Peez

With all due respect, you have done nothing of the sort. All you have done is claim that this is the case. Please do, I would be very interested. There is nothing in your synopsis that suggests to me that wolbachia is inherited as such. Further, there is no indication of how this is relevant. IF we assume that wolbachia are no longer independent organisms and are rather part of their "host" organism, and if we then assume that wolbachia are "inherited" in the same sense as mitochondria, then you still have to establish that such inheritance is non-nucleotide. I have looked at a number of them, but I found no indication that wolbachia infection is an example of non-nucleotide inheritance. Fair enough, I will consider it so. I agree that DD was oversimplifying, but he did not claim that environment plays no part in gene expression. I see nothing on page four which suggests that either DD or Oolon think that the environment is unimportant in gene expression. In fact, Oolon states on page four: Clearly Oolon, at least, accepts that the environment is important in development. I maintain that you are attacking a straw man. I did not take it to be necessarily directed at me personally, but it still appears to be an attack on a position that has not been taken by anyone here. I appreciate your attempt to clarify, and I certainly do not think that what I see as straw man arguments are being made intentionally so. Still, it is the inheritance without nucleotide sequences that is the issue here (as far as I can tell ).

Peez

RufusAtticus

Peez,

Umm, pz and I are both biologists and we don't define evolution as change in allele frequencies, quod erat demonstrandum.

Yes, wolbachia are inherited similar to mitochondria. (They can also be transmitted horizontally as well as vertically.) They are separate organisms distinct from the host cell. (As distinct as E. coli is in your gut.) They are transmitted as whole organisms, which means that it is a form of non-nucleotide inheritance. In other words, the trait of wolbachia infection and the consequences of it is inheritance through the transmission of whole wolbachia. I do not understand how you don’t see this as non-nucleotide inheritance.

~~RvFvS~~

P.S. Some more info that might help:

Zimmer, C (2001) Wolbachia: A tale of sex and survival. Science 292:1093-1095

<a href="http://unix.cc.wmich.edu/~dshoemak/research/areas/evolutionary.htm" target="_blank">http://unix.cc.wmich.edu/~dshoemak/research/areas/evolutionary.htm</a>

<a href="http://www.rochester.edu/College/BIO/labs/WerrenLab/Herit_Micro.html" target="_blank">http://www.rochester.edu/College/BIO/labs/WerrenLab/Herit_Micro.html</a>

Doubting Didymus

Rufus, I apologise. I am not elucidating properly, and my position is not clear enough.

Allow me to explain myself in more detail.

That certainly wasn't my intention. I completely agree with your explaination.

If we are dealing with fossils, it's generally bone morphology. Fossil strata can also give us a half decent look at the environment and the other organisms that the fossil in question lived in/with. So yes, we are using non-genes to determine evolutionary history, just as when dawkins delivers the theory of sexual selection and positive feedback in modern living weaverbirds, he uses no genetic data.

You do not need to see the genes in order to say something about their role in evolution.

That is simply not true.

For a start, I do not define evolution in that way. I define evolution in terms of any units with three properties:
Heritability: the units must get themselves copyied with enough precision to overcome information loss.
Mutability: A unit that cannot change its nature in any way can never change over time.
Differential replication efficacy: Some units must be capable of becoming better at copying themselves than other units (or technically, simply better at copying than they once were). Without this, units can be heritable and mutable, but selection can achieve nothing and evolution is severely limited.

For evolution to be interesting, I would add a fourth attribute, which I read about in "levels of selection" by someone or other. That is: the unit must have a large future potential. To illustrate this I like to think of the clay crystal replicator theory. Clay crystals (might) exhibit heritability, mutability, and the ability to become better replicators, but I doubt (though I may be wrong) that they have the potential for this evolution to ever acheive anything much more complex than a clay crystal. Technically, this last is not nessecary for evolution to theoretically occur, but it is certainly neccesary for evolution that produces something like us.

Dawkins defines this unit as the gene, and I would agree, but the above definition is a little broader. Certainly this unit was not always the gene, and an alien species would probably have a totally different kind of unit.

