9 Phylogeny Example: Fish Tree of Life

library(fishtree) # Fish Tree of Life package
library(ape)
library(rfishbase) # Fishbase package
library(picante) # Phylogeny package
library(fields)

9.1 Import species from Fishbase

Fishbase (https://fishbase.org/) is a global database of fish species, distributions, ecology, morphology, and photos. First, we will bring in all species names from the family Centrarchidae, a North American family that includes basses and sunfish.

species <- rfishbase::fb_tbl("species")
centrarchids <- species[species$FamCode == 302,]
centrarchids$gensp <- paste(centrarchids$Genus,centrarchids$Species)

9.2 Import phylogenetic information from the Fish Tree of Life

We can then pass on this species list to the Fish Tree of Life to get a phylogeny:

phy <- fishtree_phylogeny(species = centrarchids$gensp)

## Warning: Requested 38 but only found 33 species.
## • Lepomis peltastes
## • Micropterus cahabae
## • Micropterus chattahoochae
## • Micropterus tallapoosae
## • Micropterus warriorensis

9.3 Plot a basic phylogeny

We can then plot the Centarchid species phylogeny for species with placement

# Plot the tree
plot.phylo(
  phy,
  type = "phylogram",           # "phylogram", "cladogram", or "fan" for radial
  cex = 0.8,              # Size of tip labels
  font = 3,               # Italic font for species names
  no.margin = FALSE,
  label.offset = 0.02,    # Spacing between tip and label
  edge.width = 2          # Thicker branches
)
title("Phylogenetic Tree of the 33 placed Centrarchid species")

9.4 Annotating a phylogeny

We can also do things like annotate our phylogeny using some of the other data from Fishbase.

# Clean tip labels for matching
phy_labels_clean <- gsub("_", " ", phy$tip.label)

# Match lengths
lengths <- centrarchids$Length[match(phy_labels_clean, centrarchids$gensp)]

# Build color palette
color_palette <- colorRampPalette(c("blue", "green", "yellow", "red"))
n_colors <- 100
colors <- color_palette(n_colors)

# Scale length values to color indices
length_scaled <- round(scales::rescale(lengths, to = c(1, n_colors)))

# Assign colors, defaulting to gray for NA values
tip_colors <- ifelse(is.na(length_scaled), "gray", colors[length_scaled])

plot.phylo(
  phy,
  type = "phylogram",
  cex = 0.8,
  font = 3,
  tip.color = tip_colors,
  no.margin = FALSE,
  label.offset = 0.02,
  edge.width = 2
)
title("Phylogenetic Tree of the 33 placed Centrarchid species")

if (any(!is.na(lengths))) {
  legend_gradient <- matrix(seq(min(lengths, na.rm = TRUE), max(lengths, na.rm = TRUE), length.out = n_colors), ncol = 1)
  image.plot(
    z = legend_gradient,
    col = colors,
    legend.only = TRUE,
    horizontal = TRUE,
    legend.width = 1.2,
    legend.shrink = 0.6,
    smallplot = c(0.15, 0.85, 0.05, 0.08),
    axis.args = list(
      at = pretty(range(lengths, na.rm = TRUE)),
      labels = pretty(range(lengths, na.rm = TRUE)),
      cex.axis = 0.8
    ),
    legend.args = list(text = "Length", side = 2, line = 2, cex = 0.9)
  )
}