Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
252
datasets available to search
ShareScore release 0.9.0
Dataset results
252 results for “Plant Evolution”
Raw data and Matlab code for: Convergence in carnivorous pitcher plants reveals a mechanism for composite trait evolution
<p>Composite traits involve multiple components that, only when combined, gain a new synergistic function. Thus, how they evolve remains a puzzle. We combined field experiments, microscopy, chemical analyses and laser Doppler vibrometry with comparative phylogenetic analyses to show that two carnivorous <em>Nepenthes</em> pitcher plant species convergently evolved identical adaptations in three distinct traits to acquire a new, composite trapping mechanism. Comparative analyses suggest that this new trait arose convergently via 'spontaneous coincidence' of the required trait combination, rather than directional selection in the component traits. Our results indicate a plausible mechanism for composite trait evolution and highlight the importance of stochastic phenotypic variation as a facilitator of evolutionary novelty.</p>
Data from: The origin, deployment, and evolution of a plant-parasitic nematode effectorome
<p>Plant-parasitic nematodes constrain global food security. During parasitism, they secrete effectors into the host plant from two types of pharyngeal gland cells. These effectors elicit profound changes in host biology to suppress immunity and establish a unique feeding organ from which the nematode draws nutrition. Despite the importance of effectors in nematode parasitism, there has been no comprehensive identification and characterisation of the effector repertoire of any plant-parasitic nematode.</p> <p>To address this, we advance techniques for gland cell isolation and transcriptional analysis to define a stringent annotation of putative effectors for the cyst nematode <em>Heterodera schachtii </em>at three key life-stages. We define 659 effector gene loci: 293 "known" high-confidence homologs of plant-parasitic nematode effectors, and 366 "novel" effectors with high gland cell expression. In doing so we define a comprehensive "effectorome" of a plant-parasitic nematode.</p> <p>Using this effector definition, we provide the first systems-level understanding of the origin, deployment and evolution of a plant-parasitic nematode effectorome. The robust identification of the comprehensive effector repertoire of a plant-parasitic nematode will underpin our understanding of nematode pathology, and hence, inform strategies for crop protection.</p>
Deer grazing drove an assemblage-level evolution of plant dwarfism in an insular system
<p>Plant dwarfism, a syndrome characterised by a significant reduction in plant height and organ size, is a widely observed pattern of stress-tolerant life-form evolution that results from local adaptation to harsh environmental conditions. The drivers of assemblage-level dwarfism have primarily been attributed to abiotic factors, such as low temperature, aridity, poor soil fertility, or frequent fires. While biotic factors such as grazing pressure from herbivores can contribute to the establishment of plant dwarfism, these factors have rarely been tested at assemblage levels. Focusing on a dwarf plant assemblage comprising over 80 taxa on a small continental island in Japan with a high deer density, we hypothesised that historical deer grazing could also be a factor contributing to the large-scale convergent evolution of dwarfism. To test this hypothesis, we measured the size of 1,908 individual plants of 40 taxa-pairs, comprising both palatable and unpalatable pairs from the island and their counterpart taxa from neighbouring regions, and sought to assess which factors (i.e. low solar radiation, estimated divergence time, low nutrient conditions, and grazing pressure from deer) may have contributed to the formation of the dwarf plant assemblage on the island. We also performed genetic analysis to infer the timeframes for the establishment of dwarf taxa. Statistical analyses revealed that plant size was significantly reduced mainly among the palatable taxa growing on the island, with preferential grazing by deer being identified as the most significant factor influencing plant size. Furthermore, genetic analyses revealed that dwarf ecotypes may have evolved over tens of thousands of years.</p> <p><strong>Synthesis:</strong> To the best of our knowledge, this study is the first to demonstrate that interactions with herbivores can shape the assemblage-level convergence of plant dwarfism. These findings enhance our current understanding of the formation of plant functional diversity.</p>
Evolution of sympatric host-specialized lineages of the fungal plant pathogen Zymoseptoria passerinii in natural ecosystems
<p>This repository contains the data sets from the research paper "Evolution of sympatric host-specialized lineages of the fungal plant pathogen <em>Zymoseptoria passerinii</em> in natural ecosystems"</p>
Polyploidy promotes divergent evolution across the leaf economics spectrum and plant edaphic niche in the Dianthus broteri complex
