In this article we will show how we can map the insertions made in phylogenetic tree through the procedure realized in
FishPhyloMaker function. Mapping the insertions is of special importance since allow to understand how the gaps in phylogenetic knowledge is distributed in the phylogenetic tree. For example, we can understand if the Characidae family present more phylogenetic gaps than Loricariidae family.
This can be done by using the information contained in the output of
FishPhyloMaker function when we set the argument
return.insertions = TRUE. This returns a data frame containing the categories of insertion for each species, these categories are:
To obtain this data frame we need first to run
FishPhyloMaker setting the argument
return.insertions = TRUE. We will use data of fish occurrence in the Neotropical region present in
We need to format this data using function
With taxon_data we can run
FishPhyloMaker to obtain the phylogeny and the data frame with all the insertions made by each species
The data frame can be extracted and the categories of insertion can be plotted in the phylogenetic tree by using the information on
library(phytools) library(ggtree) library(ggplot2) insertions_org <- phylo_fish_Afrotropics$Insertions_data[match(tree$tip.label, phylo_fish_Afrotropics$Insertions_data$s), ] p.base <- ggtree(tree, layout = "circular", size = .3) %<+% insertions_org + geom_treescale(x = 0, width = 20, linesize = .5, color = "blue", fontsize = 0) + # plot the scale bar annotate("text", x = 4, y = 500, label = "20 myr", size = 1.5) # an attempt for add a scale bar p.full <- p.base + geom_tippoint(aes(color = insertions), size = .5, alpha = .8) + theme(legend.position = "bottom") + guides(color = guide_legend(override.aes = list(size = 2))) + scale_color_viridis_d(name = NULL, na.translate = F, labels = c("Congeneric F", "Congeneric", "Family", "Order", "Present"))
In Figure 1 we can see all the insertions made in the insertion process.