Hello,
I have identified clades with fair support values (BI >0.7) in my backbone tree. I would like to reinforce these supports so I rebuilt ingroup trees for each of the clades using their respective sister and basal groups as outgroups, and using more markers. The ingroup tree contains only a subset of individuals of the clade due to sample and seqeunce availability, but it does encompass all of the subclades. Suppose the ingroup and the backbone trees share the same topology, is it reasonable for me to substitute the backbone branch support with that of the ingroup? (with annotation noting that the branch support is reinforced by a ingroup tree)
Thank you very much in advance!
Briefly, the answer is no, you should not substitute these support values. First, your motive should not be to increase the apparent support for the prospective clades but to examine whether they are correct in the first place. If the support values are not very strong, it might not be due to lack of data but instead occur because the identified clades are incorrect or else ambiguous due to factors such as incomplete lineage sorting.
Second, the stronger support with the subsets of samples is probably due simply to having fewer taxa in the tree that could come out in different places in different bootstrap or MCMC samples, and not necessarily because you've added more marker or sequence data.
It is unclear from your explanation what kind of data you are using (genome-wide markers? gene sequences?), what your OTUs represent (different species and/or multiple samples within identified species?), your tree construction methods, and whether your support comes from bootstrap values or Bayesian posteriors.
David L Remington Thank you for your comments.
I am building a genus/species-level tree of a family using three genes for the backbone, and both ML and BI. Instead of substituting the support values, how about I keep all the trees (perhaps in the appendix), and create a summary dendrogram without showing the support to give a general picture about the most probable grouping that can be obtained? I am thinking of highlighting the poorly supported branches in grey and those additionally supported or further resolved by ingroup trees in red. In this case, the building of ingroup trees will also be based on all of the taxa (or approaching all) in the clade.
@LaHim, I think that approach makes sense overall. I would also suggest including the actual support values on the summary tree that are over some threshold (e.g. 60%). With the subtrees, it sounds like there is a trade-off between including additional sequence data vs. not including some taxa within the presumed clades because data are not available. There's no single right answer to how to make that decision, but I would avoid simply picking the combination that gives you the highest support values.
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