When we attempt to apply to organisms that are not obligately sexual (that is, which don't have to have sex to reproduce) concepts that were specified to use with those that are, we have problems. The Recombination Model is one such attempt. Sure, some microbial species exchange genes. Others do it more frequently and more completely. There appears to be a continuum of gene exchange all the way from almost never to almost every time. So why should we expect that gene transfer will provide us with the sort of homogeneity of lineages and quasispecies that it does in obligate sexuals?
In part I believe this is because we always start from what we know. As I mentioned, the existence and ubiquity of asexual organisms has been resisted from a long time, and treated as exceptional rather than the rule, because biology began with large scale plants and animals, where the paradigm cases were encountered for the biospecies concept. As exceptional cases were encountered, these concepts were stretched, and modified, to serve the increasingly "deviant" cases, until now we realise that deviance is relative to the paradigm conceptions rather than a fact about the organisms. What should we say instead?
I believe we should treat this continuum idea more seriously and as the basis from which the metazoan and metaphyte conceptions are drawn out. And we should consider how the two factors of the Templeton conception - exchange and ecological niche - play differing roles according to the degree of sex a lineage has.
Before I deal with this in detail, let me note for the record that there can be, and must certainly often be, other reasons why the carpet is not smooth, but is patchy. Extinction can cause there to be patches in genome space. Some varieties die out. While this can be because of selection, often it will be due to plain old genetic drift, and contingency. A lineage of asexuals can stochastically drift due to random biases in the direction of mutation, for instance, while earlier forms can go extinct simply because of random drift or random termination of that clone. Moreover, if a genome evolves in a habitat that is sensitive to sudden changes in climate or even geological change that degrades it, then that genome and its neighbours will become extinct. Evolution doesn't explore the same coordinates in genome space all the time and everywhere. This is similar to the phylogenetic trends that occur through simple stochasticity, because clonal evolution is phylogeny.
So, back to the notion that sex is not an all-or-nothing affair, so to speak. If the continuum ranges from 0% gene exchange (total asexuality) to 50% gene exchange (total sexuality), then it follows that at the asexual end, exchange can have only limited to no effect on maintaining homogeneity, while at the sexual end, it can have a very great role in maintaining homogeneity. Likewise, at the asexual end, homogeneity not due to stochastic effects will be due largely to ecological selection (fitness peak tracking), while for sexuals this will not be so great a cause. I have given a schematic graph to illustrate this.
This will be why we find that gene exchange doesn't have a simple relationship to genomic homogeneity. It will depend on the rate and amount of genes shared across lineages case by case, as well as the degree to which the quasispecies is maintained by ecological interchangeability. Following on from my discussion about speciation earlier, and my 2001 paper on species concepts, where I employed this evolutionary aspect of the nature of sex to argue that being a species is an evolved trait, not a natural kind, we ought to expect that each species and group of species has its own unique evolutionary history and therefore properties, just as limbs and lungs and livers do. There will be a more general theoretical context of adaptive landscapes, genetic dynamics, and so on, but given that each evolutionary group has encountered different conditions, this means that each modality will be shared in a fairly limited way.
Moreover, this means that biospecies is not the most basal notion of species. In fact, biospecies, or reproductive conceptions of species in general, are derived modalities. The basal notion is quasispecies. All species are at least quasispecies; some are in addition reproductive cohesion or isolation conceptions. This means that some standard requirements for biospecies, such as reciprocal monophyly, do not need to apply to all species. But there is one rather interesting aspect to this approach that I find illuminating, although your mileage may vary: a simple quasispecies is cohered by more or less one adaptive peak (if it is cohered; stochastic clustering does not imply this), while a biospecies famously can be and often is adapted as a generalist or have polytypic traits for differing adaptive peaks.
What maintains a sexual species in this case will be, therefore, the combination of extrinsic selection, and internal or intrinsic cohesion, due to selection for reproductive compatibility with potential mates. I have a paper forthcoming in Biology and Philosophy which argues this in detail. Microbial species will tend to depend on adaptive peak cohesion inversely to the degree that they do share their genes and directly to what functional value of those genes they share have ecologically.
Here is a nice image that shows that even among eukaryotes, reciprocal monophyly is not always the case for species. It's from a paper in PLOS Computational Biology critical of the DNA Barcoding proposal.
Each version shows two species, X and Y. In A, X and Y are reciprocally monophyletic, which means that the coalescent (or last common shared genomic node in the tree, shown by the open stars) is different for each of them and is not nested within either. In B, Y is nested in X, and so X is paraphyletic, although Y is monophyletic. In C, X and Y are interspersed, phylogenetically, in each other, and so each species is polyphyletic and share a coalescent.
Of course in sexual species this raises the question of what makes X and Y species in the latter two cases (that is, why do we think they are different species? The usual answer is either based on mating behaviours, ecology or morphology, or some mix of these) but in asexuals this will occur when the two species cluster genomically as quasispecies in different ways despite being convergently evolved.
Enough for now. I'll wrap up this series next post.
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