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The circumscription of Rondeletieae has changed considerably over time. Historically, 85 genera have been included, characterized by small trees, imbricate corolla aestivation and capsules. Molecular studies led to a narrower circumscription and stressed out that Rondeletieae is mainly an Antillean clade. As historically circumscribed, Rondeletieae is both polyphyletic (involving several tribes, including Condamineae, Sipaneeae, etc.) and paraphyletic with respect to Guettardeae. Uncertainties persist on the tribal circumscription, and its generic limits and relationships. We report results of phylogenetic analyses under parsimony, maximum likelihood and Bayesian analyses including 179 taxa, using concatenated datasets of three chloroplast DNA regions (petD, trnL–F and trnK–matK), their DNA microstructural characters as well as morphology. Our objectives are to: test the monophyly of Rondeletieae and evaluate phylogenetic relationships, evaluate potential characters for tribal and generic delimitation and propose a circumscription for Rondeletieae according to phylogenetic hypothesis using morphological characters. The tribes Guettardeae and Rondeletieae are strongly supported as sister: quincuncial aestivation and spathulate corolla lobes are proposed as a unique combination of characters supporting this relationship. We did not find synapomorphies for each tribe, but there is a set of character combinations that allows distinguishing both tribes that includes the corolla and pollen ornamentation as well as fruit and seed morphology. After evaluating other genera not included in the phylogenies, our proposal is that Rondeletieae contains approximately 120 species in 20 neotropical genera: Acrosynanthus, Acunaeanthus, Blepharidium, Donnellyanthus, Mazaea, Phyllomelia, Rachicallis, Roigella, Rondeletia, Rovaeanthus, Suberanthus, Tainus, plus one tentatively included and recently described (Jamaicanthus).

The plastid genomes of early-diverging angiosperms were among the first land plant plastomes investigated. Despite their importance to understanding angiosperm evolution, no investigation has so far compared gene content or gene synteny of these plastid genomes with a focus on the Nymphaeales. Here, we report an evaluation and comparison of gene content, gene synteny and inverted repeat length for a set of 15 plastid genomes of early-diverging angiosperms. Seven plastid genomes of the Nymphaeales were newly sequenced for this investigation. We compare gene order and inverted repeat (IR) length across all genomes, review the gene annotations of previously published genomes, generate a multi-gene alignment of 77 plastid-encoded genes and reconstruct the phylogenetic relationships of the taxa under study. Our results show that gene content and synteny are highly conserved across early-diverging angiosperms: All species analyzed display complete gene synteny when accounting for expansions and contractions of the IRs. This conservation was initially obscured by ambiguous and potentially incorrect gene annotations in previously published genomes. We also report the presence of intact open reading frames across all taxa analyzed. The multi-gene phylogeny displays maximum support for the families Cabombaceae and Hydatellaceae, but no support for a clade of all Nymphaeaceae. It further indicates that the genus Victoria is embedded within Nymphaea. Plastid genomes of Trithuria were found to deviate by numerous substitutions and length changes in the IRs. Phylogenetic analyses further indicate that a previously published plastome named Nymphaea mexicana falls into a clade of N. odorata and should be re-evaluated.

Forests of SW Ethiopia constitute the native habitat of Coffea arabica and also the place where domestication of Arabica coffee started. Selection from wild populations has led to numerous landraces (farmer’s varieties) and cultivars. Inter-simple sequence repeats (ISSRs) were generated from a representative set of forest coffee populations and landraces across Ethiopia. For the broad diversity assessment, nine di- and tri-nucleotide ISSR primers were applied, as chosen from a total of 102 primers tested initially. Tetranucleotide ISSR primers differed in amplifying fingerprints that could hardly be analysed due to excessive variation. Tree building analysis (NJ, UPGMA) of 84 polymorphic loci amplified for 125 C. arabica individuals provided evidence for several groups of related genotypes occurring in certain geographical areas of Ethiopia and underscored the existence of wild coffee distinct from landraces. Landraces seem to have originated in different geographical areas of Ethiopia in a stepwise domestication process. While the overall geographical signal in the dataset was weak, analysis in a Bayesian framework using the admixture model with geographical priors in STRUCTURE recovered some genetic clustering. Based on Shannon’s diversity index, populations from Yayu (0.47) and Bonga (0.46) showed highest diversity, followed by individuals from Berhane Kontir (0.41). A likely scenario for the differentiation of C. arabica after an allopolyploidization event is that the hierarchical-geographical patterning of wild Coffea genotypes expected from stepwise range extension was obscured by recent or ancient gene flow. The diversity and geographical distribution of autochthonous C. arabica genotypes indicates the need for a multi-site in situ conservation approach.