<ol> <li>The evolution of the leaf economics spectrum (LES) is known to be constrained by genetic relatedness but also promoted at small geographic and phylogenetic scales. In those cases, we hypothesised that polyploidy would play a prominent role as an outstanding source of functional divergence and adaptive potential.</li> <li>We registered leaf-level nutrient, water and light economy related traits from the LES as well as edaphic properties in the four cytotypes of the autopolyploid <i>Dianthus broteri</i> complex (2×, 4×, 6× and 12×). We analysed the effect of ploidy level on the integration of the LES network, checked if concerted evolution occurred between LES and soil niche and tested the influence of phylogeny on the variables. Alternative evolutionary models for both sets of traits were compared.</li> <li> <span>We found higher divergence of polyploids (especially 6</span>×<span> and 12</span>×<span>) compared to diploids</span> in the LES and soil niche, but these traits are not coevolving. <span>6</span>×<span> and 12</span>× showed opposite ecological strategies regarding resource use and higher uncoupling of the LES network. Early divergence of traits prevailed in both LES and edaphic niche (supported by better fitted evolutionary models with one optimum per cytotype), but post-polyploidization processes played an important role for the photochemical behaviour.</li> <li> <i>Synthesis.</i><b> </b><span>Our results indicated shifts in ecological strategies across <i>D. broteri</i> cytotypes and suggested a powerful role of polyploidy in overcoming constraints for the evolution of plant functional traits.</span> </li> </ol>
Evolution in response to climate in the native and introduced ranges of a globally distributed plant
<p><span>The extent to which species can adapt to spatiotemporal climatic variation in their native and introduced ranges remains unresolved. To address this, we examined how clines in cyanogenesis (HCN production—an antiherbivore defense associated with decreased tolerance to freezing) have shifted in response to climatic variation in space and time over a 60-year period in both the native and introduced ranges of <em>Trifolium repens</em>. HCN production is a polymorphic trait controlled by variation at two Mendelian loci (<em>Ac</em> and <em>Li</em>). Using phenotypic assays, we estimated within-population frequencies of HCN production and dominant alleles at both loci (i.e., <em>Ac</em> and <em>Li</em>) from 10,575 plants sampled from 131 populations on 5 continents, and then compared these frequencies to those from historical data collected in the 1950s. There were no clear relationships between changes in the frequency of HCN production, <em>Ac</em>, or <em>Li</em> and changes in temperature between contemporary and historical samples. We did detect evidence of continued evolution to temperature gradients in the introduced range, whereby the slope of contemporary clines for HCN and <em>Ac</em> in relation to winter temperature became steeper than historical clines and more similar to native clines. These results suggest that cyanogenesis clines show no clear changes through time in response to global warming, but introduced populations continue to adapt to their contemporary environments.</span></p>
Data From: Evolution of woody plants to the land‐sea interface: The atypical genomic features of mangroves with atypical phenotypic adaptation
<p><span>How plants adapt and diverge in extreme environments is a key question of plant evolution and ecology. Mangrove invasion of intertidal environments is facilitated by adaptive phenotypes such as aerial roots, salt-secreting leaf, and viviparity, and genomic mechanisms including whole genome duplication and transposable element number reduction. However, a number of mangroves lack these typical phenotypes. The question we ask is whether these phenotypically atypical mangroves also have distinct genomic features? The sibling mangrove species <em>Lumnitzera littorea</em> and <em>Lumnitzera racemosa</em> provide a model to study this question. We sequenced and assembled their genomes to chromosome level, together with a closely related species <em>Combretum micranthum</em>. While most mangroves have small genomes, the genomes of both <em>Lumnitzera </em>species are large (1443 and 1317 Mb) and carry a high proportion of repeat sequences (~75%). Moreover, <em>Lumnitzera</em> species have not undergone post-gamma whole-genome duplications. Their genome size increased mainly due to the expansion of repeat sequences in their ancestors. However, <em>Lumnitzera </em>genomes have reduced transposable elements by constraining the proliferation of new LTR-RTs. Meanwhile, the two species have more gene families contracted than expanded, and some gene families with reversed size change may underlie their differentiation in root morphology and local distribution. We identified 86 chromosomal inversions, five of which are measured between 6.5 and 12.8 megabases. A number of genes located in these inversions function in pigment biosynthesis, a process likely involved in flower color differentiation between the <em>Lumnitzera </em>species. We conclude that the mangroves with atypical phenotypes also have atypical genomic evolution.</span></p>
