Sunday, December 04, 2005

Platynereis dumerlii, Acropora millepora and the Human Genome: Part Three

There are two issues. One is that a large number of genes in Drosophilia melanogaster and Caenorhabditis elegans are highly modified. Another is that, as mentioned in previous posts, D. Melanogaster and C. elegans may be more closely related to each other than to vertebrates. The two combined suggest that comparisons based only on these organisms could be misleading. What about using a different outgroup, such as the Cnidaria? The Cnidaria are regarded as a sister group to the Bilateria (that is, those organisms displaying bilateral symmetry). Results of several such comparisons are interesting. For example, the paper linked to above focused on Acropra millepora - a type of coral considered to be a basal metazoan - and discovered striking asymmetries in the frequency of gene loss across the Bilateria. More specifically, the study noted that extensive gene loss had occured in Drosophilia and Caenorhabditis while vertebrates seemed to conserve genes. In other words, vertebrates in general, and humans in particular, share more similarities with Acopora than flies and nematodes do. How is this possible? The divergence times between theses groups extend quite a ways back and one would expect humans to share few sequences in common with Acropora. According to the study:

Although a close relationship between coral and human sequences is superficially surprising given that the cnidarian and bilaterian lineages are thought to have diverged in deep Precambrian time [22], this is largely a consequence of the relative pace of change in the model invertebrates. The greater divergence in D. melanogaster and C. elegans sequences is unlikely to reflect uniform rates of change over long time periods; rather, rapid genome change is likely to have occurred recently (and probably independently) in these organisms and be associated with intense selection for small genome size, rapid developmental rates, and the highly specialized lifestyles of the fly and worm. Although D. melanogaster had the previously reported fastest rate of sequence change, the genes of C. elegans are evolving even faster [23 and 24], and genome rearrangements are occurring approximately four times faster in the worm than in the fly [24]. Typically long branch lengths in phylogenetic analyses (see Figure 2) support the idea that many D. melanogaster sequences are highly derived relative to their coral and human counterparts. This is also true of many C. elegans sequences [23 and 25]. (the numbers are to references in the original article - afarensis)

A similar study involving Platynereis dumerlii comes to much the same conclusion. PZ Meyers has a explanation of this bit of research.
This result, that humans are evolutionarily slow has been portrayed as a bit of a surprise, but is something that has been in the works for awhile. For example, as early as 1992 it was known that insulin genes in humans and apes evolved at a slower rate than in monkeys. The phenomena, called the "Hominid-rate-slowdown hypothesis". was first suggested by Goodman in a 1961 paper entitled "The Role of Immunochemical Differences in the Phyletic Development of Human Behavior" (published in Human Biology) and led to papers being published on the subject up to the present (here and here for example). Which, of course, indicates evolutionary biologists need to pay more attention to anthropologists!
The larger point to these posts is that scientific research raises more questions than it answers and leads us down new, unexpected, paths. I started this series looking at the relationship between nematodes, flies and humans and followed a path to recent rapid genome chang in flies and the hominid slowdown hypothesis. HAd we gone back in time rather than forward we would have ended up talking about the origin of methanogenesis and phototrophy or or the rise of multicellular life.