Fig 1.
Compared alternative models of speciation.
SI = strict isolation: subdivision of an ancestral diploid panmictic population (of size Nanc) in two diploid populations (of constant sizes Npop1 and Npop2) at time Tsplit. AM = ancestral migration: the two newly formed populations continue to exchange alleles until time TAM. IM = isolation with migration: the two daughter populations continuously exchange alleles until present time. SC = secondary contact: the daughter populations first evolve in isolation (forward in time), then experience a secondary contact and start exchanging alleles at time TSC. PAN: panmictic model. All individuals are sampled from the same panmictic population. Red phylogenies represent possible gene trees under each alternative model.
Fig 2.
ABC analysis of randomly simulated datasets.
Posterior probability Pmigration to support ongoing migration was estimated for a total of 116,000 simulated datasets across 16 models. A. Pmigration as a function of the net synonymous divergence Da. Dots represent datasets simulated under the IM, SC, and PAN models. The colors show datasets for which gene flow is correctly supported (green) or wrongly rejected (red). Grey dots represent datasets for which the robustness of the ABC analysis is <0.95. B. Pmigration as a function of the net synonymous divergence Da. Dots represent datasets simulated under the SI or AM models. The colors show datasets for which gene flow is correctly rejected (green; robustness ≥ 0.95) or wrongly supported (red; robustness ≥ 0.95). C. Proportion of true positives (green), false positives (red), and ambiguous analyses (grey) for different ranges of Da across IM, SC, and PAN datasets. Horizontal red line shows 5%. D. Proportion of true positives (green), false positives (red), and ambiguous analyses (grey) for different ranges of Da across SI and AM datasets.
Fig 3.
Probability of ongoing gene flow along a continuum of molecular divergence.
Each dot is for one observed pair of populations/species. x-axis: net molecular divergence Da measured at synonymous positions (log10 scale) and averaged across sequenced loci. y-axis: relative posterior probability of ongoing gene flow (i.e., SC, IM, and PAN models) estimated by ABC. Red dots: pairs with a strong support for current isolation. Grey dots: pairs with no strong statistical support for any demographic model (robustness <0.95). Blue dots: pairs with strong statistical support for genome-homogeneous ongoing gene flow. Purple dots: pairs with strong statistical support for genome-heterogeneous ongoing gene flow. Filled symbols: pairs with a strong support for genome-heterogeneous Ne. Open symbols: genome-homogeneous Ne. The light grey rectangle spans the range of net synonymous divergence in which both currently isolated and currently connected pairs are found (see S1 Data).