Everything up to this point describes one population becoming different from what it was, which would leave the earth with a single, superbly adapted species.
The previous lessons put four forces into a population: selection, mutation, migration and drift. All four operate on a pool of individuals exchanging genes, and none of them divides the pool. Yet about 2.1 million species have been described. This lesson is about what a species is, which turns out to be genuinely contested, and about how one becomes two, which turns out to be observable.
The concept, and why it is not a definition
Naturalists sorted organisms into kinds for two thousand years before anyone asked what a kind is. The answer that organised twentieth-century biology is Ernst Mayr's, stated in 1942: species are groups of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups.
The move this makes is to relocate the species from the organism to the population, exactly as the fifth lesson relocated evolution. A species is not defined by how its members look. It is defined by the boundary of gene exchange, which makes it the unit within which the previous lessons' algebra applies: inside a species, selection at one locus can be assisted by recombination with a favourable allele at another, and outside it, cannot. On this reading a species is the largest pool over which evolution can act as a single process, which is why the concept earns its place in the theory rather than merely in the filing system.
Reproductive isolation is not one thing. Barriers acting before fertilisation include living in different places, breeding at different times, failing to recognise each other's courtship, and gametes that will not fuse. Barriers acting after include hybrid embryos that die, hybrids that live but are sterile, and hybrids that are fit but whose own offspring collapse. Prezygotic barriers are cheaper, since a wasted gamete costs less than a wasted pregnancy, and there is a mechanism, called reinforcement, by which selection strengthens them: if hybrids are unfit, any allele that makes its bearer avoid mating across the boundary is favoured. That prediction is testable, and it holds. Jerry Coyne and Allen Orr's surveys of Drosophila found prezygotic isolation between species pairs that overlap geographically to be substantially stronger, at the same genetic distance, than between pairs that do not.
Where the concept breaks
An honest account has to say that the biological species concept fails, cleanly, in several large parts of the tree.
It says nothing about asexual organisms. Bacteria do not interbreed in the required sense and they do exchange genes across enormous phylogenetic distances by conjugation and transduction, so the boundary is not a boundary. It says nothing about fossils, where the character in question cannot be observed. It is awkward about the many pairs that live apart and are never tested, since "potentially interbreeding" is a counterfactual.
And it treats hybridisation as an exception when it is common. Jim Mallet's 2005 survey estimated that roughly 10 per cent of animal species and 25 per cent of plant species hybridise with at least one other. Non-African human genomes carry about 2 per cent Neanderthal sequence, which means the two lineages met and interbred, and yet nobody proposes merging them. Isolation is a matter of degree.
Example. A horse and a donkey produce a mule. Mules are healthy, strong and almost always sterile. Are horses and donkeys one species or two, and what is the mechanism?
Two, on the biological concept: a barrier that reduces gene flow to essentially zero does the work whether it acts before or after fertilisation, and hybrid sterility is as effective as never mating. The mechanism here is mechanically clear. A horse has 64 chromosomes and a donkey 62, so the mule has . At meiosis chromosomes must pair, and an odd set with two non-matching complements cannot pair reliably, so gamete formation fails. Note that this is a barrier with a physical cause you can look at down a microscope, which is unusual: most hybrid sterility is genetic rather than chromosomal, arising from combinations of alleles that have never been tested together and turn out not to work.
Now you. Ensatina salamanders form a chain of populations down the two sides of California's Central Valley. Neighbours along the chain interbreed freely all the way round, but where the two ends meet in southern California the terminal forms barely hybridise at all. How many species is that?
Answer
The biological species concept cannot answer, and that is the point of the example rather than a failure of the reader. Interbreeding is a relation between neighbouring populations and it is not transitive, so a concept built on it will break wherever a chain is long enough. Ring species were prized as living demonstrations of speciation caught halfway.
The honest addition is that the two best cases have both weakened on inspection. Detailed work on Ensatina by David Wake's group found that gene flow around the ring is not continuous: there are breaks and past separations, and the chain is better read as several formerly isolated lineages that have come back into contact than as one unbroken gradient. Genomic work published in 2014 on the greenish warbler, the other standard example, found the same thing. That does not damage the underlying claim, which is that reproductive isolation accumulates gradually with divergence. It damages the tidy illustration, and it is a good example of how a case that is repeated in every textbook can turn out to be less clean than the textbook implies.
Splitting by geography
The uncontroversial route to two species is to interrupt gene flow physically and let the forces of the previous lessons do the rest. Two populations that no longer exchange genes accumulate different mutations, drift in different directions, and experience different selection. Reproductive isolation is not selected for in this scenario; it accrues as a by-product, which is why it takes a long time and why its strength correlates with divergence rather than with anything about the barrier.
The rate at which gene flow must be cut is small. Sewall Wright's result is that the differentiation between two populations, measured as , settles at , where is the fraction of each population replaced by migrants each generation. With , meaning literally one effective migrant per generation regardless of population size, is 0.2 and the populations stay recognisably similar. With it rises to 0.5. One migrant per generation is enough to hold two populations together, which is why continuous ranges rarely split and why islands do so readily.
The clean natural experiment is the Isthmus of Panama, which closed around 3 million years ago and divided one ocean into two. Nancy Knowlton's work on Alpheus snapping shrimp identified fifteen pairs of sister species facing each other across it, each pair separated by the same event at the same moment. The pairs still recognise each other's courtship imperfectly and produce few viable clutches, and their genetic divergences cluster as they should if one date applies to all of them.
How long it takes
Because the isolation is a by-product, its accumulation can be plotted against divergence and turned into a rate.
