Recent accelerated diversification in rosids occurred outside the tropics.

Conflicting relationships have been found between diversification rate and temperature across disparate clades of life. Here, we use a supermatrix comprising nearly 20,000 species of rosids-a clade of ~25% of all angiosperm species-to understand global patterns of diversification and its climatic association. Our approach incorporates historical global temperature, assessment of species' temperature niche, and two broad-scale characterizations of tropical versus non-tropical niche occupancy. We find the diversification rates of most subclades dramatically increased over the last 15 million years (Myr) during cooling associated with global expansion of temperate habitats. Climatic niche is negatively associated with diversification rates, with tropical rosids forming older communities and experiencing speciation rates ~2-fold below rosids in cooler climates. Our results suggest long-term cooling had a disproportionate effect on non-tropical diversification rates, leading to dynamic young communities outside of the tropics, while relative stability in tropical climes led to older, slower-evolving but still species-rich communities.

Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences - a case study in the tree genus Milicia.

BACKGROUND: Species delimitation in closely related plant taxa can be challenging because (i) reproductive barriers are not always congruent with morphological differentiation, (ii) use of plastid sequences might lead to misinterpretation, (iii) rare species might not be sampled. We revisited molecular-based species delimitation in the African genus Milicia, currently divided into M. regia (West Africa) and M. excelsa (from West to East Africa). We used 435 samples collected in West, Central and East Africa. We genotyped SNP and SSR loci to identify genetic clusters, and sequenced two plastid regions (psbA-trnH, trnC-ycf6) and a nuclear gene (At103) to confirm species' divergence and compare species delimitation methods. We also examined whether ecological niche differentiation was congruent with sampled genetic structure. RESULTS: West African M. regia, West African and East African M. excelsa samples constituted three well distinct genetic clusters according to SNPs and SSRs. In Central Africa, two genetic clusters were consistently inferred by both types of markers, while a few scattered samples, sympatric with the preceding clusters but exhibiting leaf traits of M. regia, were grouped with the West African M. regia cluster based on SNPs or formed a distinct cluster based on SSRs. SSR results were confirmed by sequence data from the nuclear region At103 which revealed three distinct 'Fields For Recombination' corresponding to (i) West African M. regia, (ii) Central African samples with leaf traits of M. regia, and (iii) all M. excelsa samples. None of the plastid sequences provide indication of distinct clades of the three species-like units. Niche modelling techniques yielded a significant correlation between niche overlap and genetic distance. CONCLUSIONS: Our genetic data suggest that three species of Milicia could be recognized. It is surprising that the occurrence of two species in Central Africa was not reported for this well-known timber tree. Globally, our work highlights the importance of collecting samples in a systematic way and the need for combining different nuclear markers when dealing with species complexes. Recognizing cryptic species is particularly crucial for economically exploited species because some hidden taxa might actually be endangered as they are merged with more abundant species.

Should genes with missing data be excluded from phylogenetic analyses?

Phylogeneticists often design their studies to maximize the number of genes included but minimize the overall amount of missing data. However, few studies have addressed the costs and benefits of adding characters with missing data, especially for likelihood analyses of multiple loci. In this paper, we address this topic using two empirical data sets (in yeast and plants) with well-resolved phylogenies. We introduce varying amounts of missing data into varying numbers of genes and test whether the benefits of excluding genes with missing data outweigh the costs of excluding the non-missing data that are associated with them. We also test if there is a proportion of missing data in the incomplete genes at which they cease to be beneficial or harmful, and whether missing data consistently bias branch length estimates. Our results indicate that adding incomplete genes generally increases the accuracy of phylogenetic analyses relative to excluding them, especially when there is a high proportion of incomplete genes in the overall dataset (and thus few complete genes). Detailed analyses suggest that adding incomplete genes is especially helpful for resolving poorly supported nodes. Given that we find that excluding genes with missing data often decreases accuracy relative to including these genes (and that decreases are generally of greater magnitude than increases), there is little basis for assuming that excluding these genes is necessarily the safer or more conservative approach. We also find no evidence that missing data consistently bias branch length estimates.

