Monday, February 28, 2005 the light of genetics.

Theodosius Dobzhanksy famously wrote, "Nothing in biology makes sense except in the light of evolution." Dobzhansky, considered one of the foremost figures of the modern synthesis, grossly underestimated his importance to the field of biology. Given the modern state of both evolutionary biology and molecular genetics, I propose that the twenty-first century edition of Dobzhanksy's quote should be:
Ecologists and paleontologists may sneer at my comment and claim that I am approaching evolutionary biology from an extanto-centric (ok, I just made that word up) and far too genetical perspective. I highly disagree, for while there is much to learn from ecological and paleontological studies, they mean nothing if we cannot prove that any observed variation is heritable. In it's purest form, the biological theory of evolution refers to the change in allele frequencies over time -- this is studied by population geneticists and researchers looking at molecular data.

The most important discovery in evolutionary biology of the twentieth century was not made by Dobzhansky, Ernst Mayr, R.A. Fisher, J.B.S Haldane, or Sewall Wright, but by G.H. Hardy and Wilhelm Weinberg. Hardy and Weinberg independently came up with what is now referred to as the Hardy-Weinberg equilibrium. Assuming no mutation, no migration into the population, no natural selection, large population size, and random mating, they showed that allele frequencies will not change and genotype frequencies will stabilize at certain equilibrium values after one to two generations of random mating. Hardy and Weinberg proved that MENDELIAN INHERITANCE DOES NOT CHANGE ALLELE FREQUENCIES.

Prior to their discovery, no one had synergized Mendel's findings with Darwin's theory. From Mendel's experiments, it appeared that genotype and allele frequencies could change over time because different crosses produced different numbers of phenotypes. However, when examining all of the mating in a population, it turns out that allele frequencies do not change. This simple theory laid the groundwork for all of the theoretical population geneticists to formulate the modern synthesis (these simple populations were later referred to as "Wright-Fisher populations").

Only by violating one or more Hardy-Weinberg assumptions can we cause allele frequencies to change. For instance, if we impose directional selection, one allele will approach fixation while the other allele will be lost (a deterministic process). On the other hand, if we have a small population, genetic drift (a stochastic process) can lead to the loss or fixation of an allele via random chance. As you can see, both of these violations of the Hardy-Weinberg assumptions lead to changes in allele frequencies and evolution.

Every theory in population genetics, from the earliest models by Wright and Fisher to modern coalescent theory, relies on the important discovery by Hardy and Weinberg: random mating does not change allele frequencies. In order for evolution to occur within a population allele frequencies must change. When evolution occurs between populations or leads new species (speciation) allele frequencies at at least one locus must change. By showing that Mendelian inheritance alone cannot lead to these changes, Hardy and Weinberg gave birth to the field of population genetics and allowed us to study evolution using molecular data (the material of heredity). Whether population structure, genetic drift or natural selection are the main forces of evolution and speciation are debatable, but you never hear any legitimate biologist say that random mating causes evolution thanks to a clever physician and a curious mathematician.

Monday, February 21, 2005

Human Inversion Under Selection

Chromosomal inversions have been studied for nearly a century by geneticists and cytologists. Early researchers could visualize inversions in Drosophila via polytene chromosomes, and Sturtevant (1926) realized that inversions suppress recombination in laboratory experiments. This helped Dobzhansky and others develop the theory of coadaptation to explain how inversions can maintain favorable combinations of alleles in cis (i.e., on the same chromosome). There has also been extensive work done on inversions and sex ratio biases in Drosophila -- from both a molecular and evolutionary perspective. Recent work on speciation has shed light on the role inversions can play in patterns of nucleotide diversity between diverging taxa as well as actively encouraging speciation by suppressing recombination in heterokaryotypic individuals.

I do not want to give the impression that polymorphic genome rearrangements are a quirk relegated to
Drosophila and research on these chromosomal rearrangements does not have implications outside of Dipterans. It just so happens that a majority of the work was performed on these convenient laboratory creatures, but research in marsupials, mice, and now human (see here and here for reviews) suggests that chromosomal rearrangements segregate in natural populations of mammals as well. The question to ask is "What role do these inversions and Robertsonian fusions play in evolution?" Recent work on chromosomal inversions and human and chimp speciation has been inconclusive (see here and here for critiques and here for a rebuttal); in my opinion, the main limitation is that the model assumes sympatry or parapatry, and we have no conclusive evidence that humans and chimps speciated with gene flow.

New findings by Stefansson et al show that natural selection may act on human inversion polymorphisms and shape their frequencies in natural populations. They discovered this inversion polymorphism by accident when they were examining a gene associated with Parkinson disease. By comparing the sequence from multiple individuals in the region surrounding the gene, they were able to determine that one of the haplotypes was inverted relative to the other. (There is also a duplication associated with the inversion.)

Inversion polymorphisms are expected to maintain different alleles in different arrangements because the inversions suppress recombination. This can be seen in the phylogenies created using sequence from within the inverted region.

H1 is the wild-type arrangement, and H2 is the inverted arrangement. As you can see, in both phylogenies, the H2 allele is found outside of the H1 clade. This suggests that the two groups (H1 and H2) diverged a long time ago and that the inversion is fairly ancient. In fact, the authors date the inversion event to 3 million years ago -- half as long ago as the divergence between humans and chimps.

The authors also show that individuals carrying the inversion have more children than wild-type parents. They say that this may be due to increased recombination in mothers who carry the inversion. This may be confusing, since I told you that inversions suppress recombination. Inversions only suppress recombination within the inversion and in the area surrounding the inversion. In this study, the researchers show that females who carry the inversion have an elevated recombination rate in the rest of their genome (the inverted region is fairly small so it probably plays a minor role in suppressing recombination).