Supporting data and code for: Host plant and insecticides shape the evolution of genetic and clonal diversity in a major aphid crop pest
<p>This is the first release of the final data and code for the article accepted for publication in <em>Evolutionary Applications</em> journal. It contains the necessary scripts to produce most of the analyses and figures of the manuscript. All the necessary data can be found in the 'data' folder.</p>
Complete telomere-to-telomere genomes uncover virulence evolution conferred by chromosome fusion in oomycete plant pathogens
<p><span>Variations in chromosome number are occasionally observed among oomycetes, a group that includes many plant pathogens, but the emergence of such variations and their effects on genome and virulence evolution remain ambiguous. We generated complete telomere-to-telomere genome assemblies for <em>Phytophthora sojae</em>, <em>Globisporangium ultimum</em>, <em>Pythium oligandrum</em>, and <em>G. spinosum</em>. Reconstructing the karyotype of the most recent common ancestor in Peronosporales revealed that frequent chromosome fusion and fission drove changes in chromosome number. Centromeres enriched with <em>Copia</em>-like transposons may contribute to chromosome fusion and fission events. Chromosome fusion facilitated the emergence of pathogenicity genes and their adaptive evolution. Effectors tended to duplicate in the sub-telomere regions of fused chromosomes, which exhibited evolutionary features distinct to the non-fused chromosomes. By integrating ancestral genomic dynamics and structural predictions, we have identified secreted Ankyrin repeat-containing proteins (ANKs) as a novel class of effectors in <em>P. sojae</em>. Phylogenetic analysis and experiments further revealed that ANK is a specifically expanded effector family in oomycetes. These results revealed chromosome dynamics in oomycete plant pathogens, and provided novel insights into karyotype and effector evolution.</span></p>
Data from: Evolutionary déjà vu? A case of convergent evolution in an ant-plant association
<p>Obligatory ant-plant symbioses often appear to be single evolutionary shifts within particular ant lineages; however, convergence can be revealed once natural history observations are complemented with molecular phylogenetics. Here we describe a remarkable example of convergent evolution in an ant-plant symbiotic system. Exclusively arboreal, <em>Myrmelachista</em> species can be generalized opportunists nesting in several plant species or obligately symbiotic, live-stem nesters of a narrow set of plant species. Instances of specialization within <em>Myrmelachista</em> are known from northern South America and throughout Middle America. In Middle America, a diverse radiation of specialists occupies understory treelets of lowland rainforests. The morphological and behavioural uniformity of specialists suggests that they form a monophyletic assemblage, diversifying after a single origin of specialization. Using ultraconserved element phylogenomics and ancestral state reconstruction, we show that shifts from opportunistic to obligately symbiotic evolved independently in South and Middle America. Furthermore, our analyses strongly support a remarkable case of convergence within the Middle American radiation, with two independently evolved specialist clades, arising nearly simultaneously from putative opportunistic ancestors during the late Pliocene. This repeated evolution of a complex phenotype suggests similar mechanisms behind trait shifts from opportunists to specialists, generating further questions about the selective forces driving specialization.</p>
FIGURE 1 in The Integrated Plant Record (IPR) analysis: Methodological advances and new insights into the evolution of European Palaeogene/Neogene vegetation
FIGURE 1. Zelkova zelkovifolia is a representative of the broad-leaved deciduous component.
Processed data supporting the manuscript "Cutting the sap: first molecular phylogeny of twig-girdler longhorn beetles (Coleoptera: Cerambycidae: Lamiinae: Onciderini) suggests shifts in host plant attack behaviors contributed to morphological evolution"
<div><strong>Processed data supporting the manuscript: </strong>Cutting the sap: first molecular phylogeny of twig-girdler longhorn beetles (Coleoptera: Cerambycidae: Lamiinae: Onciderini) suggests shifts in host plant attack behaviors contributed to morphological evolution</div> <div> </div> <div><strong>By:</strong> Diego de S. Souza 1, 2, Rowan L. K. French 3, José O. Silva Júnior 4, Eugenio H. Nearns 5, Luciane Marinoni 4, Ian P. Swift 6, Kelly B. Miller 7, Felix A. H. Sperling 2 & Marcela L. Monné 1</div> <div> </div> <div>1 Department of Entomology, National Museum, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.</div> <div>2 Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.</div> <div>3 Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.</div> <div>4 Department of Zoology, Federal University of Paraná, Curitiba, Paraná, Brazil.