I have drawn a maximum clade credibility tree using BEAST. When viewing the tree in FigTree, checking the Root box and selecting midpoint changes the years of divergence at the node of some of my taxa. I would like to know the correct way of quoting the divergence times since the years are different. Which one do I use?
The divergence times in a phylogenetic tree are all relative to the root. When you change the root, which is considered your point of reference, then the times of divergence will change to reflect their distances from that new point of reference.
This is why a species sequence which is outside your intended group of study is often used in a phylogenetic analysis as the root. If you have included such a species in your analysis I would suggest you use it as your root. If you haven't, then it might be worth redoing.
Read here for some information about rooting:
http://cabbagesofdoom.blogspot.fi/2012/06/how-to-root-phylogenetic-tree.html
http://cabbagesofdoom.blogspot.fi/2012/06/how-to-root-phylogenetic-tree.html
The relaxed clock algorithm in BEAST has an interesting way of rooting and there are two options - I don't know what kind of analysis you were doing!
1. You were inferring the age of divergence between species based on a clock rate or some fossil calibration and the tree is ultrametric (all tips align in the present). In that case BEAST infers the root itself - you actually don't need to use an outgroup! I would suggest leaving the tree as is.
2. You work with microbes sampled over years and infer the rate of the clock from the differences, in which case the tips will not be aligned, but they should still fit with a time access. Again, I probably wouldn't change the rooting. Generally FigTree roots the BEAST trees the way they should look.
I would advise to only change the rooting if you have a non-ultrametric (and thus not BEAST) tree. IMHO...
Good luck!
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