Oliver Purschke 01 Oktober, 2017
This document describes the workflow (with contributions from Brody Sandel) that was used to generate the phylogenetic tree for the taxa in the global vegetation plot database sPlot (v. 2.1).
library(ape)
library(geiger)
library(dplyr)load("../backbone.splot2.1.try3.is.vascular.Rdata")head(backbone.splot2.1.try3[,c(2,32,34,35)])## names.sPlot.TRY name.short.correct is.vascular.species
## 1 ? <NA> NA
## 2 0 <NA> NA
## 3 [1269 Chlorophytum platt] Chlorophytum TRUE
## 4 [1284 Echinochloa] Echinochloa TRUE
## 5 [1285 Indigofera lange Bl-Stiele] Indigofera TRUE
## 6 [1304 Polygala] Polygala TRUE
## sPlot2.1.TRY
## 1 S
## 2 S
## 3 S
## 4 S
## 5 S
## 6 S
tail(backbone.splot2.1.try3[,c(2,32,34,35)])## names.sPlot.TRY name.short.correct
## 130597 Chlorocyperus longus Chlorocyperus longus
## 130598 Glyceria fluitans subsp. poiformis Glyceria fluitans
## 130599 Hydrodictyon utriculatum <NA>
## 130600 Bryum pseudotriquetrum var. duvalioides Bryum pseudotriquetrum
## 130601 Hylocomium squarrosum Hylocomium squarrosum
## 130602 Carex hornschuchiana Carex hornschuchiana
## is.vascular.species sPlot2.1.TRY
## 130597 TRUE S
## 130598 TRUE S
## 130599 NA S
## 130600 NA S
## 130601 NA S
## 130602 TRUE S
Because the taxonomic backbone includes combines and standardizes names from both, the sPlot and TRY databases, we need to exclude those names that are only found in the TRY database:
splot.nam <- backbone.splot2.1.try3[backbone.splot2.1.try3$sPlot.TRY != "T", c(4,32)]How many entries in the backbone are only found in sPlot (S) as well as in both, sPlot and TRY (ST)?
table(splot.nam$sPlot.TRY)##
## S ST
## 70329 24796
Generate vector of unique names.
splot.nam.2 <- unique(splot.nam$name.short.correct)Check for NA entries and get rid of them:
any(is.na(splot.nam.2))## [1] TRUE
na.ind <- which(is.na(splot.nam.2))
splot.nam.3 <- splot.nam.2[-na.ind]
any(is.na(splot.nam.3))## [1] FALSE
length(splot.nam.3)## [1] 61214
There are 61,214 unique names in the backbone that belong to sPlot as well to sPlot and TRY. However, some of them are non-vascular names and/or are only found in the previous version of sPlot (sPlot 2.0) but not in sPlot 2.1, which will be dealt with the last section.
Insert underscores to make names match with the tip.labels of the phylogeny.
splot.nam.4 <- gsub(" ", "_", splot.nam.3)I started with the fully resolved reference phylogeny for 31,749 vascular plants by Zanne et al. (2014), that was generated by David Tank and folks and therefore is referred to as tank tree in the subsequent text.
tank.tree <- read.tree("/home/oliver/Dokumente/PhD/PostPhD/IDiv/sDiv/sPlot/Analyses/Data/Phylogeny/2/PhylogeneticResources/Vascular_Plants_rooted.dated.tre")ind.miss <- splot.nam.4 %in% tank.tree$tip.label How many taxon names in sPlot are found/not found in the tank tree?:
table(ind.miss)## ind.miss
## FALSE TRUE
## 45784 15430
Only 25.2% of the taxa in sPlot are in the tank tree.
Before grafting the missing taxa onto the reference phylogeny, we might inspect those taxa, to see whether there are taxa that obviously should be in the tree.
