Most evolutionists think that speciation, which we see as the origin of a new group whose members are unable to produce fertile hybrids with other such groups (but whose members are interfertile with each other) occurs in the following way. Populations of a single species become geographically isolated by the interposition of geographic barriers like mountains, deserts, water, continental drift, etc. These barriers can either arise de novo, like the Andes, thus isolating populations on either side of them, or result from a rare migration event that is a one-off, like the invasion of the Galápagos by ancestral iguanas, tortoises, or finches. By preventing the mixing of genes among populations of what was initially a single species, the populations can then diverge genetically, often by natural or sexual selection, but also by processes like genetic drift. Different environments, different selective pressures and different mutations will then assure that the geographically isolated populations will travel along different evolutionary pathways.

When sufficient genetic divergence has occurred that the populations can no longer produce fertile hybrids if they were once again to come into contact, we say that they are separate biological species. The genetic barriers preventing successful hybridization, called reproductive isolating barriers, are diverse: they can include a preference for different environments, mating at different times (“temporal isolation,” which occurs in corals), a dislike of mating with the other species (“sexual isolation”, very common in birds and flies) or the production of either inviable or sterile hybrids (e.g., the sterile mule) when members of different species do mate. What has happened is that the geographic isolation allows the evolution of genetic isolation up to the point of speciation.

The scenario I just described is called allopatric speciation (from the Greek meaning “different places”). But there is evidence that species can form without such geographic isolation, especially in the case of polyploidy in plants, in which two species hybridize (or a single species doubles its genome), and genetic processes in the hybrid make it a different species from either parent. This can take only a handful of generations. And we are learning that, more often than we thought, species can still split while exchanging some of their genes.

Now all of this represents our best current take about the origin of species, which is summed up in the technical book I wrote with Allen Orr in 2004, Speciation. These views were not developed by Darwin, as he didn’t have a clear idea of the relationship between species and reproductive isolation. Although his most famous book is called On the Origin of Species, it says little about that issue, but rather deals more with the origin of adaptations within a species.

But how long does it take for this process to occur? That’s harder, as only in very rare cases can we actually observe new species arising, and only when it’s fast—as in polyploidy (about 3 generations to get a new plant species). Without our having been there, we have to use indirect methods. Allen Orr and I, in a pair of papers in Evolution (references below), tried to do that with the fruit fly Drosophila.

What we did was take named species of flies whose degree of reproductive isolation—only sexual isolation and hybrid inviability and sterility—had been measured in the lab, and estimated the “genetic distance” between those species using early electrophoretic data. In that way we could correlate the degree of reproductive isolation of different species with the degree of genetic divergence between them. Assuming the latter statistic accumulates roughly linearly with time (the so-called “molecular clock”), we could then get an idea of how fast reproductive isolation accumulates. Our admittedly rough estimate—for we neglected forms of reproductive isolation impossible to measure in the lab (i.e., ecological differences)—was that it took between 200,000 and 2.7 million years for one species of Drosophila to split into two. (The faster estimates are for species now found in the same area, for in such cases natural selection against hybridization, if hybrids are sterile or inviable, can speed up the evolution of reproductive isolation.)

In our book Speciation, Allen and I considered many other groups, and concluded that in general speciation takes between 0.5 and 5 million years, with some exceptions like polyploidy. But that’s a very rough guess based on many kinds of data, including fossils. That is, by the way, ample time to generate the millions of species living today, even taking pervasive extinction into account.

A new paper in PLOS Biology by Camille Roux et al. (reference and free link below) uses a related method to see how much genetic distance between groups is sufficient to make them different species, although in this case the species were designated simply by nomenclature rather than by strict consideration of reproductive isolation. The methods are complex, but I’ll oversimplify them to give the general result.

Roux et al. used data on 61 pairs of species or populations; these were diverse, including worms, fish, crustaceans, mammals, and insects. All of these pairs had extensive molecular data known for them. Ten were pairs taken from the literature, 22 were pairs of named, distinct species, and 29 were pairs of populations considered to be within the same species.

Using various complex models, the authors attempted to see how much gene flow was going on between these pairs of taxa, relating that to the genetic distance between them. (There are ways to do this without it being circular.) They used various models, including complete allopatric speciation, speciation occurring while gene flow was going on between the separating groups, and gene flow that occurred after geographically isolated groups once again came to live in the same place. What they came up with is a plot showing the relationship between the degree of genetic difference between pairs of species or populations (Da below) and the probability of ongoing gene flow between taxa (P in the diagram below).

