What could be the reasons for Bayesian Inference tree having a different topology from Maximum Likelihood Tree?

Question

[anuragm]

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 ?

Answer 1

[5heikki]

Are you using the same substitution model in both cases?

[anuragm]

Yes, using GTR in both

[5heikki]

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

[Brice Sarver]

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).