Reposted from the old blog.
OK, this is one of a series of posts in which I will play with ideas that might will become a paper.
The problem is this: usually we define a species as a group of related organisms that share genes (or a gene pool, which amounts to the same thing). Sometimes we include also ecological considerations (either in the form of natural selection, or in terms of sharing a niche).
But many microbial species either do not share genes to reproduce, or they can but do not need to. So, the question is sometimes raised whether microbes (of this kind) form species at all, or if there is some replacement term or concept for microbial taxonomy.
Historically, it took a long time to even accept that there were asexual organisms. Darwin discussed hermaphroditic species, but they still had mating types or genders; it was just that a single individual had both kinds. It was long recognised that some plants could propagate vegetatively. But the notion that there were obligately asexual organisms was doubted, for instance, by Fisher as late as 1958 (in the second edition of the Genetical Theory of Natural Selection). George Gaylord Simpson, the famous joint architect of the synthesis and paleontologist, simply denied that asexuals formed species. Call them something else, he said.
But bacteriologists, mycologists, and virologists all continued to name and describe species, even though they could not really make use of the Biological Species Concept of Dobzhansky and Mayr. They relied on their staining properties, the colony shape, the microscopic morphology of the cells, and of course the ecological conditions under which they lived. There was lacking, though, a clear definition of what a species could be for these organisms.
Part of the problem is this: if a species were obligately clonal, then each mutation would make a new clonal lineage:
and we would expect to find not clusters but a carpet of strains more or less evenly distributed. How can we account for this? I will call this the Problem of Homogeneity: why are asexual lineages ever found as groups at all? Why are they homogeneous over time, and stable enough to be called "species"?
I will follow this up in the next post, but I want to get your feedback first. [Still interested - JSW]
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John,
before you get too far along in this, you must check out Fred M. Cohan's theoretical and population genetics work on bacterial speciation. In a nutshell, Fred (I was his post-doc & have published with him on this issue) argues that if you use a Templeton-like definition of species (i.e., a species is the domain of organisms through which a mutation could spread), then species boundaries are 'fixed' by periodic selection purges: the species is the domain of bacterial lineages that could be removed by selection of one of the genotypes within species. (The model is actually quite sophisticated and is based on coalescent theory).
The upshot of this is that the phylogenetic structure of bacteria groups should have clusters or star-like radiations seperated by deep branches (which is what one typically observes in bacterial 'populations').
Hope this is useful.
Thanks. Mike. I know Cohan's work, of course, but not that particular bit, so a ref would be handy. But I do address this in the subsequent entries (which are also from my old blog). Be patient... or go read them at the the old blog.
I'm giving this, suitably expanded and academicked up, as a talk at a conference in Exeter next month, and as a paper in Studies in the History and Philosophy of Biology special edition that will come out of it. So any comments will be welcomed.
I've set up the blog to post these one a day for the next four days...
I've always preferred the spectrum analogy.
Similar to the way (in chemistry) mixtures of complex hydrocarbons are often referred to with their C-chain #'s rather than as individual compounds.
If you're considering something like volatility, the C# is readily useful as a predictor. I'm not sure how i would translate out to microbial genomics, but there must be structural (at a genetic or expression level) elements that are sufficiently identifiable.
heady blog you got here.