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Author | Topic: Is convergent evolution evidence against common descent? | |||||||||||||||||||||||
Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined: |
Comparing whole genomes is a pretty major task, the sort of thing that takes research groups a year or more of work to do properly and several years of computing time.
It might be better to identify some specific genes which we think might be relevant and try and find sequences for them amongst the selected groups. I fear this will prove difficult outside of well studied organisms or organisms whose genomes are being, or have been, sequenced. There are any number of well conserved genes involved in development which might effect morphology in the sort of ways we see in some convergent forms, the problem is pinpointing which ones. Most of the sequence data we have been looking at is totally divorced from the question of convergent evolution and more to do with the extenet to which molecular genetic phylogenies for mitochondrial sequences match up to the morphologically derived phylogenies, which is a relatively worthwhile exercise but seems to be a bit straying from the actual topic. One problem with your selection of organisms is that there is only moderately complete genomic data on 3 of them. You might be able to do whole genome comparisons of their mitochondria, the data is there for all of those species I think, but that sort of analysis requires considerably more sophistication than what we have been doing. You cant just plug 16kb sequences into ClustalW and have much faith in the results being meaningful. Having just typed that I was then seized by a compulsion to do just that, so treat the meaningful character of these results with caution. I wont post the sequences for this alignment, for obvious reasons, but the Genbank accessions are as follows :- Kangaroo - Y10524Human - NC_001807 Mouse - NC_006914 Turtle (not snapping I'm afraid) - NC_000886 Opossum -NC_001610 Sequence type explicitly set to DNA Sequence format is Pearson Sequence 1: Chelonia 16497 bp Sequence 2: Homo 16571 bp Sequence 3: Mus 16300 bp Sequence 4: Macropus 16896 bp Sequence 5: Didelphis 17084 bpStart of Pairwise alignments Aligning... Sequences (1:2) Aligned. Score: 20.4643Sequences (1:3) Aligned. Score: 23.2147 Sequences (1:4) Aligned. Score: 19.2277 Sequences (1:5) Aligned. Score: 18.561 Sequences (2:2) Aligned. Score: 53.2134 Sequences (2:3) Aligned. Score: 21.1718 Sequences (2:4) Aligned. Score: 20.7592 Sequences (2:5) Aligned. Score: 19.9807 Sequences (3:2) Aligned. Score: 21.1718 Sequences (3:3) Aligned. Score: 48.8589 Sequences (3:4) Aligned. Score: 20.7117 Sequences (3:5) Aligned. Score: 18.2209 Sequences (4:2) Aligned. Score: 20.7592 Sequences (4:3) Aligned. Score: 20.7117 Sequences (4:4) Aligned. Score: 49.6982 Sequences (4:5) Aligned. Score: 27.9179 Sequences (5:2) Aligned. Score: 19.9807 Sequences (5:3) Aligned. Score: 18.2209 Sequences (5:4) Aligned. Score: 27.9179 Sequences (5:5) Aligned. Score: 45.3641 You may notice that the pairwise alignments even of the same sequence only produce values of around 50%. The tree produced is like this :-
Which looks like it conforms to our expectations, but as I say, treat this analysis with a degree of scepticism. TTFN, WK
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Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined: |
Some research puts the estimate as low as 95%, if one takes indels into account (Britten, 2002). Another paper shows 98.6% sequence identity in the MHC/HLA locus between human's and chimps drops to as low as 86.7% when indels are taken into account (Anzai, et al., 2003)
TTFN, WK
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RAZD Member (Idle past 1405 days) Posts: 20714 From: the other end of the sidewalk Joined: |
Thanks. What about data on specific mutations common to both chimps and humans (and gorillas) that are in unused portions and thus have no reason to be the same except by common ancestry? I know that ecrine glands are on the body areas of these three apes versus palms and feet of other apes, but that also has to do with sexual pheromones I believe.
I had started with 96% from memory but changed that to 97% from the googled data spread. The interesting thing for me on that 2nd to last paper was the number of differences between humans and chimps (h-c) was greater than the differences between chimps and gorillas (c-g) even though there was less time since divergence of (h-c) than (c-g). This implies a selection process operating on human evolution that was more active than the one operating on chimps and gorillas. And given that humans are homogeneous within 0.25% or so (+/- 0.1%?) even after tremendous dispersal of humans by several different routes to cover the globe, that would imply that the human genome was pretty well fixed before Homo sapiens walked out of Africa, including not just such known features as bipedalism, large brain, small jaw and the like, but the apparent skin bareness, long head hair, enlarged buttocks, female breasts and sexual readiness, and enlarged male penis. Runaway sexual selection offers an obvious additional mechanism for incorporation of mutations within the genome at such an increased rate, and many of these features would also fit the scenario of sexually selected features, but this is at best circumstantial evidence, and there was certainly some natural selection going on at the same time. A large part of it could be just mental development and a threshold of awareness also leading to conscious selection feedback. we are limited in our ability to understand by our ability to understand RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}
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randman  Suspended Member (Idle past 4899 days) Posts: 6367 Joined: |
WK, why only around 50% for the same species? That doesn't make sense. I know you said take it with a grain of salt, so to speak, but that's more like a whole block of salt there.
Shouldn't it be near 100%?
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wj Inactive Member |
Sequence, not species.
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Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined: |
I suspect the problem is based on the method the CLustalW program uses to do its faster but less accurate method. I have rerun the data using the slower more accurate method and there were no self sequence comparisons and the similarity scores were considerably higher.
Sequence type explicitly set to DNA Sequence format is Pearson Sequence 1: Chelonia 16497 bp Sequence 2: Homo 16571 bp Sequence 3: Mus 16300 bp Sequence 4: Macropus 16896 bp Sequence 5: Didelphis 17084 bp Start of Pairwise alignments Aligning... Sequences (1:2) Aligned. Score: 65 Sequences (2:3) Aligned. Score: 69 Sequences (3:4) Aligned. Score: 70 Sequences (4:5) Aligned. Score: 75 Sequences (1:3) Aligned. Score: 68 Sequences (2:4) Aligned. Score: 66 Sequences (3:5) Aligned. Score: 71 Sequences (1:4) Aligned. Score: 68 Sequences (2:5) Aligned. Score: 65 Sequences (1:5) Aligned. Score: 67 I then bootstrapped the alignment and mapped the resulting tree getting a pretty robust result.
Perhaps I could have taken some time to adjust the parameters for the quick alignment, different parameters produce more reliable results for longer sequences, and the 16,000 odd base pairs in the mitochondrial genome is orders of magnitude beyond the length of amino acid sequences we have been looking at previously. TTFN, WK
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mark24 Member (Idle past 5195 days) Posts: 3857 From: UK Joined: |
WK,
What program did you use for this? Can I download it? Thanks, Mark There are 10 kinds of people in this world; those that understand binary, & those that don't
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Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined: |
I used the web based ClustalW program to do the initial alignment. I then used a local version of ClustalX, which you can download, to perform the bootstrap analysis and then Treeview to to produce the tree with bootstrap values. If you are performing a bootstrap it helps to set the program to label the nodes rather than the branches, the plotting programs don't seem to see labelled branches for some reason.
TTFN, WK
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mark24 Member (Idle past 5195 days) Posts: 3857 From: UK Joined: |
WK,
Great, thanks mate. Mark There are 10 kinds of people in this world; those that understand binary, & those that don't
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mark24 Member (Idle past 5195 days) Posts: 3857 From: UK Joined: |
Bah! I'm running WinXP, & there isn't a version of that.
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