Concordance factor

[Minh Bui]

Dear Users,

We’d like to draw your attention to a new feature in IQ-TREE v1.7 (currently in beta release): The concordance factor allows you to assess the (dis)agreement between species tree and gene trees. We implemented two measures of gene concordance factor (gCF) and the new site concordance factor (sCF), that quantify the concordance at gene- and site-level, respectively. We also provide a new option to infer gene trees separately. The preprint is available at

https://www.biorxiv.org/content/early/2018/12/05/487801.

And a Tutorial for how to use these features:

http://www.iqtree.org/doc/Concordance-Factor

Cheers
Minh, Matt Hahn and Rob Lanfear

[brucea...@gmail.com]

Hi, I very much like the gcf and scf option but I'm struggling to understand exactly which gene trees would be considered both decisive and concordant.

Suppose I have a branch in the species tree with four clades around it, each containing four taxa, {A1,A2,A3,A4 ∪ B1.B2,B3B4}|{C1,C2,C3,C4 ∪ D1,D2,D3,D4}. Now,as I understand from the explanation, a gene tree is "decisive" for this branch if all these four clades A,B,C and D are non-empty. And a concardant gene tree has the same bipartition of these clades as the species tree.

However, what if a genetree has a topology that mixes taxa from the clades, so that, for example, the new topology is {A1,A2,C1,C2 ∪ B1.B2,B3,B4}|{C3,C4,A3,A4 ∪ D1,D2,D3,D4}? Is this topology concordant or not with the species tree?

In general, my question is how are the clades defined and mapped between the species tree and gene tree when the taxa vary in presence and topological position?

Many thanks.

[Bui Quang Minh]

Hi there,

It is not concordant with the species tree.

Cheers,

Minh

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[Bruce Murphy]

Thank you for your answer. Am I right in thinking that because a single misplaced branch may be sufficient to make a genetree discordant, therefore the probability of concordant branches diminishes with more tips in the relevant clades or trees and gcf values will be lower? (Similarly to the way bootstrap values tend to be lower when more tips are involved). 

(This was sent from my phone).

[Minh Bui]

Yes that's right. When some tips moved away from its “usual” clade to the other side (e.g. some C go to A in your case), then it makes the gene tree discordant with the species tree (same with standard bootstrap).

Cheers

Minh