I've been meaning to write about this article in Nature for about a week now. I started writing about a half-hour ago, got about halfway through, then accidentally deleted the post. Now, I'm off to start again. I'd like to point out that this is an essay, not a research article, and I've learned that it's a lot harder to comment on essays and reviews than on primary research.
The authors deal with the problems associated with cryptic species. I've taken cryptic species to mean, "morphologically indistinguishable to the researcher examining the population." This definition leads me to conclude that cryptic species are not a true biological phenomenon, but a byproduct of the study of natural populations. They are only called cryptic because we cannot tell them apart, just like we have categorized all Drosophila species into a single genus, when we could have put them in an order or family if we so desired.
I will use the biological species concept (BSC) for my discussion since it is the most widely accepted species concept for dealing with sexually reproducing species -- I'll ignore asexually reproducing species for now even though they make up the majority of life on earth. The BSC states that two populations (or lineages) deserve species status if they cannot form viable and fertile hybrids. Conversely, all populations within a single species are capable of exchanging genetic information in a process known as gene flow, which can be diagnosed using molecular markers and used to infer species status if hybridization cannot be observed or studied in the lab or the field.
Getting back to the essay, the authors describe a scenario whereby cryptic species are found:
[A] number of individuals belonging to a morphologically recognized species are sequenced (or otherwise genetically characterized), normally at several points (loci) within the genome. Then, often unexpectedly, the various genotypes will cluster in reciprocally monophyletic groups, with no signs of genetic exchange between them. Similar evolutionary scenarios are evident at each locus, suggesting that the corresponding populations are reproductively isolated from each other, yet the sampled populations are not geographically isolated.This type of pattern is expected for geographically isolated (allopatric) populations, but a single population of a species is expected to be randomly mating so that monophyletic groups are not consistently observed at multiple loci. The pattern described by the authors is a telltale sign of two distinct populations -- determining species status is a whole other process.
All one can conclude from monophyletic groups are distinct evolutionary lineages. It is important to determine how genetically differentiated the two groups are, and if they truly are sympatric. They may appear sympatric (i.e., collected in the same geographic area), but if their mating patterns are asynchronous or their mating ranges do not overlap, they have an excellent potential to speciate (if they haven't already) because of their extrinsic reproductive isolation. This is similar to problems we encounter when defining niches because we are limited by what we can observe and describe. Just because it looks like the two evolutionary lineages inferred from the molecular markers are sympatric, does not necessarily mean they are -- we may be missing something, as nature is a very complicated place.
In my opinion, the most interesting questions are those that deal with the mechanisms of speciation. Determining whether two indistinguishable groups are cryptic/sister/true-species is only the first step in the study of speciation. By examining closely related species (for instance Drosophila pseudoobscura and D. persimilis) we may be able to detect the remnants or current processes involved in creating complete reproductive isolation between these close relatives. The authors miss the boat on this key point, as they conclude we should be
looking for the conditions in which cryptic species will thrive — pursuing their causes whilst decrypting their natureSince cryptic species is an artifact of the scientific process being used, simply identifying, describing, and characterizing patterns of cryptic species is not sufficient in itself. These are excellent initial observations that should then lead to many questions regarding the process of speciation (this is going from the what/observation to the how/hypothesis). Only by examining pairs of taxa at different points in the process of speciation can we fully understand how speciation works in sexual organisms.