5. Getting studies and trees supporting relationships in a synthetic subtree

Overview

Teaching: 5 min
Exercises: 5 min

Questions

What are the original studies supporting relationships in my synthetic subtree?

Objectives

Get supporting trees for certain regions of the synthetic Open Tree of Life.

To get the source trees supporting a node from our synthetic tree we will need two functions. The function source_list() gets the study and tree ids (and other info) from source studies (not the trees). It is applied to a ‘tol_node’ object.

We already have one that we generated with tol_node_info(), do you remember how we called it?

Hands on! Get all supporting trees.

Get the supporting study metadata from the Canis node info. Store it in an object called canis_node_studies. Look at its class and the information it contains.

canis_node_studies <- rotl::source_list(canis_node_info)

class(canis_node_studies)

[1] "data.frame"

str(canis_node_studies)

'data.frame':	5 obs. of  3 variables:
 $ study_id: chr  "ot_278" "ot_328" "pg_1428" "pg_2647" ...
 $ tree_id : chr  "tree1" "tree1" "tree2855" "tree6169" ...
 $ git_sha : chr  "3008105691283414a18a6c8a728263b2aa8e7960" "3008105691283414a18a6c8a728263b2aa8e7960" "3008105691283414a18a6c8a728263b2aa8e7960" "3008105691283414a18a6c8a728263b2aa8e7960" ...

Now that we have the ids, we can use the function get_study_tree(), which will get us the actual supporting trees. This function takes one study id and tree id at a time, like this:

x <- 1
rotl::get_study_tree(study_id = canis_node_studies$study_id[x], tree_id = canis_node_studies$tree_id[x], tip_label="ott_taxon_name", deduplicate = TRUE)

Warning: Some tip labels were duplicated and have been modified: Leptocyon,
Leptocyon, Leptocyon, Leptocyon, Leptocyon, Leptocyon, Leptocyon, Canidae,
Canidae, Urocyon, Urocyon, Urocyon, Cerdocyon, Canis, Canis, Canis, Canis,
Canis, Canis, Canis, Canis, Canis, Canidae, Cynarctoides

Phylogenetic tree with 142 tips and 141 internal nodes.

Tip labels:
	Prohesperocyon_wilsoni, Ectopocynus_antiquus, Ectopocynus_intermedius, Ectopocynus_simplicidens, Hesperocyon, Hesperocyon_gregarius, ...

Rooted; includes branch lengths.

Hands on! Get all supporting trees.

Call the output canis_source_trees

Hint: You can use a “for” loop or an apply() function to get them all.

Solution

With a ‘for’ loop.

canis_source_trees <- vector(mode = "list") # generate an empty list
for (i in seq(nrow(canis_node_studies))){
  source_tree <- rotl::get_study_tree(study_id = canis_node_studies$study_id[i], tree_id = canis_node_studies$tree_id[i], tip_label="ott_taxon_name", deduplicate = TRUE)
  canis_source_trees <- c(canis_source_trees, list(source_tree))
}

Warning: Some tip labels were duplicated and have been modified: Leptocyon,
Leptocyon, Leptocyon, Leptocyon, Leptocyon, Leptocyon, Leptocyon, Canidae,
Canidae, Urocyon, Urocyon, Urocyon, Cerdocyon, Canis, Canis, Canis, Canis,
Canis, Canis, Canis, Canis, Canis, Canidae, Cynarctoides

canis_source_trees

[[1]]

Phylogenetic tree with 142 tips and 141 internal nodes.

Tip labels:
	Prohesperocyon_wilsoni, Ectopocynus_antiquus, Ectopocynus_intermedius, Ectopocynus_simplicidens, Hesperocyon, Hesperocyon_gregarius, ...

Rooted; includes branch lengths.

[[2]]

Phylogenetic tree with 294 tips and 272 internal nodes.

Tip labels:
	Homo_sapiens, Rattus_norvegicus, Mus_musculus, Artibeus_jamaicensis, Mystacina_tuberculata, Tadarida_brasiliensis, ...

Rooted; includes branch lengths.

[[3]]

Phylogenetic tree with 169 tips and 168 internal nodes.

Tip labels:
	Xenopus_laevis, Anolis_carolinensis, Gallus_gallus, Taeniopygia_guttata, Tachyglossus_aculeatus, Ornithorhynchus_anatinus, ...

Rooted; includes branch lengths.

[[4]]

Phylogenetic tree with 86 tips and 85 internal nodes.

Tip labels:
	*tip_#1_not_mapped_to_OTT._Original_label_-_Morganucodon_oehleri, *tip_#2_not_mapped_to_OTT._Original_label_-_Morganucodon_watsoni, *tip_#3_not_mapped_to_OTT._Original_label_-_Haldanodon_exspectatus, Eomaia_scansoria, Amblysomus_hottentotus, Echinops_telfairi, ...