I do not think the gene centric definition is hampered by not having access to the genes, any more than a hypothetical 'environment-centric' definition would be hampered if we could not detect the environment of the fossil.

If evolution is highly specific to genes (hypothetically), then a gene - centric definition is appropriate no matter how much access we have to those genes. If we discovered that evolution was driven by aliens, than an alien - centric definition would be appropriate even if we could not directly assess the aliens involvement in fossils.

Not neccesarily. As a completely fantastic hypothetical, imagine for a moment that beaver dams are living organisms. Imagine that a new dam is built by the beaver by taking the offspring of an old dam and guiding its growth by instinct. The genes of the dam would be important, but even more important to the evolution of dams would be changes in the genes of the beavers.

This example is to show that gene centrism is not limited when it tries to explain the effects of one organism on another. Its a weird and silly example, but it's early morning here, so cut me some slack.

This kind of thing is what dawkins talks about (much better than I can) in the extended phenotype. The effects of genes are not restricted to the organism they are in. They can extend outside to 'cause' effects on the environment, and on the phenotypes of other species.

What makes them able to destroy spindle fibres? Since they can pass the ability on to the next wolbachia generation, it is an inheritable ability and thus, the genes of the wolbachia have phenotypic power over it. That it why I say wolbachia infection is consistent with gene centrism.

Well, I would consider wolbachia part of the insects environment, wouldn't you? The insects evolution is being influenced by an environmental factor that influences its genes. I have read about a species of fly that is sometimes divided into two cryptid species, simply because one population only ever lands on the bottom of leaves, and the other only ever lands on the top. They can interbreed if you make them, but they never do it in the wild. This is a phenotypic factor of the fly, but it is also an environmental or geographic factor and it certainly will influence the gene pools of the cryptids. Speciation may be just around the corner. It makes no difference to me whether the environmental factor is abiotic, is caused by the phenoype of the organism itself, or whether that phenotype is in turn produced by the interaction of another species, it's still an environmental factor.

Now the insect phenotype has changed due to an environmental factor, true, but in this case you could say that it inherited the environmental factor from its parent. Is this non-genetic inheritance? I say no, because the only reason you can say that wolbachia are heritable in the first place is because they pass on their features via their genes.

Just to clear this up: do you consider that speciation has occured as soon as the infected population can no longer interbreed with the clean population, or would you wait until the host genome has changed enough to prevent interbreeding even if the wolbachia were removed?

There is probably no easy answer, 'species' being as elusive a term as it is.

When do we say the host population has changed? In this case, I would say straight away. I have inherited a phenotype changing feature from my parent insect. Evolution has occured. Is this consistent with gene centrism? I say yes, because what I have actually inherited is a little gene pool, and it could easily be said that my phenotype is being influenced by more genes than just my own. The same thing already applies to mitochondria. The genes that have phenotypic power over me are a bit more than just my own. This is not just compatible with gene centrism, I think it illustrates its usefulness as an evolutionary perspective.

Re reading my post, I see that I have not been much more clear than last time. Alas, this is a difficult subject and you will just have to deal with my scribbly attempts at explaining my veiwpoint.

Peez

My appologies, this was not clear to me. Then I can accept that some biologists do not use what I would consider to be the standard definition. Meaning that some wolbachia genes have been transmitted to the nuclear genome? That would be my assessment as well. I disagree. For one thing, I would not define the transmission of a parasite as "inheritance". If an insect gets wolbachia from its mother, I would not call that "inheritance", if a child gets syphilis from its mother, I would not call that "inheritance", if calf gets E. coli infection from its mother's faeces, I would not call that inheritance, if a dog gets tapeworms from a dead pig, I would not call that inheritance, when a robin gets lice from another bird, I would not call that inheritance, and when a mosquito lands on my arm, I would not call that inheritance. Quite simply I see two populations living in close association, I do not see inheritance. But that is beside the point. hy do you think that wolbachia "inheritance" is non-nucleotide? Does wolbachia lack DNA? Even if we were to accept that transmission of a parasite is "inheritance", it is still nucleotide inheritance unless the parasite has some non-nucleotide inheritance system. I do not have time to track down this article right now, does it address non-nucleotide inheritance? nteresting, but does not indicate that wolbachia infection is "inherited", nor that evolution should be defined to include non-nucleotide changes. In fact, as far as I can tell, it implicitly uses the "gene-centric" definition. This at least refers to wolbachia infection being "inherited". Though I do not agree with such usage, it is a semantic argument. In any event it does not address the issue of non-nucleotide inheritance.

