-
Notifications
You must be signed in to change notification settings - Fork 4
/
MS1_Fig5_compare_LTTs.R
375 lines (315 loc) · 15.9 KB
/
MS1_Fig5_compare_LTTs.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# R Code - MamPhy MS1 -- Upham et al. 2019 -- PLOS Biology
###
# Figure 5 - comparing LTT plots among Mammalia species-level studies
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# PLOTTING OTHER BIG TREES
####
setwd("/Users/Nate/Desktop/VertLife_Project/MAMMALS-phylo-analyses/12_PhyloAnalyses/")
source("source_functions/DR_circleTree_functions.R")
library(ape); library(phytools); library(viridis); library(phangorn); library(geiger); library(magick); library(phyloch)
library(dplyr)
##
# All BIG TREES TOGETHER in a loop, same timescale and color scale.
# Load trees
dir<-"_DATA/"
mamMCC1<-read.nexus(file=paste0(dir,"MamPhy_fullPosterior_BDvr_Completed_5911sp_topoCons_NDexp_MCC_target.tre"))
mamMCC <- ladderize(drop.tip(mamMCC1, "_Anolis_carolinensis"))
#r1<-max(nodeHeights(plottree1))
BE_etAl_phy1<-read.nexus(file=paste0(dir,"bininda-emonds-et-al2007_treeFile_Supp1.nex"))
BE_etAl_phy <- ladderize(BE_etAl_phy1[[1]])
#rX<-max(nodeHeights(plottreeX))
KuhnEtAl_100<-read.nexus(file=paste0(dir,"FritzTree.rs200k.100trees.nex"))
mamPhy_100<-read.nexus(file=paste0(dir,"MamPhy_fullPosterior_BDvr_Completed_5911sp_topoCons_NDexp_sample100_nexus.trees"))
FS2015_100<-read.nexus(file=paste0(dir,"FS2015_Fully_resolved_phylogeny_random100trees.nex")) # 100 trees, 5747 taxa each
Hedges_phySmooth<-read.tree(file=paste0(dir,"9.TTOL_mammals_smoothed_interpolated.tre"))
###
# Make the LTT comparisons plot
########
# get PER-STUDY colors...
colKuhn<-viridis(10, alpha=0.4)[1]
colBE<-viridis(10, alpha=1)[2]
colFS<-viridis(10, alpha=0.4)[6]
colHedges<-viridis(10, alpha=1)[9]
colThisStudy<-rgb((as.vector(col2rgb("goldenrod1"))/255)[1],(as.vector(col2rgb("goldenrod1"))/255)[2],(as.vector(col2rgb("goldenrod1"))/255)[3],alpha=0.5)
RESDIR<-"Fig5_compare_LTTs/"
png(file=paste0(RESDIR,"comparing_MamPhys_LTT_all_BE-Kuhn-FS-Hedges_viridis_legByType_withMamPhy.png"), width=6, height=6, res=400, units="in")
# ltt.plot(KuhnEtAl_100[[1]], log="y", col=rgb(0,0,1,alpha=0.5), lwd=1, xlim=c(-100,0), bty="n", ylab="", xlab="", xaxt="n",yaxt="n")#, ylim=c(4,5500))
# KUHN
ltt.plot(KuhnEtAl_100[[1]], log="y", col=rgb(0,0,1,alpha=0.5), lwd=1, xlim=c(-100,0), bty="n", ylab="log (Lineages)", xlab="Time before present (Ma)")#, ylim=c(4,5500))
