Phylotypic stages and evolutionary development: Part II -- The flies
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It’s just a stage. A phylotypic stage. Part II: The flies. by Stephen F. Matheson Originally posted on Panda's Thumb, December 2010. The controversy about the existence of the phylotypic stage is more than some bickering about whether one blobby, slimy fish-thing looks more like a Roswell alien than another one does. It’s about whether the phylotypic stage means something, whether it tells us something important about development and how developmental changes contribute to evolution. To answer such a question, we need more than another set of comparisons of the shape and movements of embryos and their parts. We need a completely different way of looking at the phylotypic stage, to see ifsomething notable is going on under the hood. So vertebrates all look the same at the tailbud stage. What does that mean? Embryos look the way they do because of the positions and behaviors of the cel ls that make them up. The cells in an embryo all have the same DNA, and the link between that DNA and those specific cell behaviors is the basic process of gene expression. (This is a fundamental principle ofdevelopmental biology.) And by gene expression, we usually mean the synthesis of messenger RNAunder the direction of genes in the DNA. Different cell types express different sets of genes, and the orchestration of the expression of particular genes at particular times is a big part of what makes development happen. When considering the phylotypic stage, then, developmental biologists wondered: is the apparent similarity of embryos at that stage reflected by similarities in gene expression. Or, more specifically, does the hourglass model hold up when we look at gene expression? This was the focus of the two articles in the 9 December 2010 issue ofNature that inspired the cool cover. The first report was authored by a collaborative research group headed byPavel Tomancakat the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden ; the co-first authors are Alex Kalinka and Karolina Varga, and you can find the paper (and lots more) at their excellent site.After a brief review of the hourglass model and rumors of its non-existence, they state their purpose: to address "the extent to which expression divergence underpins the morphological hourglass pattern at the genome-wide level." Their hypothesis, grounded in evo-devo ideas, was that gene expression variation would parallel the morphological variation. Put simply, theypredicted that gene expression variation would display that same hourglass pattern: lots ofvariation early and late, with less variation during that curiously conserved phylotypic stage. The investigators focused their analysis on a set of six species of fruit fly ( the famous genus Drosophila). This gave them two key advantages in their work. First, the complete genome sequence is known for all six of those species , and so the team had access to powerful comparative tools in assessing variations in gene expression. Second, the six species span some 40 million years of evolutionary divergence. That enabled the researchers to look for variation over a significant evolutionary timescale, and it was a critical aspect of their experimental design. To see why, we need to look briefly at what they actually measured. The goal was to detect variations in the level of expression of particular genes and to assess howthese changes were related both to developmental time (the age or embryonic stage of one species) and to evolutionary time (the evolutionary "distance" between one species and another). So theydeveloped a parameter called the GST, which represents the amount of variation (over time) in expression exhibited by a particular gene. The authors’ description of this analysis might be interesting and comprehensible to many readers: Our measure of temporal divergence is the three-way interaction between genes, species, and time points, the GST values. These values capture the extent to which the 1