What does this diagram show? Well, as you move along the horizontal (X) axis from left to right, the genetic distance at “neutral” sites increases, meaning that the species or population pairs get older. And you see from the Y axis (gene flow) that as the age between taxa increases, the amount of gene flow between them decreases, finally winding up at zero—at which point they are full biological species (in red). The Big Deal about the paper, however, is the fairly narrow transitional “gray zone”: the bar that marks the transition between fairly free gene flow (populations or incipient species) and full species. That gray bar extends from 0.5% to 2% sequence difference at “neutral” sites.

Surprisingly, the transition zone is about the same regardless of whether the groups are geographically isolated or not; I would have expected that geographic isolation would speed up speciation by impeding “annoying” divergence-preventing evolutionary difference. The authors were also surprised at this, but said this may be because their range data were not so great. Further, the authors recognized several new species, which looked pretty much the same but whose genetic distance put them on the right (i.e., not left) side of the speciation threshold.

The fact that diverse taxa adhere to the same “threshold” of speciation seems surprising, implying that the amount of neutral genetic difference associated with speciation is roughly the same for very different groups. From that observation the authors conclude this (my emphasis):

. . . our report of a strong and general relationship between molecular divergence and genetic isolation across a wide diversity of animals suggests that, at the genome level, speciation operates in a more or less similar fashion in distinct taxa, irrespective of biological and ecological particularities.

This conclusion is echoed by a PLOS blog post on the paper by grad student Jenns Hegg from the University of Idaho:

Does this paper tell us what is and isn’t a species? No, it doesn’t. But, it gives us an idea of how to understand the process of speciation across species. It also indicates that speciation happens (genetically at least) in pretty similar ways in all species regardless of the specifics of the population…which is good news for anyone interested in developing better ecological and evolutionary theories to explain how species come about through natural selection.

Well, both of these conclusions are dubious. Yes, it was surprising that the “gray zone” wasn’t so different among diverse taxa, but remember that these taxa are not all phylogenetically independent. Some groups are used more than once, so we can’t be sure that every data point represents an evolutionarily independent pair of taxa. Further, the sample size is limited (e.g., no Drosophila!) Also, there are these problems:

We know of some cases of speciation that are very rapid, including about 4000 years in some cichlids, 50 years in polyploid plants, and a few hundred years in sunflowers (see here for some fast cases of speciation that are outside the gray zone). Polyploidy, or rapid ecological speciation, obviate these conclusions. One cannot conclude that all speciation events adhere to the pattern above.

A constant genetic distance of 0.5%-2% does not necessarily mean that species take roughly the same time to evolve in nature. That’s because the molecular clock ticks at different rates in different taxa, so a divergence of 1% in flies could represent a very different time for a divergence of 1% in mammals or worms.

We already know that different taxa speciate in different ways, so saying that “speciation happens in similar ways in all species regardless of the specifics of the population” is just wrong. (Polyploidy instantly invalidates that statement!) And it’s wrong to say, as the authors do, that “speciation operates in a more or less similar fashion in distinct taxa.” What the data show is that the neutral genetic distance associated with the reduction of gene flow is similar in this small sample of species. The paper doesn’t—and cannot—say anything about the process or “mechanism” of speciation, which we already know differs in different groups. We can’t even say that the rate of speciation is similar in different groups until we know how neutral genetic distance translates into years among different groups.

I think, then, that too much is being made of this paper, though the results are still quite interesting. But we need a much better data set, a much better calibration of the molecular clock in different groups, and some clearer thinking about what the authors mean by “speciation operating in a similar fashion.” We already know that in different groups different reproductive isolating barriers are important (pollinator isolation in orchids, sexual isolation in birds, etc.—see Speciation). And if by “similar fashion” the authors mean “similar rates,” well, that remains to be seen as well.

The authors discuss the use of this gray-zone metric as a conservation tool—a way to distinguish taxa to put them within the regulations for protection of endangered groups—but I won’t open that can of worms.

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Coyne, J. A. and H.A. Orr. 1989. Patterns of speciation in Drosophila. Evolution 43: 362-381.

Coyne, J. A., and H. A. Orr. 1997. “Patterns of speciation in Drosophila” revisited. Evolution 51:295-303.

Roux C, Fraïsse C, Romiguier J, Anciaux Y, Galtier N, et al. (2016) Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLOS Biology 14(12): e2000234. doi: 10.1371/journal.pbio.2000234