#axis(side=1, at=c(0,-20,-40,-60,-80,-100),labels=c(0,-20,-40,-60,-80,-100))
for(i in 2:length(KuhnEtAl_100)){
ltt.lines(KuhnEtAl_100[[i]], col=colKuhn, lwd=1) #rgb(0,0,1,alpha=0.5)
}
ltt.lines(BE_etAl_phy, col=colBE, lwd=2) #"purple"
# MAMPHY
for(i in 1:length(mamPhy_100)){
ltt.lines(mamPhy_100[[i]], col=colThisStudy, lwd=1) #grey(0.5,alpha=0.4)
}
ltt.lines(mamMCC, col="black", lwd=2)
# FS2015
for(i in 1:length(FS2015_100)){
ltt.lines(FS2015_100[[i]], col=colFS, lwd=1) #rgb(1,0,0,alpha=0.4)
}
par(new=TRUE)
#HEDGES
ltt.lines(Hedges_phySmooth, col=colHedges, lwd=2) #"goldenrod1"
rect(xleft= 0, ybottom=1, xright=10, ytop=6000, angle = 90, col = "white", border = "white", lwd=3)
#ltt.plot(KuhnEtAl_100[[1]], log="y", col=rgb(0,0,1,alpha=0.5), lwd=1, xlim=c(-100,0), bty="n",ylab="log ( Lineages )")#, ylim=c(4,5500))
#legend(x= -100, y= 6500, legend=c(" ","Supertree w/ polytomies", "","Supertree resolved credible set"," ",
# "Supertree resolved credible set", " ", "Consensus timetree smoothed", " ",
# "Backbone-and-patch credible set", "Backbone-and-patch MCC"),
# col=c(NA, colBE, NA, colKuhn,NA, colFS,NA, colHedges,NA, "goldenrod1","black"), #col=c(NA, "purple", NA, "blue",NA,"red",NA,"goldenrod1",NA,grey(0.5),"black"),
# lwd=2, lty=1, cex=0.7)
#text(x= -98, y= 4900, label="Bininda-Emonds et al. 2007", font=2, cex=0.7, adj=0)
#text(x= -98, y= 2550, label="Kuhn et al. 2011", font=2, cex=0.7, adj=0)
#text(x= -98, y= 1350, label="Faurby and Svenning 2015", font=2, cex=0.7, adj=0)
#text(x= -98, y= 720, label="Hedges et al. 2015", font=2, cex=0.7, adj=0)
#text(x= -98, y= 400, label="This study", font=2, cex=0.7, adj=0)
legend(x= -100, y= 6500, legend=c(" ","Bininda-Emonds et al. 2007 (one tree)", "Kuhn et al. 2011 (set of trees)"," ","Faurby & Svenning 2015 (set of trees)",
" ", "Hedges et al. 2015 (one tree)", " ",
"This study (set of trees)", "This study (MCC tree)"),
col=c(NA, colBE, colKuhn,NA, colFS,NA, colHedges,NA, "goldenrod1","black"), #col=c(NA, "purple", NA, "blue",NA,"red",NA,"goldenrod1",NA,grey(0.5),"black"),
lwd=2, lty=1, cex=0.7)
text(x= -98, y= 4900, label="MRP supertree", font=2, cex=0.7, adj=0)
text(x= -98, y= 1850, label="DNA supertree", font=2, cex=0.7, adj=0)
text(x= -98, y= 1030, label="Consensus timetree", font=2, cex=0.7, adj=0)
text(x= -98, y= 520, label="Backbone-and-patch", font=2, cex=0.7, adj=0)
dev.off()