</div> <div>5 National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.</div> <div>6 California State Collection of Arthropods, Sacramento, California, USA.</div> <div>7 Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA.</div> <div> </div> <div>Corresponding author: Diego de S. Souza, dsouza@fieldmuseum.org. Current affiliation: Field Museum of Natural History, Chicago, Illinois, USA.</div> <div> </div> <div> </div> <div><strong>List of Contents: </strong></div> <div> </div> <div><strong>Onciderini_concat_matrix.phy</strong></div> <div>Concatenated matrix (cox1, Wg and CPS) used for the phylogenetic analyses of Onciderini (Coleoptera: Cerambycidae: Lamiinae: Onciderini). </div> <div> </div> <div><strong>PartitionFinder_AICc_best_scheme.txt</strong></div> <div>Results from PartitionFinder v2.1.1, containing the best partitioning scheme for the concatenated matrix of Onciderini, identified using the corrected Akaike Information Criterion (AICc), with model definitions for use in the phylogenetic analyses.</div> <div> </div> <div><strong>RAxML_Onciderini_concat_matrix (zip file)</strong></div> <div>- Onciderini_concat_matrix.phy: concatenated matrix (cox1, Wg and CPS) used in the RAxML phylogenetic analyses of Onciderini (Coleoptera: Cerambycidae: Lamiinae: Onciderini).</div> <div>- Partitions_AICc_RAxML.txt: partitioning scheme used in the RAxML analysis as predefined by PartitionFinder v2.1.1 using the corrected Akaike Information Criterion (AICc).</div> <div>- RAxML_bestTree.Onciderini_concat_matrix_ML: best-scoring maximum likelihood tree inferred by RAxML for the concatenated matrix of Onciderini.</div> <div>- RAxML_bipartitions.Onciderini_concat_matrix_final: bipartitions (clades) of the maximum likelihood tree inferred by RAxML with support values estimated from 1,000 pseudoreplicates.</div> <div>- RAxML_bipartitionsBranchLabels.Onciderini_concat_matrix_final: final maximum likelihood tree inferred by RAxML for the concatenated matrix of Onciderini, with labeled branches showing bootstrap support values.</div> <div>- RAxML_bootstrap.Onciderini_concat_matrix_bootstrap: bootstrap trees generated from a non-parametric bootstrap analysis in RAxML based on 1,000 pseudoreplicates.</div> <div>- RAxML_info.Onciderini_concat_matrix_bootstrap: log file containing details of the bootstrap analysis, including the settings and parameters used in the non-parametric bootstrap runs in RAxML.</div> <div>- RAxML_info.Onciderini_concat_matrix_final: log file summarizing the RAxML analysis, including settings and convergence statistics for the final maximum likelihood tree.</div> <div>- RAxML_info.Onciderini_concat_matrix_ML: log file containing details of the maximum likelihood tree search, including the parameters and models applied during the maximum likelihood analysis conducted by RAxML.</div> <div>- RAxML_log.Onciderini_concat_matrix_ML: log file of the maximum likelihood tree search for the concatenated matrix of Onciderini.</div> <div>- RAxML_parsimonyTree.Onciderini_concat_matrix_ML: parsimony starting tree used by RAxML during the maximum likelihood analysis for the concatenated matrix of Onciderini.</div> <div>- RAxML_result.Onciderini_concat_matrix_ML: maximum likelihood tree inferred by RAxML from the concatenated matrix of Onciderini, summarizing the tree topology and likelihood score for the best tree obtained.</div> <div> </div> <div><strong>BI_AICc_Onciderini_concat_matrix (zip file)</strong></div> <div>- BI_AICc_Onciderini_concat_matrix.nex: nexus file containing the concatenated matrix of Onciderini used for Bayesian Inference (BI), including the best-fit model scheme identified by PartitionFinder and MCMC parameters for running the analysis in MrBayes.</div> <div>- BI_AICc_Onciderini_concat_matrix.nex_r1_r2_combined_consensus.tree: consensus tree from two combined independent Bayesian Inference (BI) runs based on the concatenated matrix of Onciderini, after discarding the first 25% of initial generations as burn-in.</div> <div>- BI_AICc_Onciderini_concat_matrix.nex.run1.p: log file containing parameter values and likelihood scores from the first run of the Bayesian Inference (BI) based on the concatenated matrix of Onciderini.</div> <div>- BI_AICc_Onciderini_concat_matrix.nex.run2.p: log file containing parameter values and likelihood scores from the second run of the Bayesian Inference (BI) based on the concatenated matrix of Onciderini.</div> <div> </div> <div><strong>BEAST2_Onciderini_BD_lognormal (zip file)</strong></div> <div>- BEAUTi_Onciderini_BD_lognormal.xml: XML file generated by BEAUTi for running BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution.</div> <div>- BEAST2_Onciderini_BD_lognormal_run[1-8].log: log files from eight independent runs of BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution.</div> <div>- TreeAnnotator_Onciderini_BD_lognormal_run1-run8_consensus.out: TreeAnnotator output file combining the results of eight BEAST2 runs based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution.