Collapse branches in a phylogenetic tree based on partially matching taxa labels in R

Question

I have built a phylogenetic tree for a DNA bacterial region, where same bacterial species, in general, clustered together in close branches. Now, I would like to collapse branches, which have labels in common. I tried to define labels to collapse based on the following keywords which partially match names of terminal taxa:

keywords:

("vulneris","ulcerans","blattae","coli","hermannii","albertii","periodonticum","fergusonii")

In R, I upload the following file.newick:

(((((((((E_vulneris_otu44:0.03924,((E_vulneris_otu97:0.00766,
E_vulneris_otu96:0)0.8:0.00914,E_fergusonii_otu74:0.00725)0:0.0072)0:0,
((E_vulneris_otu95:0,
(((gi_undefined_HMPREF0402_04011_HMPREF0402_04011_E_ulcerans:0,
fig_768594rna24_RO08_01535_E_vulneris:0)0:0.00373,
(gi_undefined_HMPREF1766_00665_HMPREF1766_00665_E_vulneris:0,
fig_768595rna53_CBG60_05850_E_vulneris:0)0:0.00373)0.8:0.00701,
fig_7685910rna43_CI114_11510_E_vulneris:0)0.84:0.00717)0:0,
E_fergusonii_otu78:0.0072)0.85:0.00718)0:0,E_vulneris_otu94:0)0.82:0.00753,
E_vulneris_otu77:0)0.82:0.00698,(E_vulneris_otu93:0,((E_vulneris_otu89:0,
E_vulneris_otu90:0.00754)0:0.00765,E_vulneris_otu91:0)0.83:0.01608)0:0)
0.8:0.02319,(((E_vulneris_otu35:0,E_vulneris_otu34:0.00752)0.83:0.00766,
E_vulneris_otu28:0.00688)0:0,(E_vulneris_otu2:0.01715,E_vulneris_otu1:0)
0.89:0.01482)0.8:0.01541)0.89:0.02013,E_periodonticum_otu73:0)0.75:0.01535,
fig_86016rna55_CTM98_06410_E_periodonticum:0.00831)0.97:0.1808,
((((((E_blattae_otu76:0,E_blattae_otu75:0.01744)0.82:0.00698,
(E_blattae_otu4:0.00771,E_blattae_otu39:0)0.8:0.00762)0:0,
((gi_undefined_HMPREF1540_00319_HMPREF1540_00319_E_vulneris:0,
fig_8616rna58_DXA30_07775_E_ulcerans:0)0.81:0.00724,
gi_undefined_C4N16_02505_E_albertii:0)0.92:0.01676)0.78:0.01261,
E_blattae_otu92:0.004)0.78:0.02469,(((E_coli_otu8:0.01561,
E_coli_otu38:0.00378)0:0.00378,E_coli_otu33:0)0:0,
(((E_coli_otu54:0.00713,gi_undefined_C4N19_02700_E_coli:0)
0.73:0.00675,(((E_coli_otu57:0,E_coli_otu43:0.00715)0.84:0.00715,
E_coli_otu53:0)0.79:0.00852,((((E_coli_otu40:0,
E_coli_otu56:0.0076)0:0.00376,E_coli_otu55:0.00703)0:0.00376,
E_coli_otu37:0)0:0.0028,(E_coli_otu41:0,E_coli_otu4:0.00715)
0.9:0.00714)0:0.00395)0.79:0.00862)0.77:0.00764,E_coli_otu36:0)
0.82:0.00761)0.89:0.04396)0.83:0.0832,(gi_undefined_C4N18_07110_E_blattae:0,
gi_undefined_FUSO3_01390_E_hermannii:0.04598)0.92:0.1457)0.97:0.1015);

tree.test<-read.tree(file = "file.newick")

and build the tree by using ape and phytools packages:

ggtree(tree.test) + geom_tiplab()

but I cannot figure out how to collapse at the keyword level. Any suggestions would be very appreciated. Thank you!

Answer 1

One way to do that would be to drop all the OTUs but one in each species group using the ape::drop.tip function:

library(ape)

## List of clades
clades <- c("vulneris","ulcerans","blattae","coli","hermannii","albertii","periodonticum","fergusonii")

## New tree placeholder
trimmed_tree <- tree.test

## Loop through each tip to drop
for(one_clade in clades) {
    ## Find the tips matching the species name
    species <- grep(one_clade, trimmed_tree$tip.label)
    ## Removing all the species but the first one
    trimmed_tree <- drop.tip(trimmed_tree, trimmed_tree$tip.label[species[-1]])
}

## Displaying the trimmed tree (with one OTU per species)
plot(trimmed_tree)