Multi-gene analysis provides a well-supported phylogeny of Rosales.

Despite many attempts to resolve evolutionary relationships among the major clades of Rosales, some nodes have been extremely problematic and have remained unresolved. In this study, we use two nuclear and 10 plastid loci to infer phylogenetic relationships among all nine families of Rosales. Rosales were strongly supported as monophyletic; within Rosales all family relationships are well-supported with Rosaceae sister to all other members of the order. Remaining Rosales can be divided into two subclades: (1) Ulmaceae are sister to Cannabaceae plus (Urticaceae+Moraceae); (2) Rhamnaceae are sister to Elaeagnaceae plus (Barbeyaceae+Dirachmaceae). One noteworthy result is that we recover the first strong support for a sister relationship between the enigmatic Dirachmaceae and Barbeyaceae. These two small families have distinct morphologies and potential synapomorphies remain unclear. Future studies should try to identify nonDNA synapomorphies uniting Barbeyaceae with Dirachmaceae.

Taxonomic discrimination of higher plants by pyrolysis mass spectrometry.

Pyrolysis mass spectrometry (PyMS) is a rapid, simple, high-resolution analytical method based on thermal degradation of complex material in a vacuum and has been widely applied to the discrimination of closely related microbial strains. Leaf samples of six species and one variety of higher plants (Rosa multiflora, R. multiflora var. platyphylla, Sedum kamtschaticum, S. takesimense, S. sarmentosum, Hepatica insularis, and H. asiatica) were subjected to PyMS for spectral fingerprinting. Principal component analysis of PyMS data was not able to discriminate these plants in discrete clusters. However, canonical variate analysis of PyMS data separated these plants from one another. A hierarchical dendrogram based on canonical variate analysis was in agreement with the known taxonomy of the plants at the variety level. These results indicate that PyMS is able to discriminate higher plants based on taxonomic classification at the family, genus, species, and variety level.

The radiation of the Cape flora, southern Africa.

The flora of the south-western tip of southern Africa, the Cape flora, with some 9000 species in an area of 90,000 km2 is much more speciose than can be expected from its area or latitude, and is comparable to that expected from the most diverse equatorial areas. The endemism of almost 70%, on the other hand, is comparable to that found on islands. This high endemism is accounted for by the ecological and geographical isolation of the Cape Floristic Region, but explanations for the high species richness are not so easily found. The high species richness is accentuated when its taxonomic distribution is investigated: almost half of the total species richness of the area is accounted for by 33 'Cape floral clades'. These are clades which may have initially diversified in the region, and of which at least half the species are still found in the Cape Floristic Region. Such a high contribution by a very small number of clades is typical of island floras, not of mainland floras. The start of the radiation of these clades has been dated by molecular clock techniques to between 18 million years ago (Mya) (Pelargonium) and 8 Mya (Phylica), but only six radiations have been dated to date. The fossil evidence for the dating of the radiation is shown to be largely speculative. The Cenozoic environmental history of southern Africa is reviewed in search of possible triggers for the radiations, climatic changes emerge as the most likely candidate. Due to a very poor fossil record, the climatic history has to be inferred from larger scale patterns, these suggest large-scale fluctuations between summer wet (Palaeocene, Early Miocene) and summer dry climates (Oligocene, Middle Miocene to present). The massive speciation in the Cape flora might be accounted for by the diverse limitations to gene flow (dissected landscapes, pollinator specialisation, long flowering times allowing much phenological specialisation), as well as a richly complex environment providing a diversity of selective forces (geographically variable climate, much altitude variation, different soil types, rocky terrain providing many micro-niches, and regular fires providing both intermediate disturbances, as well as different ways of surviving the fires). However, much of this is based on correlation, and there is a great need for (a) experimental testing of the proposed speciation mechanisms, (b) more molecular clock estimates of the age and pattern of the radiations, and (c) more fossil evidence bearing on the past climates.