What would be helpful would be an article on non-nucleotide inheritance, or that at least deals with evolution as something other than genetic change. We can quibble about the meaning of "inheritance", but I don't believe that this will be fruitful. The issue (as I see it) is whether not non-nucleotide inheritance can occur. I am not adverse to the idea that it may, but I have yet to see any evidence that it does, or any mechanism by which it might, or any phenomenon that requires anything other than nucleotide inheritance. I would be very interested in learning about anything that contradicts this.

Peez

Doubting Didymus

Peez, I would like to discuss some of your points with you.

Wolbachia are definitely heritable in exactly the same way as our mitochondria are heritable. It is not directly a part of our nuclear genome, but we do have genuine copies and they are obtained from the parent. Mitochondria are ancestral endoparasites that evolved a co existence with eukaryotes prior to the advent of multicellularity.

Mitochondria and wolbachia can therefore be considered equally heritable, and both have phenotypic effects.

I would argue, however, that the only reason my mitochondria and my wolbachia can even be considered copies in the first place is because they pass on their traits via their genetics.

You need to be careful about statements like this:

As you must therefore exclude mitochondria from your evolutionary definition. Wolbachia are just as heritable. I got it from my mother, it effects my phenotype, and I will pass it on to my child. This much is true, but I am still arguing that wolbachia (and mitochondria) are only heritable because they pass on their traits via genes.

RufusAtticus

Doubting Didymus,

I thought so, but I just wanted to make sure.

I can agree with these. In fact, I like how they’re phrased since “unit” is scalable from nucleotide to species. Are these of your own devising? If not, can you send me a reference for them?

With this step you have gone from “evolution” to “selection,” as such I think it should be separated from the above two to prevent the pan-adaptationist misconception.

The problem is near impossible to go from a phenotype to a gene that contributes to that phenotype without some pedigree information or experimental genetic manipulation. I say this to point out that there is no simple access to genetic information from phenotypic information. What do you think about the following description of evolutionary genetics?

• Evolution is the change of properties of a population or frequencies of such properties over time, i.e. between generations. Evolution happens almost exclusively by changes in heritable material, such as genes.

I think we are view the allele-centric definition differently. I see it as not saying that evolution happens because of changes in genes, but rather that a population evolves by changes to its gene pool. Could it be perhaps that you are promoting a gene-centric definition and I am poopooing a gene-pool-centric one? I think that might be why we are not communicating properly with one another.

Yes and no. The fact that such parasites exist and can infect insects would be environmental. But once such an infection occurs, wolbachia parasites are now a heritable trait. It all boils down to at what scale you are looking for the “environment.”

Again, I think it has to do with the scale we decided to look at it. From the perspective of the host, the reproductive phenotypes are traits that are inherited not through its genes but rather through a cytoplasmic parasite.

I take the view that the possibility of two isolated populations coming back together in the future is not sufficient to say that they are not behaving as separate biological species right now. So I would say that if wolbachia infection has isolated two populations of an organism, then they would in fact be separate biological species, even if the incompatibility was not due divergence of nuclear genomes.

~~RvFvS~~

RufusAtticus

Peez,

Not that I know of. Although it might have occurred, the damaging effects of wolbachia infection to host reproduction suggests to me that it would benefit the hosts to get rid of the parasite rather than assimilate it.

So you would argue that you did not inherit your mother’s mitochondria. What then do you call it?

