Lotus (120–130 species) is the largest genus of the tribe Loteae. The taxonomy of Lotus is complicated, and a comprehensive taxonomic revision of the genus is needed. We have conducted phylogenetic analyses of Lotus based on nrITS data alone and combined with data on 46 morphological characters. Eighty-one ingroup nrITS accessions representing 71 Lotus species are studied; among them 47 accessions representing 40 species are new. Representatives of all other genera of the tribe Loteae are included in the outgroup (for three genera, nrITS sequences are published for the first time). Forty-two of 71 ingroup species were not included in previous morphological phylogenetic studies. The most important conclusions of the present study are (1) addition of morphological data to the nrITS matrix produces a better resolved phylogeny of Lotus; (2) previous findings that Dorycnium and Tetragonolobus cannot be separated from Lotus at the generic level are well supported; (3) Lotus creticus should be placed in section Pedrosia rather than in section Lotea; (4) a broad treatment of section Ononidium is unnatural and the section should possibly not be recognized at all; (5) section Heinekenia is paraphyletic; (6) section Lotus should include Lotus conimbricensis; then the section is monophyletic; (7) a basic chromosome number of x = 6 is an important synapomorphy for the expanded section Lotus; (8) the segregation of Lotus schimperi and allies into section Chamaelotus is well supported; (9) there is an apparent functional correlation between stylodium and keel evolution in Lotus.

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Lotus comprises ca. 130 species of herbs, semishrubs and shrubs native to the Old World, including important pasture crops and a model legume, L. japonicus. Earlier nrITS‐based phylogenies were incongruent with all taxonomic classifications of the genus. In particular, members of the former genus Dorycnium were unexpectedly placed near species of L. sect. Lotus. The primary goal of the present study is to explore whether the unexpected placement of members of sect. Lotus and the former genus Dorycnium in earlier phylogenetic studies resulted from (1) insufficient taxon sampling and/or (2) the use of only one DNA marker. The rooting of the Lotus phylogeny, its major clades and basic biogeographic patterns are also discussed. This is the first global phylogenetic study of Lotus that uses both plastid and nuclear markers. The nrITS region was analyzed in 155 ingroup specimens representing 98 species of Lotus. Sequences of nrITS, nrETS, psbA‐trnH spacer and rps16 intron were analyzed for 70 ingroup specimens representing 54 species. The placement of the segregate genera Dorycnium and Tetragonolobus in the synonymy of Lotus was confirmed. Analyses of plastid data strongly supported a basal split of Lotus into two clades, one comprising species of sect. Lotus plus those traditionally placed in Dorycnium and the other including the rest of the species. The former clade has a centre of species diversity in Europe and N Asia, and the latter in Macaronesia, Africa and S Asia. Only the "Southern" clade is resolved in analyses of nrITS and nrETS data. Trees inferred from plastid, nrITS and nrETS data shared the occurrence of several smaller clades corresponding to traditionally recognized infrageneric taxa or species groups as well as the occurrence of some well‐supported clades that differ from traditional taxonomic concepts. Several instances of incongruence were documented between nuclear and plastid markers and between the two nuclear markers, possibly resulting from reticulate evolution. The extant geographic patterns of Lotus are likely biased by at least one round of area fragmentation followed by expansion coupled with extensive speciation associated with the complex history of the Mediterranean biome.

The genus Pinguicula (Lentibulariaceae) is unusual within the dicot order Lamiales because of the occurrence of both embryos with two cotyledons and those with just one cotyledon. In order to elucidate the infrageneric relationships and the evolutionary history of the embryo, we analysed (1) the internal transcribed spacers ITS1 and ITS2 of the nuclear ribosomal DNA (nrITS) of 29 Old and New World taxa of Pinguicula, and (2) the morphological and anatomical characters of the seeds. We suggest that the cotyledon number and spermoderm structure were quite unstable in the evolution of Pinguicula. Although basal nodes of the nrITS tree are sensitive to taxon sampling, all tree topologies found in this study imply homoplasy in the cotyledon number.

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