Hello,
suppose I have constructed a phylogenetic tree with all OTU sequences and reference sequences. I now want to have a tree containing only the OTU sequences. Is it a good practical to remove the reference sequences from the original tree? Will such handling interfere the topology/clustering of the OTU sequences.
I read somewhere in web stating "Deleting nodes from phylogenies is risky business! Deleting nodes is unlikely to give you the same phylogeny as re-running the tree with the corresponding sequences removed." how will node deleting interfere with the clustering alone? Are there relevant literatures on this matter?
Thank you in advance and best regards
There is not enough information to give any exact suggestions. But in general, any removing or adding taxa into a phylogenetic tree can affect to its topology. These changes are in relation to math model used for a phylogenetic tree construction, general number of OTUs and general variability changes in sampling caused by such deletion.
Hello,
taxon sampling is known to affect the accuracy of inferred phylogenies. The main reason is that additional taxons may break some long branches of the tree and reduce problems caused by homoplasy
http://materiais.dbio.uevora.pt/Evo/A_review_of_long-branch_attraction.pdf
http://www.plantsystematics.com/qikan/manage/wenzhang/jse08016.pdf
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000602
I hope this help,
sincerely
Hi Vincent,
Nice papers to get some understanding. Why I have the impression that more sequences / taxa yield better phylogenetic inference. The problem I am currently dealing with is OTUs of some bacterial functional gene homologues. The dataset has been processed by mothur and contains OTUs with at least 5% sequence differences between each other, and reference sequences from NCBI.
provided my impression is right, it should be ok or even better to construct phylogenetic trees will All available sequences and then prune the tree down to one tree containing only the sequences/taxa that I am interested. Am I right or I get it wrong?
Best wishes
Hello Yiyu,
I deem that your suggestion to use all available sequences for the construction of the phylogenetic tree and then prune the outgroup (reference) sequences ia a good idea. Outgroups are very important in the construction of a tree; if you do not include them in the phylogenetic analysis, the overall topology of the tree will change.
If you are using Dendroscope for tree visualization, then you can simply collaple the "outgroup" node.
However, you can try re-constructing the tree using different sequences and see what you get.
Regards
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