Plastid Rps16 Intron Research Articles

Berberocarum (Apiaceae), a new genus from the High Atlas Mountains (Morocco), with notes on some other NW African Umbelliferae–Apioideae

In Northwest Africa (Morocco), Carum (Apiaceae/Umbelliferae) is represented by six little known species. In order to clarify the relationships of these species within Carum, we conducted detailed morphological studies and molecular sequence analysis of four species (C. atlanticum, C. jahandiezii, C. lacuum and C. proliferum) based on the nuclear DNA internal transcribed spacer (ITS) and plastid rps16 intron (rps16) regions. According to the molecular data, the Moroccan Carum species form three isolated evolutionary lines distant from that of the generitype C. carvi. The morphological study demonstrated that fruits of C. atlanticum belong to a carpological type markedly different from that of other Carum species. Based on the correlation of obtained carpological and molecular data, we propose to transfer C. atlanticum to the new monotypic genus Berberocarum, endemic to the High Atlas Mountains.

Disentangling relationships among the members of the Silene saxífraga alliance (Caryophyllaceae): Phylogenetic structure is geographically rather than taxonomically segregated

AbstractOut of ca. 700 species belonging to Silene, 15 to 35 were classified in S. sect. Saxifragoideae. This section has its highest diversity on the Balkan Peninsula, which was the most important European Pleistocene refugium. The most widespread of the species is S. saxifraga ranging from the Pyrenees to the Carpathians. Together with ten morphologically similar taxa it is often treated as the S. saxifraga group, but the relationships among the taxa are unclear and blurred due to the occurrence of transitional forms. In this study, we used sequences of the nuclear ribosomal internal transcribed spacer (ITS) and the plastid rps16 intron as well as amplified fragment length polymorphisms (AFLPs) to elucidate phylogenetic relationships among the taxa belonging to—or hypothesized to be closely related to—S. sect. Saxifragoideae, covering the section’s entire geographical range. Phylogenetic analyses of 112 populations belonging to 33 taxa clarified previous classifications and showed that S. cephallenia, S. congesta, S. linoides, S. multicaulis, S. schwarzenbergeri and S. waldsteinii are clearly differentiated from all other taxa, which in turn form the newly circumscribed S. saxifraga group. Phylogenetic relationships within the latter are unresolved, and are governed by geographic proximity rather than by taxonomic identity. This is likely a result of recent rapid radiation and range expansion, as well as of convergent morphological evolution triggered by similar environmental selection pressures. The southern parts of the Balkan Peninsula are the centre of genetic diversity of the group, underlining the area’s importance as a sanctuary of diversification of European biota.

Molecular phylogeny of subgenus Polypompholyx (Utricularia; Lentibulariaceae) based on three plastid markers: diversification and proposal for a new section

Phylogenetic relationships among all of the 47 recognised species and 10 putative new taxa of Utricularia subgenus Polypompholyx, were assessed using maximum parsimony and Bayesian inference analyses of DNA sequences representing the plastid rps16 intron, trnL–F intron and spacer regions and the trnD–T intron. We found strong jackknife and posterior-probability support for a monophyletic subgenus Polypompholyx and a sister relationship between the sections Polypompholyx+Tridentaria and Pleiochasia. Within the section Pleiochasia, are two well-supported major clades, each containing three supported clades. Our S-DIVA biogeographic analysis, using five major Australian drainage basins and New Zealand as geographic areas, estimated two early vicariance events between south-western and north-western mainland regions, corresponding with known periods of increased aridity at 15 and 6million years ago. Subsequent dispersal events were estimated between northern and south-eastern Australia, with recent dispersal of species from south-western regions to the south-east and New Zealand occurring between 4million and 1million years ago. There were 28 speciation events inferred within the north-western region, followed by 9 for the south-western and south-eastern regions, indicating that the north-western monsoonal savanna habitats are a biodiversity hotspot for the lineage. We also show the evolutionary shifts in growth habit, and show that lifecycle corresponds strongly with shifts in seasonality between temperate and monsoonal regions. On the basis of our molecular phylogenetic results and morphology, we here designate a new sectional ranking for subgenus Polypompholyx.

A phylogenetic study of subgenus Polypompholyx: a parallel radiation of Utricularia (Lentibulariaceae) throughout Australasia

Phylogenetic relationships among 26 of the 37 recognised taxa of Utricularia subgenus Polypompholyx sensu Müller & Borsch were assessed by cladistic analysis of DNA sequences from the plastid rps16 intron. We also examined the placement of the recently described U. simmonsii (sect. Minutae), which was reported to share some morphological characters with subgenus Polypompholyx. We found strong jackknife support for a monophyletic subgenus Polypompholyx lineage; however, our strict consensus tree shows an unresolved relationship between the sections Polypompholyx and Pleiochasia. Within the section Pleiochasia, we found two supported clades, generally differing in a more northern or southern distribution. Despite high levels of morphological heterogeneity and convergence, we found some clade-specific character homogeneity within these two clades, particularly that of growth and bladder-trap form, and floral structure. Bladder-trap form corresponds most strongly with terrestrial v. aquatic habits. The evolution of filiform corolla appendages corresponds with floral colour, and is possibly associated with sexual mimicry, with those of the upper corolla arising twice independently. Furthermore, we found that U. monanthos and U. novae-zelandiae remain synonyms of U. dichotoma, and that U. simmonsii is not included in the subgenus Polypompholyx, but instead is allied with sections Stomoisia and Enskide of subgenus Bivalvaria.

