Nuclear and plastid DNA sequences reveal complex reticulate patterns in Australian water-lilies (Nymphaea subgenus Anecphya, Nymphaeaceae)

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Abstract
This study represents the first comprehensive analysis of phylogenetic relationships within the Australian water-lilies, Nymphaea subg. Anecphya. Our 51-accession dataset covers all 10 species of the subgenus, except the newly described N. alexii, and includes information from the nuclear ITS as well as from the chloroplast trnT–trnF region. The results show that molecular data are consistent with morphology, because the subdivision of subg. Anecphya into two major clades, a large-seeded and a small-seeded group, could be confirmed. Within the large-seeded group, Nymphaea atrans and N. immutabilis seem to form one clade, whereas samples of N. gigantea, N. georginae, N. macrosperma and N. carpentariae form another. Relationships within the small-seeded group, containing all samples of N. violacea, N. elleniae and N. hastifolia, are less clear, since the trees obtained from the chloroplast and the nuclear marker are incongruent. The samples of N. violacea do not form a monophyletic group in each of the trees, but—at least in the ITS tree—group with either N. elleniae or N. hastifolia/Ondinea, respectively. Polymorphisms among ITS paralogues, i.e. substitutions at single nucleotide positions and length polymorphisms, have been observed in some samples of N. violacea. This fact as well as the incongruent phylogenetic signal obtained from the chloroplast and the nuclear genomes point to recent hybridisation or introgression in this group. Remarkably, Ondinea purpurea is resolved within the small-seeded group by both markers and seems to have a close relationship to N. hastifolia. Although incomplete lineage sorting cannot be fully excluded to explain high variability in N. violacea, molecular data potentially hint to a case of still imperfect taxonomy.

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