##
# Plot just the RODENTIA portions...
###
# plot each big tree with node labels numbered and TIPS
pdf(file=paste0(RESDIR,"comparing_MamPhys_fullplots_nodeNumsTips.pdf"), width=120, height=100, onefile=TRUE)
par(oma = rep(3,4) + 0.1,
mar = c(4,1.5,4,1) + 0.1) #‘c(bottom, left, top, right)’
layout(matrix(1:6,1,6, byrow=TRUE))#,widths=rep(0.25,4),heights=rep(,4))
plot(ladderize(KuhnEtAl_100[[1]]), cex=0.2, label.offset=1)
nodelabels(cex=0.2)
mtext(side=3, "Kuhn 2011 tree 1 of 100", cex=5)
plot(ladderize(BE_etAl_phy), cex=0.2, label.offset=1)
nodelabels(cex=0.2)
mtext(side=3, "BE2007 1 tree ", cex=5)
plot(ladderize(FS2015_100[[1]]), cex=0.2, label.offset=1)
nodelabels(cex=0.2)
mtext(side=3, "FS2015 tree 1 of 100", cex=5)
plot(ladderize(Hedges_phySmooth), cex=0.2, label.offset=1)
nodelabels(cex=0.2)
mtext(side=3, "Hedges 1 tree", cex=5)
plot(ladderize(mamPhy_100[[1]]), cex=0.2, label.offset=1)
nodelabels(cex=0.2)
mtext(side=3, "MamPhy tree 1 of 100", cex=5)
plot(ladderize(mamMCC), cex=0.2, label.offset=1)
nodelabels(cex=0.2)
mtext(side=3, "MamPhy MCC", cex=5)
dev.off()
# GET TAXON LISTS & PRUNE
###
# BE_etAl_phy --
# Rodentia -- node 4520
toKeep<-as.vector(na.omit(BE_etAl_phy$tip.label[getDescendants((BE_etAl_phy), node=4520)]))
toDrop<-setdiff(BE_etAl_phy$tip.label,toKeep)
BE_Rodentia<-drop.tip(BE_etAl_phy,toDrop)
# Chiroptera -- node 5842
toKeep<-as.vector(na.omit(BE_etAl_phy$tip.label[getDescendants((BE_etAl_phy), node=5842)]))
toDrop<-setdiff(BE_etAl_phy$tip.label,toKeep)
BE_Chiroptera<-drop.tip(BE_etAl_phy,toDrop)
# Primates -- node 5259
toKeep<-as.vector(na.omit(BE_etAl_phy$tip.label[getDescendants((BE_etAl_phy), node=5259)]))
toDrop<-setdiff(BE_etAl_phy$tip.label,toKeep)
BE_Primates<-drop.tip(BE_etAl_phy,toDrop)
# Hedges_phySmooth --
# Rodentia -- node 5371
toKeep<-as.vector(na.omit(Hedges_phySmooth$tip.label[getDescendants((Hedges_phySmooth), node=5371)]))
toDrop<-setdiff(Hedges_phySmooth$tip.label,toKeep)
Hedges_Rodentia<-drop.tip(Hedges_phySmooth,toDrop)
# Chiroptera -- node 8027
toKeep<-as.vector(na.omit(Hedges_phySmooth$tip.label[getDescendants((Hedges_phySmooth), node=8027)]))
toDrop<-setdiff(Hedges_phySmooth$tip.label,toKeep)
Hedges_Chiroptera<-drop.tip(Hedges_phySmooth,toDrop)
# Primates -- node 7581
toKeep<-as.vector(na.omit(Hedges_phySmooth$tip.label[getDescendants((Hedges_phySmooth), node=7581)]))
toDrop<-setdiff(Hedges_phySmooth$tip.label,toKeep)
Hedges_Primates<-drop.tip(Hedges_phySmooth,toDrop)
# MamPhy --
# Rodentia tag
toKeep<-mamMCC$tip.label[grep(pattern="RODENTIA", x=mamMCC$tip.label, ignore.case=FALSE)]
toDrop<-setdiff(mamMCC$tip.label,toKeep)
MamMCC_Rodentia<-drop.tip(mamMCC,toDrop)
MamPhy100_Rodentia<-list()
for(i in 1:length(mamPhy_100)){
