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Phylogeny of the genus Lotus (Leguminosae-Loteae) was studied using several molecular markers (internal (ITS1-2) and external (ETS) transcribed spacers of nrDNA and a spacer psbA-trnH of plastid DNA) and different methods of analysis (Strict Consensus, Maximum Parsimony (MP) and Bayesian analysis). The results obtained are considered in view of the evolution of basic chromosome numbers, polyploidy and hybridization in the genus Lotus. In the tribe Loteae basic chromosome number x=7 is probably plesiomorphic, x=6 has arosen in parallel in several clades well-defined also by morphology, and x=8 is quite rare in contrast to other temperate herbaceous legume tribes. In the majority of phylogenetic trees of the genus Lotus obtained for ITS1-2 region members of the section Chamaelotus with x=7 on diploid level occupied the basal position. In other trees (MP analyses of ITS and ETS data and of a concatenated dataset of ITS+ETS+psbA-trnH) section Chamaelotus shared basal position with sections Bonjeanea and Dorycnium (both with x=7 on diploid level) and a part of section Lotus (with x=6). The remaining species of the genus Lotus cluster in two large subclades, Subclade 1 with basic chromosome number x=7 and Subclade 2 with x=6. The taxonomic composition of Subclade 1 is very stable in all phylogenetic trees constructed for all DNA markers. It includes four large (i. e. Pedrosia, Lotea, Tetragonolobus, and non-monophyletic Heinekenia) and several small sections. In three of them tetraploid species or 2x-4x polyploid complexes occur. In the section Pedrosia many species are polyploid, a hybrid origin was demonstrated for some of them on the basis of morphology and molecular markers. In the section Lotea polyploidy occurs in the former “Lotus creticus group” and in the Lotus peregrinus group. In the section Heinekenia only two Australian species are characterized by tetraploid level with 2n=28, however, a considerable part of the section has not been studied yet as to its cytological features. The large Subclade 2 is subdivided into 3 or 4 subclades: 1) Lotus corniculatus group, 2) L. angustissimus group + L. uliginosus group, 3) L. parviflorus group (in some analyses). In each of these secondary level subclades polyploid formation took place on the basis of x=6. The largest Lotus corniculatus group includes diploid, heteroploid (2x, 4x) and tetraploid species. The position of polyploid species on phylogenetic trees is often not resolved due to their hybrid origin and reticulate evolution of the group. Several cases of hybridization within L. corniculatus complex on homoploid and heteroploid level were confirmed by ISSR DNA markers.