Existing Phylogenetic Trees Generated For Eukaryotes Using Degenerate Sites From Alignments

Question

[kajendiran56]

Dear All, I was wondering if there are any existing phylogenetic trees generated where entire eukaryotic genomes have been aligned. I am not an expert in evolution but I am aware that a tree with accurate branch lengths can be created using degenerate sites extracted from such an alignment, and thus whilst do not have the computational resource to conduct such alignments, maybe they already exist?

Thank you in advance

Answer 1

[Josh Herr]

The answer to your question (as far as I am aware) is no. No one has generated phylogenetic trees from existing whole Eukaryotic genome alignments.

This question has come up numerous times here for Help With Multiple Whole Genome Alignment. Aligning Over 400 Whole Genomes, Pairwise Genome Alignment, and almost identical questions to yours about whole genome alignment and phylogenetics from Whole Genome Phylogeny and Phylogenetic Analysis Of Whole Genomes. Please read these posts for more information on your question.

I have a question for you: Given that you can construct a highly robust phylogenetic tree from dozens of standardized markers in a reasonable amount of time for Eukaryotes, why would you want to construct a phylogenetic tree of the entire genome when computationally this would take a ridiculous amount of time and most of the data would be uninformative?

[kajendiran56]

Hi there, sorry for the delay. Thanks for pointing out the other posts. Regarding your question, what you say makes sense, using markers will cut down the processing time and in honesty I had not thought of this approach. One question however is would omitting the majority of the data produce a tree that would markedly differ from one where the entire genome was aligned? Thank you for your time

[Josh Herr]

Of course you'd be limiting data by focusing on markers, but you need to find the right signal to noise ratio. You could spend your whole life collecting data for a single experiment. The point I was trying to make is that you could save a lot of time by focusing on a series of phylogenetically informative markers (you'd have to decide this based on your own analysis and those of others) instead of trying to analyze entire genomes. When you're using a whole genome alignment you'll have so much uninformative data you might actually get a more robust analysis by just looking at your suite of genes. Genome rearrangements would be quite informative, but these could be coded in a phylogenetic data matrix along with your suite of genetic data.

If you still unsure, try it yourself using both a suite of markers and then our whole genome alignments and show both phylogenies with some comparative statistical measures.

[kajendiran56]

Sorry for not getting back until now. Thank you for your help, I appreciate your time.