Path: ...!2.eu.feeder.erje.net!feeder.erje.net!feeds.news.ox.ac.uk!news.ox.ac.uk!nntp-feed.chiark.greenend.org.uk!ewrotcd!news.eyrie.org!beagle.ediacara.org!.POSTED.beagle.ediacara.org!not-for-mail
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
Lines: 32
Sender: to%beagle.ediacara.org
Approved: moderator@beagle.ediacara.org
Message-ID: <E9icnc7BV66euDH7nZ2dnZfqlJ-dnZ2d@giganews.com>
References: <v8gmal$2b76f$1@dont-email.me>
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8; format=flowed
Content-Transfer-Encoding: 8bit
Injection-Info: beagle.ediacara.org; posting-host="beagle.ediacara.org:3.132.105.89";
	logging-data="15053"; mail-complaints-to="usenet@beagle.ediacara.org"
User-Agent: Mozilla Thunderbird
To: talk-origins@moderators.isc.org
Return-Path: <poster@giganews.com>
X-Original-To: talk-origins@ediacara.org
Delivered-To: talk-origins@ediacara.org
	id 625E6229782; Thu, 01 Aug 2024 20:15:00 -0400 (EDT)
	by beagle.ediacara.org (Postfix) with ESMTP id 4471E229765
	for <talk-origins@ediacara.org>; Thu, 01 Aug 2024 20:14:58 -0400 (EDT)
	id 20A545DC29; Fri,  2 Aug 2024 00:15:31 +0000 (UTC)
Delivered-To: talk-origins@moderators.isc.org
	by mod-relay-1.kamens.us (Postfix) with ESMTP id 13DF85DC26
	for <talk-origins@moderators.isc.org>; Fri,  2 Aug 2024 00:15:31 +0000 (UTC)
	by egress-mx.phmgmt.com (Postfix) with ESMTP id A6E816037D
	for <talk-origins@moderators.isc.org>; Fri,  2 Aug 2024 00:13:30 +0000 (UTC)
	by serv-4.ord.giganews.com (Postfix) with ESMTP id D8F4B44069B
	for <talk-origins@moderators.isc.org>; Thu,  1 Aug 2024 19:14:59 -0500 (CDT)
	by serv-4.i.ord.giganews.com (8.14.4/8.14.4/Submit) id 4720Ex8e057050;
	Thu, 1 Aug 2024 19:14:59 -0500
X-Authentication-Warning: serv-4.i.ord.giganews.com: news set sender to poster@giganews.com using -f
X-Path: news.giganews.com.POSTED!not-for-mail
X-NNTP-Posting-Date: Fri, 02 Aug 2024 00:14:59 +0000
Content-Language: en-US
In-Reply-To: <v8gmal$2b76f$1@dont-email.me>
X-Usenet-Provider: http://www.giganews.com
X-Original-Complaints-To: abuse@giganews.com
X-DMCA-Notifications: http://www.giganews.com/info/dmca.html
X-Abuse-and-DMCA-Info: Please be sure to forward a copy of ALL headers
X-Abuse-and-DMCA-Info: Otherwise we will be unable to process your complaint properly
X-Postfilter: 1.3.40
Bytes: 4283

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.