I see the transmission of wolbachia from parent to offspring as being non-nucleotide inheritance? I see the division of wolbachia into daughter cells as being nucleotide based. I’m not arguing that the ability of wolbachia to affect their host’s phenotype is not inherited via wolbachia DNA. What I am stating is that the wolbachia infection itself is inherited by the transmission of wolbachia themselves and not their DNA when gametes form.

The Zimmer article is a good overview of wolbachia and there effects on reproduction and evolution. The other two were just some sites that were to give you a better picture of the bacteria, its life cycle, and the effects on the host.

Here is something pz mentioned earlier that you might have missed: cortical inheritance.
<a href="http://www.devbio.com/chap02/link0203b.shtml" target="_blank">Inheritance in Ciliates</a>

~~RvFvS~~

Doubting Didymus

I wrote these particular ones from scratch, but I see them everywhere, all the time. The most recent occasion I came across them was near the start of a book called 'levels of selection', a compilation on the subject that includes some input from John Maynard Smith, but the actual editing author I can not remember.

I think you read too much into this one, But I see what you mean. However, you can't deny that at least for evolution as we know it to occur, some units must be able to improve their replicability.

I am not totally clear on this division, but I would certainly extend my definition to include the total of all phenotype-altering heritable factors, regardless of their locations. I don't know of anyone (except peez, maybe) who wants to restrict evolution entirely to the gene pools of individual species. Certainly that is not Dawkins's position.

I can agree with that, but I would put a little more emphasis on heritablility than you do.

I think this is what you meant by the difference between gene-centric and gene-pool centric definitions?

I do not restrict my definition to the specific gene pool of any one species. I do, however, 'reduce' (there's that word again) the majority of heritable features to genes. That the genes are not part of the insects gene pool does not bother me.

I do not want to say I have the answer to when a species is diverged, but how does your definition hold up to the reductio ad absurdum? If wolbachia - isolated populations are now a new species, are the cryptid species of flies I spoke of earlier a recognisable new species? If so, What about a population of flies that I am just holding in a closed box? They are reproductively isolated, so when can I name them?

I am not saying you are wrong, just pointing out that 'species' is really hard to properly define.

Peez

I'm keen Wolbachia are "inherited" as separate organisms, with their own distinct genome. Mitochondria are not separate organisms, do not have their own distinct genome, and are thus not "inherited" the same way that wolbachia are. I disagree. One is part of the organism and is "inherited" both through nuclear and mitochondrial DNA, the other is a separate organism that is "inherited" on its own. Obviously both have phenotypic effects, just as mosquitoes do on us. Agreed. I believe that I was being careful when I made that statement. I consider mitochondria to be part of a cell, not a symbiont. I realize that this might be a semantic distinction, as I mentioned earlier, but it is a distinction that I make. A cell with mitochondria is a single organism (as I see it), while a cell with wolbachia is made up of two organisms. Mitochondria are inherited from our parents, while we are infected with wolbachia by our parents. I realize that this is, perhaps, a semantic argument, but again it is a distinction that I make.

Peez

Peez

I realize that this was not addressed to me, but if I may... This definition does not seem to be very precise. For example, a simple increase in population size would be considered evolution. A change in the average age of a population would be considered evolution. A change in the distribution of a population would be considered evolution. On the other hand, you may consider these changes to be "evolution". Could you post a more precise version? It might help to clarify things. Just to clarify, according to what I am calling the standard definition of evolution, evolution does not occur because of a change in allele frequencies, it is a change in allele frequencies. I realize that you probably meant the same thing, but I wanted to be clear since definitions are an issue here.

When we say that evolution is a change in allele frequency over time, we are talking about the frequency of alleles in a population. That is, we are talking about the gene pool. Evolution (by this definition) does not happen to individuals, it happens to populations. I would consider "a change in genes" to be a very sloppy definition of evolution, and not one that I have seen any biologist use. I don't believe that Dawkins has used it. We are inevitably getting into semantics here, but "environment" is not restricted to extra-cellular environment by evolutionary biologists. Dawkins obviously considers everything other than genes to be "environment". To be more precise, "inherited" though the genes of the cytoplasmic parasite.

Peez