Coyne and Orr assembled data on 171 pairs of Drosophila species in 1989 and extended it in 1997, scoring prezygotic and postzygotic isolation on scales from 0 to 1 and plotting both against Nei's genetic distance . Both rise steadily. Complete isolation appears around of 0.5 to 1.0, which on the standard Drosophila calibration of roughly 5 million years per unit of corresponds to 2.5 to 5 million years. Vertebrate estimates from the same approach tend to run longer, birds longer still.
Those are averages with enormous scatter, and the scatter is the interesting part: some pairs are fully isolated at a tenth of that distance and others still hybridise at twice it. Speciation has no characteristic timescale because the barrier is built from whatever incompatibilities happen to arise, and that is a matter of which mutations occurred, not of how much time passed.
Splitting without geography
Whether a lineage can divide while its members are still in contact was disputed for most of the twentieth century, and Mayr thought it essentially impossible: any incipient divergence should be swamped by gene flow. The objection is quantitative and can be answered quantitatively. A locus under selection against migration maintains a difference only when exceeds , and settles at a frequency of about .
The best-studied case is a fly. Rhagoletis pomonella lays its eggs in the fruit of hawthorn, its native host in North America. Apples were introduced, and in 1864 the fly was first recorded attacking them in the Hudson Valley. The two host races now differ measurably. Apples fruit about three weeks earlier than hawthorns, so the apple race emerges earlier and its diapause is under different selection; the flies mate on or near the fruit, so host preference is also mate choice; and allele frequencies at several loci differ consistently between races collected from trees a few metres apart.
Example. Gene flow between the host races is estimated at about 6 per cent per generation. If selection on a diapause-timing allele is , what frequency difference can be maintained, and what does the answer establish?
The equilibrium frequency in the face of one-way migration is roughly . A locus under that much selection therefore holds a difference of 70 percentage points between populations exchanging 6 per cent of their members every generation. Had selection been weaker than migration, against , the difference would collapse entirely. So the answer is that sympatric divergence is possible but conditional: it requires selection stronger than gene flow at the loci that matter, and it works best when the selected trait is also the trait that determines who mates with whom, as host preference is here.
Now you. The Rhagoletis case is usually described as speciation in progress rather than speciation. What is still missing, and what would settle it?
Answer
What is missing is the barrier itself. The races are partially isolated by host fidelity and timing, and 6 per cent gene flow is a long way from zero; they remain interfertile in the laboratory with no reduction in hybrid viability. Under the biological species concept they are one species with structure, not two species.
Settling it needs one of two observations, and both take longer than a career. Either gene flow falls to effectively zero while the two remain in contact, or hybrids become unfit, which would let reinforcement take over and finish the job quickly. What the case does establish, which is what it is cited for, is that the first step of sympatric divergence is not merely possible but happened in the nineteenth century in an orchard, on a schedule short enough that the founding event has a date.
Splitting in one generation
There is one route that skips all of this, and it is responsible for a large share of plant species.
If a cell fails to halve its chromosome number at meiosis it produces an unreduced gamete. Two of those fusing give a tetraploid, with four sets of chromosomes instead of two. The tetraploid can pair its chromosomes at meiosis perfectly well, since it has an even number of matching sets, so it is fertile with itself and with other tetraploids. Crossed back to its diploid parents it gives triploids, which have three sets, cannot pair them, and are sterile. The barrier is complete in the first generation, and it is the only mechanism in this lesson that produces a new species without any period of divergence at all.
Example. Unreduced gametes occur in perhaps 0.5 per cent of meioses in some plants. What is the chance that a given fertilisation produces a tetraploid, and why is polyploid speciation nonetheless common?
Two independent unreduced gametes must meet, so the probability is , one in 40,000 fertilisations. A single flowering plant can produce far more ovules than that over a season, and a field contains thousands of plants, so the event is not rare in absolute terms even though it is rare per fertilisation. It also does not need to succeed twice: many polyploids can self-pollinate or reproduce vegetatively, so one individual is a viable founding population. Estimates from the distribution of chromosome numbers across the plant tree put polyploidy behind about 15 per cent of speciation events in flowering plants and 31 per cent in ferns.
Now you. Tragopogon miscellus, a goatsbeard, is an allopolyploid formed from two European species introduced to eastern Washington State in the 1920s and first collected in 1949. Why is this case more useful as evidence than any number of ancient polyploids?
Answer
Because it has a date on both ends. The parent species were absent from North America before their introduction, so the hybrid cannot predate it, and the new species was collected within about twenty years and has since spread and been resampled repeatedly. That converts a claim about the past into an observation: a reproductively isolated, self-sustaining species originated in a known decade in a known place, and the same event has been shown to have occurred independently more than a dozen times in that region.
Ancient polyploids, which include wheat, cotton, tobacco and the ancestor of all vertebrates, are inferred from duplicated gene sets and are entirely convincing as history. What they cannot do is answer the objection that speciation has never been seen. This one has, twice over, and it is worth pairing with the observation that the whole process here is mechanical: nothing about it requires selection at all.
What splitting implies
Repeated splitting has a consequence that the first lesson raised and could not explain. If lineages divide and rarely rejoin, then the history of life is a tree, and the pattern of similarity among living things is not an arbitrary arrangement but a record of how recently any two of them shared an ancestor.
That is a very strong claim, far stronger than it sounds, because it predicts that characters drawn from anatomy, embryology and sequence must all agree on the same branching diagram, and there is no reason on any other account that they should. The next lesson takes that prediction apart and tests it.