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Author Topic:   Human Evolution (re: If evolved from apes, why still apes?)
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 67 of 128 (455375)
02-12-2008 8:27 AM
Reply to: Message 64 by molbiogirl
02-01-2008 11:14 PM


Keeping up with the literature
You really need to keep up with the literature!
I'm sorry to say this molbiogirl but this statement make you look both arrogant and ignorant.
The fact that you have one press release which quotes someone using the 1% value hardly makes it the cutting edge of the scientific literature. The study which suggested a ~5% divergence when insertion-deletion events were incorporated (Britten, 2002)was widely publicised and as far as I know there have been no studies suggesting this is inaccurate and many supporting it and suggesting important roles for indels in human/chimp evolution (Wetterbom ,et al., 2006; Chen, et al.2007; Sakate, et al., 2007).
Looking at the paper the press release refers to (Clark, et al., 2003), they were looking at alignments of specific genes and seem to be talking specifically about nucleotide divergence in classical protein-coding genes. That can arguably support your claim that, 'Chimps differ from humans by less than 1% genetically', but only in a very limited way. It really needs some context to explain exactly what level of divergence you are talking about, 'genetically' is really too vague to encompass the many different comparative methods which have been used over the years for comparing the genes and now the genomes of humans and chimps.
SkepticFaith is closer to the mark when he says that such values don't tell the whole story. Having said that, his 5-7% is probably a better estimate when the entire genomic structure is taken into account rather than just the nucleotide sequences in orthologous genes.
TTFN,
WK

This message is a reply to:
 Message 64 by molbiogirl, posted 02-01-2008 11:14 PM molbiogirl has replied

Replies to this message:
 Message 71 by Blue Jay, posted 02-12-2008 9:20 PM Wounded King has replied
 Message 73 by molbiogirl, posted 02-13-2008 9:36 AM Wounded King has not replied

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


Message 72 of 128 (455621)
02-13-2008 5:09 AM
Reply to: Message 71 by Blue Jay
02-12-2008 9:20 PM


Re: Keeping up with the literature
Indels don't change the overall sequence, though
Sure they do, if by 'overall sequence' we mean the sequence within the genome. If you are talking about the 'overall sequence' of a gene which the indel is not occurring in then sure, they don't change it.
In terms of gauging evolutionary relatedness, frameshifts are largely misleading, because, even though there is a difference in location, the sequence is still the same.
Can you give some rationale for why small stretches of homologous sequence conservation are the best way of guaging 'evolutionary relatedness'.
If you think that only the protein coding sequence of traditional genes is important to evolution then you are well behind the curve.
Homology reaches farther than the 95% you give it by incorporating frameshifts.
This isn't just about frameshifts, you are still thinking at the gene level when we should be talking about the genome level.
If you want to say something overall about the genetic similarity of humans and chimps then why not look at the overall organisation of the genome. If you only restrict yourself to sequences from ORFs similar enough to align, as the research molbiogirl referenced did, then you are just front loading your search to give you higher similarity than might actually be the case in the genome as a whole.
So, skepticfaith's assertion--that we've now found that we're not so close to chimpanzees because the difference is 5%--is flawed.
In what way? molbiogirl said were were 1% different 'genetically', a vague term that could encompass any level of genetic organisation. Skeptic faith simply said he had heard a value for genetic divergence of 5-7%. In what way is his assertion any more flawed than molbiogirl's? They are both using the vague concept of genetic similarity but providing figures base on different specific genetic metrics.
Why should nucleotide divergence in alignable coding gene sequences be the holy grail of genetic divergence. We know that a large number of the mutations which appear to account for the differences between humans and chimps are not of this type.
Why is a single nucleotide substitution a better guage than a 2bp deletion for evolutionary distance? I can understand that indels can be more complex to dissect but discounting them for that reason is just one more way of biasing your analysis towards finding higher similarity.
Why restrict ourselves now that we have the tools for doing real full scale genome comparisons?
TTFN,
WK

This message is a reply to:
 Message 71 by Blue Jay, posted 02-12-2008 9:20 PM Blue Jay has replied

Replies to this message:
 Message 74 by Blue Jay, posted 02-13-2008 2:42 PM Wounded King has replied

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


Message 75 of 128 (455796)
02-13-2008 7:36 PM
Reply to: Message 74 by Blue Jay
02-13-2008 2:42 PM


Re: Keeping up with the literature
Using deletion lengths (as Britten did) to represent how close humans are to chimpanzees would inflate their importance relative to point mutations, making it look like we diverged X+Y mya when, in fact, we diverged only X mya (X and Y >0).
In terms of genetic similarity throughout the genome, which was what Britten was discussing, they are more important. I don't think Britten was ever suggesting that indel length should be used to estimate the time of divergence.
So, if you're talking just about genetic similarity (as I assume you are), then skepticfaith's estimate is probably closer. But, if you're talking about evolutionary relatedness (which is closer to the topic of this thread), skepticfaith's estimate is an inflation of the distinction between us and chimps.
I have to disagree. In terms of the topic in the immediate past molbiogirl was specifically talking about genetic similarity. In a broader sense the topic seems to me more about the genetic differences between the various primate species than about divergence times. I certainly don't see how what you are talking about is more relevant to 'evolutionary relatedness'.
I would agree that for constructing a phylogenetic tree you would probably be better of going with traditional approaches, I'm not sure if anyone has really tried using indels and other forms of copy number variation as a basis for such analyses. Building a phylogeny is not the be all and end all of evolutionary relatedness I would suggest.
What we are developing now is the ability to really identify mutations which are the basis of specific diferences between humans and our closest relatives, as well as learning more about variation within the human species.
TTFN,
WK

This message is a reply to:
 Message 74 by Blue Jay, posted 02-13-2008 2:42 PM Blue Jay has replied

Replies to this message:
 Message 76 by Blue Jay, posted 02-14-2008 12:17 AM Wounded King has replied

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


Message 77 of 128 (455845)
02-14-2008 4:28 AM
Reply to: Message 76 by Blue Jay
02-14-2008 12:17 AM


Re: Keeping up with the literature
I'm not sure I understand what else you think there could be to evolutionary relatedness than phylogeny. After all, phylogenies, when done correctly, are taken to directly represent evolutionary relatedness.
...
Anyway, this is all off-topic. Maybe we could start a new thread to discuss genetic factors in evolutionary relatedness.
I'm not sure that there is a thread's worth to it. All I mean is that while classical phylogenetics can tell you plenty about who is most closely related to you and reconstruct an evolutionary history of cladogenesis, it tells you very little about what the actual functional basis is for the differences between one species from another in terms of phenotype.
My own research is in Developmental biology and I come at this more from an evo-devo perspective. I am therefore more interested in changes in gene regulation and the effects of large scale genetic events such as gene duplication and divergence, or even wholesale genome duplications. I don't really care when chickens and frogs last had a common ancestor, I just want to know what is different and what is the same in the way they develop and what the genetic basis of those differences is.
You might think of it as a more functional form of evolutionary relatedness, connected to the genetic basis of functional morphological/phenotypic change rather than to in many cases neutral genetic change used as a yardstick for measuring divergence times and determining phylogeny.
TTFN,
WK

This message is a reply to:
 Message 76 by Blue Jay, posted 02-14-2008 12:17 AM Blue Jay has replied

Replies to this message:
 Message 78 by Blue Jay, posted 02-16-2008 6:04 PM Wounded King has not replied

  
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