If this inversion increases fitness (by increasing fecundity), shouldn't it be found throughout the world? This is especially true if it is as old as the authors claim it is. The authors found that it is common in Europe, but rare in the rest of the world:

The black wedges on the pie charts indicate the approximate frequency of the inversion in each of the populations sampled. One possible explanation is that the inversion is under balancing selection (natural selection favoring heterozygotes), which leads to a stable polymorphism. Another explanation is that the inversion only confers a fitness benefit in the European population, but it is neutral or deleterious in the rest of the world.

If this allele is beneficial (as the authors claim) and has been under directional selection due to the fitness effect it confers on its carriers, the estimates of divergence time may be flawed. The authors assumed a neutral process when calculating divergence times. Directional selection leads to an elevated rate of evolution, and, in turn, an overestimate of divergence times. Given the data the authors present, it seems highly unlikely that this inversion really is 3 million years old. It is more probable that natural selection has acted on this recent inversion event causing it to increase in frequency in European populations. This would explain the low frequency of the allele in the rest of the world and the high frequency within Europe as well as the ancient divergence time estimate (an overestimate).

The error in the paper is minute, and this finding is still quite important. It could very well be possible that this human inversion maintains alleles that interact favorably, much like what has been Drosophila inversions. It is difficult to detect polymorphic inversions in mammals because they do not produce polytene chromosomes. More inversions may be found through rigorous examination of particular loci. Through detailed comparisons of sequence data from different inversion types, we may be able to locate signatures of selection at the sequence level (decreased polymorphism, excess non-synonymous substitutions, elevated linkage disequilibrium) and test whether Dobzhansky's theory of coadaptation applies to taxa outside of Drosophila, such as mammals.

Wednesday, February 16, 2005

The Cambrian Explosion Never Happened.

Blair and Hedges just published an article where they use molecular clocks to examine the validity of the Cambrian explosion. They conclude, "molecular clocks continue to support a long period of animal evolution before the Cambrian explosion of fossils." Their results indicate that the Cambrian explosion (a period ~520 million years ago [mya] when many animal phyla first appear in the fossil record) is an artifact of the fossilization process and not an adequate description of animal evolution.

Molecular clock estimates of divergence times work by determining the rate at which DNA sequences diverge (the rate of DNA evolution). Rates of sequence evolution are calibrated to real time (years) using the fossil record. Estimates of the divergence time of two taxa from the fossil record are used to determine the age of divergence, which can then be used to figure out how fast a genomic sequence should evolve. For instance, if two taxa diverged 50 mya and they differ at 10% of their nucleotide sites, we can say that the nucleotide sequence evolves at a rate of 2% divergence every 10 million years or 0.2% divergence every 1 million years. This rate of evolution is then used to calculate the divergence times of other taxa in which fossil evidence is scarce or non-existent.

Previous molecular studies have been inconsistent -- some support the Cambrian explosion and some refute it. Blair and Hedges argue that the results that support the Cambrian explosion are flawed because they either misapplied calibration points or used an improper model of nucleotide substitution. The allegation of calibration point misconduct is a bold one coming from the Hedges lab, considering a recent review in which the authors conclude that Hedges and collaborators' "divergence-time estimates were generated through improper methodology on the basis of a single calibration point that has been unjustly denuded of error." I'll stop at that, as I don't want any grief from the folks upstairs (and, no I don't mean god -- the Hedges lab is literally "upstairs" from me), but I will point out that Hedges and Kumar did refute the allegations here.

The concept of the Cambrian explosion is often used by anti-evolutionists as support for divine intervention during the origin of animals. If most animals appeared at the same time, they argue, evolution would fall apart since Darwin's theory depends on gradual change over time. It now appears, however, that the Cambrian explosion is a mere artifact of the fossilization process. Because fossilization is a chance process that requires multiple events of varying probabilities, the fossil record can be misleading as a true history of life on Earth. It provides a general guideline, but the first appearance of an organism or taxon in the fossil record cannot be taken as the first appearance of the taxon in history. Instead, the first appearance of a taxon in the fossil record is the first discovered fossilized account of that taxon.

If Blair and Hedges's interpretation of the molecular data is correct, many of the animal taxa that were thought to have arisen in a very short time period may have evolved over hundreds of millions of years. This is extremely consistent with Darwin's view of evolution as a gradual process, and it puts an axe through the anti-evolutionists claims that the Cambrian explosion is inconsistent with evolution.

Thursday, February 10, 2005

Science Channel - Top 100 Discoveries.

The Science Channel aired the Top 10 Science Discoveries as voted on by the viewers last night. I caught a couple of them as I was flipping through channels:

#4. The periodic table. This was cool because Bill Nye (the host of the show) interviewed my introductory chemistry professor, Roald Hoffmann. I finally realized that Nye probably selected Hoffmann because he, too, attended Cornell. It was pretty neat having a Nobel Laureate teaching my first semester chemistry course. One of the most interested assignments that semester was a book report on The Periodic Table by Primo Levi -- a semi-autobiographical tale of a young man's interest in chemistry.

#1. Natural selection. Nye introduced it as a controversial theory, which it is amongst lay-people, but not amongst biologists. It is pretty awesome, though, that even with all the attacks on evolution by the IDist/creationists, the general public still recognize the importance of this revolutionary theory. They did an adequate treatment of Charles Darwin, but they introduced him as the Naturalist on the Beagle, when, in fact, he was merely the Captain's companion. I didn't really pay much attention to this segment, as it wasn't extremely interesting and I've heard the stories so many times.