• Demography;
  • gene flow;
  • Juniperus;
  • Qinghai–Tibetan Plateau;
  • selection;
  • speciation

Population genetics data based on multiple nuclear loci provide invaluable information to understand demographic, selective, and divergence histories of the current species. We studied nucleotide variation at 13 nuclear loci in 53 populations distributed among four closely related, but morphologically distinct juniper species of the Qinghai–Tibetan Plateau (QTP). We used a novel approach combining Approximate Bayesian Computation and a recently developed neutrality test based on the maximum frequency of derived mutations to examine the demographic and selective histories of individual species, and isolation-with-migration analyses to study the joint history of the species and detect gene flow between them. We found that (1) the four species, which diverged in response to the extensive QTP uplifts, have different demographic histories; (2) two loci, Pgi and CC0822, depart significantly from neutrality in one species and Pgi, is also marginally significant in another; and (3) shared polymorphisms are common, indicating both incomplete lineage sorting and gene flow after species divergence. In addition, the detected unidirectional gene flow provides indirect support for the theoretical prediction that introgression should mostly take place from local to invading species. Our results, together with previous studies, underscore complex evolutionary histories of plant diversification in the biodiversity-hotspot QTP.