</div> <div>- TreeAnnotator_Onciderini_BD_lognormal_run1-run8_consensus.tre: consensus tree from eight combined BEAST2 runs, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution, after discarding the first 10% of initial generations as burn-in.</div> <div> </div> <div><strong>BEAST2_Onciderini_BD_exponential (zip file)</strong></div> <div>- BEAUTi_Onciderini_BD_exponential.xml: XML file generated by BEAUTi for running BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution.</div> <div>- BEAST2_Onciderini_BD_exponential_[1-8].log: log files from eight independent runs of BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution.</div> <div>- TreeAnnotator_Onciderini_BD_exponential_run1-run8_consensus.out: TreeAnnotator output file combining the results of eight BEAST2 runs based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution.</div> <div>- TreeAnnotator_Onciderini_BD_exponential_run1-run8_consensus.tre: consensus tree from eight combined BEAST2 runs, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution, after discarding the first 10% of initial generations as burn-in.</div> <div> </div> <div><strong>BEAST2_Onciderini_BD_uniform (zip file)</strong></div> <div>- BEAUTi_Onciderini_BD_uniform.xml: XML file generated by BEAUTi for running BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution.</div> <div>- BEAST2_Onciderini_BD_uniform_[1-8].log: log files from eight independent runs of BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution.</div> <div>- TreeAnnotator_Onciderini_BD_uniform_run1-run8_consensus.out: TreeAnnotator output file combining the results of eight BEAST2 runs based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution.</div> <div>- TreeAnnotator_Onciderini_BD_uniform_run1-run8_consensus.tre: consensus tree from eight combined BEAST2 runs, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution, after discarding the first 10% of initial generations as burn-in.</div> <div> </div> <div><strong>Comparative_analyses (zip file)</strong></div> <div><strong>RawData (folder):</strong> raw morphometric and girdling data, plus tree that was later pruned for downstream comparative analyses; these data were used as input for the OncidHeadDimorphism-DatasetPREP-FINAL.R data cleaning script. </div> <div>- Onciderini_BD_lognormal_run1-run8_consensus.nwk: newick version of TreeAnnotator_Onciderini_BD_lognormal_run1-run8_consensus.tre (outputted as a newick file by importing the .tre file into FigTree and exporting in newick format).</div> <div>- Measurements_Onciderini_Raw_Final.csv: individual-level raw morphometric data for Onciderini.</div> <div>- Behav_Matrix_2_states_trimmed_2022-12-15.csv: species-level data on girdling status for Onciderini species, with all Lochmaeocles species classified as girdlers (2 behavioral states across Onciderini species). </div> <div>- Matrix_3_states_trimmed_final.csv: species-level data on girdling status for Onciderini species, with all Lochmaeocles species classified as facultative girdlers (3 behavioral states across Onciderini species). </div> <div>- Matrix_2_states_trimmed_1LochGirdler_Final.csv: species-level data on girdling status for Onciderini species, with only one Lochmaeocles species (L. tessellatus) classified as a girdler (2 behavioral states across Onciderini species). </div> <div> </div> <div><strong>ProcessedData (folder): </strong>filtered data and pruned trees outputted by the OncidHeadDimorphism-DatasetPREP-FINAL.R script</div> <div>- oncid_f_36spp_clean.csv: dataset of species means and log-ratios for morphometric traits in females, plus girdling data; only includes species that have girdling data and are in the phylogenetic tree</div> <div>- oncid_m_42spp_clean.csv: dataset of species means and log-ratios for morphometric traits in males, plus girdling data; only includes species that have girdling data and are in the phylogenetic tree</div> <div>- oncid_sd_35spp_clean.csv: dataset of species means for sexual dimorphism in morphometric traits, plus girdling data; only includes species that have girdling data and are in the phylogenetic tree</div> <div>- oncid_girdlingbehav_allingroupspp_clean.csv: full dataset of girdling behavior for 56 Onciderini species that are in the phylogenetic tree; includes separate columns for the three alternative girdling classification schemes</div> <div>- oncid_tree_behavfull_56spp.nwk: pruned phylogenetic tree for the full girdling dataset (56 species)</div> <div>- oncid_tree_f_36spp.nwk: pruned phylogenetic tree for the female morphometric dataset (36 species)</div> <div>- oncid_tree_m_42spp.nwk: pruned phylogenetic tree for the male morphometric dataset (42 species)</div> <div>- oncid_tree_mf_43spp.nwk: pruned phylogenetic tree for all species with morphometric data for males or females; used for the stochastic character map next to the heatmap plot (Fig 4)</div> <div>- oncid_tree_sd_35spp.nwk: pruned phylogenetic tree for the sexual dimorphism dataset (35 species)</div> <div> </div> <div><strong>FittedModels (folder): </strong>fitted models (mvgls, model comparison analyses, OUM models, simmaps) outputted by the OncidHeadDimorphism-Analysis-FINAL.R script </div> <div>- MacroModelFits_logRtraits_f_36spp-2024-10-12.Rdata: summary