Speciation

Speciation is the formation of distinct species through evolution. Detecting a difference between biological populations is a starting observation; its interpretation depends on the stated species concept and the evidence for lasting separation. Reproductive isolation is one important route to limiting gene flow in sexual reproduction.

A hybrid zone is a region where genetically differentiated populations meet and produce offspring through interbreeding. Its spatial pattern reflects gene flow, dispersal and possible differences in biological fitness. A narrow transition can persist despite interbreeding; observing hybrids does not by itself show that the parental populations will merge completely.

In a Scottish contact zone between red deer and introduced sika deer, microsatellite genetic markers and the mitochondrial genome revealed introgression within populations that still formed two distinguishable genetic groups. Rare interbreeding can therefore leave a broader inherited signal than inspection of external appearance suggests.^[ref] Comparing multiple genetic markers helps distinguish contemporary interbreeding from ancestry accumulated across generations.

Divergence of adjacent populations into distinct species while some gene flow persists across their contact region. Spatially varying natural selection and the development of reproductive isolation can maintain differences despite exchange. It is a geographical mode distinct from complete separation in allopatric speciation and initial coexistence without such a barrier in sympatric speciation.

Origin of a reproductively distinct lineage through hybridization. A surviving hybrid individual alone is not a new species.

Evolution of increased premating isolation because interpopulation mating has fitness costs. Ecological divergence without such selection is not sufficient evidence.

Secondary contact is renewed geographic contact between biological populations that diverged during an interval of separation. The resulting interaction can involve gene flow, a hybrid zone or continued reproductive isolation.

Present-day sympatry therefore does not alone establish sympatric speciation: the populations may have become distinct elsewhere before meeting again. Historical inference needs evidence about both the earlier separation and the later exchange.

Origin of distinct species without initial geographic separation at the relevant scale. Current sympatry alone does not establish this historical route.

Evolution of distinct species during geographic separation. Persistence of isolation after renewed contact is a further test.

Evolution of reproductive isolation as a consequence of divergent ecological natural selection. Ecological differences or distinct reaction norms alone are insufficient unless they reduce gene flow.

Divergence of sensory systems and signals associated with the physical or ecological environment, potentially generating mating barriers.

A trait affected by divergent ecological selection that also contributes to assortative mating. Distinguish one pleiotropic trait from tightly linked separate loci.

Reproductive isolation consists of barriers that reduce gene flow through sexual reproduction. Distinguish premating isolation from barriers after mating. Barriers before fertilization also include incompatible gametes; barriers after fertilization can reduce offspring survival or fertility. ^[ref]

An assay should state which step it measures. Observing fewer cross-group matings does not measure offspring fertility; observing fertilization does not demonstrate that the offspring will reproduce. These distinctions make a partial barrier informative without declaring completed speciation.

Barriers to gene exchange acting before a zygote forms. Habitat separation, differing breeding times, behavioral discrimination and mechanical mismatch can reduce mating or gamete transfer; gametic incompatibility can act after mating while still preventing fertilization. Thus prezygotic isolation is broader than premating isolation and distinct from postzygotic isolation. The time and biological stage measured by an assay determine which category it tests.

Reproductive incompatibility associated with an inherited cytoplasmic factor, including some bacterial symbionts. Reciprocal crosses, microbial manipulations and host-background controls identify its cause.

Greater divergence of mating signals or preferences in sympatry than outside contact. The pattern can follow reinforcement, but also ecological differences, sorting or interference without reduced hybrid fitness.

When one sex of first-generation hybrids is absent, rare or sterile, it tends to be the heterogametic sex. This predicts a sex bias within crosses, rather than a universal difference in isolation between birds and mammals.^[ref]

A harmful interaction between alleles that evolved in separate lineages and are compatible with their own genetic backgrounds. For example, substitutions yielding $Ab$ and $aB$ can each be tolerated, while the combination $AB$ is harmful in a hybrid. This is a form of epistasis.

Premating isolation reduces mating between biological populations. The dietary divergence and mating isolation in Drosophila pseudoobscura assay measures this stage using observed pairings.

Postmating reproductive isolation acts after mating. Specify whether the test concerns fertilization, offspring survival, or the offspring's own reproduction; those outcomes are not interchangeable.

Reduced survival or fertility appearing in later-generation or backcross descendants of hybrids, even when first-generation offspring are fertile. genetic recombination can expose harmful combinations previously masked in the first generation.

A barrier to gene flow acting after fertilization, through reduced survival or fertility of hybrids. Test both sexes and later generations: survival of first-generation offspring does not establish their fertility.

Reduced or absent fertility of hybrid offspring. It must be distinguished from failure to mate or reduced viability before reproductive maturity.

The 1989 experiment used eight Drosophila pseudoobscura biological populations from one Bryce Canyon population: four maintained on starch medium, four on maltose, in CAGEs at $25{}^{\circ }\mathrm{C}$. Testing began about a year after establishment. ^[ref]

Before testing, flies spent one generation on cornmeal–molasses–agar. Virgins aged 3–6 days entered multiple-choice chambers: twelve females from each population, followed by males from both populations introduced nearly simultaneously without anesthesia. Observers scored matings for 60–90 minutes under bright indirect lighting. One group's right wing tips were clipped for identification, with clipping reversed between replicates. ^[ref]

All sixteen cross-diet comparisons had positive mating assortment contrasts; eleven departed significantly from random mating. Same-diet comparisons did not show significant departures. Common-medium rearing addressed immediate diet conditioning; same-diet controls addressed separation and establishment population bottlenecks. Mate choice was not the selection target; the biological populations were maintained separately. The result supports partial premating isolation accompanying dietary divergence, not completed speciation. ^[ref]

The causal inference remains limited. A negative same-diet hypothesis test does not prove zero reproductive isolation. One generation under common conditions does not exclude every persistent environmental influence. The chamber readout alone cannot identify a particular gene, establish offspring fertility, or predict gene flow after sustained contact in nature. Further experiments would need to target those questions separately.

For observed pairings between two labels $A,B$, let $N_{\mathrm{same}}=N_{AA}+N_{BB}$ and $N_{\mathrm{cross}}=N_{AB}+N_{BA}$, where the first label denotes the female's group and the second the male's. A mating assortment contrast isIt lies between $-1$ and $1$. Positive $I$ describes an excess of same-label pairings over cross-label pairings; whether that is evidence of assortative mating depends on the null mathematical model and the assay. The four counts form a contingency table.

Here is an original scope check. Suppose independently paired females and males have probabilities $p_f,p_m$ of carrying label $A$. ThenWith $p_f=p_m=1/2$, the expected value is zero. With $p_f=p_m=4/5$, it is $9/25=0.36$, despite pairing being independent of label. This counterexample concerns unequal pool composition; it does not replace the group introductions and contingency table tests in the dietary divergence and mating isolation in Drosophila pseudoobscura experiment. Even with balanced pools, finite observed samples fluctuate: a positive $I$ alone is not a hypothesis test, much less a universal species boundary.