The Genotype and the Phenotype and How to Measure Divergence
PZ Myers has ventured out from Minnesota to visit Toronto. His car died on the way back to Morris, and he decided to do some reading, which led to some blogging on, what else, evo-devo, which, in turn, led to a discussion of Endless Forms Most Beautiful, and Jerry Coyne's review of the book. Coyne was somewhat critical of the book, and I'm a bit more apologetic of Coyne (being a population geneticist) than is Myers (being a developmental biologist). Myers writes:
"Carroll begins by noting the disparity between the rates of evolution in proteins vs. the rates of anatomical change. Compare chimpanzees and humans, for instance, and you see major differences in morphology, but the differences at the level of the gene sequences are relatively small."My biggest problem with comparing sequence level divergence with anatomical/morphological/phenotypic change results in how well we understand the two processes and how we measure the two types of divergence (genotypic vs. phenotypic).
For those unfamiliar, sequence level divergence is much easier to calculate and is extremely more objective than phenotypic divergence. Of course, choosing the sequences to study is somewhat subjective, but with whole genome sequences we can examine the entire genome at whatever scale is appropriate (DNA level for closely related taxa, and protein level for more distantly related taxa); this removes some of the subjectivity.
Morphological divergence, on the other hand, is more difficult to get your head around. How do we choose characters to study? How do we measure those characters? What role do our predispositions and preconceptions play in these analyses? Molecular data is not immune from these limitations in any way, but they pose a much bigger problem for anatomical characters (in my opinion).
Who is to say that the "major differences in morphology" between humans and chimps can't be explained by the protein divergence between the two species? Well, me, for one. I do believe that expression divergence (in both cis and trans), as well as splicoforms, is important for morphological/phenotypic diversification. I'm not sure, however, what proportion of morphological divergence is due to changes in cis elements and what proportion is because of evolution of protein sequence. Oh, and don't forget the role gene duplication can play in allowing genes to evolve novel expression profiles.
We have a hard enough time trying to figure out how to measure expression divergence, and this seems to be the next step up in complexity from the sequence level. I'd shy away from comparing sequence level divergence to morphological divergence until we have better statistics for estimating phenotypic divergence (at any level, from mRNA expression to anatomy). Some neat work on the evolution of gene expression, by the way, is being done by one of Sean Carroll's former students, Tricia Wittkopp. Wittkopp is working to unravel the relative roles cis elements (i.e., regulatory sequences) and trans elements (transcription factors and their cis and trans elements) play in the divergence of gene expression. Plus, she gets mad props for doing a post-doc with Andy Clark, a top-notch population geneticists, showing you can straddle the line between developmental biology and population genetics.
Basically, comparing sequence divergence to anatomical divergence is -- to overuse the metaphor -- like comparing apples to oranges. Before anyone starts saying the amount of morphological divergence cannot be explained by the amount of protein sequence divergence, wait until we have more objective measures of morphological divergence.