of model comparison results for Brownian Motion (BM), single-peak Ornstein-Uhlenbeck (OU), multipeak OU (OUM), and multi-rate Brownian motion (BMM) models (univariate and multivariate) fitted to female morphometric data across 100 stochastic character maps of girdling behavior</div> <div>- MacroModelFits_logRtraits_m_42spp-2024-10-12.Rdata: summary of model comparison results for Brownian Motion (BM), single-peak Ornstein-Uhlenbeck (OU), multipeak OU (OUM), and multi-rate Brownian motion (BMM) models (univariate and multivariate) fitted to male morphometric data across 100 stochastic character maps of girdling behavior</div> <div>- MacroModelFits-SDDI-35spp_2024-10-11.Rdata: summary of model comparison results for Brownian Motion (BM), single-peak Ornstein-Uhlenbeck (OU), multipeak OU (OUM), and multi-rate Brownian motion (BMM) models (univariate and multivariate) fitted to sexual dimorphism data across 100 stochastic character maps of girdling behavior</div> <div>- mvgls-results-headsize-mf-2024-10-12.Rdata: fitted mvgls regression models for male and female traits (analyzed separately)</div> <div>- mvgls-results-sddi-2024-10-12.Rdata: fitted mvgls regression models for sexual dimorphism</div> <div>- OUM_headtraits_f_36spp-2024-10-12.Rdata: fitted OUM models and summary statistics for female head traits</div> <div>- OUM_headtraits_m_42spp-2024-10-12.Rdata: fitted OUM models and summary statistics for male head traits</div> <div>- OUM-SDDI-35spp-2024-10-12.Rdata: fitted OUM models and summary statistics for sexual dimorphism in head traits</div> <div>- simmaps_ard_full_2state.RDS: stochastic character maps of girdling behaviour for all 56 species with girdling data, with two behavioral states (girdling or non-girdling) - all Lochmaeocles species are classified as girdlers</div> <div>- simmaps_ard_full_3state.RDS: stochastic character maps of girdling behaviour for all 56 species with girdling data, with three behavioral states (girdling, non-girdling, or facultative girdling)</div> <div>- simmaps_ard_full_1Loch.RDS: stochastic character maps of girdling behaviour for all 56 species with girdling data, with two behavioral states (girdling or non-girdling) - only one Lochmaeocles species (L. tessellatus) is classified as a girdler</div> <div>- simmaps_ard_m.RDS: stochastic character map for the 42 species used in the analyses of male morphometric traits</div> <div>- simmaps_ard_f.RDS: stochastic character map for the 36 species used in the analyses of female morphometric traits</div> <div>- simmaps_ard.RDS: stochastic character map for the 35 species used in the sexual dimorphism analyses; 2 behavioral states.</div> <div> </div> <div><strong>Rscripts (folder): </strong>R scripts used to process data and run phylogenetic comparative analyses of head size and girdling behavior.</div> <div>- OncidHeadDimorphism-DatasetPREP-FINAL.R: R script used to filter data and prune trees from the RawData folder for downstream phylogenetic comparative analyses; outputs of this script are in the ProcessedData folder.</div> <div>- OncidHeadDimorphism-Analysis-FINAL.R: R script used to analyze data in the ProcessedData folder to answer questions about the origin and evolution of girdling behavior and the relationship between girdling and head size or head size sexual dimorphism; fitted models outputted by this script are in the FittedModels folder</div> <div>- OncidHeadDimorphism-Plots-FINAL.R: R script used to generate plots for the manuscript<br><br></div>
Data from: Repeated evolution of vertebrate pollination syndromes in a recently diverged Andean plant clade
While specialized interactions, including those involving plants and their pollinators, are often invoked to explain high species diversity, they are rarely explored at macroevolutionary scales. We investigate the dynamic evolution of hummingbird and bat pollination syndromes in the centropogonid clade (Lobelioideae: Campanulaceae), an Andean-centered group of ∼550 angiosperm species. We demonstrate that flowers hypothesized to be adapted to different pollinators based on flower color fall into distinct regions of morphospace, and this is validated by morphology of species with known pollinators. This supports the existence of pollination syndromes in centropogonids, an idea corroborated by ecological studies. We further demonstrate that hummingbird pollination is ancestral, and that bat pollination has evolved ∼13 times independently, with ∼11 reversals. This convergence is associated with correlated evolution of floral traits within selective regimes corresponding to pollination syndrome. Collectively, our results suggest that floral morphological diversity is extremely labile, likely resulting from selection imposed by pollinators. Finally, even though this clade's rapid diversification is partially attributed to their association with vertebrate pollinators, we detect no difference in diversification rates between hummingbird- and bat-pollinated lineages. Our study demonstrates the utility of pollination syndromes as a proxy for ecological relationships in macroevolutionary studies of certain species-rich clades.
