How to generate topological constraints using the Open Tree of Life

Stuff for the Jupyter notebook which you can ignore...



In [86]:

    
library(repr)
options(repr.plot.width = 8, repr.plot.height = 3)

To retrieve topologies from the Open Tree of Life, we need the rotl R package. We'll also load the ape package to manipulate the tree.



In [91]:

    
install.packages("rotl")
library("rotl")
library("ape")









    



Installing package into ‘/home/dgkontopoulos/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)

Now, let's create a vector of species names for which we want a tree topology and match them to those of the Open Tree taxonomy:



In [94]:

    
species <- c(
    "Homo sapiens", "Felis catus", "Crocodylus niloticus", "Nymphicus hollandicus", 
    "Vitis vinifera", "Geobacter daltonii", "Thermoplasma acidophilum", "Caulophacus agassizi", 
    "Caulophacus arcticus", "Caulophacus cyanae", "Caulophacus galatheae"
)

resolved_names <- tnrs_match_names(species)
resolved_names









    





search_string unique_name approximate_match ott_id is_synonym flags number_matches

	homo sapiens            Homo sapiens            FALSE                   770315                  FALSE                                           1                       
	felis catus             Felis catus             FALSE                   563166                  FALSE                                           2                       
	crocodylus niloticus    Crocodylus niloticus    FALSE                   35864                   FALSE                                           2                       
	nymphicus hollandicus   Nymphicus hollandicus   FALSE                   630645                  FALSE                                           1                       
	vitis vinifera          Vitis vinifera          FALSE                   756728                  FALSE                                           6                       
	geobacter daltonii      Geobacter daltonii      FALSE                   489275                  FALSE                                           1                       
	thermoplasma acidophilum Thermoplasma acidophilum FALSE                   891210                  FALSE                                           1                       
	caulophacus agassizi    Caulophacus agassizi    FALSE                   2832726                 FALSE                                           1                       
	caulophacus arcticus    Caulophacus arcticus    FALSE                   612407                  FALSE                                           1                       
	caulophacus cyanae      Caulophacus cyanae      FALSE                   4939783                 FALSE                                           1                       
	caulophacus galatheae   Caulophacus galatheae   FALSE                   2832723                 FALSE                                           1

Return the subset of the Open Tree of Life that contains the matched species:



In [81]:

    
tree <- tol_induced_subtree(ott_ids=ott_id(resolved_names))
plot(tree, cex = 0.8, no.margin = TRUE)

The tree may also contain the names of some of its clades:



In [80]:

    
plot(tree, cex = 0.8, show.node.label = TRUE, no.margin = TRUE)

To infer phylogenies under the constraints of this tree, we have to remove the ott* IDs from species names and save the tree to a file.

The former can be done with a small regular expression:



In [92]:

    
tree$tip.label <- gsub("_ott\\d+$", "", tree$tip.label)
tree$tip.label

write.tree(tree, file = 'constraint_tree.phy')









    





	'Homo_sapiens'
	'Felis_catus'
	'Nymphicus_hollandicus'
	'Crocodylus_niloticus'
	'Caulophacus_agassizi'
	'Caulophacus_arcticus'
	'Caulophacus_cyanae'
	'Caulophacus_galatheae'
	'Vitis_vinifera'
	'Thermoplasma_acidophilum'
	'Geobacter_daltonii'

Ta-daaa! Our constraint tree is ready! A number of phylogeny inference programs can use it to constrain topological exploration:

RAxML and IQ-TREE: -g path_to_constraint_tree

PhyML: -u=path_to_constraint_tree --constraint_file=path_to_constraint_tree

MrBayes: use the function createMrBayesConstraints in the R package paleotree to generate a MrBayes NEXUS block of topological constraints from the tree. Next, paste the block to the input file to be read by MrBayes.

search_string	unique_name	approximate_match	ott_id	is_synonym	number_matches
homo sapiens	Homo sapiens	FALSE	770315	FALSE	1
felis catus	Felis catus	FALSE	563166	FALSE	2
crocodylus niloticus	Crocodylus niloticus	FALSE	35864	FALSE	2
nymphicus hollandicus	Nymphicus hollandicus	FALSE	630645	FALSE	1
vitis vinifera	Vitis vinifera	FALSE	756728	FALSE	6
geobacter daltonii	Geobacter daltonii	FALSE	489275	FALSE	1
thermoplasma acidophilum	Thermoplasma acidophilum	FALSE	891210	FALSE	1
caulophacus agassizi	Caulophacus agassizi	FALSE	2832726	FALSE	1
caulophacus arcticus	Caulophacus arcticus	FALSE	612407	FALSE	1
caulophacus cyanae	Caulophacus cyanae	FALSE	4939783	FALSE	1
caulophacus galatheae	Caulophacus galatheae	FALSE	2832723	FALSE	1