I have generated a tree and I'm having difficulty rooting it in 'ape', and I am unsure if my method of specifying an outgroup is correct.
Here is the species list:
Agaricus_silvicola
Amanita_citrina
Amanita_echinocephala
Amanita_fulva
Amanita_pantherina
Amanita_phalloides
Amanita_rubescens
Amanita_strobiliformis
Amanita_vaginata
Amanita_virosa
Ampulloclitocybe_clavipes
Xerocomellus_chrysenteron
Boletus_edulis
Boletus_erythropus
Boletus_luridiformis
Boletus_luridus
Boletus_subtomentosus
Cantharellus_cibarius
Craterellus_tubaeformis
Clitocybe_fragrans
Infundibulicybe_geotropa
Clitocybe_gibba
Clitocybe_nebularis
Clitocybe_odora
Clitocybe_phyllophila
Clitocybe_vibecina
Clitopilus_prunulus
Coprinus_silvaticus
Cortinarius_anomalus
Cortinarius_decipiens
Cortinarius_flexipes
Cortinarius_hemitrichus
Cortinarius_hinnuleus
Craterellus_cornucopioides
Cystolepiota_seminuda
Geastrum_fimbriatum
Geastrum_triplex
Gymnopus_androsaceus
Gymnopus_confluens
Gymnopus_dryophilus
Gymnopus_peronatus
Hebeloma_crustuliniforme
Hebeloma_leucosarx
Hebeloma_mesophaeum
Hebeloma_sacchariolens
Hemimycena_cucullata
Hydnum_repandum
Inocybe_assimilata
Inocybe_asterospora
Inocybe_bongardii
Inocybe_flocculosa
Inocybe_fraudans
Inocybe_geophylla
Inocybe_lacera
Inocybe_napipes
Inocybe_petiginosa
Inocybe_rimosa
Laccaria_laccata
Lactarius_azonites
Lactarius_piperatus
Lactarius_sphagneti
Lactarius_tabidus
Lactarius_vellereus
Lactarius_zonarius
Lepiota_castanea
Lepiota_cristata
Lepista_flaccida
Lepista_nuda
Lycoperdon_molle
Lycoperdon_nigrescens
Lycoperdon_perlatum
Macrocystidia_cucumis
Marasmius_cohaerens
Marasmius_epiphyllus
Marasmius_wynneae
Mutinus_caninus
Mycena_metata
Mycena_pelianthina
Mycena_polyadelpha
Mycena_rosella
Mycena_vitilis
Paxillus_involutus
Phallus_impudicus
Psathyrella_obtusata
Pseudoclitocybe_cyathiformis
Rhodocollybia_butyracea
Rhodocollybia_maculata
Russula_aeruginea
Russula_atropurpurea
Russula_cyanoxantha
Russula_delica
Russula_foetens
Russula_fragilis
Russula_heterophylla
Russula_nigricans
Russula_ochroleuca
Russula_rosea
Russula_virescens
Russula_xerampelina
Scleroderma_areolatum
Scleroderma_verrucosum
Stropharia_aeruginosa
Tricholoma_album
Tricholoma_fulvum
Tricholoma_ustale
Tubaria_conspersa
Tubaria_furfuracea
Tylopilus_felleus
Hymenopellis_radicata
I have installed a lot of packages, and not entirely sure which ones I use:
library(ggtree)
library(ggplot2)
library(motmot.2.0)
library(caper)
library(geiger)
library(ape)
library(MASS)
library(phytools)
library(adephylo)#
library(quantreg)#
library(phangorn)
library(rotl)
library(MuMIn)
Read in data:
data<- read.csv("filename.csv")
create species list:
species.list <- as.character(levels(as.factor(data$unique_name)))
create taxonomy:
taxonomy <- tnrs_match_names(species.list[1:109], context_name = "Basidiomycetes")
download tree:
downloaded.tree <- tol_induced_subtree(ott_ids = taxonomy$ott_id, label_format = "name")
compute branch lengths:
computed_brlen_tree <-compute.brlen(downloaded.tree)
when plot(computed_brlen_tree) I notice that there is no single outgroup, why is this?
I need to root the tree so I tried this:
rooted_tree = root(computed_brlen_tree, outgroup = "Russula_foetens", resolve.root = TRUE)
it changes how the tree looks, and I receive this confirmation:
Phylogenetic tree with 109 tips and 57 internal nodes.
Tip labels:
Rhodocollybia_butyracea, Rhodocollybia_maculata, Gymnopus_confluens, Gymnopus_peronatus, Gymnopus_dryophilus, Gymnopus_androsaceus, ...
Node labels:
Root, mrcaott109ott2361, mrcaott109ott1939, mrcaott109ott471, mrcaott109ott206, mrcaott109ott2427, ...
Rooted; includes branch lengths.
However:
> is.rooted(computed_brlen_tree)
[1] FALSE
The tree is still not rooted. what is the best method for specifying an outgroup in this instance? I just used the one appearing at the bottom of the unrooted tree plot. Any assistance here greatly appreciated, I am a beginner so I may be missing obvious things.