Data from: Detailed characterization of the UMAMITs proteins provides insight into their evolution, amino acid transport properties, and role in the plant
<p>Amino acid transporters play a critical role in distributing amino acids within the cell compartments and between the plant organs. Despite this importance, relatively few amino acid transporter genes have been characterized and their role elucidated with certainty. Two main families of proteins encode amino acid transporters in plants: the Amino Acid-Polyamine-Organocation superfamily, containing mostly importers, and the Usually Multiple Acids Move In and out Transporter family, apparently encoding exporters, totaling 63 and 44 genes in Arabidopsis, respectively. Knowledge on UMAMITs is scarce, based on six Arabidopsis genes and a handful of genes from other species. To get insight into the role of the members of this family and provide data to be used for future characterization, we studied the evolution of the UMAMITs in plants, and determined the functional properties, the structure, and the localization of the 47 Arabidopsis UMAMITs. Our analysis showed that the AtUMAMITs are essentially localized at the tonoplast or the plasma membrane, and that most of them are able to export amino acids from the cytosol, confirming a role in intra- and inter-cellular amino acid transport. As an example, this set of data was used to hypothesize the role of a few AtUMAMITs in the plant and the cell.</p>
Rapid adaptive evolution to drought in a subset of plant traits in a large-scale climate change experiment
<p>Rapid evolution of traits and of plasticity may enable adaptation to climate change, yet solid experimental evidence under natural conditions is scarce. Here, we imposed rainfall manipulations (+30%, control, -30%) for ten years on entire natural plant communities in two Eastern Mediterranean sites. Additional sites along a natural rainfall gradient and selection analyses in a greenhouse assessed whether potential responses were adaptive. In both sites, our annual target species <i>Biscutella didyma</i> consistently evolved earlier phenology and higher reproductive allocation under drought. Multiple arguments suggest that this response was adaptive: it aligned with theory, corresponding trait shifts along the natural rainfall gradient, and selection analyses under differential watering in the greenhouse. However, another seven candidate traits did not evolve, and there was little support for evolution of plasticity. Our results provide compelling evidence for rapid adaptive evolution under climate change. Yet, several non-evolving traits may indicate potential constraints to full adaptation.</p>
Rapid divergent evolution of an annual plant across a latitudinal gradient revealed by seed resurrection
<p>Global change is expected to drive short-term evolution of natural populations. However, it remains unclear whether different populations are changing in unison. Here, we study contemporary evolution of growth-related and reproductive traits of three populations of <i>Cyanus segetum</i> face to warming and pollinator decline across a latitudinal gradient in France. We resurrected stored seeds sampled up to 24 years apart from northern, central-western, and southern populations and conducted an <i>in situ</i> common-garden experiment. To disentangle neutral from selection-driven differentiation, we calculated neutral genetic differentiation (<i>F<sub>ST</sub></i>) and quantitative trait differentiation (<i>Q<sub>ST</sub></i>) between temporal samples. We found that phenotypic evolution was divergent across populations exhibiting different trends for rosette size, date of flowering, and capitula size. By measuring seed set as a proxy of fitness, we showed that samples with larger mean capitula size outperformed samples with smaller mean capitula size in the western and southern populations. Regression of traits on seed set showed that flowering date and capitula size are the primary determinants of fitness, and <i>Q<sub>ST</sub>-F<sub>S</sub></i><i><sub>T</sub></i> comparisons indicated that natural selection has likely contributed to the shifts in flowering phenology and rosette size. These findings outline the potential for rescue of natural populations through contemporary evolution and emphasize the complex interplay between spatial and temporal variation in species' responses to global change.</p>
Supplementary Dataset for Trenner et al. 2022: Evolution and Functions of Plant U-box proteins (PUBs): From protein quality control to signalling
<p>This record contains additional information and a supplementary dataset of sequence alignment files and phylograms that support the publication:</p> <p>Trenner J, Monaghan J, Saeed B, Quint M, Shabek N, Trujillo M. 2022. Evolution and Functions of Plant U-box proteins (PUBs): From protein quality control to signalling. (submitted to Annual Review of Plant Biology)</p> <p>Included files:</p> <p><em>Additional information.pdf</em></p> <p>This file contains Supplementary Methods and References.</p> <p><br> <em>Supp_Fig1_Ubox_full_protein_maximum_likelihood_phylogram_linear.pdf</em></p> <p>A multiple protein sequence alignment by MAFFT of 1121 U-box protein sequences from 21 species and four outgroup sequences containing a RING finger domain (<em>A. thaliana</em> RBX1, <em>A. thaliana</em> RMA1, <em>S. cerevisiae</em> RAD18, <em>Homo sapiens</em> TRAF6 ) was used to infer a phylogenetic tree by maximum likelihood with IQ-TREE. The implemented ultrafast bootstrap approximation, set to 2000 bootstrap samples, was used for branch support. The consensus tree was annotated using iTOL.</p> <p> </p> <p><em>Supp_Fig2_Ubox_domain_maximum_likelihood_phylogram_linear.pdf</em></p> <p>In order to analyse specifically the evolution of the U-box domain, the U-box domain of the final 1121 U-box protein sequences as well as the RING finger domain of the four outgroup sequences were isolated and aligned by MAFFT. The U-box domain alignment was then used to infer a phylogenetic tree by maximum likelihood with IQ-TREE. The implemented ultrafast bootstrap approximation, set to 2000 bootstrap samples, was used for branch support. The consensus tree was annotated using iTOL. This tree was used to interpret the evolutionary history of U-box proteins in the main text.</p> <p> </p> <p><em>MAFFT_alignment _1121seqs_Ubox_full_protein_plus_4seqs_RING_outgroup.fasta</em></p> <p>Multiple protein sequences alignment by MAFFT of 1121 U-box full length protein sequences and four RING finger protein sequences, FASTA formatted.</p> <p> </p> <p><em>MAFFT_alignment _1121seqs_Ubox_domain_plus_4seqs_RING_outgroup.fasta</em></p> <p>Multiple protein sequences alignment by MAFFT of U-box domain sequences of 1121 U-box protein and four RING finger domain sequences of outgroup sequences, FASTA formatted.</p> <p> </p> <p><em>Ubox_protein_sequences_information.xlsx</em></p> <p>Spreadsheet with sequence ID information and source databases.</p>