Generate vector of the 45,784 names in sPlot that missing from the tree.
splot.nam.miss <- splot.nam.4[ind.miss==F]Before grafting the missing species onto the reference phylogeny, we might inspect missing species to see whether there are species that obviously should be there.
write.csv(sort(splot.nam.miss), file = "splot.nam.miss.csv")length(splot.nam.miss)## [1] 45784
The following function addCongeners takes a tree and species list, each containing "Genus_species" or "Genus" formatted names. For each species in the list, if it has a congener on the tree but is not itself on the tree, add it next to a randomly selected congener at a random position along the edge returns a larger tree (see also the approach that was used to generate the BIEN-Phylogeny (Maitner et al.) here). Such approach has been demonstrated to introduce less bias into subsequent analysis than adding missing species as polytomies to the respective genera (Davies et al. 2012). I did not add species based on taxonomic information above genus level.
addCongeners = function(tree,speciesToAdd){
resample <- function(x, ...) x[sample.int(length(x), ...)]
staGenus = unlist(lapply(strsplit(speciesToAdd,"_"),function(i){i[[1]]}))
gtree = tree
for(i in sample(1:length(speciesToAdd),length(speciesToAdd),replace = F)){
gtreeGenera = unlist(lapply(strsplit(gtree$tip,"_"),function(i){i[[1]]}))
#If the species isn't on the tree but a congener is
if(!speciesToAdd[i] %in% tree$tip.label & staGenus[i] %in% gtreeGenera){
branchName = gtree$tip[resample(which(gtreeGenera == staGenus[i]),1)]
newtree = sim.bdtree(n=2)
newtree$tip.label = c(branchName,speciesToAdd[i])
edgeL = gtree$edge.length[which.edge(gtree,branchName)]
#Splice in at a random depth between 0 and 1
depth = runif(1,0,1)
newtree$edge.length = depth*newtree$edge.length*edgeL/max(newtree$edge.length)
whereToGraft = which(gtree$tip == branchName)
gtree = bind.tree(gtree,newtree,where = whereToGraft,position = edgeL*depth)
#The grafting process duplicates the branchName tip. Drop one of them.
gtree = drop.tip(gtree, which(gtree$tip == branchName)[1])}
}
return(gtree)
}tank.tree.added <- addCongeners(tank.tree, splot.nam.miss)
splot2.1.tank.tree.70287 <- tank.tree.addedTook 4.5 hours (on the RStudio-server) to add the missing 45,784 taxa in sPlot that were not included in the tank tree. This resulted in an extended tank tree with 70,287 taxa.
... and check which names could not be added:
splot2.1.tank.tree.70287 <- read.tree("/home/oliver/Dokumente/PhD/PostPhD/IDiv/sDiv/sPlot/Analyses/Data/Phylogeny/sPlot2.1Phylo/splot2.1.tank.tree.70287.tre")
ind.miss.2 <- splot.nam.miss %in% splot2.1.tank.tree.70287$tip.label
splot.nam.miss.2 <- splot.nam.miss[ind.miss.2==F]
write.csv(sort(splot.nam.miss.2), file = "splot.nam.miss.2.csv")
length(splot.nam.miss.2)length(splot.nam.miss.2)## [1] 7246
Because they had no congeners in the reference phylogeny, 7,246 species could not be added (11.8% of all resolved taxa in sPlot). This resulted in a phylogeny with 53,967 names from a total of 61,214 standardized taxa in sPlot. Anyway, lichens, mosses as well as species that are not found in sPlot 2.1 are still included in that sPlot species list. We will take care of that in a later section.
The reference phylogeny by Zanne et al. (2014) has recently been updated by Qian & Jin (2016), subsequently referred to as the Qian tree. So we will use that tree to generate our final phylogeny.
phyto.phylo.tree <- read.tree("/home/oliver/Dokumente/PhD/PostPhD/IDiv/sDiv/sPlot/Analyses/Data/Phylogeny/Qian_PhytoPhylo/AppendixS5/PhytoPhylo.tre")
ind.miss <- splot.nam.4 %in% phyto.phylo.tree$tip.label table(ind.miss)## ind.miss
## FALSE TRUE
## 45784 15430
16,121 names in sPlot are found in the Qian tree.