Introns and spacers are a rich and well-appreciated information source for evolutionary studies in plants. Compared to coding sequences, the mutational dynamics of introns and spacers is very different, involving frequent microstructural changes in addition to substitutions of individual nucleotides. An understanding of the biology of sequence change is required for correct application of molecular characters in phylogenetic analyses, including homology assessment, alignment coding, and tree inference. The widely used term “indel” is very general, and different kinds of microstructural mutations, such as simple sequence repeats, short tandem repeats, homonucleotide repeats, inversions, inverted repeats, and deletions, need to be distinguished. Noncoding DNA has been indispensable for analyses at the species level because coding sequences usually do not offer sufficient variability. A variety of introns and spacers has been successfully applied for phylogeny inference at deeper levels (major lineages of angiosperms and land plants) in past years, and phylogenetic structure R in intron and spacer data sets usually outperforms that of coding-sequence data sets. In order to fully utilize their potential, the molecular evolution and applicability of the most important noncoding markers (the trnT–trnF region comprising two spacers and a group I intron; the trnS–G region comprising one spacer and a group II intron in trnG; the group II introns in petD, rpl16, rps16, and trnK; and the atpB–rbcL and psbA–trnG spacers) are reviewed. The study argues for the use of noncoding DNA in a spectrum of applications from deep-level phylogenetics to speciation studies and barcoding, and aims at outlining molecular evolutionary principles needed for effective analysis.

Malpighiales are one of the most diverse orders of angiosperms. Molecular phylogenetic studies based on combined sequences of coding genes allowed to identify major lineages but hitherto were unable to resolve relationships among most families. Spacers and introns of the chloroplast genome have recently been shown to provide strong signal for inferring relationships among major angiosperm lineages and within difficult clades. In this study, we employed sequence data of the petD group II intron and the petB-petD spacer for a set of 64 Malpighiales taxa, representing all major lineages. Celastrales and Oxalidales served as outgroups. Sequence alignment was straightforward due to frequent microstructural changes with easily recognizable motifs (e.g., simple sequence repeats), and well defined mutational hotspots. The secondary structure of the complete petD intron was calculated for Idesia polycarpa as an example. Domains I and IV are the most length variable parts of the intron. They contain terminal A/T-rich stem-loop elements that are suggested to elongate independently in different lineages with a slippage mechanism earlier reported from the P8 stem-loop of the trnL intron. Parsimony and Bayesian analyses of the petD dataset yielded trees largely congruent with results from earlier multigene studies but statistical support of nodes was generally higher. For the first time a deep node of the Malpighiales backbone, a clade comprising Achariaceae, Violaceae, Malesherbiaceae, Turneraceae, Passifloraceae, and a Lacistemataceae–Salicaceae lineage received significant statistical support (83% JK, 1.00 PP) from plastid DNA sequences.

