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Background  During glacial periods, glacial advances caused temperate plant extirpation or retreat into localized warmer areas, and subsequent postglacial glacial retreats resulted in range expansions, which facilitated secondary contact of previously allopatric isolated lineages. The evolutionary outcomes of secondary contact, including hybrid zones, dynamic hybrid swarm, and resultant hybrid speciation, depends on the strengths of reproductive barriers that have arisen through epistatic and pleiotropic effects during allopatric isolation. The aim of this study was to demonstrate refugia isolation and subsequent secondary contact between two perennial Asclepioid species and to assess the genetic consequences of the secondary contact. We modeled the range shift of two ecologically distinct  Vincetoxicum  species using the species distribution model (SDM) and assessed the genetic consequences of secondary contact by combining morphological and genetic approaches. We performed morphometric analysis (592 individuals) and examined 10 nuclear microsatellites (671 individuals) in  V. atratum ,  V. japonicum , and putative hybrid populations.    Results  Multivariate analysis, model-based Bayesian analysis, and non-model-based discriminant analysis of principal components confirmed the hybridization between  V. atratum  and  V. japonicum . High pollen fertility and a lack of linkage disequilibrium suggested that the hybrid populations may be self-sustaining and have persisted since  V. atratum  and  V. japonicum  came into contact during the post-glacial period. Moreover, our findings show that the pattern of hybridization between  V. atratum  and  V. japonicum  is unidirectional and differs among populations. Geographically-isolated hybrid populations exist as genetically distinct hybrid swarms that consist of  V. atratum -like genotypes,  V. japonicum -like genotypes, or admixed genotypes. In addition, Bayesian-based clustering analysis and coalescent-based estimates of long-term gene flow showed patterns of introgressive hybridization in three morphologically ‘pure’  V. japonicum  populations.    Conclusion  In this study, we demonstrated that climatic oscillations during the Quaternary period likely led to species range shift and subsequently secondary contact. Hybrid populations may be self-sustaining and have persisted since  V. atratum  and  V. japonicum  came into contact during the post-glacial period. Pattern of hybridization between  V. atratum  and  V. japonicum  is unidirectional and differs among populations. We concluded that these differences in the genetic consequences of secondary contact are caused by historical colonization processes and/or natural selection.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-016-0587-2) contains supplementary material, which is available to authorized users.

bmc evolutionary biology

Long-term persisting hybrid swarm and geographic difference in hybridization pattern: genetic consequences of secondary contact between two Vincetoxicum species (Apocynaceae–Asclepiadoideae)