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Neutral mutations, pseudogenes, and evolution

Genetics as it applies to evolution, molecular biology, and medical aspects.

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Neutral mutations, pseudogenes, and evolution

Postby JimmyJazz » Sun Mar 06, 2011 12:05 am

Hello, this is my first post - thanks in advance for the help.

I have been reading a few books on evolution lately - I just finished Jerry Coyne's Why Evolution is True, and right now I'm reading Relics of Eden: The Powerful Evidence of Evolution in Human DNA by Daniel J. Fairbanks.

One issue that's come up in both books, but especially in Relics of Eden, is the issue of pseudogenes and neutral mutations.

From what I can gather, pseudogenes are characterized by neutral mutations. So for example, with a duplication pseudogene or a retropseudogene, there are two copies of a gene where only one copy is needed for functionality; thus, the second gene is free to mutate without negatively affecting fitness. Proof for evolution can be seen in making a comparison between the pseudogene mutations in humans and the pseudogene mutations in other primates--since it is all but impossible for these neutral mutations to have occurred, independently, in the exact same spots on the pseudogene's DNA sequence. Furthermore, pseudogenes can help us establish taxonomy, since the closer the match between two species, the more recently did they branch off from their common ancestor (pseudogene comparisons have been a part of the convergent genetic evidence showing that humans and chimps are more closely related to each other than either of them is to gorillas). This is my understanding, but correct me if anything I've said is mistaken.

My question then, if I am correct in thinking that mutations to pseudogenes are considered examples of neutral mutations, is: Why are the same pseudogenes found throughout an entire species? Why do all humans have the same mutations in the same spots on the same pseudogenes--or, hell, why do we even have the same duplicated genes in the first place? If this whole process--gene duplication, followed by mutations rendering one of the two genes into a nonfunctional pseudogene--does not affect fitness, then why would we expect to see everyone showing the same pseudogenes with the same mutations on them? Wouldn't only certain lineages have them? And I'm not talking about 'race' here - I'm talking about possibly even something more specific, like just a single family or something. Blue-eye and brown-eye alleles BOTH still exist, because neither one is more 'fit' than the other, so there is no reason for either of them to be extinguished over time. Why doesn't the same thing apply to pseudogenes and the mutations that occur on them?

I should add one more thing: I can fully understand why unitary ('disabled') pseudogenes might exist throughout the entire population. For one thing, it is simply more metabolically efficient not to carry a gene that expends energy creating proteins which we no longer need (such as the GULO gene in primates, which is disabled because we have always had sufficient Vitamin C in our diet, or the gene that once made eyesight possible in the now-vestigial eyeballs of moles who no longer have any need for vision). But it's the retropseudogenes and duplication pseudogenes that really confuse me - I can't imagine how they would affect fitness in any way, and if they don't, then I can't imagine why they'd exist throughout entire populations, much less entire species.

This was way longer than I intended it to be, but hopefully it was at least clear.
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No takers?

Postby JimmyJazz » Tue Mar 08, 2011 8:18 pm

No takers? Maybe I can ask my question more succinctly using a quote from Relics of Eden: The Powerful Evidence of Evolution in Human DNA:


When a gene generates a pseudogene copy of itself, the original gene and the copy should be identical. Because the pseudogene is not functional, any mutations it acquires after its insertion are selectively neutral. Because they are neither favored nor disfavored, the mutations should accumulate at a fairly constant rate. Therefore, the more a pseudogene differs from its original gene, the older it must be.

By this logic, if a pseudogene arose after the divergence of human and chimpanzee ancestral lineages, it should be present in either the human or chimpanzee genome but not both.



But if mutations on pseudogenes are selectively neutral - neither favored nor disfavored - then why do we see the same set of mutations in the entire human species and the same mutations in the entire chimpanzee species, rather than only in certain human lineages and in certain chimpanzee lineages? If natural selection is not at work, what is the mechanism that would have caused this mutation to be widespread throughout an entire population of early humans or an entire population of early chimps?
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Postby canalon » Tue Mar 08, 2011 9:53 pm

Note: I am a bacteriologist, so not familiar with human genome content. Or chimp for that matter. :)

If I understand you, you fail to see why some pseudo genes are found throughout each species with the same mutations while you would expect them to have slowly diverged within the species by accumulation of neutral mutations.

