Question: Correspondence between unlabeled/different tips of different phylogenetic trees
gravatar for rfm
2.8 years ago by
rfm0 wrote:


I've been thinking about and searching for strategies to combine information of phylogenetic trees. My problem is a little different than what is usually done. Suppose I have 2 phylogenetic trees, constructed from sequences of 2 different loci (each tree from one single locus). I know that the trees were obtained from the same organisms, but I don't know the correspondence between the tips of the trees. That means that the trees can be considered as unlabeled or having different labels.

What I want to figure out, is a way to match tips from one tree with tips from the other tree so that in the end I get as close as possible of having sets of 2 tips each, one from one tree and one from the other that are from the same species, meaning that by comparing the trees in some way I could match sequences from different loci without knowing their order or having a common labeling.

Imagine that this represents the tips of the trees:

species1_locusA    species4_locusB
species4_locusA    species1_locusB
species2_locusA    species3_locusB
species3_locusA    species2_locusB

I only know that one tree is from locus A of 4 species and the other tree is from locus B of the same species. They don't have labels or have different labels so I can't match things by labels. Due to tree discordance and use of different loci, the trees won't match in terms of topology but might have some similarities.

Does anyone know a way to start looking into this or know some research that might help? As far as I've seen, most programs need trees with the same labels or a correspondence between labels.

Thanks in advance for any help.

ADD COMMENTlink written 2.8 years ago by rfm0

It seems like a graph matching problem to me.

ADD REPLYlink written 2.8 years ago by Jean-Karim Heriche24k

Thanks for the suggestion. I don't know much about graphs but I'll definitely look into that to see if it helps.

ADD REPLYlink written 2.8 years ago by rfm0

Do you actually know the species corresponding to each tip on each tree, or are they unknown?

ADD REPLYlink written 2.8 years ago by Selenocysteine600

I don't know the species corresponding to each tip. I only know that the tree is from one locus and that the group and number of species in both trees should be the same. Identity of tips is uncertain. I don't know if I can somewhat identify signals in the trees topologies that can actually help.

ADD REPLYlink written 2.8 years ago by rfm0
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