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Author Topic:   Is convergent evolution evidence against common descent?
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 301 of 311 (216266)
06-11-2005 8:17 PM
Reply to: Message 292 by randman
06-11-2005 3:49 AM


Re: Genomic data on a marsupial
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 - Y10524
Human - 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 bp
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 20.4643
Sequences (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

This message is a reply to:
 Message 292 by randman, posted 06-11-2005 3:49 AM randman has replied

Replies to this message:
 Message 304 by randman, posted 06-12-2005 1:55 AM Wounded King has replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 302 of 311 (216270)
06-11-2005 8:27 PM
Reply to: Message 300 by RAZD
06-11-2005 12:57 PM


Re: common descent goes deeper
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

This message is a reply to:
 Message 300 by RAZD, posted 06-11-2005 12:57 PM RAZD has replied

Replies to this message:
 Message 303 by RAZD, posted 06-11-2005 9:28 PM Wounded King has not replied

RAZD
Member (Idle past 1395 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 303 of 311 (216287)
06-11-2005 9:28 PM
Reply to: Message 302 by Wounded King
06-11-2005 8:27 PM


Re: common descent goes deeper
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}}}

This message is a reply to:
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randman 
Suspended Member (Idle past 4889 days)
Posts: 6367
Joined: 05-26-2005


Message 304 of 311 (216324)
06-12-2005 1:55 AM
Reply to: Message 301 by Wounded King
06-11-2005 8:17 PM


Re: Genomic data on a marsupial
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%?

This message is a reply to:
 Message 301 by Wounded King, posted 06-11-2005 8:17 PM Wounded King has replied

Replies to this message:
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 Message 306 by Wounded King, posted 06-12-2005 8:04 AM randman has not replied

wj
Inactive Member


Message 305 of 311 (216351)
06-12-2005 7:05 AM
Reply to: Message 304 by randman
06-12-2005 1:55 AM


Re: Genomic data on a marsupial
Sequence, not species.

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 306 of 311 (216358)
06-12-2005 8:04 AM
Reply to: Message 304 by randman
06-12-2005 1:55 AM


Re: Genomic data on a marsupial
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

This message is a reply to:
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Replies to this message:
 Message 307 by mark24, posted 06-12-2005 8:13 AM Wounded King has replied

mark24
Member (Idle past 5185 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 307 of 311 (216360)
06-12-2005 8:13 AM
Reply to: Message 306 by Wounded King
06-12-2005 8:04 AM


Re: Genomic data on a marsupial
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

This message is a reply to:
 Message 306 by Wounded King, posted 06-12-2005 8:04 AM Wounded King has replied

Replies to this message:
 Message 308 by Wounded King, posted 06-12-2005 8:36 AM mark24 has replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 308 of 311 (216363)
06-12-2005 8:36 AM
Reply to: Message 307 by mark24
06-12-2005 8:13 AM


Re: Genomic data on a marsupial
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

This message is a reply to:
 Message 307 by mark24, posted 06-12-2005 8:13 AM mark24 has replied

Replies to this message:
 Message 309 by mark24, posted 06-12-2005 8:37 AM Wounded King has not replied
 Message 310 by mark24, posted 06-12-2005 8:40 AM Wounded King has not replied

mark24
Member (Idle past 5185 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 309 of 311 (216364)
06-12-2005 8:37 AM
Reply to: Message 308 by Wounded King
06-12-2005 8:36 AM


Re: Genomic data on a marsupial
WK,
Great, thanks mate.
Mark

There are 10 kinds of people in this world; those that understand binary, & those that don't

This message is a reply to:
 Message 308 by Wounded King, posted 06-12-2005 8:36 AM Wounded King has not replied

mark24
Member (Idle past 5185 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 310 of 311 (216366)
06-12-2005 8:40 AM
Reply to: Message 308 by Wounded King
06-12-2005 8:36 AM


Re: Genomic data on a marsupial
Bah! I'm running WinXP, & there isn't a version of that.

This message is a reply to:
 Message 308 by Wounded King, posted 06-12-2005 8:36 AM Wounded King has not replied

AdminJar
Inactive Member


Message 311 of 311 (216367)
06-12-2005 8:47 AM


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Time to put this puppy to bed.
"Aw, just when it's getting interesting!"
You and your sister, up, straight to bed. No backtalk! NOW!

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