Tuesday, October 25, 2016

Mapping sampled changes on the tree from stochastic character mapping

A cool (in my opinion) phytools plotting function that I've yet to see applied in a published study is markChanges, which can be used to visualize the posterior density of changes (as opposed to trait values) from a sample of stochastically mapped trees.

Here are a couple of different examples - one with lots of uncertainty about the location of trait changes on the tree (feeding mode in elopomorph eel evolution; from Collar et al. 2014); and another in which there should be much less (piscivory vs. non-piscivory in Centrarchidae).

First, the elopomorph dataset:

library(phytools)
eel.tree
## 
## Phylogenetic tree with 61 tips and 60 internal nodes.
## 
## Tip labels:
##  Moringua_edwardsi, Kaupichthys_nuchalis, Gorgasia_taiwanensis, Heteroconger_hassi, Venefica_proboscidea, Anguilla_rostrata, ...
## 
## Rooted; includes branch lengths.
feed.mode
##                 Albula_vulpes             Anguilla_anguilla 
##                       suction                       suction 
##              Anguilla_bicolor             Anguilla_japonica 
##                       suction                       suction 
##             Anguilla_rostrata                Ariosoma_anago 
##                       suction                       suction 
##           Ariosoma_balearicum           Ariosoma_shiroanago 
##                       suction                       suction 
##        Bathyuroconger_vicinus   Brachysomophis_crocodilinus 
##                          bite                          bite 
##              Conger_japonicus              Conger_myriaster 
##                       suction                       suction 
##               Conger_verreaxi                Conger_wilsoni 
##                       suction                       suction 
##        Congresox_talabonoides            Cynoponticus_ferox 
##                       suction                          bite 
##            Dysomma_anguillare                  Elops_saurus 
##                          bite                       suction 
##         Facciolella_gilbertii          Gavialiceps_taeniola 
##                          bite                          bite 
##         Gnathophis_longicauda          Gorgasia_taiwanensis 
##                       suction                       suction 
##         Gymnothorax_castaneus   Gymnothorax_flavimarginatus 
##                          bite                          bite 
##            Gymnothorax_kidako           Gymnothorax_moringa 
##                          bite                          bite 
## Gymnothorax_pseudothyrsoideus       Gymnothorax_reticularis 
##                          bite                          bite 
##            Heteroconger_hassi          Ichthyapus_ophioneus 
##                       suction                          bite 
##      Kaupichthys_hyoproroides          Kaupichthys_nuchalis 
##                          bite                          bite 
##          Megalops_cyprinoides             Moringua_edwardsi 
##                       suction                          bite 
##             Moringua_javanica              Muraenesox_bagio 
##                          bite                          bite 
##           Muraenesox_cinereus          Myrichthys_breviceps 
##                          bite                       suction 
##          Myrichthys_maculosus         Myrichthys_magnificus 
##                       suction                       suction 
##                Myrophis_vafer        Nemichthys_scolopaceus 
##                          bite                          bite 
##          Nettastoma_melanurum        Ophichthus_serpentinus 
##                          bite                       suction 
##          Ophichthus_zophochir        Oxyconger_leptognathus 
##                       suction                          bite 
## Parabathymyrus_macrophthalmus           Paraconger_notialis 
##                       suction                       suction 
##      Pisodonophis_cancrivorus          Poeciloconger_kapala 
##                          bite                       suction 
##         Rhinomuraena_quaesita          Rhynchoconger_flavus 
##                          bite                       suction 
##        Saurenchelys_fierasfer      Scolecenchelys_breviceps 
##                          bite                       suction 
##            Scuticaria_tigrina             Serrivomer_beanii 
##                          bite                          bite 
##             Serrivomer_sector        Simenchelys_parasitica 
##                          bite                       suction 
##            Uroconger_lepturus      Uropterygius_micropterus 
##                       suction                          bite 
##          Venefica_proboscidea 
##                          bite 
## Levels: bite suction
mtrees<-make.simmap(eel.tree,feed.mode,nsim=100)
## make.simmap is sampling character histories conditioned on the transition matrix
## 
## Q =
##                bite     suction
## bite    -0.01582783  0.01582783
## suction  0.01582783 -0.01582783
## (estimated using likelihood);
## and (mean) root node prior probabilities
## pi =
##    bite suction 
##     0.5     0.5
## Done.
cols<-setNames(c("red","blue"),c("bite","suction"))
dotTree(eel.tree,feed.mode,colors=cols,fsize=0.7,ftype="i",
    legend=FALSE)
add.simmap.legend(x=0,y=-4,colors=cols,prompt=FALSE,
    vertical=FALSE,shape="circle")
nulo<-sapply(mtrees,markChanges,sapply(cols,
    make.transparent,0.1))
add.simmap.legend(colors=sapply(setNames(cols[2:1],
    c("bite->suction","suction->bite")),
    make.transparent,0.1),prompt=FALSE,x=50,y=-4,
    vertical=FALSE)

