Phylogeny of South African Gnaphalieae (Asteraceae) based on two noncoding chloroplast sequences

The Gnaphalieae are a group of sunflowers that have their greatest diversity in South America, Southern Africa, and Australia. The objective of this study was to reconstruct a phylogeny of the South African Gnaphalieae using sequence data from two noncoding chloroplast DNA sequences, the trnL intron and trnL/trnF intergenic spacer. Included in this investigation are the genera of the Gnaphalieae from the African basal groups, members of the subtribes Cassiniinae, Gnaphaliinae, and Relhaniinae, and African representatives from the large Old World genus Helichrysum. Results indicate that two Gnaphaloid genera, Printzia and Callilepis, should be excluded from the Gnaphalieae. In most trees the Relhaniinae s.s. (sensu stricto) and some of the basal taxa comprise a clade that is sister to the remainder of the tribe Gnaphalieae. The Relhaniinae, which are restricted to Africa, are not a monophyletic group as presently circumscribed, nor are the South African members of Helichrysum, the Cassiniinae and Gnaphaliinae. There is general agreement between our molecular analysis and that of morphology, particularly in the terminal branches of the trees.     

Principal features of the cpDNA evolution in Taraxacum (Asteraceae, Lactuceae): a conflict with taxonomy

Phylogenetic relationships based on the chloroplast genome of Taraxacum were studied. Representative samples of 44 sections or species groups and a number of isolated species were analyzed. On the basis of the sequence variation in psbA–trnH and in trnL–trnF, mutations associated with RFLPs were monitored. Five RFLPs without homoplasy were recognized and used to reconstruct four main cpDNA groups (haplotypes); Group I is ancestral and, contrary to the information in the primary sequences, the RFLPs were not distinct from those of the outgroup species of Agoseris and Prenanthes. This group corresponds to dandelions believed to be ancestral on the basis of morphological data and previous studies of the chloroplast genome. A comparison of parsimony analysis of morphological and chloroplast data showed an overall lack of congruence. The conflict can most probably be accounted for as a consequence of reticulation.     

Out in the cold: genetic variation of Nothofagus pumilio (Nothofagaceae) provides evidence for latitudinally distinct evolutionary histories in austral South America

Nothofagus pumilio is the dominant and almost ubiquitous tree species in mountainous environments of temperate South America. We used two types of molecular markers (cpDNA and isozymes) to evaluate the effects of the Paleogene paleogeography of Patagonia and more recent climatic oscillations of the Neogene on such cold‐tolerant species’ genetic makeup. Phylogeographic analysis on sequences of three cpDNA non‐coding regions at 85 populations yielded two latitudinally disjunct monophyletic clades north and south of c. 42°S containing 11 and three haplotypes, respectively. This indicates a long‐lasting vicariant event due to the presence of an extended open paleobasin at mid latitudes of Patagonia. Also distribution patterns of cpDNA haplotypes suggest regional spread following stepping‐stone models using pre‐Cenozoic mountains as corridors. Comparable genetic diversity measured along 41 sampled populations using seven polymorphic isozyme loci provides evidence of local persistence and spread from multiple ice‐free locations. In addition, significantly higher heterozygosity and allelic richness at high latitudes, i.e. in areas of larger glacial extent, suggest survival in large and isolated refugia. While, higher cpDNA diversity in lower latitudes reflects the complex orogeny that historically isolated northern populations, lower isozyme diversity and reduced F_ST values provide evidence of local glacial survival in numerous small locales. Therefore, current genetic structure of N. pumilio is the result of regional processes which took place during the Tertiary that were enhanced by contemporary local effects of drift and isolation in response to Quaternary climatic cycles.     

Pleistocene refugia and polytopic replacement of diploids by tetraploids in the Patagonian and Subantarctic plant Hypochaeris incana (Asteraceae, Cichorieae)

We report the phylogeographic pattern of the Patagonian and Subantarctic plant Hypochaeris incana endemic to southeastern South America. We applied amplified fragment length polymorphism (AFLP) and chloroplast DNA (cpDNA) analysis to 28 and 32 populations, respectively, throughout its distributional range and assessed ploidy levels using flow cytometry. While cpDNA data suggest repeated or simultaneous parallel colonization of Patagonia and Tierra del Fuego by several haplotypes and/or hybridization, AFLPs reveal three clusters corresponding to geographic regions. The central and northern Patagonian clusters (∼38–51° S), which are closer to the outgroup, contain mainly tetraploid, isolated and highly differentiated populations with low genetic diversity. To the contrary, the southern Patagonian and Fuegian cluster (∼51–55° S) contains mainly diploid populations with high genetic diversity and connected by high levels of gene flow. The data suggest that H. incana originated at the diploid level in central or northern Patagonia, from where it migrated south. All three areas, northern, central and southern, have similar levels of rare and private AFLP bands, suggesting that all three served as refugia for H. incana during glacial times. In southern Patagonia and Tierra del Fuego, the species seems to have expanded its populational system in postglacial times, when the climate became warmer and more humid. In central and northern Patagonia, the populations seem to have become restricted to favourable sites with increasing temperature and decreasing moisture and there was a parallel replacement of diploids by tetraploids in local populations.     

