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From: RonO <rokimoto557@gmail.com>
Newsgroups: talk.origins
Subject: New type of phylogenetic analysis
Date: Thu, 1 Aug 2024 14:05:57 -0500
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https://www.science.org/doi/10.1126/sciadv.adp0114

This paper is trying to identify the genomic changes that occurred 
within 5 million years of the Cretaceous extinction event that ended the 
lineages of nonavian dinos.  They are trying to figure out what changes 
occurred during this period of rapid diversification of birds.

They claim to be able to detect changes in base composition of 
mitochondrial and genomic sequence.  From their own figure 1 I do not 
know if they have enough nodes to be able to figure out what changes 
occurred during this 5 million year period.  You need a lot of branch 
points to be able to predict what the ancestral sequence was and you 
need them well spaced down through the lineages back to the convergence 
that you are trying to figure out what the sequence was.  They claim 
that they have figured out how to relax the assumption of no change in 
DNA base composition as the lineage evolves, and can estimate when base 
composition of the genomic sequences was changing.

All they have are the base compositions of the extant genomic sequences, 
and they are trying to figure out what the base compositions were in the 
past.  A neat trick if they can do it since predicting the past sequence 
using extant sequences uses the assumption that the base composition was 
the same in the past.

Ron Okimoto