Off topic:phylogenetic analyses in R program

Question

[slx865004802]

I compared two phylogenetic trees based on two different genes via Shimodaira–Hasegawa tests in R program. Here is the code:

library(ape)
library(phangorn)
tr1 <- read.tree("ND1_besttree.out")
PCGstr <- read.tree("PCGs_besttree.out")
phyDat1 <- read.phyDat("ND1.phy")
PCGsphyDat <- read.phyDat("PCGs.phy")
fit1 <- pml(tr1, phyDat1)
fit2 <- pml(PCGstr, PCGsphyDat)
X <- SH.test(fit1, fit2, B=10000)
X

And here are the results:

     Trees      ln L      Diff ln L    p-value
[1,]   1     -24837.17    195.1926     0.0000
[2,]   2     -24641.98     0.0000      0.5079

I am a beginner in R and phylogeny. I wonder how to analyse the result and how to calculate ΔLn L? And I want to know if any significant differences between the two trees. Thanks very much for your help!