Friday, June 20, 2008

The Amphioxus Genome

The amphioxus genome and the evolution of the chordate karyotype. 2008. N. H. Putnam et al. Nature 453: 1064-1071.

The newly sequenced genome of the lancelet (amphioxus) provides the evidence that vertebrates evolved over the past 550 million years through a four-fold duplication of the genes of more primitive ancestors.
From the press release:

“amphioxus and humans had a common ancestor 550 million years ago, which allows us to use amphioxus as a surrogate for that ancestor in terms of understanding how vertebrate genomes evolved. If you compare the 23 chromosomes of humans with the 19 chromosomes of amphioxus, you find that both genomes can be expressed in terms of 17 ancestral pieces. So, we can say with some confidence that 550 million years ago, the common ancestor of amphioxus and humans had 17 chromosomal elements.”

Each of those 17 ancestral segments was duplicated twice in the evolution of vertebrates, after which most of the routine "housekeeping" genes lost the extra copies. Those left, totaling a couple thousand genes, found new functions that make us different from all other creatures.

"These few thousand genes have been retooled to make humans more elaborate than their simpler ancestors. They are involved in setting up the body plan of an animal and differentiating different parts of the animal. The hypothesis, pretty strongly supported by this data, is that the multiplication of this particular kind of gene and differentiation into different functions was important in the formation of vertebrates as we know them."

The researchers are trying to reconstruct what happened at the end of the Cambrian period 550 million years ago, when a creature similar to the lancelet evolved and diverged into three types of chordates: cephalocordates like the lancelet; urochordates like the sea squirt; and vertebrates like us. Cephalocordates and urochordates are invertebrates that have a flexible notochord rather than a bony spine protecting their spinal cord.

Interestingly, the sea squirt Ciona intestinalis, a tunicate, was previously thought to belong to the the earliest chordate lineage because of the sea squirt's very simple body plan. Comparison of the lancelet, sea squirt and human genomes, however, show instead that the lancelet lineage diverged before the tunicates and vertebrates.