The smoking gun of evolution?

Synteny is the concept that gene order is conserved across species. So, for example, the hoxb gene family sits in order from hoxb1 through hoxb9 as you move along human chromosome 17. If you look at these genes in the mouse and zebrafish, they're still ordered 1 through 9, but on mouse chromosome 11 and zebrafish chromosome 19. This conservation of gene order holds true for large segments of genomes across birds, fish, insects, mammals, and probably more.

Now the reason synteny alone isn't a compelling enough argument for evolution is the idea of God's blueprint. The reason, so the argument goes, that gene order (and more detailed sequence) is conserved is because God has a general blueprint for all creatures that represents the optimal conditions for development. So our genomes are similar by design, not because of common ancestors. In fact, the general gene order on human chromosome 17 happens to be almost entirely conserved on mouse chromosome 11.

But the rest of the genome isn't such a perfect fit. The large segments of synteny are broken up between species, approximately 420 segments between mouse and human. Now that we have genomic sequence information, the breakpoints can be defined. For example, where mouse chromosome 11 stops looking like human chromosome 17, it starts looking like human chromosome 1. The immediate implication is that at some point in evolution, the human/mouse ancestor either had mouse chromosome 11 and this split in humans into human chromosomes 1 and 17 (and others), or the ancestor had human chromosome 17 and it fused with human chromosome 1 (and others) in mice.

That's where some recent papers come into play. Researchers noticed that these synteny breakpoints had an overabundance of segmental duplications surrounding them. That means that chunks of chromosome near the breakpoints somehow duplicated (probably through a process called non-homologous end joining and maybe breakage-fusion-bridge cycles). Instead of the computed 18% of breakpoints being associated with these "seg dups" if they were randomly distributed, 25% were associated. [It's important to note that this number excludes repeats at the centromere and telomere (ie, the ends) of chromosomes because those repeats are believed to occur through mechanisms that may not be involved in speciation.]

So, even if God had a blueprint for gene order, the "smoking gun" of evolution is that these segmental duplications mark events in evolutionary history where ancestral chromosomes broke apart and fused together to give the modern array of species and genomes. Furthermore, many of the synteny breakpoints occur at locations where human diseases are known to be caused by chromsome breaks and fusions. This led to the hypothesis that many breakpoints are "fragile regions" of the genome that are more likely to participate in speciation. It's the most parsimonious explanation for the data (not that that ever deterred creationists), and begins to give some insight as to what that ancestral organism was like.

Incidentally, my friend Bryan is working on creating an artificial ancestral genome of a plant pathogen by first comparing all the known variants and deriving the ancestor based on sequence and gene order. It would be exciting in the far future to find the human "missing link" genetically even without fossil evidence.  ¶ 10:55 PM

  I've moved the blog to blogspot.com because it wouldn't publish to the knapphouse website. This should motivate me a little more (or at least remove a major obstacle) to write more often. I've found that trying to record myself talking makes me too self conscious to say anything useful, so I'll have to just try and remember.  ¶ 5:24 PM