Pollen- versus seed-mediated gene flow in a scattered forest tree species.

We examined the spatial distribution of maternally inherited chloroplast DNA markers over the French part of the range of Sorbus torminalis, a scattered temperate forest tree native to most of Europe. The survey by restriction analysis of polymerase-chain-reaction amplified fragments for 880 individuals distributed among 55 populations allowed the detection of 25 haplotypes. The coefficient of differentiation among populations computed on the basis of haplotype frequency (G(STc) = 0.34) was one of the lowest found in forest trees so far, and the mean within-population diversity was relatively high, indicating multiple-mother foundation events. A significant but slight geographical pattern was observed, up to distances of about 100 km. This pattern of differentiation was compared to the genetic structure of the same populations revealed by biparentally inherited markers (isoenzymes), and a new method to quantify the relative importance of seed and pollen dispersal was derived, based on isolation-by-distance models. Neither pollen- nor seed-mediated gene flow was predominant in S. torminalis, a finding that differs from those for the majority of tree species studied so far. This result was most likely due to an extinction-recolonization dynamics based on efficient seed dispersal strategies. The joint screening of 31 individuals of the related Sorbus aria and of 163 hybrid individuals shows that hybridization occurs predominantly in one direction and is rarely followed by cytoplasmic introgression. As a consequence, interspecific gene flow should not significantly affect the diversity dynamics within S. torminalis.

Rapid and recent origin of species richness in the Cape flora of South Africa.

The Cape flora of South Africa grows in a continental area with many diverse and endemic species. We need to understand the evolutionary origins and ages of such 'hotspots' to conserve them effectively. In volcanic islands the timing of diversification can be precisely measured with potassium-argon dating. In contrast, the history of these continental species is based upon an incomplete fossil record and relatively imprecise isotopic palaeotemperature signatures. Here we use molecular phylogenetics and precise dating of two island species within the same clade as the continental taxa to show recent speciation in a species-rich genus characteristic of the Cape flora. The results indicate that diversification began approximately 7-8 Myr ago, coincident with extensive aridification caused by changes in ocean currents. The recent origin of endemic species diversity in the Cape flora shows that large continental bursts of speciation can occur rapidly over timescales comparable to those previously associated with oceanic island radiations.

Diterpenes from the bark and seeds of Colophospermum mopane.

The CHCl3 extract of the bark and seeds of Colophospermum mopane gave three new diterpenes, dihydrogrindelic acid and dihydrogrindelaldehyde and methyl labd-13E-en-15-oate. The structures were assigned on the basis of detailed spectroscopic data analyses. The aldehyde showed significant cytotoxic activity against a human breast cancer cell line.

Solid-phase microextraction of hop volatiles. Potential use for determination and verification of hop varieties.

The composition of hop essential oil is an important tool for evaluation of hop quality. As each hop variety has a typical essential oil pattern (fingerprint), hop oil analyses can be used to distinguish between hop varieties. The headspace solid-phase microextraction (SPME) method as described in this contribution is a simple sample preparation technique and represents an alternative procedure for essential oil fingerprint determination. Different SPME parameters (extraction temperature, extraction time and sample mass) were studied and the results were compared with those obtained by the routine distillation method. It is shown that SPME results can be used for determination and verification of varieties grown in Slovenia by means of principal components analysis.

Value of high-performance liquid chromatographic analysis of anthocyanins in the differentiation of red grape cultivars and red wines made from them.

A HPLC method that allows the separation of several anthocyanins present in red grapes and red wines, using a linear gradient of acetonitrile in water at pH 1.3, using perchloric acid as an acid modifier, is described. Data clearly show that the anthocyanins profile of red grapes may be complex, but quite different for each cultivar studied. Thus, those molecules may be used as chemotaxonomic markers for classifying red grape cultivars. However, the anthocyanin profile of red wines clearly differs from that presented by grapes employed in making it, because red wine contains a higher relative amount of malvidin-3-O-glucoside than grapes, and the relative amount of other anthocyanins in wines is usually lower than in grapes. Therefore, the use of anthocyanins present in wines to determine the grape cultivar used for winemaking needs a careful evaluation of the influence of different technological procedures on the anthocyanins fingerprint.

