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 OpenTree.

To get the source trees supporting a node from our OpenTree synthetic subtree 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  "" "" "" "" ...

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:

index <- 1

rotl::get_study_tree(study_id = canis_node_studies$study_id[index], tree_id = canis_node_studies$tree_id[index], 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"