Question: What Makes A Phylogenetic Tree Interesting?
gravatar for Michael Dondrup
7.1 years ago by
Bergen, Norway
Michael Dondrup48k wrote:

... or how to automatically detect "novelty" in phylogenetic trees?

Today, I have a question about one of my weak spots, phylogenetics, sorry if it is a bit vague.

Imagine we have a set (>10k) of automatically generated (unrooted) trees for groups of homologous genes for a newly sequenced organism. Assume the tree generation is more or less sane (which is possibly not true for all trees ;) ).

  • Which could be criteria to screen for genes with "interesting" characteristics in their trees for further study? Looking for indicators e.g. of horizontal gene-transfer, co-evolution, convergent evolution, or differences in selective pressure, etc.
  • Which could be good criteria for filtering out crap trees (which I am sure exist, for example those looking like a comb, all branches have equal length, possibly because of errors in orthologue selection).
  • Which algorithm or software could be used to accomplish the above?

My ideas:

  • Define a consensus evolutionary tree (either from literatures or set of selected genes or all genes) and calculate tree difference (e.g. Robinson-Foulds metric). Possibly normalize by number of branches?
  • Use taxonomic information, e.g. to detect "out-of-clade" trees, where "my organism" is situated closest to members of a different clade than it has been classified in.

I searched for +"novelty detection" phylogenetic tree and similar terms but I didn't spot an article where this was applied automatically.

phylogenetics evolution tree • 2.2k views
ADD COMMENTlink modified 7.0 years ago by Biostar ♦♦ 20 • written 7.1 years ago by Michael Dondrup48k
gravatar for Biojl
7.1 years ago by
Biojl1.7k wrote:

Maybe you want to take a look at the first part of this paper:

Genome-wide signatures of convergent evolution in echolocating mammals

ADD COMMENTlink written 7.1 years ago by Biojl1.7k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2040 users visited in the last hour