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Charlesworth on Lynch

Posted by RPM on March 5, 2008
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Brian Charlesworth has reviewed Michael Lynch’s The Origins of Genome Architecture for Current Biology. Charlesworth’s review is generally positive, and he agrees that population size may be an important factor in genome evolution. However, he thinks that Lynch overplays the role relaxed selective constraint in small populations plays in the evolution of genomic complexity.

Charlesworth argues that sexual reproduction may be partly to blame for some of the features found in the bloated genomes of many eukaryotes. For example, the abundance of transposable elements may be the result of sexual reproduction, not relaxed constraint:

It is true that, on average, bacteria have much large Ne values than most eukaryotes for which we currently have data, but they differ in numerous other respects as well, for example lack of regular sexual reproduction. As all good comparative biologists know, it is very difficult to disentangle cause and correlation from wide comparisons. Alternatives to many of Lynch’s explanations of the patterns can be envisaged, and his arguments do not seem to rule these out. For example, as he himself describes in Chapter 7, the spread of transposable elements through the genomes of a host population is dependent on some degree of sexual exchange between members of the populations, and the correlations described by Lynch could thus at least partly be explained by lack of such exchange.

Additionally, introns may be a byproduct of sexual reproduction:

Could it be that the invention of regular sexual reproduction made it easier for mobile, initially self-splicing introns to invade the genome in large numbers? This possibility is not explored by Lynch, who resorts (p. 261) to the untestable hypothesis that there was a long period of reduced Ne among ancestral eukaryotes. This is getting dangerously close to the adaptationist just-so stories that he ridicules in the final chapter.

Is Lynch committing to a frail nearly neutral hypothesis?

So, the book appears a bit biased. Oh, well. It makes some interesting arguments that warrant further inspection. Those arguments, however, should be taken with a grain of salt, as there may be adequate alternatives to the explanations proposed by Lynch.

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Comments

  1. #1 Jim Thomerson
    March 5, 2008

    This may be off the subject. Some allopatric speciation theories postulate a small population somehow isolated from the parent population. If the population remains small for several generations, I wonder if its evolution may be more a result of genetic drift, random events, blind luck, etc. rather than selection. As I understand selection, it is a statistical phenomenon. But statistics work less well in small populations. If the population survives and is able to increase in number, I would think selection would become more and more important in directing its evolution. Does this seem reasonable, and worth thinking about? Probably some population geneticist has figured all this out and I am just unaware of it.

  2. #2 RPM
    March 5, 2008

    Small founder populations do undergo extreme genetic drift. Oftentimes, the allele frequencies in the founder population will not reflect those of the parent population. I’m not sure how selection would be more important after those isolated populations increase in size. What could be real important are the new selection pressures experienced by the founder population.

  3. #3 LH
    March 5, 2008

    Good points by Dr. Charlesworth, although quite predictable that he would talk about sexual reproduction.

    RPM, do you agree with Lynch that neutral evolution is the null hypothesis?

    In light of this “Altenberg 16″ news, I have been thinking about Massimo Pigliucci’s critique of Lynch’s book in which he said that the burden of proof is on the neutral theory supporters just as much as it is on the selection supporters.

  4. #4 RPM
    March 6, 2008

    Statistically, in tests for natural selection, the neutral theory is the null hypothesis. It’s very difficult to prove neutrality. And if you read John Hawks’ blog, you’ll often see him take a position against the default assumption of neutrality.

    However, Lynch is advocating more of a nearly neutral model than a neutral model. It’s nearly neutral because it concerns slightly deleterious mutations, which are at the whim of selection and/or drift depending on population size.

  5. #5 DGS
    March 7, 2008

    I would have to think the burden of proof is on anybody, be they selectionist or neutralist, to assure that the mechanisms they propose have been considered within some approximation of a population context. This is Lynch’s main objection to many of the ideas he critiques: evolution is a population-level phenomenon, and to the extent possible we have to consider evolutionary models within a population context.

    It’s the failure to appreciate this idea that annoys me about much of Pigliucci’s recent advocacy. His ideas, and those of West-Eberhard and others, seem to me to be various ways of claiming to make an end-around out of population thinking.