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* Premise of the study: The monogeneric family Ruppiaceae is found primarily in brackish water and is widely distributed on all continents, many islands, and from subartic to tropical zones. Ruppia taxonomy has been confusing because of its simplified morphology yet high phenotypic plasticity and the existence of polyploidy and putative hybrids. This study addresses the current classification of species in the genus, the origin of putative hybrids and polyploids, and the distribution of Ruppia species. * Methods: Separate molecular phylogenetic analyses using plastid DNA and nuclear-encoded PHYB data sets were performed after chromosome observations. * Key results: The resultant trees were largely congruent between genomes, but were incongruent in two respects: the first incongruence may be caused by long outgroup branches and their effect on ingroup rooting, and the second is caused by the existence of heterogeneous PHYB sequences for several accessions that may reflect several independent hybridization events. Several morphological species recognized in previous taxonomic revisions appear paraphyletic in plastid DNA and PHYB trees. * Conclusions: Given the molecular phylogenies, and considering chromosome number and morphology, three species and one species complex comprising six lineages were discerned. A putative allotriploid, an allotetraploid, and a lineage of hybrid origin were identified within the species complex, and a hybrid was found outside the species complex, and their respective putative parental taxa were interred. With respect to biogeography, a remarkably discontinuous distribution was identified in two cases, for which bird-mediated seed dispersal may be a reasonable explanation. Key words: hybridization; matK; PHYB; phylogeny; polyploidy; rbcL; rpoB; rpoCl; Ruppia; Ruppiaceae. doi: 10.3732/ajb.0900168

Hybridization via distributional changes should be an important factor for plant speciation. Previous cpDNA analyses of the Aristolochia kaempferi group, comprising six taxa in East Asia, showed a distinct phylogeographic structure resulting from distributional changes brought about by paleoclimatic oscillations. However, the cpDNA phylogeny was incongruent with morphologically defined taxa. To explore the evolutionary processes responsible for the inconsistency between cpDNA and morphology, we made artificial crosses and performed phylogenetic analyses using multiple nuclear markers. All crosses among different taxa or cpDNA clades set fruit, if crossing direction is not considered. The five nuclear phylogenies mostly did not support either the taxa or the cpDNA clades. A combined analysis of cpDNA and the PI exon revealed the two major lineages in the group, lacking a prezygotic isolating barrier between them. However, an asymmetric prezygotic isolating barrier occurs between populations of the Japanese main islands and of other areas that belong to different cpDNA subclades. It seems reasonable to conclude that the development of a prezygotic isolating mechanism is not necessarily proportional to the degree of genetic divergence. These results suggested that species boundaries within the group are blurred due to speciational processes associated with multiple hybridization and introgression resulting from repeated contacts among differentiated populations. Key words: APETALA3; Aristolochiaceae; crossing experiments; East Asia; PhyA; PISTILLATA; reticulate evolution; secondary contact.