plot of chunk unnamed-chunk-1

Just to clarify the interpretation of this plot, the hash marks show the entire posterior sample of changes on the tree - across 100 samples from the posterior distribution. Any individual tree will have fewer (but still a lot of changes):

pd<-summary(mtrees)
pd
## 100 trees with a mapped discrete character with states:
##  bite, suction 
## 
## trees have 30.95 changes between states on average
## 
## changes are of the following types:
##      bite,suction suction,bite
## x->y        17.58        13.37
## 
## mean total time spent in each state is:
##              bite     suction    total
## raw  1155.3150660 828.7861757 1984.101
## prop    0.5822863   0.4177137    1.000

Now here is the second dataset. This one piscivory vs. non-piscovory in Centrarchidae:

cent.tree
## 
## Phylogenetic tree with 28 tips and 27 internal nodes.
## 
## Tip labels:
##  Acantharchus_pomotis, Lepomis_gibbosus, Lepomis_microlophus, Lepomis_punctatus, Lepomis_miniatus, Lepomis_auritus, ...
## 
## Rooted; includes branch lengths.
piscivory
##    Acantharchus_pomotis        Lepomis_gibbosus     Lepomis_microlophus 
##                    pisc                     non                     non 
##       Lepomis_punctatus        Lepomis_miniatus         Lepomis_auritus 
##                     non                     non                     non 
##      Lepomis_marginatus       Lepomis_megalotis         Lepomis_humilis 
##                     non                     non                     non 
##     Lepomis_macrochirus         Lepomis_gulosus     Lepomis_symmetricus 
##                     non                    pisc                     non 
##       Lepomis_cyanellus      Micropterus_coosae      Micropterus_notius 
##                    pisc                    pisc                    pisc 
##     Micropterus_treculi   Micropterus_salmoides  Micropterus_floridanus 
##                    pisc                    pisc                    pisc 
## Micropterus_punctulatus    Micropterus_dolomieu Centrarchus_macropterus 
##                    pisc                    pisc                     non 
##      Enneacantus_obesus       Pomoxis_annularis  Pomoxis_nigromaculatus 
##                     non                    pisc                    pisc 
##  Archolites_interruptus    Ambloplites_ariommus   Ambloplites_rupestris 
##                    pisc                    pisc                    pisc 
##   Ambloplites_cavifrons 
##                    pisc 
## Levels: non pisc
mtrees<-make.simmap(cent.tree,piscivory,nsim=100)
## make.simmap is sampling character histories conditioned on the transition matrix
## 
## Q =
##            non      pisc
## non  -4.228856  4.228856
## pisc  4.228856 -4.228856
## (estimated using likelihood);
## and (mean) root node prior probabilities
## pi =
##  non pisc 
##  0.5  0.5
## Done.
cols<-setNames(c("red","blue"),c("pisc","non"))
dotTree(cent.tree,piscivory,colors=cols,ftype="i")
nulo<-sapply(mtrees,markChanges,sapply(cols,
    make.transparent,0.2))
add.simmap.legend(colors=sapply(setNames(cols[2:1],
    c("non->pisc","pisc->non")),
    make.transparent,0.2),prompt=FALSE,
    x=par()$usr[1]+0.1*max(nodeHeights(cent.tree)),
    y=-1.2,vertical=FALSE)

plot of chunk unnamed-chunk-3

For comparison to our previous analysis:

summary(mtrees)
## 100 trees with a mapped discrete character with states:
##  non, pisc 
## 
## trees have 6.95 changes between states on average
## 
## changes are of the following types:
##      non,pisc pisc,non
## x->y     3.27     3.68
## 
## mean total time spent in each state is:
##            non     pisc    total
## raw  0.6532209 1.041858 1.695079
## prop 0.3853630 0.614637 1.000000

That's it.

1 comment:

  1. Quick question, I have phytools on R, but its tells me eel.tree is not present. How do you get it?

    ReplyDelete