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Author | Topic: Why is evolution so controversial? | |||||||||||||||||||||||
zaius137 Member (Idle past 3409 days) Posts: 407 Joined: |
Good post....
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zaius137 Member (Idle past 3409 days) Posts: 407 Joined: |
quote: I am sure this is accurate for what genes this paper looked at. These numbers do vary from paper to paper according to the focus of the researchers.
quote: I agree for the gene segments analyzed.
quote: I would say you can not get to 5% from 1.33% in these results. Like I say, different findings for different genes investigated. Here is a paper comparing different genes ( it covered exclusively chromosome 21 in humans and chromosome 22 in chimps) high-quality BAC clone sequences of the homologous chimpanzee chromosome 22 quote.
In 5% of the chimpanzee genes, indels or substitutions caused premature stop codons that rendered the affected transcripts nonfunctional. Taken together, our findings demonstrate that indels comprise the majority of the genomic divergence. Furthermore, indels occur frequently in coding sequences. Our results thereby support the hypothesis that indels may have a key role in primate evolution. Comparative Genomic Analysis of Human and Chimpanzee Indicates a Key Role for Indels in Primate Evolution | SpringerLink quote: Fine for the segments selected by the authors Here is a link to the paper again that promotes 5% sequence divergence. Comparative Genomic Analysis of Human and Chimpanzee Indicates a Key Role for Indels in Primate Evolution | SpringerLink Here is a shameless repost of the calculation I did with only using indel variables from the proceeding paper and reduced mutation rate for indels.
2.37% -1.52% Gives ~.8% for human and chimp divergence concerning indels this seems low but it must be true. Subbing in for indels gives: t= number of generations since divergence (Generation =20 years)k= percentage of autosomal sequence divergence Estimated at .8% (for indels) Ne= effective size of population ~10^5 (u)=mutation rate 2 x 10^-9 (for indels) t= .5(k/u-4Ne) from Estimate of the Mutation Rate per Nucleotide in Humans | Genetics | Oxford Academic t = 1.8 million generations or 36 million years since divergence considering indels. So the HCLCA was about 36 million years ago. (u) for substations is ~70 per generation. 1/7 (u) makes (u’) = 10 mutation per generation in humans for indels only. (u’) is calculated by (10/6.4x10^9 ~ 2x 10^-9). (u’) for indels is ~ 2x10^-9. In using the empirical value of measured mutation rate and assuming 1/7(u) for indels. As I have stated over and over indel and substitution rates are addable. They both reflect autosomal sequence divergence for the (k) in the calculation in question.
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zaius137 Member (Idle past 3409 days) Posts: 407 Joined: |
quote: Just what I was looking for. thanks.
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zaius137 Member (Idle past 3409 days) Posts: 407 Joined: |
Just for one minute, step back and take a overall picture.
Do you see what is driving these large divergence times? The big deal is the rate of mutation Indels rate of occurrence is slower than that of substitutions. Also the relevance of indels to human chimp divergence is only growing with new research. This is that perfect storm I mentioned way back in the posts. Regardless if you say I am misusing Nachman and Crowell’s paper. The trend is that Paleoanthropology and genetics are becoming more discordant with time. This is not supposed to happen with a healthy theory. It is evolution in decline.
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zaius137 Member (Idle past 3409 days) Posts: 407 Joined: |
quote: Look my friend not all the differences they found ended up in the percentage of autosomal variance. If they counted all divergence, humans and chimps would have a similarity less than 70%. About 700 million base pair did not even align at that time (that is .7/6.2 or about 11% of the two genomes). I have no problems with the findings except the same old 1.5% divergence (that is an interpretation). Face the fact that interpretive comparisons are a bit more than a cherry pick (especially this one). Let us talk about papers written after the initial sequencing back in 2005 for further new and hopefully more objective interpretation.
quote: So you will accept the initial sequencing interpretation over all subsequent papers? Sorry I do not
quote: And indels do the difference in mutations per site. (divergence in) Mutaions per site (k)/ mutations per site per generation (u) = generations t=.5(k/u-4Ne) which gives t the units of generation. Your argument is moot.
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zaius137 Member (Idle past 3409 days) Posts: 407 Joined: |
quote: Good count of mutations is (1) this gives (1) mutation per site. (k) = number of mutations different between species / number of sites In this case: Number of mutations = 1 Number of sites = 1 1/1 = 100% in this case. Now given 2 sites... Given 2 sites with 1 mutation. Number of mutations = 1 number of sites =2 percent divergence = 1/2 or 50%. Get it, Got it Mutations per site..
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zaius137 Member (Idle past 3409 days) Posts: 407 Joined: |
Good post... Too early for cheers.
Well maybe not in your case... Cheers!
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zaius137 Member (Idle past 3409 days) Posts: 407 Joined: |
quote: Believe it or not sfs and I have hashed this out over a year ago. I never claimed 0% homology. By the same token sfs could not claim (100%) homology. It is as I have argued here, what are the important genes and how different are they? Edited by zaius137, : No reason given.
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zaius137 Member (Idle past 3409 days) Posts: 407 Joined: |
You are wearing a hole in the carpet my friend...
Site identified, site compared. Site unidentified site not compared.
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zaius137 Member (Idle past 3409 days) Posts: 407 Joined: |
quote: I was very carful to claim that it could be as high as 70%, not that it was.
quote: Are pseudogenes important? My only complaint here it the ~1.5% divergence.
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zaius137 Member (Idle past 3409 days) Posts: 407 Joined: |
quote: I remember I maintained a point on several issues. If I remember correctly, your little program you wrote was using asexual reproduction rates contrary to our sexual reproduction discussion, your similarity in protein coding segments was not using the poisson distribution like you should have. etc. The past is the past, I always say....Ohh... by the way I did prevail in the discussion on alignment.
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zaius137 Member (Idle past 3409 days) Posts: 407 Joined: |
quote: If you identified 20 sites then it is bp per bp on each segment. You have sites 7-11 100% divergent. Divergence per site is: Number of mutations = 5 Number of sites = 20 Number of divergent sites is 5/20 or 25% divergent (75% similar). As per the definition... "compared" Mutation per site. If the site is 20 bp then you have 1 mutation per site. number of sites = 1 number of mutations = 1 divergence is 100%.. But you only compared 1 site. Would you like to use the bp per bp comparison for the entire genome? I thought you claimed that a single insertion is counted as one mutation? Are you retracting that statement? Edited by zaius137, : No reason given.
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zaius137 Member (Idle past 3409 days) Posts: 407 Joined: |
quote: Then I can use the 1/7(u) again?
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zaius137 Member (Idle past 3409 days) Posts: 407 Joined: |
quote: I understand the papers I cited claim more than 1.5% divergence counting indels. So far no argument you have made causes me to doubt The authors conclusions, since they are recognized authorities in the field. Are you still claiming they are wrong?
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zaius137 Member (Idle past 3409 days) Posts: 407 Joined: |
If (u) is 1.3%, then an additional indel rate of (u)/7 would be a total of 1.49%. That would work for me. Again (u) is not a percentage. It is rate of mutation per generation. Edited by zaius137, : No reason given.
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