Generate vector of missing names:
splot.nam.miss.phyto.phylo <- splot.nam.4[ind.miss==F]phyto.phylo.tree.added <- addCongeners(phyto.phylo.tree, splot.nam.miss.phyto.phylo)
phyto.phylo.splot2.1.69335 <- phyto.phylo.tree.addedThis resulted in an extended Qian tree with 69,335 taxa.
phyto.phylo.splot2.1.69335 <- read.tree("/home/oliver/Dokumente/PhD/PostPhD/IDiv/sDiv/sPlot/Analyses/Data/Phylogeny/sPlot2.1Phylo/phyto.phylo.splot2.1.69335.tre")
pdf("phyto.phylo.tree.splot.69335.pdf", height = 150, width = 150)
plot(phyto.phylo.splot2.1.69335, "f", cex = .1)
dev.off()
ind.miss.3 <- splot.nam.miss.phyto.phylo %in% phyto.phylo.splot2.1.69335$tip.label How many taxa in sPlot could/could not be added to the Qian & Jin (2016) tree?:
table(ind.miss.3)## ind.miss.3
## FALSE TRUE
## 7147 37946
splot.nam.miss.3 <- splot.nam.miss.phyto.phylo[ind.miss.3==F]
write.csv(sort(splot.nam.miss.3), file = "splot.nam.miss.3.csv")pruned.tree <- drop.tip(phyto.phylo.splot2.1.69335, setdiff(phyto.phylo.splot2.1.69335$tip.label, splot.nam.4))
phyto.phylo.splot2.1.54067 <- pruned.tree
write.tree(phyto.phylo.splot2.1.54067, file = "phyto.phylo.splot2.1.54067.tre")
phyto.phylo.splot2.1.54067 <- read.tree("phyto.phylo.splot2.1.54067.tre")16121/54067Out of the total of 54,067 species that are now in the sPlot2.1 tree, 29.8% are actually found in the Qian tree. The remainder was added as congeners.
pdf("phyto.phylo.tree.splot.54067.pdf", height = 220, width = 220)
plot(phyto.phylo.splot2.1.54067, "f", edge.width = .4, label.offset = .03, cex = .1)
dev.off()
png("phyto.phylo.tree.splot.54067.png", height = 10000, width = 10000, pointsize = 1, res = 4000)
plot(phyto.phylo.splot2.1.54067, "f", edge.width = .1, label.offset = .03, cex = .1)
dev.off()Select the respective set of species from the backbone.
Exclude NA entries from the backbone:
ind2.1 <- !is.na(backbone.splot2.1.try3$sPlot2.1.TRY)
back2.1 <- backbone.splot2.1.try3[ind2.1, ]Generate a version of the backbone that only includes the unique resolved names in name.short.correct. For the non-unique names, keep the first row of duplicated names:
back2.1.uni <- back2.1[!duplicated(back2.1$name.short.correct), ]
back2.1.uni <- back2.1.uni[-1, ]length(unique(back2.1.uni$name.short.correct))## [1] 86760
Select vascular species only and exclude NA entries:
df.uni <- back2.1.uni %>%
dplyr::filter(is.vascular.species == TRUE, !is.na(name.short.correct))length(df.uni$name.short.correct)## [1] 83677
table(df.uni$sPlot2.1.TRY)##
## S ST T
## 34105 20414 29158
df.uni.splot <- df.uni %>%
dplyr::filter(is.vascular.species == TRUE, !is.na(name.short.correct), df.uni$sPlot2.1.TRY!= "T")length((df.uni.splot$name.short.correct))## [1] 54519
splot_2.1_vasc_nam <- df.uni.splot$name.short.correct
length(splot_2.1_vasc_nam)## [1] 54519
splot_2.1_vasc_nam_2 <- gsub(" ", "_", splot_2.1_vasc_nam)pruned.tree.splot2.1 <- drop.tip(phyto.phylo.splot2.1.69335, setdiff(phyto.phylo.splot2.1.69335$tip.label, splot_2.1_vasc_nam_2))
phyto.phylo.splot2.1.50167.vasc <- pruned.tree.splot2.1
write.tree(phyto.phylo.splot2.1.50167.vasc, file = "phyto.phylo.splot2.1.50167.vasc.tre")
