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Lotus is the largest of 18 genera of the tribe Loteae. It includes ca. 125 species with the center of diversity in the Mediterranean. Earlier, on the basis of morphological investigations and a limited number of nrITS1-2 sequences we subdivided the genus Lotus into 14 sections and excluded from Lotus a monotypic genus Kebirita from Morocco. Dorycnium, Tetragonolobus and Benedictella are considered as sections within genus Lotus. However, many problems such as overlapping of morphological character ranges between sections, low support and lack of resolution in some clades and insufficient taxon sampling remained in phylogenetics of Lotus. At the first stage of our updated molecular phylogenetic study, we conducted analyses of nrITS1-2 DNA for a set of about one hundred Lotus species and outgroups represented by other genera of the tribe Loteae. According to the results obtained, several sections of Lotus (namely, Pedrosia s.l., Lotea, Tetragonolobus and Chamaelotus) were monophyletic, and others (i.e. sections Lotus, Heinekenia, Dorycnium and Bonjeanea) were not supported by our analyses. For a deeper insight into section evolution and relationships we included a set of four non-coding DNA regions, comprising two nuclear (i.e. ITS1-2 and ETS) and two plastid ones (i.e. psbA-trnH spacer and rps16 intron). We constructed MP and Bayesian phylogenetic trees separately for each of four markers and also for a concatenated dataset of all markers. The analysis included 46 species of Lotus but covered 11 of 14 sections of the genus. The results obtained can be summarized as follows: Nuclear marker phylogeny revealed three large and one to several minor clades within the genus Lotus, while cpDNA trees clearly split into two clades: (1) Lotus+Dorycnium+Bonjeanea and (2) remaining sections. All studied markers support sections Lotea and Chamaelotus as monophyletic groups, and the majority of them also support the section Pedrosia. On the contrary, none of the markers allows recognizing sections Heinekenia, Dorycnium, and Bonjeanea in the traditional circumscription based on morphology. According to nuclear markers and a concatenated dataset of all markers, three branches corresponding to geographical distribution are suggested within the section Heinekenia (i.e. Heinekenia SW, SE and N), and branches SE and N are closer to each other. Sections Tetragonolobus and Krokeria (each characterized by a specific set of fruit features), are in close relationships with the section Lotea according to the nuclear phylogeny, while on cpDNA trees Tetragonolobus has relations with a large group of sections (Lotea, Heinekenia, Canaria, and Chamaelotus). A monotypic section Erythrolotus represented by L. conimbricensis is always related to the section Lotus, and they possess a common feature, i.e. basic chromosome number x=6. Section Lotus (incl. Erythrolotus) is separated as monophyletic by nuclear (ITS, ETS) markers and by a concatenated set of all markers. In analyses of cpDNA sequences a part of it (excl. L. corniculatus group) becomes close and intermingles with members of sections Dorycnium and Bonjeanea, which might suggest of hybrid origin of the group.