Phylogenetic community assembly with the Fish Tree of Life

Here’s a quick example to show how we could use the fishtree package to conduct some phylogenetic community analyses. First, we load fishtree and ensure that the other packages that we need are installed.

library(ape)
library(fishtree)
loadNamespace("rfishbase")
#> <environment: namespace:rfishbase>
loadNamespace("picante")
#> <environment: namespace:picante>
loadNamespace("geiger")
#> <environment: namespace:geiger>

Next we’ll start downloading some data from rfishbase. We’ll be seeing if reef-associated ray-finned fish species are clustered or overdispersed in the Atlantic, Pacific, and Indian Oceans.

# Get reef-associated species from the `species` table
reef_species <- rfishbase::species(fields = c("Species", "DemersPelag"))
#> Joining with `by = join_by(Subfamily, GenCode, FamCode)`
#> Joining with `by = join_by(FamCode)`
#> Joining with `by = join_by(Order, Ordnum, Class, ClassNum)`
#> Joining with `by = join_by(Class, ClassNum)`
reef_species <- reef_species[reef_species$DemersPelag == "reef-associated", ]

# Get native and endemic species from the Atlantic, Pacific, and Indian Oceans
eco <- rfishbase::ecosystem(species_list = reef_species$Species)
#> Joining with `by = join_by(Subfamily, GenCode, FamCode)`
#> Joining with `by = join_by(FamCode)`
#> Joining with `by = join_by(Order, Ordnum, Class, ClassNum)`
#> Joining with `by = join_by(Class, ClassNum)`
valid_idx <- eco$Status %in% c("native", "endemic") & eco$EcosystemName %in% c("Atlantic Ocean", "Pacific Ocean", "Indian Ocean") 
eco <- eco[valid_idx, c("Species", "EcosystemName")]

# Retrieve the phylogeny of only native reef species across all three oceans.
phy <- fishtree_phylogeny(species = eco$Species)
#> Warning: Requested 5867 but only found 3938 species.
#> • Abudefduf conformis
#> • Abudefduf natalensis
#> • Abudefduf nigrimargo
#> • Acanthaluteres brownii
#> • Acanthanectes rufus
#> • ...and 1924 others

We’ll have to clean up the data in a few ways before sending it to picante for analysis. First, we’ll need to convert our species-by-site data frame into a presence-absence matrix. We’ll use base::table for this, and use unclass to convert the table into a standard matrix object.

sample_matrix <- unclass(table(eco))
dimnames(sample_matrix)$Species <- gsub(" ", "_", dimnames(sample_matrix)$Species, fixed = TRUE)

Next, we’ll use geiger::name.check to ensure the tip labels of the phylogeny and the rows of the data matrix match each other.

nc <- geiger::name.check(phy, sample_matrix)
sample_matrix <- sample_matrix[!rownames(sample_matrix) %in% nc$data_not_tree, ]

Finally, we’ll generate the cophenetic matrix based on the phylogeny, and transpose the presence-absence matrix since picante likes its columns to be species and its rows to be sites.

cophen <- cophenetic(phy)
sample_matrix <- t(sample_matrix)

We’ll run picante::ses.mpd and picante::ses.mntd with only 100 iterations, to speed up the analysis. For a real analysis you would likely increase this to 1000, and possibly test other null models if your datasets have e.g., abundance information.

picante::ses.mpd(sample_matrix, cophen, null.model = "taxa.labels", runs = 99)
#>                ntaxa  mpd.obs mpd.rand.mean mpd.rand.sd mpd.obs.rank mpd.obs.z
#> Atlantic Ocean   612 238.0090      231.7315   2.1788238          100 2.8811424
#> Indian Ocean    1207 233.2275      231.5993   1.2359893           90 1.3172917
#> Pacific Ocean   1487 231.7967      231.6420   0.8434865           57 0.1833511
#>                mpd.obs.p runs
#> Atlantic Ocean      1.00   99
#> Indian Ocean        0.90   99
#> Pacific Ocean       0.57   99
picante::ses.mntd(sample_matrix, cophen, null.model = "taxa.labels", runs = 99)
#>                ntaxa mntd.obs mntd.rand.mean mntd.rand.sd mntd.obs.rank
#> Atlantic Ocean   612 41.91627       48.55036    1.4029729             1
#> Indian Ocean    1207 34.95466       38.09685    0.8187912             1
#> Pacific Ocean   1487 34.20019       35.09422    0.5352152             6
#>                mntd.obs.z mntd.obs.p runs
#> Atlantic Ocean  -4.728594       0.01   99
#> Indian Ocean    -3.837596       0.01   99
#> Pacific Ocean   -1.670402       0.06   99

The Atlantic and Indian Oceans are overdispersed using the MPD metric, and all three oceans are clustered under the MNTD metric. MPD is thought to be more sensitive to patterns closer to the root of the tree, while MNTD is thought to more closely reflect patterns towards the tips of the phylogeny.

We can confirm these patterns visually by running the following code, which will plot the phylogeny and add colored dots (red, green, and blue) to indicate whether a tip is associated with a specific ocean basin.

plot(phy, show.tip.label = FALSE, no.margin = TRUE)
obj <- get("last_plot.phylo", .PlotPhyloEnv)

matr <- t(sample_matrix)[phy$tip.label, ]
xx <- obj$xx[1:obj$Ntip]
yy <- obj$yy[1:obj$Ntip]
cols <- c("#1b9e77", "#d95f02", "#7570b3")
for (ii in 1:ncol(matr)) {
  present_idx <- matr[, ii] == 1
  points(xx[present_idx] + ii, yy[present_idx], col = cols[ii], cex = 0.1)
}

Jonathan Chang