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Recent molecular phylogenetic studies reported high diversity of Ruppia species in the Mediterranean. Multiple taxa, including apparent endemics, are known from that region, however, they have thus far not been exposed to phylogenetic analyses aimed at studying their relationships to taxa from other parts of the world. Here we present a comprehensive phylogenetic analyses of the R. maritima complex using data sets composed of DNA sequences of the plastid genome, the multi-copy nuclear ITS region, and the low-copy nuclear phyB gene with a primary focus on the Mediterranean representatives of the complex. As a result, a new lineage, 'Drepanensis', was identified as the seventh entity of the complex. This lineage is endemic to the Mediterranean. The accessions included in the former 'Tetraploid' entity were reclassified into two entities: an Asia-Australia-Europe disjunct 'Tetraploid_α' with a paternal 'Diploid' origin, and a European 'Tetraploid_γ' originating from a maternal 'Drepanensis' lineage. Another entity, 'Tetraploid_β', is likely to have been originated as a result of chloroplast capture through backcrossing hybridization between paternal 'Tetraploid_α' and maternal 'Tetraploid_γ'. Additional discovery of multiple tetraploidizations as well as hybridization and chloroplast capture at the tetraploid level indicated that hybridization has been a significant factor in the diversification of Ruppia. [ABSTRACT FROM AUTHOR]

• Premise of the study: The monogeneric family Ruppiaceae is found primarily in brackish water and is widely 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 putarive parental taxa were inferred. With respect to biogeography, a remarkably discontinuous distribution was identified in two cases, for which bird-mediated seed dispersal may be a reasonable explanation. [ABSTRACT FROM AUTHOR]