Rooted; no branch lengths.

[[5]]

Phylogenetic tree with 78 tips and 77 internal nodes.

Tip labels:
	Ornithorhynchus, Manis, Ailuropoda, Canis, Felis, Panthera, ...

Rooted; no branch lengths.

With an apply() function.

canis_source_trees <- sapply(seq(nrow(canis_node_studies)), function(i)
  rotl::get_study_tree(study_id = canis_node_studies$study_id[i], tree_id = canis_node_studies$tree_id[i], tip_label="ott_taxon_name", deduplicate = TRUE))

Warning: Some tip labels were duplicated and have been modified: Leptocyon,
Leptocyon, Leptocyon, Leptocyon, Leptocyon, Leptocyon, Leptocyon, Canidae,
Canidae, Urocyon, Urocyon, Urocyon, Cerdocyon, Canis, Canis, Canis, Canis,
Canis, Canis, Canis, Canis, Canis, Canidae, Cynarctoides

canis_source_trees

[[1]]

Phylogenetic tree with 142 tips and 141 internal nodes.

Tip labels:
	Prohesperocyon_wilsoni, Ectopocynus_antiquus, Ectopocynus_intermedius, Ectopocynus_simplicidens, Hesperocyon, Hesperocyon_gregarius, ...

Rooted; includes branch lengths.

[[2]]

Phylogenetic tree with 294 tips and 272 internal nodes.

Tip labels:
	Homo_sapiens, Rattus_norvegicus, Mus_musculus, Artibeus_jamaicensis, Mystacina_tuberculata, Tadarida_brasiliensis, ...

Rooted; includes branch lengths.

[[3]]

Phylogenetic tree with 169 tips and 168 internal nodes.

Tip labels:
	Xenopus_laevis, Anolis_carolinensis, Gallus_gallus, Taeniopygia_guttata, Tachyglossus_aculeatus, Ornithorhynchus_anatinus, ...

Rooted; includes branch lengths.

[[4]]

Phylogenetic tree with 86 tips and 85 internal nodes.

Tip labels:
	*tip_#1_not_mapped_to_OTT._Original_label_-_Morganucodon_oehleri, *tip_#2_not_mapped_to_OTT._Original_label_-_Morganucodon_watsoni, *tip_#3_not_mapped_to_OTT._Original_label_-_Haldanodon_exspectatus, Eomaia_scansoria, Amblysomus_hottentotus, Echinops_telfairi, ...

Rooted; no branch lengths.

[[5]]

Phylogenetic tree with 78 tips and 77 internal nodes.

Tip labels:
	Ornithorhynchus, Manis, Ailuropoda, Canis, Felis, Panthera, ...

Rooted; no branch lengths.

The object canis_node_studies contains a lot of information. You can get it using a ‘for’ loop, or an apply() function.

A key piece of information are the citations from the supporting studies. We can get these for each source trees with the function get_study_meta(). Let’s do it. First we need the study meta:

canis_node_studies_meta <- lapply(seq(nrow(canis_node_studies)), function(i)
  rotl::get_study_meta(study_id = canis_node_studies$study_id[i]))

Now we can get the citations:

canis_node_studies_citations <- sapply(seq(length(canis_node_studies_meta)), function (i) canis_node_studies_meta[[i]]$nexml$`^ot:studyPublicationReference`)

Finally, let’s plot the supporting trees along with their citations.

for (i in seq(length(canis_source_trees))){
  print(paste("The supporting tree below has", length(canis_source_trees[[i]]$tip.label), "tips."))
  print(paste("Citation is:", canis_node_studies_citations[i]))
  ape::plot.phylo(canis_source_trees[[i]])
}

[1] "The supporting tree below has 142 tips."
[1] "Citation is: Tedford, Richard H.; Wang, Xiaoming; Taylor, Beryl E. (2009). Phylogenetic systematics of the North American fossil Caninae (Carnivora, Canidae). Bulletin of the American Museum of Natural History, no. 325. http://hdl.handle.net/2246/5999\n\nWang, Xiaoming; Tedford, Richard H.; Taylor, Beryl E. (1999). Phylogenetic systematics of the Borophaginae (Carnivora, Canidae). Bulletin of the American Museum of Natural History, no. 243. http://hdl.handle.net/2246/1588\n\nWang, Xiaoming (1994). Phylogenetic systematics of the Hesperocyoninae (Carnivora, Canidae). Bulletin of the  American Museum of Natural History, no. 221. http://hdl.handle.net/2246/829\n"