MamPhy100_Rodentia[[i]]<-drop.tip(mamPhy_100[[i]],toDrop)
}
class(MamPhy100_Rodentia)<-"multiPhylo"
# Chiroptera tag
toKeep<-mamMCC$tip.label[grep(pattern="CHIROPTERA", x=mamMCC$tip.label, ignore.case=FALSE)]
toDrop<-setdiff(mamMCC$tip.label,toKeep)
MamMCC_Chiroptera<-drop.tip(mamMCC,toDrop)
MamPhy100_Chiroptera<-list()
for(i in 1:length(mamPhy_100)){
MamPhy100_Chiroptera[[i]]<-drop.tip(mamPhy_100[[i]],toDrop)
}
class(MamPhy100_Chiroptera)<-"multiPhylo"
# Primates tag
toKeep<-mamMCC$tip.label[grep(pattern="PRIMATES", x=mamMCC$tip.label, ignore.case=FALSE)]
toDrop<-setdiff(mamMCC$tip.label,toKeep)
MamMCC_Primates<-drop.tip(mamMCC,toDrop)
MamPhy100_Primates<-list()
for(i in 1:length(mamPhy_100)){
MamPhy100_Primates[[i]]<-drop.tip(mamPhy_100[[i]],toDrop)
}
class(MamPhy100_Primates)<-"multiPhylo"
# Kuhn 2011
# RODENTIA
toKeep<-as.vector(unlist(read.table(file=paste0(dir,"KuhnEtAl2011_TAXA_Rodentia.txt"))))
toDrop<-setdiff(KuhnEtAl_100[[1]]$tip.label,toKeep)
Kuhn100_Rodentia<-list()
for(i in 1:100){
Kuhn100_Rodentia[[i]]<-drop.tip(KuhnEtAl_100[[i]],toDrop)
}
class(Kuhn100_Rodentia)<-"multiPhylo"
# CHIROPTERA
toKeep<-as.vector(unlist(read.table(file=paste0(dir,"KuhnEtAl2011_TAXA_Chiroptera.txt"))))
toDrop<-setdiff(KuhnEtAl_100[[1]]$tip.label,toKeep)
Kuhn100_Chiroptera<-list()
for(i in 1:100){
Kuhn100_Chiroptera[[i]]<-drop.tip(KuhnEtAl_100[[i]],toDrop)
}
class(Kuhn100_Chiroptera)<-"multiPhylo"
# PRIMATES
toKeep<-as.vector(unlist(read.table(file=paste0(dir,"KuhnEtAl2011_TAXA_Primates.txt"))))
toDrop<-setdiff(KuhnEtAl_100[[1]]$tip.label,toKeep)
Kuhn100_Primates<-list()
for(i in 1:100){
Kuhn100_Primates[[i]]<-drop.tip(KuhnEtAl_100[[i]],toDrop)
}
class(Kuhn100_Primates)<-"multiPhylo"
# FS2015
# RODENTIA
toKeep<-as.vector(unlist(read.table(file=paste0(dir,"FS2015_TAXA_Rodentia.txt"))))
toDrop<-setdiff(FS2015_100[[1]]$tip.label,toKeep)
FS100_Rodentia<-list()
for(i in 1:100){
FS100_Rodentia[[i]]<-drop.tip(FS2015_100[[i]],toDrop)
}
class(FS100_Rodentia)<-"multiPhylo"
# CHIROPTERA
toKeep<-as.vector(unlist(read.table(file=paste0(dir,"FS2015_TAXA_Chiroptera.txt"))))
toDrop<-setdiff(FS2015_100[[1]]$tip.label,toKeep)
FS100_Chiroptera<-list()
for(i in 1:100){
FS100_Chiroptera[[i]]<-drop.tip(FS2015_100[[i]],toDrop)
}
class(FS100_Chiroptera)<-"multiPhylo"
# PRIMATES
# Fixing the FS2015 PRIMATES...NEEDED because TARSIERS are non-ultrametric in all their trees! (need to email them the correction)
library(phangorn)
toKeep<-as.vector(unlist(read.table(file=paste0(dir,"FS2015_TAXA_Primates.txt"))))
toDrop<-setdiff(FS2015_100[[1]]$tip.label,toKeep)
FS100_Primates<-list()
for(i in 1:100){
toBeScaled<-drop.tip(FS2015_100[[i]],toDrop)
FS100_Primates[[i]]<-nnls.tree(cophenetic(toBeScaled),toBeScaled,rooted=TRUE)
}
class(FS100_Primates)<-"multiPhylo"
