Re: More stupid denial about DNA sequence analysis

On 5/25/2025 3:54 PM, RonO wrote:

https://evolutionnews.org/2025/05/fact-check-new-complete-chimp-genome- shows-14-9-percent-difference-from-human-genome/
 The ID perps just have to lie about how we have had to do sequence analysis to get useful information about the evolutionary relationships.   As stupid as it may be they refuse to understand that we have had to compare sequences that we could be sure were homologous.  We have always had to rely on more than just sequence similarity.  When we only had a few sequences to compare there was a big snit about the difference between sequence similarity and homology.  What has always been used for sequence analysis are the sequences that we had a good idea were homologous between species.  We have always understood that due to insertions and deletions that not all of the similar sequence had to be homologous, and that factor was always a concern for trying to align sequences for analysis.  This means that we have always not been able to deal with insertions and deletions very well, and have left the large ones out of the analysis.  We also could not compare the parts of the genome that we could not sequence accurately because they were highly repetitive or high GC and were under represented in the databases.
 Simply put in order to determine the relationship between species you need to compare sequences that all of the species have.  This means that if one species has an insertion in the sequence, the insertion cannot be used in the analysis because all the other species do not have the insertion.  Highly repetitive sequence could not be in the analysis because it could not be sequenced accurately, and was determined to have a high creation and loss rate using the old density gradient DNA analysis of satellite DNA.  This just meant that we never tried to seriously use heterochromatin in any evolutionary analysis.  You just have to look at the old data on heterochromatin to know that we knew that chimps had a lot more heterochromatin on the ends of their chromosomes than humans (I recall the estimates where that chimps had more than double the amount as humans).  This is a major part of the 13% difference that the ID perps are stupidly jumping for joy over.  Humans just do not have as much heterochromatin on the ends of their chromosomes as chimps, and what they have has been known to have a high variation rate before we could easily sequence the DNA.  These large regions of short tandem repeats have a very high mutation rate.  Most of the larger regions likely change in copy number every replication cycle.
 Telomere to telomere sequences of the ape genomes have been published.
 https://www.nature.com/articles/s41586-025-08816-3
 The article is open access.  They used the same technology that allowed the sequencing of nearly all of the human genome to sequence.  They were able to sequence through most of the large regions containing tandem repeats, but not all, and they couldn't get through all the repetitive sequence around some of the centromeres.  So what they found was a lot of basically junk DNA that is a different sequence between chimps and humans.
 All of this just doesn't matter.  The sequence analysis that places chimps as our closest relatives still stands because we used sequence that chimps and the other apes have that we could compare, like coding sequences and the noncoding regions around known genes that we could determine were the same sequences relative to their positions around known genes.  We do not have to use the sequence that we cannot reliably determine is the homologous sequence in all taxa in any particular analysis, so we still will not use the highly repetitive sequences and indels.  We cannot use sequence that chimps may have, but humans do not have and vice versa.  Chimps just have a lot more heterochromatin on the ends of their chromosomes than humans have, and the additional sequence is useless for the way sequence analysis has to be done.
 Ron Okimoto
 

What is of note is that all the ape genomes were larger than the telomere to telomere human assembly (3.055 Gb).  The human sequence would contain all the duplications and transposon and viral insertions that occurred after we shared a common ancestor with the other ape lineages (the other apes would not have these sequences in their genomes).  Just as humans do not have the duplications, and transposon and viral insertions that occurred in the other ape lineages after we split from a common ancestral population.  Heterochromatin evolves very rapidly in size and tandem repeat sequence.  Apes have been known to have a lot more heterochromatin at the ends of their chromosomes than humans for a very long time.
Chimps (3.14 Gb), Bonobo (3.21 Gb), Gorilla (3.55 Gb), Bornean orangutan (3.16 Gb), Sumatran orangutan (3.17 Gb), Siamang (3.24 Gb).
Just in genome length we differ from gorillas by over 13%.
Ron Okimoto