From: Bart Hazes
Date: 24 January 2012 21:31
On 12-01-24 11:20 AM, Jacob Keller wrote:
Inspired by the recent post about "quasispecies:"
I have been bothered recently by the following problem: why do species
of genetic uniformity exist at all (or do they?)? This first came up
when I saw a Nature paper describing live bacteria extracted from a
supposedly 250-million-year-old salt crystal whose 16S RNA was 99%
identical to marismortui bacteria (ref below). What? Are the bacteria
the same now as 250 million years ago? But there is a further
question: given the assumptions of evolution, why should there be any
bacterium whose genome is the same as any other, assuming that
equivalent codons are really equivalent (or at least roughly so), and
that even at the protein level, there is such a thing as "neutral
drift?" After all, we even see in our lab cultures that they (at least
e coli) mutate fairly frequently, so why is there such a thing as "e
coli" at all, at least at the nucleotide level? I don't think we
usually say that each bacterial species is totally optimized in all
its features, do we? Even assuming that every single protein must be
just so, shouldn't there be as many species of e coli as there are
possible genomes encoding the same protein set, i.e. some extremely
large number? Why is there any uniformity at all? Or IS there--maybe
the bacteria too are only quasispecies...? And maybe also...
JPK
To my knowledge there is no universally accepted definition of a species but it certainly does not involved genetic identity. You use "genetic uniformity" but I am not sure how you define uniform. Even in a single generation, the chromosomes of a child have half a dozen or so mutations relative to the source chromosomes from its parents.
Many definitions focus on genetic isolation but that implies that in past centuries protestants and catholics were distinct species as inter-denominational marriage was a definite no-no. It also gets really messy for all life forms with non-sexual reproduction. For instance, if you consider a bacterium to reproduce clonally, then each individual is genetically isolated from every other, and thus there is one species per individual. In one form or another it all boils down to genetic affinity to a shared common ancestor, but that does not give you a neat criteria to define what is a species and some people are going to bring up horizontal gene transfer to further muddy the waters.
To get the official word on the concept of a quasi species you have to asked an evolutionary biologist, but since you were asking on the CCP4 here is my interpretation:
For some RNA viruses the rate of mutation is so high that they basically sample a flat region of the fitness-landscape. If you could take two individual viruses out of this sample to establish two independent infections than over time each will start to re-sample the same flat landscape. In other words, there is not a single unique, or predominant, sequence that represents the species but a pool of "near-equal" fitness variants.
To some extend I feel that this is always the case but for "normal" organisms the sampling rate of fitness space is slow and genetic differences between individuals are dominated by mutations passed down by vertical descend. In contrast, if you sequence two viruses from the above two infections there genetic distance will be similar to the genetic distances between individuals within a single infection.
Bart
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From: Saul Hazledine
This way of looking at species is described in a paper I once presented in a journal club. The work is computer based and describes putting an evolutionary algorithm in control of its own mutation rate. Its not my field, but I found the paper very approachable and extremely interesting.
Emergence of species in evolutionary "simulated annealing":
Saul Hazledine
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From: Carter, Charlie
Begin forwarded message:
Date: January 24, 2012 7:16:42 PM EST
To: Bart Hazes
Subject: Re: [ccp4bb] quasispecies
This remark brings to mind a paper published recently by Ariel Fernandez and Mike Lynch:
Nature 474:502, 2011: Non-adaptive Origins of Interactome Complexity
The point, if I understand it correctly, is that when population sizes are small, as they are in multicellular eukaryotes, the effect of "drift" becomes more significant, and mutations to the surfaces of proteins that impair the protein surface - solvent interaction are established more easily in the population. A consequence suggested by the authors is that these "surface defects" provide an enhanced manifold from which to recruit novel surface-surface contacts that lead to an increase in the interactome".
Charlie
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