Data from: Ancestral area analyses reveal Pleistocene-influenced evolution in a clade of Coastal Plain endemic plants
<p><strong>AIM:</strong> The North American Coastal Plain is currently recognized as a global biodiversity hotspot. However, the mechanisms driving high levels of species richness in a region with relatively low topographic relief and homogeneous climate are unclear. We investigated the evolutionary processes driving ancestral area evolution and diversification in a biodiversity hotspot from both a systematic and biogeographic context using a clade endemic to the hotspot.</p> <p><strong>LOCATION</strong>: North American Coastal Plain</p> <p><strong>TAXON</strong>: The Scrub Mint clade comprises <em>Dicerandra</em>, <em>Conradina</em>, <em>Piloblephis</em>, <em>Stachydeoma</em>, and four species of <em>Clinopodium</em> (Mentheae; Lamiaceae), almost all of which are endemic to the North American Coastal Plain. </p> <p><strong>METHODS</strong>: We generated a dated phylogeny using a target enrichment/capture dataset and then calculated ancestral area using biogeographic models. We uncovered neo- and paleo-endemism hotspots and inferred ancestral potential ranges at each node based on ancestral niche reconstructions and paleoclimatic data to understand the geographic range evolution of subclades. </p> <p><strong>RESULTS</strong>: Ancestral area for the SMC was inferred to be the Florida Panhandle/Apalachicola River basin. A diversification event likely happened around the mid-Pleistocene Transition. Endemism hotspots were recovered in NE Florida, the Atlantic Coastal Ridge, and along the Lake Wales Ridge. Reconstructions of potential ranges support biogeographic findings, with the ancestor of the SMC likely located in the vicinity of the northeastern Gulf Coast during interglacial and glacial periods.</p> <p><strong>MAIN</strong> <strong>CONCLUSIONS</strong>: The timing of diversification events and colonization of new areas by ancestors of the SMC is consistent with the timing of major geological events in the region. The presence of multiple types of endemism highlights the complexity of evolutionary and ecological processes that foster the large number of endemic taxa found in this region. Efforts to identify hotspots in this region will be critical to preserving the remaining pockets of biodiversity threatened by global change.</p>
Population bottleneck associated with but likely preceded the recent evolution of self-fertilization in a coastal dune plant
<p>Evolution of self-fertilization may be initiated by a historical population bottleneck, which should diagnostically reduce lineage-wide genetic variation. However, selfing can also strongly reduce genetic variation after it evolves. Distinguishing process from pattern is less problematic if mating system divergence is recent and geographically simple. Dramatically reduced diversity is associated with the transition from outcrossing to selfing in the Pacific coastal endemic Abronia umbellata that includes large-flowered, self-incompatible populations (var. umbellata) south of San Francisco Bay and small-flowered, autogamous populations (var. breviflora) to the north. Compared to umbellata, synonymous nucleotide diversity across 10 single-copy nuclear genes was reduced by 94% within individual populations and 90% across the whole selfing breviflora lineage, which contained no unique polymorphisms. The geographic pattern of genetic variation is consistent with a single origin of selfing that occurred recently (7–28 kya). These results are best explained by a historical bottleneck, but the two most northerly umbellata populations also contained little variation and clustered with selfing populations, suggesting that substantial diversity loss preceded the origin of selfing. A bottleneck may have set the stage for the eventual evolution of selfing by purging genetic load that prevents the spread of selfing.</p>
Data for: Mycorrhizas drive the evolution of plant adaptation to drought
<p class="MsoNormal">Plant adaptation to drought facilitates major ecological transitions, and will likely play a vital role under looming climate change. Mycorrhizas, i.e. strategic associations between plant roots and soil-borne symbiotic fungi, can exert strong influence on the tolerance to drought of extant plants. Here, I show how mycorrhizal strategy and drought adaptation have been shaping one another throughout the course of plant evolution. To characterize the evolutions of both plant characters, I applied a phylogenetic comparative method using data of 1,638 extant species globally distributed. The detected correlated evolution unveiled gains and losses of drought tolerance occurring at faster rates in lineages with ecto- or ericoid mycorrhizas, which were on average about 15 and 300 times faster than in lineages with the arbuscular mycorrhizal and naked root (non-mycorrhizal alone or with facultatively arbuscular mycorrhizal) strategy, respectively. My study suggests that mycorrhizas can play a key facilitator role in the evolutionary processes of plant adaptation to critical changes in water availability across global climates.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.