Wednesday, December 28, 2005

Why Study Speciation Genes?

I mentioned previously that John Wilkins has gotten me thinking about speciation, and his most recent post on speciation contains a bit of a poke at geneticists studying speciation:

“Some researchers, such as Chung-I Wu . . . seek to find ‘speciation genes’ which are modified through this inadvertent selection. This is, I believe, a category mistake, and a logical fallacy.

”The category mistake is to presume that because a genetic distance causes speciation, it is therefore a gene ‘for’ speciation. But there is no prior specification of genes that cause reproductive isolation. A genetic change may do so, or it may not. Identifying that it has done so is something that can only be done post hoc. And there appears to be no particular genes that cause speciation over large evolutionary distances - there may be an active gene complex in Drosophila which when changed causes reproductive isolation, but it doesn't therefore follow that a homolog of that complex will do the same thing in other flies, or in insects generally, or in all animals, etc. In fact, it doesn't even follow that we will find this is the complex involved in all cases of Drosophila speciation, either.”

I will argue that Drosophila geneticists are not so much interested in finding “speciation genes”, but rather interested in understanding the genetics of speciation. To do so requires finding mutations that allow the species boundary to be surmounted. As I have mentioned previously, good species are reproductively isolated, preventing any genetical analysis of the factors that lead to this isolation. Mutations in the “speciation genes” (especially the extremely useful Hybrid Male Rescue mutation), however, allow researchers to cross individuals from different species and study the genetics of speciation.

Geneticists like to find generalities. That is why we study model organisms; they are easy to work with in a laboratory setting and allow us to extend our discoveries regarding molecular biology, cellular function, development, physiology, etc to other related taxa (both closely related and more distant relatives). Wilkins makes a valid point that it is difficult to generalize discoveries regarding the genetics of speciation made within one system (compared to the generalizing done in other fields). For example, finding a speciation gene in one species pair does not say anything about that gene’s involvement in speciation in general. I don’t think you will find a single geneticist who would disagree with that.

Other research on the genetics of speciation does provide the potential to generalize across different taxa (finding these “speciation genes”’ is merely a necessary step in this process for some species pairs). It is difficult to say how common certain patterns are in speciation, but some of the following insights from Drosophila have the potential to be applicable in distantly related taxa.

Researchers have shown that genome rearrangements can influence the distribution of genes responsible for reproductive isolation throughout the genome between sympatric and parapatric species pairs. Some have argued for the same type of relationship between chromosomal inversions and speciation in humans and chimps, but they may have done the analysis incorrectly or even violated one of the assumptions of their model (humans and chimps probably speciated allopatrically). The findings in Drosophila are similar to those observed in Rhagoletis and in sunflowers, suggesting that this model may be common for parapatric speciation.

With the development of high throughput technologies for studying genome wide patterns of gene expression in Drosophila, researchers have begun to investigate expression changes in species hybrids. The disproportionate effect of cis regulatory changes between species pairs (compared to trans changes) has not been tested outside of the D. melanogaster species group. This type of find differs from the discovery of a “speciation gene” because it is a trend observed from the study of a large set of genes mis-expressed in species hybrids. These experiments would not be possible without the use of speciation gene mutants so that interspecific hybrids could be created.

Wilkins will be happy to know that some researchers are interested specifically in finding which genes are involved in maintaining species boundaries. They do so not for the sake of finding the genes, but for determining how those genes evolve. Some focus on the role of natural selection in speciation. Many others are interested in understanding how genetic changes between species lead to behavioral differences that underlie the prezygotic isolation of the species. And yes, some do study individual speciation genes, but they do so to understand why natural selection would favor the evolution of a particular protein and how it interacts with other gene products to prevent interspecific hybridization.

While the individual genes responsible for speciation may not be the same between different species pairs, “speciation genes” are probably under the same evolutionary forces regardless of which species pair one studies. As researchers discover more speciation genes, it will become possible to determine if certain classes of proteins (such as transcription factors) are disproportionately present within the catalog. Biologists do not study the genetics of speciation simply to find speciation genes; they search for speciation genes (and QTLs) to determine how organisms, the environment, and the genome interact to produce reproductive isolation between species.


At 11:18 PM, Blogger John Wilkins said...

Thanks for this response, RPM. I agree that studying genes that cause speciation in particular cases is both iteresting and instructive. All I am opposing is the too-quick generalisation across phylogenetic distances.

There is a tendency to overgeneralise in biology, and this is in part due to the misleading assumption that there must be general rules in a science - of course there are, but biology is a historical science and historical events are singular, even when general rules apply. Some like to think that biology is a sui generis science, and has its own laws. I am of the view that the only laws in operation in biology are those of physics and chemistry. Everything else is a particular event or process.

At 12:54 PM, Blogger RPM said...

I agree with your view on laws. I disagree with the view that biology is purely historical. Even in a field like physics, we study the formation (or destruction) of a particular star despite its singularity in order to figure out how those processes occur. The same goes for biology. While the same exact pathways are not present in the development of both zebrafish and mammals, we can still use the fish model to elucidate some of the mechanisms in mammals. That’s why people study model organisms in cell biology, developmental biology, biochemistry, and, yes, evolution.

In speciation research, they’re trying to come up with a suite of ways speciation can occur, and identifying “speciation genes” is necessary in some instances. You’re doing the same thing when you categorize different types of speciation. Part of speciation is the genetical aspect (I’d argue that it’s a large part) and I see nothing wrong with generalizing when the evidence makes it possible.


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