Insecticidal flavaglines and other compounds from Fijian Aglaia species.

Bioassays with lipophilic crude extracts of four Fijian Aglaia species against Spodoptera littoralis displayed strong insecticidal activity for A. basiphylla and A. gracilis, whereas A. archboldiana and A. vitiensis did not have any significant effects. The insect toxicity of A. basiphylla was caused by the well known benzofuran flavaglines rocaglamide, desmethylrocaglamide and aglafoline. In contrast, A. gracilis contained four related pyrimidinone derivatives in the root and stem bark, including two new congeners named marikarin and 3'-hydroxymarikarin. Moreover, two new putrescine bisamides, secoodorine and secopiriferine, a new benzopyran flavagline. desacetylaglain A. and a new norsesquiterpene were isolated from the leaves together with three known bisamides and 3-hydroxy-5,7,4'-trimethoxyflavone. The structures of the new compounds were elucidated by spectroscopic methods. Comparative feeding assays within the active pyrimidinone flavaglines showed that the free hydroxy group in aromatic ring A of marikarin diminishes insecticidal activity.

Influence of food and larval age on the defensive chemistry of Saturnia pyri.

Scolus secretions and hemolymph of caterpillars of Saturnia pyri fed with two different foodplants (Crataegis monogyna, Prunus spinosa) were chemically analyzed and their chemical similarities determined. The secondary-compound patterns obtained for the two body fluids showed no significant differences when compared between the two groups of alternatively fed last-instar larvae. Thus, the composition of these fluids of full-grown caterpillars is not influenced by the larval diet. However, younger larvae on P. spinosa revealed a diversity of compounds differing significantly from that of larger caterpillars fed with either C. monogyna (both body fluids) or P. spinosa (hemolymph only). This indicates that, on the one hand, the hemolymph composition is adapted to the changing physiological requirements of the given instars whereas, on the other hand, the defensive mixtures remain unaltered in the late larval instars due to a constant spectrum of potential enemies.

High resolution microsatellite based analysis of the mating system allows the detection of significant biparental inbreeding in Caryocar brasiliense, an endangered tropical tree species.

In this work we investigate the mating system of four populations of the endangered tropical tree species Caryocar brasiliense, using genetic data from 10 microsatellite loci. Eight to 10 open-pollinated progeny arrays of 16 individuals, together with their mother tree, were sampled per population. Mating system parameters were estimated under the mixed mating model, implemented by the software MLTR. The single-locus outcrossing rate (ts) varied among loci and populations, but multilocus outcrossing rates (tm) were equal to one for all four populations. Nevertheless, biparental inbreeding (tm - ts) was different from zero for all populations, indicating that outcrossing events may occur between relatives. Our results also indicate that the high polymorphism of microsatellite markers provide an extraordinary resolution to discriminate precisely selfing events from outcrossing events between close relatives. Our results indicate that, although highly outcrossed, C. brasiliense shows high levels of biparental inbreeding, most likely due to the limited flight range of pollinators and restriction in seed dispersal. Furthermore, these results suggest that Cerrado fragmentation could limit gene flow by isolating seed dispersers and territorial small sized bat pollinators inside fragments, increasing the rate of mating between close relatives. The conservation of nonisolated populations in large preserved areas may be necessary to foster outcrossing events between unrelated individuals and thus maintain species viability.

The ecological and taxonomic importance of flower volatiles of Clusia species (Guttiferae).

The chemical composition of floral volatiles of sixteen species of Clusia (Guttiferae) belonging to four different taxonomic sections of the genus was investigated. The volatiles were extracted from fresh petals by microhydrodistillation and analysed by GC/MS. The composition of the volatiles was in part, but not always, related to the taxonomic position of the species, and to a minor extent to the type of pollinator observed on the flowers as revealed by clustering analysis. The composition of the volatile components of female and male flowers belonging to the same species (C. grandiflora, C. lanceolata, C. paralicola, C. parviflora and C. spiritu-sanctensis) was found to be almost identical. Field bioassays showed the petal extracts to be attractive to pollinating bees.

