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From: John Harshman <john.harshman@gmail.com>
Newsgroups: talk.origins
Subject: Re: New type of phylogenetic analysis
Date: Thu, 1 Aug 2024 17:14:59 -0700
Organization: University of Ediacara
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On 8/1/24 12:05 PM, RonO wrote:
> 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.

Not necessarily. There are in fact likelihood models that allow base 
composition to vary over time, and even to do so convergently in 
different lineages. They can actually help to estimate phylogeny better 
when base composition has changed, as when a gene moves from an AT-rich 
genomic region to a GC-rich one.