Tuesday, September 02, 2008

Evolution: Bacterial DNA exchange

DNA refers to complex molecules that contain genetic data for all living organisms. The most commonly understood locus for that data is the genomic DNA in the nucleus of each cell in an organism - or in the nucleoid (a somewhat nucleus-like region), in the case of prokaryotes (less complex, mostly single-celled organisms that lack a nucleus per se).

There are various other loci for that genetic data, beyond the core genomic DNA in cell nuclei - for example, mitochondria, viruses and plasmids, for example.

DNA is typically transmitted direct by direct inheritance, sexual reproduction in most more complex organisms, binary fission in more elemental organisms such as bacteria. Yet we see evidence that as well as that "vertical" data transmission, some "horizontal" exchange of genetic data takes place. I noted here that Bdelloid rotifers somehow acquire DNA from a number of sources outside the species.

Bacteria apparently exchange DNA too. A recent paper in the journal Science discusses this (also reported in New Scientist). Two species of bacteria, Campylobacter jejuni and Campylobacter coli, share about 87% of their genetic material, suggesting they diverged about 100 million years ago (by contrast, humans and chimpanzees share about 94%, having diverged about 6 million years ago). These bacterial species don't normally run into each other in the wild, as they inhabit different animals. But the artificial environment of farms has brought their environmental niches together, where they have both been able to infect chickens and cattle.

Samuel Shepherd and colleagues from Oxford University found one variety of C. coli was carrying more genes from C. jejuni than others studied; in nearly all cases, the genetic sequence in question was unchanged between species. This suggested they were exchanging DNA recently; the scientists' analysis indicated they were converging more quickly than mutation was diverging them.

This is said to be the first concrete evidence that speciation of bacteria is affected by environment in a similar fashion to more complex animals. I find it very surprising that it is a first; intuitively, it makes good sense that environment influences evolution in bacteria just as much as in other living things.

Further, I would be very reluctant to call this species convergence, as the report's authors do. The bacteria's genetic driftage would be a trend, but it would be hard to call it an absolute. I reckon it would be particularly unlikely for species to perfectly converge such that their genetic material is cleanly lined up identically at all points. I'm happy to be proven wrong, but I don't think this will happen. I would posit a randomness to the exchange, similar to the randomness of mutation. (However, at this stage we don't know the speed of the exchange: whether environment or proximity can hasten it to the point of a blur.)

Aside from the exchange of genetic material, the article makes the point that there remains disagreement over the nature of speciation in bacteria, and how the boundaries of species are maintained. My understanding of this issue would related to the nature of species stability in more complex organisms: the fact that sexual reproduction necessitates an exchange of genetic material at each generation would inherently stabilise species, whereas surely binary fission would normally destabilise. Mutations in sexual reproduction have only a 50% chance of being carried forwards, whereas in binary fission (perfect replication or no), any mutations are carried forward at each generation.

So why would bacterial species ever maintain stability? Two possibilities are the DNA exchange mechanism (a stabiliser in the immediate term), and environmental factors over the longer term.

All this is a mere curtain raiser for the role in DNA propagation of... viruses.

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