This study provides new information on phylogenetic relationships in the Ephedra distachya / E. sinica complex (Ephedraceae, gymnosperms) based on sequence variation and morphology-based delimitation of individual species. Altogether we have included 50 samples from this complex and closely related species with 39 samples sequenced for the first time. Our sampling scheme provides a much broader sampling both in respect of the number of species as well as the number of samples per species than has been accomplished in previous studies. Sequences for E. dahurica and E. pseudodistachya are given here for the first time. We sequenced the nuclear ribosomal internal transcribed spacer regions (nr ITS1 ITS2) as well as the chloroplast intergenic spacer between rnL and trnF (cp trnL-F), but only ITS1 was sufficiently informative for phylogeny reconstruction. Our data show, for the first time, (1) a well supported E. strobilacea / E. sarcocarpa / E. transitoria clade as sister to the “L” or “Asia 2” clade, furthermore (2) a distinct E. distachya clade, (3) a composite E. dahurica clade that also includes E. sinica and a fraction of E. intermedia, (4) a well supported E. regeliana clade and (5) an unresolved agglomeration of E. intermedia, E. przewalskii, E. lomatolepis and E. pseudodistachya. Most noteworthy is the support derived from the molecular data for (1) the separation of the hitherto doubtful E. pseudodistachya from E. distachya and E. dahurica and (2) the high degree of sequence similarity of E. sinica and E. dahurica. Based on morphological, molecular, ecological and biogeographical evidence, E. sinica is reduced to a subspecies of E. dahurica.
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