phyto.phylo.splot2.1.50167.vasc <- read.tree("phyto.phylo.splot2.1.50167.vasc.tre")
pdf("phyto.phylo.splot2.1.50167.vasc.pdf", height = 220, width = 220)
plot(phyto.phylo.splot2.1.50167.vasc, "f", edge.width = .4, label.offset = .03, cex = .1)
dev.off()
png("phyto.phylo.splot2.1.50167.vasc.png", height = 10000, width = 10000, pointsize = 1, res = 4000)
plot(phyto.phylo.splot2.1.50167.vasc, "f", edge.width = .1, label.offset = .03, cex = .1)
dev.off()knitr::include_graphics("/home/oliver/Dokumente/PhD/PostPhD/IDiv/sDiv/sPlot/Analyses/Code/sPlot_Phylogeny/phyto.phylo.splot2.1.50167.vasc_small.png")
From a total of 54,519 vascular taxon names in sPlot 2.1, 50,167 names (92%) are contained in the extended version of the Qian tree (extended by the names in sPlot 2.1).
How many vascular species in sPlot 2.1 are found in the Qian-tree?:
ind.miss <- splot_2.1_vasc_nam_2 %in% phyto.phylo.tree$tip.label
table(ind.miss)## ind.miss
## FALSE TRUE
## 39759 14760
There are 14,760 vascular names in sPlot 2.1 that are also found in the Qian reference tree (which contains 31,389 names), which are 47% from the total number of taxa in the Qian tree.
Of the in total 54,519 vascular taxon names in sPlot 2.1, 14,760 names (27.1%) are contained in the Qian tree.
sessionInfo()## R version 3.4.1 (2017-06-30)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.3 LTS
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## attached base packages:
## [1] grid stats graphics grDevices utils datasets methods
## [8] base
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## other attached packages:
## [1] png_0.1-7 bindrcpp_0.2 dplyr_0.7.3 rmarkdown_1.6 geiger_2.0.6
## [6] ape_4.1
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## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.12 knitr_1.17 bindr_0.1 magrittr_1.5
## [5] MASS_7.3-47 lattice_0.20-35 R6_2.2.2 rlang_0.1.2
## [9] subplex_1.4-1 stringr_1.2.0 tcltk_3.4.1 tools_3.4.1
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## [21] tibble_1.3.4 glue_1.1.1 deSolve_1.20 evaluate_0.10.1
## [25] stringi_1.1.5 compiler_3.4.1 backports_1.1.1 mvtnorm_1.0-6
## [29] pkgconfig_2.0.1
Davies, T.J., Kraft, N.J., Salamin, N. & Wolkovich, E.M. (2012) Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism. Ecology, 93, 242–247.
Maitner, B.S., Boyle, B., Casler, N., Condit, R., Donoghue, J., Durán, S.M., Guaderrama, D., Hinchliff, C.E., Jørgensen, P.M., Kraft, N.J., McGill, B., Merow, C., Morueta-Holme, N., Peet, R.K., Sandel, B., Schildhauer, M., Smith, S.A., Svenning, J.-C., Thiers, B., Violle, C., Wiser, S. & Enquist, B.J. The bien r package: A tool to access the Botanical Information and Ecology Network (BIEN) database. Methods in Ecology and Evolution, n/a–n/a.
Qian, H. & Jin, Y. (2016) An updated megaphylogeny of plants, a tool for generating plant phylogenies and an analysis of phylogenetic community structure. Journal of Plant Ecology, 9, 233–239.
Zanne, A.E., Tank, D.C., Cornwell, W.K., Eastman, J.M., Smith, S.A., FitzJohn, R.G., McGlinn, D.J., O’Meara, B.C., Moles, A.T., Reich, P.B. & others. (2014) Three keys to the radiation of angiosperms into freezing environments. Nature, 506, 89.