The bladderworts (Utricularia, Lentibulariaceae) are the most diverse carnivorous plant genus, with a nearly worldwide distribution. In the present study, chloroplast DNA sequences of the trnK intron were used to reconstruct phylogenetic relationships within the genus. Parsimony, likelihood, and Bayesian analyses resulted in highly congruent and well-resolved trees. The phylogenetic signal provided by the noncoding trnK intron partition of the dataset is similar to that of the matK coding region, although the latter is twice as long. Within matK, indels appeared in multiples of three except very close to the 3′ end of the gene. Substitutions were found to result in or eliminate stop codons, thus creating a length variable gene end. Indels in both trnK and matK exhibit low degrees of homoplasy, irrespective of their size. A tree based on indels alone is largely congruent to the substitution-based trees but less resolved. Three major clades found within Utricularia are classified as subgen. Utricularia, subgen. Bivalvia, and subgen. Polypompholyx. The immediate common ancestor of Utricularia is suggested to have been a terrestrial plant whereas epiphytic and aquatic habits evolved later in terminal clades.

Aristolochiaceae, a family of worldwide distribution comprising about 500 species, is a member of Piperales. Although Piperales is clearly monophyletic, the precise relationship within the order is ambiguous due to inconsistent placement of Lactoris fernandeziana. The appearance in some studies of Lactoris within Aristolochiaceae and the incongruence in generic treatments have also raised questions about the infrastructure of the family. This study addresses the overall generic relationships in Aristolochiaceae and its position in Piperales based on dense taxon sampling and sequence data from the plastid trnL-F region. The study resolved Piperales consisting of two major clades (Piperaceae plus Saururaceae and Lactoridaceae plus Aristolochiaceae) and Lactoris nested within Aristolochiaceae but with low support. The concept of two subfamilies in Aristolochiaceae, Asaroideae and Aristolochioideae, gains maximum statistical support. A generic treatment of Aristolochiaceae based on trnL-F is proposed which is congruent with recent analyses based on morphological characters.

The analysis of non-coding DNA in evolutionary studies of plants is witnessing an ever-increasing popularity in addition to the widespread application of sequences of protein coding genes like plastid rbcL and matK, mitochondrial coxI and matR or the 18 and 26S parts of the nuclear ribosomal array. For the chloroplast genome, the use of universal primers annealing to highly conserved tandemly repeated tRNA genes allowed the routine amplification and sequencing of variable chloroplast spacers and the trnL intron since the beginning of the 1990s. Protocols for other spacers followed shortly after, facilitated by the availability of several completely sequenced green plant plastid genomes. At around the same time the use of nuclear internal transcribed spacer (ITS) sequences was proposed for phylogenetic analyses. This has led to a large proportion of non-coding sequences available in EMBL/GenBank. For example, trnL intron sequences have so far been published for approximately 30% of all 450,000 species of land plants. Similar numbers can be found for nrITS sequences. Nevertheless, recent years have also witnessed a trend to look for new non-coding markers in all three genomic compartments of plants. Organellar and nuclear genomes of plants are made up to a large extent by non-coding sequences. There is a broad spectrum of different non-coding genomic regions such as introns, spacers, satellite regions. Therefore, non-coding DNA constitutes an immense source of information which will be accessible through the more and more completely sequenced genomes. The information content of non-coding DNA has been predominantly used for phylogeny reconstruction among closely related species or genera, and in population level studies, for example to create haplotype networks or in the form of fragment size analyses of microsatellites. More recently, the application of non-coding DNA for phylogeny reconstruction at deeper levels became more prominent because well resolved and statistically highly supported angiosperm trees could be inferred based on relatively few nucleotides of plastid spacers and introns. This growing awareness for the potential of non-coding DNA markers at the same time requires a careful implementation of analytical tools in order to deal with the complexity of evolutionary patterns in non-coding sequences that are largely caused by frequent micro-structural mutations in addition to substitutions of nucleotides. To explore the potential of non-coding genomic regions and recent developments for their analysis were the objectives of a workshop ‘‘Molecular evolution and phylogenetic utility of non-coding DNA: applications from species to deep level questions’’ that was held during the T. Borsch (&) Botanischer Garten und Botanisches Museum Berlin-Dahlem und Institut fur Biologie/Botanik, Freie Universitat Berlin, Konigin-Luise Str. 6-8, 14195 Berlin, Germany e-mail: t.borsch@bgbm.org