# PLOT the PER-STUDY-based LTTs by 3 taxa...
colRod<-plasma(10, alpha=0.3)[2]
colChir<-plasma(10, alpha=0.3)[5]
colPri<-plasma(10, alpha=0.3)[8]
colRod_2<-plasma(10, alpha=0.9)[2]
colChir_2<-plasma(10, alpha=0.9)[5]
colPri_2<-plasma(10, alpha=0.9)[8]
# COMBO
png(file=paste0(RESDIR,"comparing_MamPhys_LTT_all_COMBO_ROD-CHIR-PRI_plasma.png"), width=6, height=6, res=600, units="in")
#pdf(file=paste0(RESDIR,"comparing_MamPhys_LTT_all_COMBO_ROD-CHIR-PRI_plasma.pdf"), width=6, height=6)
par(oma = c(4,4,0.1,0.1) + 0.1,
mar = c(0.5,0.5,1,0.5) + 0.1) #‘c(bottom, left, top, right)’
layout(matrix(1:4,2,2, byrow=TRUE))#,widths=rep(0.25,4),heights=rep(,4))
# THIS STUDY (MamPhy)
###
#png(file=paste0(RESDIR,"comparing_MamPhys_LTT_all_THISSTUDY_ROD-CHIR-PRI_plasma.png"), width=6, height=6, res=600, units="in")
#pdf(file=paste0(RESDIR,"comparing_MamPhys_LTT_all_THISSTUDY_ROD-CHIR-PRI_plasma.pdf"), width=6, height=6, onefile=TRUE)#, res=400, units="in")
# ltt.plot(KuhnEtAl_100[[1]], log="y", col=rgb(0,0,1,alpha=0.5), lwd=1, xlim=c(-100,0), bty="n", ylab="", xlab="", xaxt="n",yaxt="n")#, ylim=c(4,5500))
# RODENTIA
#ltt.plot(MamPhy100_Rodentia[[1]], log="y", col=colRod, lwd=1, xlim=c(-100,0), bty="n", ylab="log (Lineages)", xlab="Time before present (Ma)")#, ylim=c(4,5500))
ltt.plot(MamPhy100_Rodentia[[1]], log="y", col=colRod, lwd=1, xlim=c(-100,0), bty="n", xaxt="n",ylab="", xlab="")#, ylim=c(4,5500))
axis(side=1, at=c(0,-20,-40,-60,-80,-100),labels=NA)#c(0,-20,-40,-60,-80,-100))
for(i in 2:100){
ltt.lines(MamPhy100_Rodentia[[i]], col=colRod, lwd=1)
}
# CHIROP
for(i in 1:100){
ltt.lines(MamPhy100_Chiroptera[[i]], col=colChir, lwd=1)
}
# PRIMATES
for(i in 1:100){
ltt.lines(MamPhy100_Primates[[i]], col=colPri, lwd=1)
}
# ltt.lines(MamMCC_Rodentia, col=colRod_2, lwd=3)
# ltt.lines(MamMCC_Chiroptera, col=colChir_2, lwd=3)
# ltt.lines(MamMCC_Primates, col=colPri_2, lwd=3)
#par(new=TRUE)
#rect(xleft= -80, ybottom=1, xright=10, ytop=2, angle = 90, col = "white", border = "white", lwd=0.1)
#dev.off()
# FS2015
###
#png(file=paste0(RESDIR,"comparing_MamPhys_LTT_all_FS2015_ROD-CHIR-PRI_plasma.png"), width=6, height=6, res=600, units="in")
#pdf(file=paste0(RESDIR,"comparing_MamPhys_LTT_all_FS2015_ROD-CHIR-PRI_plasma.pdf"), width=6, height=6)#, res=400, units="in")
# ltt.plot(KuhnEtAl_100[[1]], log="y", col=rgb(0,0,1,alpha=0.5), lwd=1, xlim=c(-100,0), bty="n", ylab="", xlab="", xaxt="n",yaxt="n")#, ylim=c(4,5500))
# RODENTIA
#ltt.plot(FS100_Rodentia[[1]], log="y", col=colRod, lwd=1, xlim=c(-100,0), bty="n",ylab="log (Lineages)", xlab="Time before present (Ma)")#, ylim=c(4,5500))
ltt.plot(FS100_Rodentia[[1]], log="y", col=colRod, lwd=1, xlim=c(-100,0), bty="n", xaxt="n",yaxt="n",ylab="", xlab="")#, ylim=c(4,5500))
axis(side=1, at=c(0,-20,-40,-60,-80,-100),labels=NA)#c(0,-20,-40,-60,-80,-100))