The only guess I could make is that the insertion of the pseudogenes happened early enough that they got in all the species. from what I understand from human evolution, it is probable that some serious bottlenecks have happened at the beginning and that may explain why we share so many of those pseudogenes.
Then for the mutations in those and the addition of new pseudogenes, it does depends on the rate of creation of pseudogenes (quite low I guess) and of mutations (probably a little bit higher than that of pseudogene creation, I guess). If we take that no pseudogenes were integrated in our species genome since the divergence from the chimp) what we would see is that we share those genes, with a different set of mutations which would directly depends on our genetic history. Then again some migration patterns will have induced serious bottlenecks which would have heavily influenced the outcome that would be observed now.
And that is where I am at a loss in my ignorance of the human genome. Is that what we observe, or do you say that some how those genes have been stable and no mutations accumulated since?
Patrick

Science has proof without any certainty. Creationists have certainty without
any proof. (Ashley Montague)
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Postby JimmyJazz » Mon Mar 14, 2011 3:37 am

Thanks canalon. I unexpectedly lost my internet access for a few days or I would have replied sooner. I think that I've found my answer in the concepts of genetic drift and fixation. Well, I don't quite understand it yet, but at least now I know where to look.

Thanks again.
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Re:

Postby JimmyJazz » Sun Apr 24, 2011 7:45 am

canalon wrote:Then again some migration patterns will have induced serious bottlenecks which would have heavily influenced the outcome that would be observed now.
And that is where I am at a loss in my ignorance of the human genome. Is that what we observe, or do you say that some how those genes have been stable and no mutations accumulated since?


Regarding bottlenecks, I recently read this passage which sheds some light on why there would not have to be any population bottlenecks in order for everyone today to share certain common ancestors (and therefore, all of that ancestor's mutations):

Tracing one person's lineage back in time forms a binary tree of parents, grandparents, great-grandparents and so on. However, the number of individuals in such an ancestor tree grows exponentially and will eventually become impossibly high. For example, an individual human alive today would, over 30 generations, going back to about the High Middle Ages, have 230 or about 1.07 billion ancestors, more than the total world population at the time.[1]

In reality, an ancestor tree is not a binary tree. Rather, pedigree collapse changes the binary tree to a directed acyclic graph.

Consider the formation, one generation at a time, of the ancestor graph of all currently living humans with no descendants. Start with living people with no descendants at the bottom of the graph. Adding the parents of all those individuals at the top of the graph will connect (half-) siblings via one or two common ancestors, their parent(s). Adding the next generation will connect all first cousins. As each of the following generations of ancestors is added to the top of the graph, the relationship between more and more people is mapped (second cousins, third cousins and so on). Eventually a generation is reached where one or more of the many top-level ancestors is an MRCA from whom it is possible to trace a path of direct descendants all the way down to every living person at the bottom generations of the graph.

The MRCA of everyone alive today could thus have co-existed with a large human population, most of whom either have no living descendants today or else are ancestors of a subset of people alive today. The existence of an MRCA does therefore not imply the existence of a population bottleneck or first couple.


http://en.wikipedia.org/wiki/Most_recen ... n_ancestor
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Postby BioSULTAN » Mon Apr 25, 2011 7:14 pm

While it is true that new variant of a gene spreads through a population, the population will have evolved. The definition does not really seem to get to the heart of the matter.

Evolution is not simply change. Changes that occur in embryo or aging processes or mutation in non-germline cells are not counted as Evolution :roll:

My best wishes

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Postby JackBean » Tue Apr 26, 2011 11:55 am

Are really all the pseudogenes conserved across the whole humankind? I think we have still only few human genomes sequenced to conclude that. It may still be present only in some sub-populations.
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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