Revision of the genus Clibadium (Asteraceae, Heliantheae)

Clibadium L. (Asteraceae, Heliantheae) is a genus of 29 species distributed throughout latin America, from Mexico to Peru, and in the West Indies, with high numbers of species in Costa Rica, Colombia, and Ecuador.Clibadium includes shrubs and small trees; usually with loosely aggregated capitula; herbaceous phyllaries arranged in 1–5 series; receptacles usually paleaceous throughout; corollas of pistillate florets 2–4-lobed; corollas of the staminate florets 4–5-lobed; purple to black anthers; and chromosome numbers alln=16. Two sections of species previously recognized are here considered as subgenera (subg.Paleata and subg.Clibadium) containing two and four sections, respectively.Clibadium subg.Paleata contains five species distributed in sects.Eggersia (3 spp.) andTrixidium (2 spp.), and subg.Clibadium has 24 species distributed among sects.Clibadium (6 spp.),Glomerata (9 spp.),Grandifolia (5 spp.), andOswalda (4 spp.).     

Mitochondrial restriction fragment length polymorphism (RFLP) and sequence variation among closely related avian species and the genetic characterization of hybrid Dendroica warblers

To address several interconnected goals, we used mitochondrial DNA (mtDNA) sequences to explore evolutionary relationships among four potentially hybridizing taxa in a North American avian superspecies (Dendroica occidentalis, D. townsendi, D. virens, and D. nigrescens). We first compared the results of a previous restriction fragment length polymorphism (RFLP)-based study with 1453 nucleotides from the mitochondrial cytochrome oxidase subunit I (COI), ATP-synthase 6 (ATPase 6), and ATP-synthase 8 (ATPase 8) genes. Separate phylogenetic analyses of the RFLP and sequence data provided identical and well-supported hierarchical species-level reconstructions that grouped occidentalis and townsendi as sister taxa. We then explored several general features of mitochondrial evolution via a comparison of the RFLP and sequence data sets. Qualitative rate differences that seemed evident in highly autocorrelated comparisons of RFLP vs. sequence pairwise distances were not supported when autocorrelation was removed. We also noted a high variance in corresponding RFLP and sequence distances after the removal of autocorrelation effects. This variance suggests that caution should be used when combining RFLP and sequence-based data in studies that require the large-scale synthesis of divergence estimates drawn from sources employing different molecular techniques. Finally, we used our parallel RFLP and sequence data to design and validate a rapid and inexpensive polymerase chain reaction-RFLP (PCR-RFLP) protocol for determining species-specific mitochondrial haplotypes. This PCR-RFLP technique will be applied in ongoing studies of the occidentalis/townsendi hybrid zone, where the historic and geographical complexity of the interbreeding populations necessitates the genotyping of thousands of individual warblers.     

The central Mediterranean as a phytodiversity hotchpotch: phylogeographical patterns of the Anthemis secundiramea group (Compositae,Anthemideae) across the Sicilian Channel

Aim We investigated the phylogeography of the Anthemis secundiramea group (Compositae, Anthemideae) to assess the role of palaeogeographical events in its genetic and taxonomic differentiation. We also evaluated the contribution of hybridization to the complexity of these diversification processes in an area of phytogeographical overlap. Location Central Mediterranean: North Africa, Tyrrhenian Islands, Sicily, and its surrounding islands and islets. Methods The geographical distribution of the genetic variability and differentiation of 207 individuals belonging to 42 populations was analysed through chloroplast DNA variation (sequences of the two spacer regions psbA–trnH and trnC–petN), and 290 individuals belonging to 35 populations were analysed using amplified fragment length polymorphism (AFLP) fingerprinting. Results We found three well‐defined groups of taxa. The first includes all populations located in North Africa belonging to the species Anthemis confusa, A. glareosa and A. ubensis, which show a significant pattern of isolation by distance from one another. They share the same chloroplast DNA haplotypes, possibly reflecting range expansion/contraction during the Quaternary. Within the second group, which comprises all populations belonging to A. secundiramea, an absence of genetic structure suggests contemporary or at least recent gene flow among its populations. The third group includes the populations belonging to Anthemis urvilleana, which is endemic to the Maltese archipelago. While hybridization with Anthemis arvensis or A. peregrina is hypothesized for four populations of A. urvilleana, the sharing of a haplotype between one population and A. muricata, endemic to Sicily, is interpreted as a relict of the ancient connection between the Maltese archipelago and south‐eastern Sicily. Main conclusions The strong genetic differentiation observed between circum‐Sicilian and North African populations of the A. secundiramea group suggests the paramount importance of the Sicilian Strait as a barrier to dispersal and gene flow. The present distribution of A. secundiramea, however, demonstrates that this barrier may be crossed by long‐distance dispersal overseas, or by anthropogenic dispersal. Sea‐level oscillations during the Pleistocene were responsible for the divergence between the Sicilian endemic A. muricata and the Maltese endemic A. urvilleana. Incongruent AFLP patterns and chloroplast haplotype distributions indicate that hybridization of members of the A. secundiramea group with eastern (A. arvensis or A. peregrina) as well as with western (the clade of A. maritima and A. pedunculata) Mediterranean elements has strongly influenced the genetic and taxonomic diversity in this species group.