The Juncaceae-Cyperaceae Interface: A Combined Plastid Sequence Analysis

Phylogenetic relationships of Juncaceae and related families of Cyperales were investigated using DNA sequence data from the plastid rps16 intron, trnL intron, and trnL-F intergenic spacer. Results using parsimony analysis of the aligned matrices find Juncaceae and Cyperaceae to be monophyletic families, which form a clade sister to a monophyletic Thurniaceae that includes Prionium (Prioniaceae), all three clades with 100% bootstrap support. Within Juncaceae, the genus Lazula is monophyletic with 100% bootstrap support and sister to the rest of Juncaceae. Further groupings within the family indicate that the genus Juncus may be monophyletic only with the inclusion of the single-flowered genera of Juncaceae (Distichia, Oxychloe, Marsippospermum, and Rostkovia; sequences of Patosia were not included). Major groupings within Juncus are supported by the morphological characters of septate or non-septate leaves and the presence or absence of bracts subtending the flowers, which have been used to define subgenera and sections within Juncus.

Aglaia (Meliaceae): an evaluation of taxonomic concepts based on DNA data and secondary metabolites

We performed maximum parsimony and Bayesian analyses (nuclear ITS rDNA, plastid rps16 intron) to estimate phylogenetic relationships within Aglaia (over 100 species in Southeast Asia, the Pacific, and Australia) and its relations among Aglaieae (Meliaceae). Based on 67 accessions of Aglaieae, three taxa of Guareae, and two taxa of Melieae (outgroup), this study provides the first assessment of the current circumscription of Aglaieae, Aglaia, and its sections and to a more limited extent of species concepts in Aglaia. DNA data are compared to recently collected data on chemical profiles. Our analyses indicate (1) the monophyly of Aglaieae; (2) the polyphyly of Aphanamixis; (3) the paraphyly of Aglaia; (4) the existence of at least three entities with respect to Aglaia: (a) the core group of Aglaia section Amoora (dehiscent fruits) with close relationships to Lansium and Reinwardtiodendron, (b) a group comprising morphological intermediates between the two sections, and (c) the core group of Aglaia section Aglaia (indehiscent fruits). Macro- and micromolecular data indicate that complex species are more heterogeneous, i.e., probably containing more than one taxon each, than taxonomically isolated species. A third section in Aglaia is recognized to accommodate A. lawii, A. teysmanniana, and A. beccarii.

Molecular Phylogenetics of Lentibulariaceae Inferred from Plastid rps16 Intron and trnL-F DNA Sequences: Implications for Character Evolution and Biogeography

Phylogenetic relationships among 75 species of Lentibulariaceae, representing the three recognized genera, were assessed by cladistic analysis of DNA sequences from the plastid rps16 intron and the trnL-F region. Sequence data from the two loci were analyzed both separately and in combination. Consensus trees from all analyses are congruent, and parsimony jackknife results demonstrate strong support for relationships both between and within each of the three de- monstrably monophyletic genera. The genus Pinguicula is sister to a Genlisea-Utricularia clade, the phylogenetic structure within this clade closely follows Taylor's recent sectional delimitations based on morphology. Three principal clades are shown within Utricularia, with the basal sections Polypompholyx and Pleiochasia together forming the sister lineage of the remaining Utricularia species. Of the fundamental morphological specializations, the stoloniferous growth form apparently arose independently within Genlisea and Utricularia three times, and within Utricularia itself, perhaps more than once. The epiphytic habit has evolved independently at least three times, in Pinguicula ,i nUtricularia section Phyllaria, and within the two sections Orchidioides and Iperua (in the latter as bromeliad tank-epiphytes). The suspended aquatic habit may have evolved independently within sections Utricularia and Vesiculina. Biogeographic optimization on the phylogeny demonstrates patterns commonly associated with the boreotropics hypothesis and limits the spatial origin of Lentibulariaceae to temperate Eurasia or tropical America.

CIRCUMSCRIPTION AND PHYLOGENETIC RELATIONSHIPS OF GYMNOCARPOS (CARYOPHYLLACEAE-PARONYCHIOIDEAE)

A molecular phylogenetic study based on nuclear ribosomal internal transcribed spacer sequences and plastid rps16 intron sequences on the status of the genus Gymnocarpos (Paronychioideae, Caryophyllaceae) is presented. Gymnocarpos decandrus and Sclerocephalus arabicus form a strongly supported clade within a well-supported group consisting also of G. przewalskii, and the rest of Gymnocarpos. Re-examination of morphological characters also supports this conclusion. Paronychia is found to be polyphyletic, with the subgenera Paronychia and Siphonychia forming a strongly supported sister group to Gymnocarpos, whereas P. kapela and P. chlorothyrsa (representing subgen. Anoplonychia) are found to be related to Herniaria and Philippiella. A key to the 10 species recognized in Gymnocarpos is presented, as well as synoptical information on nomenclature and distributions.

Inferring the History of the Polyploid Silene aegaea (Caryophyllaceae) Using Plastid and Homoeologous Nuclear DNA Sequences

The origin of the rare allotetraploid Silene aegaea was inferred from plastid rps16 intron sequences, homoeologous copies of nuclear ribosomal internal transcribed spacer (ITS) sequences, and an intron from the nuclear gene coding for the second largest subunit of RNA polymerase II (RPB2). The nuclear DNA regions support the S. sedoides and S. pentelica lineages as most closely related to the two S. aegaea paralogues. A few recombinant ITS sequences were found, but as PCR recombination could be demonstrated, no true recombination could be demonstrated. No recombination was found in the RPB2 sequences. Plastid rps16 intron sequences strongly support S. pentelica as the maternal lineage. The strength of the approach of using homoeologous sequences of several loci is demonstrated, and its usefulness for the study of phylogenies of groups including polyploids is emphasized.