, III and IV. The following ambiguity code has been applied: A/C = M, C/U = Y, G/A = R.
Figure 7 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)
Figure 7. Neighbour-joining tree based on structural differences in the variable areas S1–S6 (compare with Fig. 1) of the small-subunit (18S) rRNA in taxa of the genus Zygaena. The topology is rooted with Reissita simonyi and Epizygaenella caschmirensis as outgroup. Taxa of the subgenus Mesembrynus are indicated by shading. Numbers in parentheses specify the number of species in a particular group.
Figure 5 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)
Figure 5. Consensus structure and base pair probability matrix of the proximal part of helix 43 (S6, Fig. 1) in Lepidoptera. Nucleotides in circles indicate consistent and/or compensatory substitutions. The size of squares in the grid is proportional to the probability of a base pairing. Note that the unpaired nucleotides C and G in the helix will most likely bind in individual structures having this specific nucleotide combination, but non-Watson–Crick pairings are too frequent in the alignment for assuming a generally nucleotide interaction at this position in the consensus structure.
Figure S50 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S50. Optimisation of tropical and temperate niches across the Mimosoid phylogeny. Ancestral niches were estimated using a complete metachronogram for Caesalpinioideae, including non-Mimosoid Caesalpinioideae taxa, but only the Mimosoid clade is shown here.
Figure S48 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S48. Speciation rates estimated across the Caesalpinioideae metachronogram under eight scenarios with different fixed extinction rates. Extinction rates are shown above each subfigure, while speciation rates are indicated by branch colours.
Figure S49 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S49. Top: Speciation rates in the Mimosoid clade through time, estimated under different extinction rate scenarios using BAMM. Middle: Paleotemperature inferred from delta O18 measurements, using data from Zachos et al. (179). Bottom: Phenogram of mean annual precipitation in the Mimosoid clade through time. Coloured lines with dots show the median, wettest, and driest reconstructed rainfall niche of all nodes in the phylogeny per time bin of one million years.
Figure S47 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S47. Ancestral range estimation of Caesalpinioideae, performed using BioGeoBEARS with the best-fitting model (i.e., DEC+J). Trans-oceanic dispersal events in the Mimosoid clade, based on a model with seven regions, are indicated with numbered green circles.
Figure S46 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S46. Optimisation of dry season length across the Mimosoid phylogeny. Inset shows the fraction of dry season length niche shifs per speciation event through time. See caption Figure 1 for explanation.
Figure S45 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S45. Variation partitioning results obtained using the genus-level Mimosoid phylogeny (rather than the metachronogram). See caption Figure 2 for explanation.
Figure S42 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time
Figure S42. Phyloregionalization per continent using the metachronogram, showing global distribution of isohyets. Caption otherwise as for Figure 3.
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