From: rokimoto557@gmail.com   
      
   On 6/30/2025 10:02 PM, John Harshman wrote:   
   > On 6/30/25 1:32 PM, RonO wrote:   
   >> On 6/30/2025 1:44 PM, John Harshman wrote:   
   >>> On 6/30/25 9:01 AM, RonO wrote:   
   >>>> https://evolutionnews.org/2025/06/on-human-chimp-genetic-   
   >>>> differences- the-critics-misstate-my-arguments/   
   >>>>   
   >>>> He is claiming that his critics are not addressing his claims or   
   >>>> misstating them.  Luskin is falsely claiming that the 1% difference   
   >>>> between chimp and human genomic DNA that had been determined for the   
   >>>> sequence that was compared in order to determine the evolutionary   
   >>>> relationship between extant life forms is some type of Icon of   
   >>>> evolution.  It is just what the sequence difference was.  It wasn't   
   >>>> the 1% number that determined that chimps are the most closely   
   >>>> related species to humans it was how that 1% difference related to   
   >>>> all the other species that we had the same sequence for and could   
   >>>> compare them.   
   >>>>   
   >>>> Coding sequence is still 0.7% different between chimps and humans,   
   >>>> and the sequence around the genes that we can compare are between 1   
   >>>> and 1.8% different.  We can't use a lot of the sequence around the   
   >>>> coding sequence to compare extant species to each other because it   
   >>>> is so different between species that we can't compare it   
   >>>> accurately.  I took around 800 base-pairs of the tyrosinase exon 1   
   >>>> coding sequence and the following 900 base-pairs of the first   
   >>>> intron.  Chimps and humans were 99% similar by BLAST for this   
   >>>> sequence.  Green monkey was 95% similar for the sequence compared to   
   >>>> humans, but the coding sequence was less than 3% different and the   
   >>>> intron sequence was almost 9% different (there were also a couple of   
   >>>> indels in the intron).  I tried the same sequence for mouse and   
   >>>> BLAST would not align the intron sequence.  It was just too   
   >>>> different.  Even under BLAST for more relaxed conditions it would   
   >>>> only align bits of the intron in around 60 base-pair pieces where   
   >>>> there was enough similarity where they might be the same sequence   
   >>>> (many of these short matches were not the same sequence and were on   
   >>>> other chromosomes of the genome assembly).  The 826 base-pairs of   
   >>>> coding sequence was 87% similar, but the intron sequence was not   
   >>>> matched up. It might be expected to be around 60% similar if you   
   >>>> could align it, but any alignment likely would not be that accurate.   
   >>>>   
   >>>> This just means that the sequence that we determined to be around 1%   
   >>>> different (coding sequence) is the sequence that would be used to   
   >>>> determine evolutionary relationships between mammals.  It is the   
   >>>> sequence that can be used to determine that chimps are the most   
   >>>> closely related species to humans that exist on this planet today.   
   >>>> But outside of mammals the accuracy of coding sequence decreases   
   >>>> because of the degenerate code and multiple substitutions at the   
   >>>> third position of codons that you can't tell if they have been   
   >>>> mutated multiple times or not.  You can only use noncoding sequence   
   >>>> like introns to compare closely related taxa because they change too   
   >>>> fast to be useful.   
   >>>   
   >>> All fine except for that last bit. Introns and other junk sequences   
   >>> are perfectly useful to considrable phylogenetic depth. They work for   
   >>> the deepest divergences in birds, for example, and I imagine they   
   >>> work for pretty deep divergences in mammals too, certainly for all   
   >>> primates.   
   >>   
   >> That is what I meant when I wrote that "You can only use noncoding   
   >> sequence like introns to compare closely related taxa because they   
   >> change too fast to be useful."  I just didn't put in useful to   
   >> descriminate deeper divergences.   
   >   
   > Perhaps we have different understandings of "closely related". Are all   
   > mammals closely related?   
      
   No.  I did not mean as deeply as you seem to be claiming.  I noted that   
   the human and mouse intron sequence could not be matched up.  Humans and   
   mice separated before a lot of avian lineages in terms of time of   
   separation, but not by much, and you can't use introns for any accurate   
   type of phylogenetic analysis for such mammalian lineages.  Birds seem   
   to be a separate case.  The introns are shorter and more conserved in   
   some of the sequence.  I knew that they used intron sequences in the   
   phylogenetic analysis to place some avian lineages, but it was not for   
   the deepest branch nodes.   
      
   I checked the same Tyrosinase intron sequence that could not be matched   
   up between mice and humans for chickens and pigeons, and about 1/3 of   
   the sequence was likely not good for phylogenetic analysis (60%   
   similarity with multiple indels to make those matches) but the other 2/3   
   was as high as 80% similar for 60 bp stretches with only a few indels,   
   so you could pick intron sequences that you could still align.  I   
   wouldn't like to maximize sequence similarity by inserting indels for   
   intron sequence.  The conserved regions likely averaged 75% similarity.   
      
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