Evolving Thoughts

Evolution, culture, philosophy and chocolate! John Wilkins' continuing struggle to come to terms with impermanence... "Humanus sum, nihil humanum a me alienum puto" - Terence

Thursday, June 01, 2006

Microbial species 5: A new beginning

Well after reading many papers by various bacteriologists, mycologists, and other non-vertebrates specialists, I have come to the conclusion that there is no single set of conceptions or criteria (that much abused word!) for something being a species in non-sexual organisms, which I am here calling "microbial". Of course, as I noted, microbes can be "sexual" in various ways. They can share genes via cross-species viral infection (transfection or transduction), via gene fragment uptake (transformation), via sharing in a protosexual way (conjugation), and so on, with it being occasional and rare through to being frequent. They can do this across many clades or only a few. As Butch Cassidy's opponent Harvey Logan observed, there are no rules in a knife fight...

So the Problem of Homogeneity stands in need of explanation. One way it can be explained is in terms of a Branching Random Walk (BRW) with extinction (Pie and Weitz 2005). This generates heterogeneity in the absence of selection even if the extinction is stochastic. If developmental entrenchment is permitted (that is, the longer a gene has been in the lineage, the more tightly developmentally integrated the lineage is to that gene, making change likely to disrupt viability of the organisms, the less heterogeneous the genome distribution, but arguably that involves prior selection for genetic harmony. Still, the "null model" here allows for some heterogeneity just from random events.

As selective pressures are introduced, we get a range of homogeneity-causing processes. Endogenous selection for harmonious genes, which occurs in sexual species through reproductive compatibility, also occurs in microbial species through developmental entrenchment, and possibly also via lateral transfer, although this while sometimes sufficient, appears not to be necessary nor always sufficient. As the frequency and degree of genetic exchange increases, so too does the contribution of exchange to maintaining homogeneity, and this I call endogenous selection.

Ecological selection, or tracking fitness peaks, is, I think, going to be a much stronger "force" in maintaining genomic homogeneity, and this I call exogenous selection. However, given that stochastic "forces" can cause both differentiation (heterogeneity) and clustering (homogeneity), we might expect that ecological selection is indistinguishable from the BRW model, unless there is both a strong signal of ecological adaptation and functionality of the shared genes, and a relative stability of the genome itself. Of course, sometimes neither information is available, but that is an epistemological problem rather than an ontological or causal one.

Note that this is not going to specify exact and constant criteria for microbial specieshood. There are sexual species that are ephemeral, and there are microbial species that have all the "right" preconditions for being a species in place and yet do not behave like them. This is a first-approximation conception of microbial species, and deviants are highlighted by its adoption, so that the reasons why each one is not a species, or species that fail to meet these conditions are, can be further investigated.

That the basic notion of species is a quasipsecies model is not exactly to return to a phenetic or "typological" notion of species*. Rather it is the recognition that there has to be some phenomenally salient clustering of properties for something to be a species. What we do with it afterwards, how we explain it, or identify it, is a matter of empirical work.

Now to sum up the lessons. I argued that the best way to think of microbial, and by extension all sexual, species is twofold: Templeton's Cohesion concept, and Mallet's Genetic Cluster concept. We need to add to this something like de Querioz's General Lineage concept as well. Templeton gives us a causal requirement. Mallet' gives us a phenomenal requirement. De Querioz gives us the evolutionary, or phylogenetic, precondition. We might therefore specify that a species, microbial or otherwise, is this:
A species is a lineage or set of closely related lineages [De Querioz] that clusters genomically [Mallet] through either stochastic [Pie and Weitz] or cohesive [Templeton] mechanisms and processes, which can be due to exogenous selection tracking fitness peaks or endogenous selection for compatibility with genetic exchange, or some admixture of both.
Add to this my Synapomorphic Species Concept, which is a general specification of the notion of biological species rather than a particular conception:
A species is a lineage separated from other lineages by causal differences in
and you have more than enough from me on species definitions for now...

* I object to the caricature of types that one finds in the biological literature. Types were always more-or-less notions, and they were rarely, if ever, identified with static entities. It's time to put that notion to bed (Winsor 2003)


de Queiroz, Kevin (1998), "The general lineage concept of species, species criteria, and the process of speciation", in Daniel J Howard and Stewart H Berlocher (eds.), Endless forms: species and speciation, New York: Oxford University Press, 57-75.

Mallet, J (1995), "The species definition for the modern synthesis", Trends in Ecology and Evolution 10 (7):294-299.

Pie, Marcio R., and Joshua S. Weitz (2005), "A Null Model of Morphospace Occupation", Am Nat 166 (1):E1-E13. [This paper is not specifically about species concepts, but it transfers nicely to phylogenetic clustering of asexuals.]

Templeton, Alan R. (1989), "The meaning of species and speciation: A genetic perspective", in D Otte and JA Endler (eds.), Speciation and its consequences, Sunderland, MA: Sinauer, 3-27.

Winsor, Mary Pickard (2003), "Non-essentialist methods in pre-Darwinian taxonomy", Biology & Philosophy 18:387-400.