Glopl, a global data base on pollen limitation of plant reproduction

Plant reproduction relies on transfer of pollen from anthers to stigmas, and the majority of flowering plants depend on biotic or abiotic agents for this transfer. A key metric for characterizing if pollen receipt is insufficient for reproduction is pollen limitation, which is assessed by pollen supplementation experiments. In a pollen supplementation experiment, fruit or seed production by flowers exposed to natural pollination is compared to that following hand pollination either by pollen supplementation (i.e. manual outcross pollen addition without bagging) or manual outcrossing of bagged flowers, which excludes natural pollination. The GloPL database brings together data from 2969 unique pollen supplementation experiments reported in 927 publications published from 1981 to 2015, allowing assessment of the strength and variability of pollen limitation in 1265 wild plant species across all biomes and geographic regions globally. The GloPL database will be updated and curated with the aim of enabling the continued study of pollen limitation in natural ecosystems and highlighting significant gaps in our understanding of pollen limitation.<p>Correction in: Scientific Data, vol. 6, article number: 2. DOI: 10.1038/s41597-018-0006-1</p

Morphological, phenological and molecular data

Data in Excel format with three working sheets

Data Paper. Data Paper

<h2>File List</h2><div> <p><a href="DaPhnE_01.zip">DaPhnE_01.zip</a> -- contains all four data files described below. [d93c96544d106a7ce37f99c7a631ecbc]</p> <p><a href="DaPhnE_01_Synonymy.txt">DaPhnE_01_Synonymy.txt</a> -- tab-delimited ASCII file containing the list of the binomials used by the German, British, the Netherlands, and Swiss source databases and the respective binomials used in DaPhnE. [0785c354ec81a96b0453bcf36de29a65]</p> <p><a href="DaPhnE_01.tre">DaPhnE_01.tre</a> -- ASCII file of the phylogeny in Newick format. [1ecfc21ba9c8a754ac8c784768cb1fb3]</p> <p><a href="DaPhnE_01_nodes_with_references.txt">DaPhnE_01_nodes_with_references.txt</a> -- tab-delimited ASCII file containing 1212 lines listing nodes with either a reference for the partial phylogenies used to construct the supertree or to the node ages. [abcd006cd50353dcc3839f703c68401d]</p> <p><a href="DaPhnE_01_reference_list.txt">DaPhnE_01_reference_list.txt</a> -- tab-delimited ASCII file containing 738 references for phylogenies and node dates given in DaPhnE_01_nodes_with_references.txt. [01e130037c617d0f6e392497a9af4177]</p> </div><h2>Description</h2><div> <p> This data set represents a comprehensive, dated phylogeny of a large European flora comprising the vascular plants of the British Isles, Germany, the Netherlands, and Switzerland, totalling 4685 species. The phylogeny thus encompasses all species in the trait databases BIOLFLOR, PLANTATT, and BioBase 2003. The topology of the phylogenetic tree is based on a backbone family phylogeny of the Angiosperm Phylogeny Group III. Subsequently, partial phylogenetic subtrees derived from a total of 518 recent molecular studies were manually pruned onto the backbone tree, using multi-gene consensus topologies if possible. Similarly, 1103 internal nodes and the root node were dated based on 261 recent studies. Finally, an ultrametric tree was calculated by placing undated nodes evenly between dated nodes. The phylogeny provides a reference data set for comparative analyses of trait correlations, trait evolution, trait based ecological processes, community assembly, or other phylogenetically informed analyses across a large taxon of European plant species. It can readily be used in phylogenetic analysis tools like ape, phytools, picante, or MESQUITE. </p> <p> <i>BIOLFLOR; British flora; German flora; macroecology; Netherlands flora; phylogeny; PLANTATT; supertree; Swiss flora; vascular plants.</i> </p> </div

MSAP data

MSAP data at different levels of data processing: The spreadsheet “Raw_msap_calc” contains the input file for msap_calc.R, spreadsheet “MSAP Raw Data” contains the multistate data of combined HpaII and MspI profiles at the epilocus level, and spreadsheet “MSAP Subepiloci Data” contains the final binary data at the subepilocus level. For “Raw_msap_calc” the first three columns provide the population ID, the sample ID (population ID + individual sample number) and used methylation sensitive restriction enzymes (H=HpaII, M=MspI). The first row provides the marker ID (selective primer combination + fragment size). For “MSAP Raw Data” and “MSAP Subepiloci Data” the first column provides the sample ID and the first row provides the marker ID. In addition, for “MSAP Subepiloci” the three subepiloci types (n, m, h) are indicated in the second row

AFLP data

Presence/absence matrix (1/0) of AFLP markers. The first column provides the sample ID (population ID + individual sample number) and the first row provides the marker ID (selective primer combination + fragment size)

AFLP_microsatellites_Senecio_inaequidens_Corr

AFLP_microsatellites_Senecio_inaequidens_Cor

plant sampling & hemispherical photography

Grid based distribution maps (1 x 1m) and results of hemispherical photography based light measurements for the six surveyed populations of Viola elatior. Populated grid cells, grid cells for plant sampling and grid cells for hemispherical photographs are indicated by different colors, respectively

No genetic adaptation of the Mediterranean keystone shrub <i>Cistus ladanifer</i> in response to experimental fire and extreme drought

<div><p>In Mediterranean ecosystems, climate change is projected to increase fire danger and summer drought, thus reducing post-fire recruitment of obligate seeder species, and possibly affecting the population genetic structure. We performed a genome-wide genetic marker study, using AFLP markers, on individuals from one Central Spain population of the obligate post-fire seeder <i>Cistus ladanifer</i> L. that established after experimental fire and survived during four subsequent years under simulated drought implemented with a rainout shelter system. We explored the effects of the treatments on marker diversity, spatial genetic structure and presence of outlier loci suggestive of selection. We found no effect of fire or drought on any of the genetic diversity metrics. Analysis of Molecular Variance showed very low genetic differentiation among treatments. Neither fire nor drought altered the small-scale spatial genetic structure of the population. Only one locus was significantly associated with the fire treatment, but inconsistently across outlier detection methods. Neither fire nor drought are likely to affect the genetic makeup of emerging <i>C</i>. <i>ladanifer</i>, despite reduced recruitment caused by drought. The lack of genetic change suggests that reduced recruitment is a random, non-selective process with no genome-wide consequences on this keystone, drought- and fire tolerant Mediterranean species.</p></div

List of potentially adaptive loci and their F_ST as identified by the DFDIST/FDIST genome scan approach in pairwise comparisons of drought and fire treatments in <i>Cistus ladanifer</i>.

<p>List of potentially adaptive loci and their F_ST as identified by the DFDIST/FDIST genome scan approach in pairwise comparisons of drought and fire treatments in <i>Cistus ladanifer</i>.</p

Spatial genetic analysis for <i>Cistus ladanifer</i> at the unburned plots (EC-, EC- add).

<p>A) Spatial autocorrelogram showing mean r-values per distance class. Filled symbols indicate significant spatial autocorrelation. Dashed lines represent 95% confidence intervals as determined by 9,999 permutations; symbols outside of confidence intervals indicate significance. Error bars depict the 95% confidence interval as determined by 1,000 bootstrap resampling. B) Genetic distance, expressed as pairwise Ф_PT among plots, vs. geographic distance.</p