axis(side=2, at=c(1,5,10,50,100,500,1000),labels=NA)#c(0,-20,-40,-60,-80,-100))
for(i in 2:length(FS100_Rodentia)){
ltt.lines(FS100_Rodentia[[i]], col=colRod, lwd=1)
} # CHIROP
for(i in 1:length(FS100_Chiroptera)){
ltt.lines(FS100_Chiroptera[[i]], col=colChir, lwd=1)
}
# PRIMATES
for(i in 1:length(FS100_Primates)){
ltt.lines(FS100_Primates[[i]], col=colPri, lwd=1)
}
par(new=TRUE)
rect(xleft= 0, ybottom=1, xright=10, ytop=6000, angle = 90, col = "white", border = "white", lwd=3)
#dev.off()
# HEDGES2015
###
#png(file=paste0(RESDIR,"comparing_MamPhys_LTT_all_HEDGES2015_ROD-CHIR-PRI_plasma.png"), width=6, height=6, res=600, units="in")
#pdf(file=paste0(RESDIR,"comparing_MamPhys_LTT_all_FS2015_ROD-CHIR-PRI_plasma.pdf"), width=6, height=6)#, res=400, units="in")
# ltt.plot(KuhnEtAl_100[[1]], log="y", col=rgb(0,0,1,alpha=0.5), lwd=1, xlim=c(-100,0), bty="n", ylab="", xlab="", xaxt="n",yaxt="n")#, ylim=c(4,5500))
# RODENTIA
#ltt.plot(Hedges_Rodentia, log="y", col=colRod_2, lwd=3, xlim=c(-100,0), bty="n", ylab="log (Lineages)", xlab="Time before present (Ma)")#, ylim=c(4,5500))
ltt.plot(Hedges_Rodentia, log="y", col=colRod_2, lwd=2, xlim=c(-100,0), bty="n", ylab="", xlab="")#, ylim=c(4,5500))
ltt.lines(Hedges_Chiroptera, col=colChir_2, lwd=2)
ltt.lines(Hedges_Primates, col=colPri_2, lwd=2)
#dev.off()
# KUHN2011 and BE2007
###
#png(file=paste0(RESDIR,"comparing_MamPhys_LTT_all_KUHN2011_ROD-CHIR-PRI_plasma.png"), width=6, height=6, res=600, units="in")
#pdf(file=paste0(RESDIR,"comparing_MamPhys_LTT_all_FS2015_ROD-CHIR-PRI_plasma.pdf"), width=6, height=6)#, res=400, units="in")
# ltt.plot(KuhnEtAl_100[[1]], log="y", col=rgb(0,0,1,alpha=0.5), lwd=1, xlim=c(-100,0), bty="n", ylab="", xlab="", xaxt="n",yaxt="n")#, ylim=c(4,5500))
# RODENTIA
#ltt.plot(Kuhn100_Rodentia[[1]], log="y", col=colRod, lwd=1, xlim=c(-100,0), bty="n", ylab="log (Lineages)", xlab="Time before present (Ma)")#, ylim=c(4,5500))
ltt.plot(Kuhn100_Rodentia[[1]], log="y", col=colRod, lwd=1, xlim=c(-100,0), bty="n", yaxt="n", ylab="", xlab="")#, ylim=c(4,5500))
#axis(side=1, at=c(0,-20,-40,-60,-80,-100),labels=NA)#c(0,-20,-40,-60,-80,-100))
axis(side=2, at=c(1,5,10,50,100,500,1000),labels=NA)#c(0,-20,-40,-60,-80,-100))
ltt.lines(BE_Rodentia, col="grey", lwd=3)
ltt.lines(BE_Chiroptera, col="grey", lwd=3)
ltt.lines(BE_Primates, col="grey", lwd=3)
for(i in 2:100){
ltt.lines(Kuhn100_Rodentia[[i]], col=colRod, lwd=1)
}
# CHIROP
for(i in 1:100){
ltt.lines(Kuhn100_Chiroptera[[i]], col=colChir, lwd=1)
}
# PRIMATES
for(i in 1:100){
ltt.lines(Kuhn100_Primates[[i]], col=colPri, lwd=1)
}
title(main="",sub="", xlab="Time before present (Ma)", ylab="log (Lineages)", line=2,
outer=TRUE, cex.axis=1,cex.lab=1.2,font.axis=1, font.lab=1)
#dev.off()
dev.off()