You'll remember, because you have all memorised my blog going back two years, that I blogged on what microbial species are before, and have a paper on that subject coming out in History and Philosophy of the Life Sciences. In it I argue that microbial species, particularly bacterial species, are maintained as phenomenal clusters by two mechanisms. One is the exchangeability of genetic material, which is akin to interfertility in sexual organisms, a hypothesis proposed by Dykhuizen and Green called the "core genome" hypothesis. The other is adaptive niche tracking.
Now a paper has come out in Science, in which Adam C. Retchless and Jeffrey G. Lawrence of the University of Pittsburgh test the proposed separation mechanisms of bacterial species. Their abstract reads:
Because bacterial recombination involves the occasional transfer of small DNA fragments between strains, different sets of niche-specific genes may be maintained in populations that freely recombine at other loci. Therefore, genetic isolation may be established at different times for different chromosomal regions during speciation as recombination at niche-specific genes is curtailed. To test this model, we separated sequence divergence into rate and time components, revealing that different regions of the Escherichia coli and Salmonella enterica chromosomes diverged over a ~70-million-year period. Genetic isolation first occurred at regions carrying species-specific genes, indicating that physiological distinctiveness between the nascent Escherichia and Salmonella lineages was maintained for tens of millions of years before the complete genetic isolation of their chromosomes.
The "biological species concept" of Dykhuizen and Green for bacterial species is shown to work well for long-separated species like S enterica and E coli, but not for bacterial species in the process of separation, so-called incipient species. This is because their genomes haven't yet diverged enough so that horizontally transferred genes are non-functional (forming the "reproductive isolation" needed for this kind of species to exist). Selection for adaptive niche functional genes will be localised to those genes that are functional in the particular niche these species exploit.
It's nice to be shown to be more or less on the right track...
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Interesting. How sharp or fuzzy is the line between pairs of long-separated species versus pairs of incipient species?
I'll have to take a look at this one. Could be interesting from the whole "Darwinian threshold" concept of early bacterial phylogeny (which I'm not really a fan of, but that's a story for another time).
Jonathan: I'd expect that "long-separated" vs. "incipient" would grade into each other - two extremes of the spectrum. Even widely separated organisms (such as a eubacterium and an archaeon) can still occassionally swap genes on rare occassions.
Because bacterial recombination involves the occasional transfer of small DNA fragments between strains, different sets of niche-specific genes may be maintained in populations that freely recombine at other loci.
If that was written:
"Because hybridization involves the occasional transfer of genes between populations/sub-species, different sets of niche-specific genes may be maintained in populations that freely recombine at other loci."
I could have sworn it came out of the Rieseberg lab or some similar creature. In fact, the stuff about heterogeneity in divergence between different regions of the genome is now standard fare in studies of parapatric animal and plant populations. Of course, the differences in divergence between different regions are due to structural features, but result in the genes contained within those structural features becoming "speciation genes". Alas, bacterial recombination is an entire beast altogether, so I doubt that structural features play a large role in heterogeneous divergence between bacterial genomes.
Bacterial recombination is also "an entirely different beast"....
Speciation taking 70 million years... hmpf. I'll let Darwin speak (letter to Joseph Hooker, 24 December 1856):
Why do any bacteriologists want to import the "species problem"? They really don't need to. With asexual organisms, you can simply work with clades all the way down, and there is no "cladogenesis problem".
On another note, how was the molecular divergence date estimate calibrated, in the absence of a fossil record?
And yet I can quote Darwin on many occasions trying to work through what species are. He did not, contrary to popular opinion, deny that they existed, temporarily, but that they had some definition that worked in all cases.
Bacteriologists and other microbiologists have to work with species for the same reason that other biologists do - they are phenomenal realities that call for explanation. If you like I can send you my paper...
The real reason, it seems to me, is that the nomenclature codes require that every organism must belong to a species, so, in order to name the taxa they want to talk about, people must give them species rank. Except when they talk about inofficial phenomena like "strains" anyway.
But please send me your paper. Have you got my e-mail address?