WGDs across the angiosperm phylogeny
Query options
Phylogenetic tree with WGD events
Note: dates of WGDs marked in orange (N = 13) are discordant with their expected phylogenetic locations, probably due to shifts in substitution rates. See FAQ for more details on how WGDs are positioned in nodes of the tree. Use the toolbar on top of the plot to activate pan/zoom.
WGD ages
Search WGDs by species
WGD events per species
Explore WGD events for each species. You can visualize posterior age distribution(s) for a WGD event by selecting a row and clicking the 'Show age distributions' button.
Posterior distributions of WGD age
Access original data used in this resource
Species included in this resource
Explore taxonomic information for all species included in this resource and download FASTA and GFF3 files with CDS and gene annotation, respectively.
Frequently Asked Questions
1) How are WGD events positioned in nodes of the tree?
To place a WGD on the tree, we use the following steps:
- Extract the names of all species that share that WGD event;
- Identify the ID of the node with the most recent common ancestor (MRCA) of all species extracted in step 1 - this node ID is used to obtain the y-axis coordinate of the rectangle indicating a WGD;
- Extract mean and Highest Convergence Region (HCR) of the posterior distribution of WGD age to represent the age and uncertainties of a WGD event - these are used to obtain start and end coordinates of the rectangle indicating a WGD.
For 13 WGD events (IDs: POAC, POAL, DIOS, PASE b, CALY, LARD, TROC a, NEOL, SALV, PASS, MANG, POZO, AESC), simply using the mean and 90% HCR to obtain x-axis coordinates of the WGD rectangles leads to an apparent placement of WGD rectangles ‘outside’ the node where it must be. This is likely due to shifts in substitution rates, as reported in Vanneste et al. (2014). However, even when WGD rectangles seem out of the node, the uncertainties around WGD dates still overlap with uncertainties around divergence times estimates. For example, the figure below shows the POAC WGD (shared by all Poaceae species) on the tree.
Note that, although the rectangle seems out of the node where it should be (indicated with an arrow), uncertainties overlap, supporting their correct placement.
2) How do I report an issue or suggest a feature?
You can open an issue in the GitHub repository where the source code for this app is.
3) How do I save figures/tables to files?
Boxes in all tabs with figures and tables have a download button (
) at the top right corner. By clicking it, you can specify the output file format (.pdf/.svg for figures, .tsv/.tsv.gz for tables), and download the file to your local machine.
4) In the posterior distributions of WGD ages, how do you obtain the ‘consensus’ distribution?
The ‘consensus’ distribution is obtained from data points from all species combined. For example, signatures of the JUGL WGD event (shared by all Juglandaceae species) were identified in four species. When visualizing age distributions for this WGD, you will be able to see four different distributions (each with 20,000 data points) on the left-hand side. On the right-hand side, you will see a single distribution with all data points combined, regardless of the species from which they were obtained (in this case, 4 x 20k = 80,000 data points).