Making a fern family tree

Recently I was asked by a researcher for a family-level phylogenetic tree of ferns. The Fern Tree of Life (FTOL) project that I maintain generates a maximally sampled global fern phylogeny, but it is at the species level. So how can we go from that to a family-level tree?

Basically it involves the following steps:

1. Load a list of all species in the tree and the name of the family each belongs to.
2. Check that each family is monophyletic or monotypic (this must be true for the next step to work¹).
3. Select a single exemplar species for each family (this could be any species within the family, as long as the family is monophyletic).
4. Trim the tree to only the exemplar species (one per family).
5. Rename the exemplar species with the family name.

The code to do all of this is provided below, and is also available at this repo: https://github.com/fernphy/ftol_family.

A few packages used here bear extra mention. The MonoPhy package is great at doing exactly what the name would suggest: checking for monophyly. I am a huge fan of the assertr package for proactive assertion about data. In this case, the code would fail (issue an error) if the assumption of monophyletic/monotypic families did not hold. Finally, the ftolr package by yours truly provides the most recent fern tree and associated taxonomic data.

Of course, this approach should work for any tree assuming the two requirements are met (the higher level taxa are all monophyletic or monotypic and the tree is ultrametric).

# Load packages
library(tidyverse)
library(ftolr)
library(ape)
library(MonoPhy)
library(assertr)

# Check FTOL version and cutoff date
ft_data_ver()

[1] "1.5.0"

ft_data_ver("cutoff")

[1] "2023-06-15"

# Load ultrametric fern tree, drop outgroup
phy <- ft_tree(branch_len = "ultra", rooted = TRUE, drop_og = TRUE)

# Inspect:
phy

Phylogenetic tree with 5750 tips and 5749 internal nodes.

Tip labels:
  Acrostichum_danaeifolium, Acrostichum_speciosum, Acrostichum_aureum, Ceratopteris_richardii, Ceratopteris_cornuta, Ceratopteris_pteridoides, ...
Node labels:
  100/100, 100/100, 100, 100/100, 100, 90/100, ...

Rooted; includes branch lengths.

# Load fern taxonomy
taxonomy <- ftol_taxonomy %>%
  # Subset to only species in tree
  filter(species %in% phy$tip.label)

# Inspect:
taxonomy

# A tibble: 5,750 × 8
   species                      genus         subfamily     family      suborder    order        major_clade outgroup
   <chr>                        <chr>         <chr>         <chr>       <chr>       <chr>        <chr>       <lgl>   
 1 Acrostichum_danaeifolium     Acrostichum   Parkerioideae Pteridaceae Pteridineae Polypodiales Pteridineae FALSE   
 2 Actiniopteris_dimorpha       Actiniopteris Pteridoideae  Pteridaceae Pteridineae Polypodiales Pteridineae FALSE   
 3 Actiniopteris_semiflabellata Actiniopteris Pteridoideae  Pteridaceae Pteridineae Polypodiales Pteridineae FALSE   
 4 Actiniopteris_australis      Actiniopteris Pteridoideae  Pteridaceae Pteridineae Polypodiales Pteridineae FALSE   
 5 Actiniopteris_radiata        Actiniopteris Pteridoideae  Pteridaceae Pteridineae Polypodiales Pteridineae FALSE   
 6 Onychium_cryptogrammoides    Onychium      Pteridoideae  Pteridaceae Pteridineae Polypodiales Pteridineae FALSE   
 7 Onychium_moupinense          Onychium      Pteridoideae  Pteridaceae Pteridineae Polypodiales Pteridineae FALSE   
 8 Onychium_japonicum           Onychium      Pteridoideae  Pteridaceae Pteridineae Polypodiales Pteridineae FALSE   
 9 Onychium_lucidum             Onychium      Pteridoideae  Pteridaceae Pteridineae Polypodiales Pteridineae FALSE   
10 Onychium_plumosum            Onychium      Pteridoideae  Pteridaceae Pteridineae Polypodiales Pteridineae FALSE   
# ℹ 5,740 more rows

# Analyze monophyly of each family
family_mono_test <- AssessMonophyly(
  phy,
  as.data.frame(taxonomy[, c("species", "family")])
)

# Check that all families are monophyletic or monotypic
family_mono_summary <-
  family_mono_test$family$result %>%
  rownames_to_column("family") %>%
  as_tibble() %>%
  assert(in_set("Yes", "Monotypic"), Monophyly)

# Inspect:
family_mono_summary

# A tibble: 48 × 9
   family            Monophyly MRCA  `#Tips` `Delta-Tips` `#Intruders` Intruders `#Outliers` Outliers
   <chr>             <chr>     <chr> <chr>   <chr>        <chr>        <chr>     <chr>       <chr>   
 1 Pteridaceae       Yes       5760  897     0            0            ""        NA          ""      
 2 Polypodiaceae     Yes       6666  935     0            0            ""        NA          ""      
 3 Davalliaceae      Yes       7600  42      0            0            ""        NA          ""      
 4 Oleandraceae      Yes       7641  10      0            0            ""        NA          ""      
 5 Tectariaceae      Yes       7650  138     0            0            ""        NA          ""      
 6 Nephrolepidaceae  Yes       7787  19      0            0            ""        NA          ""      
 7 Lomariopsidaceae  Yes       7805  44      0            0            ""        NA          ""      
 8 Dryopteridaceae   Yes       7848  984     0            0            ""        NA          ""      
 9 Didymochlaenaceae Yes       8831  9       0            0            ""        NA          ""      
10 Hypodematiaceae   Yes       8839  26      0            0            ""        NA          ""      
# ℹ 38 more rows

# Get one exemplar tip (species) per family
rep_tips <-
  taxonomy %>%
  group_by(family) %>%
  slice(1) %>%
  ungroup()

# Subset phylogeny to one tip per family
phy_family <- ape::keep.tip(phy, rep_tips$species)

# Relabel with family names
new_tips <-
tibble(species = phy_family$tip.label) %>%
  left_join(rep_tips, by = "species") %>%
  pull(family)

phy_family$tip.label <- new_tips

# Visualize tree
plot(ladderize(phy_family), no.margin = TRUE)

Reproducibility

• Source code
• renv lockfile

脚注

1. Another condition of this approach is that that the tree must be ultrametric (all tips at the same depth). If that is not true, then the choice of exemplar species would affect the branchlengths in the family-level tree.