Question: What could be the reasons for Bayesian Inference tree having a different topology from Maximum Likelihood Tree?
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gravatar for anuragm
5.6 years ago by
anuragm130
India
anuragm130 wrote:

I am trying to look at evolutionary relationships using BI and ML trees. If I have 3 different evolutionary lineages BI gives a node between lineages 1 and 2 (1 and 2 diverged from a common ancestor) whereas ML gives a node between lineages 2 and 3 (2 and 3 diverged from a common ancestor). What could be the possible reasons for this ?

ADD COMMENTlink modified 5.6 years ago by 5heikki9.0k • written 5.6 years ago by anuragm130
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gravatar for 5heikki
5.6 years ago by
5heikki9.0k
Finland
5heikki9.0k wrote:

Are you using the same substitution model in both cases?

ADD COMMENTlink written 5.6 years ago by 5heikki9.0k

Yes, using GTR in both

 

ADD REPLYlink written 5.6 years ago by anuragm130
1

And are the likelihood/confidence values for the conflicting nodes robust (at least 80)?

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by 5heikki9.0k

This is the crux here. OP says nothing about assessing statistical support or how they went from a posterior distribution of trees to a consensus/MCC tree in the Bayesian approaches. If they are high and the topologies disagree, perhaps the dataset is difficult to resolve, there could be methodological bias, or branch lengths are short (among lots of other things).

ADD REPLYlink written 5.6 years ago by Brice Sarver3.5k
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