Proving Evolution the Hard Way

Using genomes and codon ratios to estimate selective pressures was so easy... why is it not working?

The fruits of evolution surround us with abundance, from the tallest tree to the tiniest bacterium, and the viruses of that bacterium. But the process behind it is not immediately evident. It was relatively late in the enlightenment before Darwin came up with the stroke of insight that explained it all. Yet that mechanism of natural selection remains an abstract concept requiring an analytical mind and due respect for very inhuman scales of the time and space in play. Many people remain dumbfounded, and in denial, while evolutionary biology has forged ahead, powered by new discoveries in geology and molecular biology.

A recent paper (with review) offered a fascinating perspective, both critical and productive, on the study of evolutionary biology. It deals with the opsin protein that hosts the visual pigment 11-cis-retinal, by which we see. The retinal molecule is the same across all opsins, but different opsin proteins can "tune" the light wavelength of greatest sensitivity, creating the various retinal-opsin combinations for all visual needs, across the cone cells and rod cells. This paper considered the rhodopsin version of opsin, which we use in rod cells to perceive dim light. They observed that in fish species, the sensitivity of rhodopsin has been repeatedly adjusted to accommodate light at different depths of the water column. At shallow levels, sunlight is similar to what we see, and rhodopsin is tuned to about 500 nm, while deeper down, when the light is more blue-ish, rhodopsin is tuned towards about 480 nm maximum sensitivity. There are also special super-deep fish who see by their own red-tinged bioluminescence, and their rhodopsins are tuned to 526 nm. 

This "spectrum" of sensitivities of rhodopsin has a variety of useful scientific properties. First, the evolutionary logic is clear enough, matching the fish's vision to its environment. Second, the molecular structure of these opsins is well-understood, the genes are sequenced, and the history can be reconstructed. Third, the opsin properties can be objectively measured, unlike many sequence variations which affect more qualitative, difficult-to-observe, or impossible-to-observe biological properties. The authors used all this to carefully reconstruct exactly which amino acids in these rhodopsins were the important ones that changed between major fish lineages, going back about 500 million years.

The authors' phylogenetic tree of fish and other species they analyzed rhodopsin molecules from. Note how mammals occupy the bottom small branch, indicating how deeply the rest of the tree reaches. The numbers in the nodes indicate the wavelength sensitivity of each (current or imputed) rhodopsin. Many branches carry the author's inference, from a reconstructed and measured protein molecule, of what precise changes happened, via positive selection, to get that lineage.

An alternative approach to evolutionary inference is a second target of these authors. That is a codon-based method, that evaluates the rate of change of DNA sites under selection versus sites not under selection. In protein coding genes (such as rhodopsin), every amino acid is encoded by a triplet of DNA nucleotides, per the genetic code. With 64 codons for ~20 amino acids, it is a redundant code where many DNA changes do not change the protein sequence. These changes are called "synonymous". If one studies the rate of change of synonymous sites in the DNA, (which form sort of a control in the experiment), compared with the rate of change of non-synonymous sites, one can get a sense of evolution at work. Changing the protein sequence is something that is "seen" by natural selection, and especially at important positions in the protein, some of which are "conserved" over billions of years. Such sites are subject to "negative" selection, which to say rapid elimination due to the deleterious effect of that DNA and protein change.

Mutations in protein coding sequence can be synonymous, (bottom), with no effect, or non-synonymous (middle two cases), changing the resulting protein sequence and having some effect that may be biologically significant, thus visible to natural selection.

This analysis has been developed into a high art, also being harnessed to reveal "positive" selection. In this scenario, if the rate of change of the non-synonymous DNA sites is higher than that of the synonymous sites, or even just higher than one would expect by random chance, one can conclude that these non-synonymous sites were not just not being selected against, but were being selected for, an instance of evolution establishing change for the sake of improvement, instead of avoiding change, as usual.

Now back to the rhodopsin study. These authors found that a very small number of amino acids in this protein, only 15, were the ones that influenced changes to the spectral sensitivity of these protein complexes over evolutionary time. Typically only two or three changes occurred over a shift in sensitivity in a particular lineage, and would have been the ones subject to natural selection, with all the other changes seen in the sequence being unrelated, either neutral or selected for other purposes. It is a tour de force of structural analysis, biochemical measurement, and historical reconstruction to come up with this fully explanatory model of the history of piscene rhodopsins. 

But then they went on to compare what they found with what the codon-based methods had said about the matter. And they found that there was no overlap whatsover. The amino acids identified by the "positive selection" codon based methods were completely different than the ones they had found by spectral analysis and phylogenetic reconstruction over the history of fish rhodopsins. The accompanying review is particularly harsh about the pseudoscientific nature of this codon analysis, rubbishing the entire field. There have been other, less drastic, critiques as well.

But there is method to all this madness. The codon based methods were originally conceived in the analysis of closely related lineages. Specifically, various Drosophia (fly) species that might have diverged over a few million years. On this time scale, positive selection has two effects. One is that a desirable amino acid (or other) variation is selected for, and thus swept to fixation in the population. The other, and corresponding effect, is that all the other variations surrounding this desirable variation (that is, which are nearby on the same chromosome) are likewise swept to fixation (as part of what is called a haplotype). That dramatically reduces the neutral variation in this region of the genome. Indeed, the effect on neutral alleles (over millions of nearby base pairs) is going to vastly overwhelm the effect from the newly established single variant that was the object of positive selection, and this imbalance will be stronger the stronger the positive selection. In the limit case, the entire genomes of those without the new positive trait/allele will be eliminated, leaving no variation at all.

Yet, on the longer time scale, over hundreds of millions of years, as was the scope of visual variation in fish, all these effects on the neutral variation level wash out, as mutation and variation processes resume, after the positively selected allele is fixed in the population. So my view of this tempest in an evolutionary teapot is that these recent authors (and whatever other authors were deploying codon analysis against this rhodopsin problem) are barking up the wrong tree, mistaking the proper scope of these analyses. Which, after all, focus on the ratio between synonymous and non-synonymous change in the genome, and thus intrinsically on recent change, not deep change in genomes.

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