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The Arabidopsis arenosa complex is closely related to the model plant Arabidopsis thaliana. Species and subspecies in the complex are mainly biennial, predominantly outcrossing, herbaceous, and with a distribution range covering most parts of latitudes and the eastern reaches of Europe. In this study we present the first comprehensive evolutionary history of the A. arenosa species complex, covering its natural range, by using chromosome counts, nuclear AFLP data, and a maternally inherited marker from the chloroplast genome [trnL intron (trnL) and trnL/F intergenic spacer (trnL/F-IGS) of tRNALeu and tRNAPhe, respectively]. We unravel the broad-scale cytogeographic and phylogeographic patterns of diploids and tetraploids. Diploid cytotypes were exclusively found on the Balkan Peninsula and in the Carpathians while tetraploid cytotypes were found throughout the remaining distribution range of the A. arenosa complex. Three centers of genetic diversity were identified: the Balkan Peninsula, the Carpathians, and the unglaciated Eastern and Southeastern Alps. All three could have served as long-term refugia during Pleistocene climate oscillations. We hypothesize that the Western Carpathians were and still are the cradle of speciation within the A. arenosa complex due to the high species number and genetic diversity and the concurrence of both cytotypes there.
Sedum, containing approximately 470 species, is by far the largest genus of Crassulaceae. Three decades of molecular phylogenetic work have provided evidence for the non‐monophyly of Sedum and many more of the 30 genera of Crassulaceae subfam. Sempervivoideae. In this study, we present a broadly sampled and dated molecular phylogeny of Sempervivoideae including 80% of all infrageneric taxa described in Sedum as well as most other genera of the subfamily. We used sequences of one nuclear (ITS) and three plastid markers (matK, rps16, trnL‐trnF). The five major lineages of Sempervivoideae (i.e., Telephium clade, Petrosedum clade, Sempervivum/Jovibarba, Aeonium clade, Leucosedum plus Acre clades) were resolved as successive sister to each other in the phylogenetic analysis of the plastid markers, while in the ITS phylogeny the Petrosedum clade is the closest relative of the Aeonium clade. Our dating analysis of ITS suggests that Sempervivoideae diversified rapidly throughout the Paleocene and Eocene, possibly in the area of the former Tethys and Paratethys archipelago. A biogeographic pattern emerges in which migration out of this ancestral area is linked to pronounced morphological evolution resulting in several distinct lineages recognized as segregate genera thought to be derived from Sedum. These segregate genera, however, have been defined on the basis of strongly homoplasious characters such as degree of petal fusion, petal colouration or flower merism. Moreover, all character states currently used for the delimitation of segregate genera seem to be homoplasious, and each of them can be found in at least one species of Sedum. Extensive literature work led to the conclusion that only few of the monophyletic clades found by us can be defined unambiguously by morphological characters. Mainly for these two reasons, we believe that combination of all 14 genera currently recognized in tribe Sedeae (= clades Leucosedum plus Acre) into Sedum might be the most stable solution of the “Sedum problem”. This new Sedum s.l. would then comprise approximately 755 species.
RaxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used software for phylogenetic inference using maximum likelihood. Here we present raxmlGUI 2.0-beta, a complete rewrite of the GUI, which replaces raxmlGUI and seamlessly integrates RAxML binaries for all major operating systems providing an intuitive graphical front-end to set up and run phylogenetic analyses. Our program offers automated pipelines for analyses that require multiple successive calls of RAxML and built-in functions to concatenate alignment files while automatically specifying the appropriate partition settings. While the program presented here is a beta version, the most important functions and analyses are already implemented and functional and we encourage users to send us any feedback they may have. RaxmlGUI facilitates phylogenetic analyses by coupling an intuitive interface with the unmatched performance of RAxML.
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