Monomer composition of polysaccharides of seed cell walls and the taxonomy of the Vochysiaceae.

The distribution of polysaccharides from the seed cell walls of 57 samples of Vochysiaceae native to Brazil were studied, comprising 16 species distributed among the genera Callisthene, Qualea, Salvertia and Vochysia. The polysaccharides were extracted with hot water, then hydrolyzed with the resulting monomers analyzed by HPLC. All samples yielded arabinose, galactose, glucose. mannose and rhamnose, the relative amounts of each monomer, however, varying from one sample to another. Arabinose was always the predominant component, which implies that it might possibly be used as a marker of the Vochysiaceae. The quantitative distribution of monosaccharides was similar between the species of Qualea and Callisthene, characterized by the predominance of arabinose and mannose, and between the species of Salvertia and Vochysia, which contained higher amounts of arabinose and galactose. Such results are consistent with affinities inferred from floral morphology, wood anatomy and molecular data. Substantial intraspecific variation was observed for some species. UPGMA analysis based on the distribution of the monosaccharides reveals two main clusters, according to the links commented above. The resultant phenogram is not coherent with the current sectional classification of the Vochysiaceae, but the differences in the monosaccharides distribution between the two clusters are strongly supported by ANOVA.

Combined analyses of RAPDs, cpDNA and morphology demonstrate spontaneous hybridization in the plant genus Chaenomeles.

Evidence of spontaneous hybridization between two partially sympatric species of Chaenomeles, C. cathayensis and C. speciosa, has been obtained through analysis of offspring families from these two species, as well as from two presumed interspecific hybrid populations. A combination of different methods was applied. Analysis of diagnostic RAPD markers and of chloroplast DNA haplotypes supported the notion of spontaneous hybridization, and suggested that there has been symmetrical, rather than unidirectional, introgression between C. cathayensis and C. speciosa. RAPDs and morphological characters revealed concordant patterns of genetic relatedness among the studied offspring families. Some putative hybrid families had mainly intermediate characters, whereas others appeared to be later generation hybrids as they were genetically and phenotypically rather similar to families that appeared to represent pure species. The RAPD-based proportion of between-family variability was considerably higher in the putatively hybridogenous populations than in populations of the pure species. Within-family gene diversity estimates ranged from C. speciosa (max. Hj = 0.235) to C. cathayensis (min. Hj = 0.094) with the presumed hybrid families taking intermediate values.

Manipulation of the phenolic chemistry of willows by gall-inducing sawflies.

The ability to induce galls on plants has evolved independently in many insect orders, but the adaptive significance and evolutionary consequences of gall induction are still largely unknown. We studied these questions by analyzing the concentrations of various plant defense compounds in willow leaves and sawfly galls. We found that the galls are probably nutritionally beneficial for the sawfly larvae, because the concentrations of most defensive phenolics are substantially lower in gall interiors than in leaves. More importantly, changes in chemistry occur in a similar coordinated pattern in all studied willow species, which suggests that the insects control the phenolic biosynthesis in their hosts. The resulting convergence of the chemical properties of the galls both within and between host species indicates that the role of plant chemistry in the evolution of host shifts may be fundamentally less significant in gallers than in other phytophagous insects.

[Variations of flower coloration in garden rose spontaneous mutants]. / Izmenchivost' okraski tsvetkov u spontannykh mutantov sadovykh roz.

Twenty two varieties were isolated as a result of studying the world assortment of garden roses, from which many natural bud variations (sports) were selected. The genealogy of these varieties and variations of flower coloration in their sports were studied. It was shown that flower coloration may have a certain direction, depending on the origin of initial forms, i.e., on their genotype. The possible genetic causes of changes in the flower coloration in a certain predominant direction upon mutation are discussed.