Carnivorous plants: phylogeny and structural evolution

Parallel developmental genetic features underlie stickleback gill raker evolution

Background

Convergent evolution, the repeated evolution of similar phenotypes in independent lineages, provides natural replicates to study mechanisms of evolution. Cases of convergent evolution might have the same underlying developmental and genetic bases, implying that some evolutionary trajectories might be predictable. In a classic example of convergent evolution, most freshwater populations of threespine stickleback fish have independently evolved a reduction of gill raker number to adapt to novel diets. Gill rakers are a segmentally reiterated set of dermal bones important for fish feeding. A previous large quantitative trait locus (QTL) mapping study using a marine × freshwater F2 cross identified QTL on chromosomes 4 and 20 with large effects on evolved gill raker reduction.

Results

By examining skeletal morphology in adult and developing sticklebacks, we find heritable marine/freshwater differences in gill raker number and spacing that are specified early in development. Using the expression of the Ectodysplasin receptor (Edar) gene as a marker of raker primordia, we find that the differences are present before the budding of gill rakers occurs, suggesting an early change to a lateral inhibition process controlling raker primordia spacing. Through linkage mapping in F2 fish from crosses with three independently derived freshwater populations, we find in all three crosses QTL overlapping both previously identified QTL on chromosomes 4 and 20 that control raker number. These two QTL affect the early spacing of gill raker buds.

Conclusions

Collectively, these data demonstrate that parallel developmental genetic features underlie the convergent evolution of gill raker reduction in freshwater sticklebacks, suggesting that even highly polygenic adaptive traits can have a predictable developmental genetic basis.

Venus Flytrap Seedlings Show Growth-Related Prey Size Specificity

Venus flytrap (Dionaea muscipula) has had a conservation status of vulnerable since the 1970s. Little research has focussed on the ecology and even less has examined its juvenile stages. For the first time, reliance on invertebrate prey for growth was assessed in seedling Venus flytrap by systematic elimination of invertebrates from the growing environment. Prey were experimentally removed from a subset of Venus flytrap seedlings within a laboratory environment. The amount of growth was measured by measuring trap midrib length as a function of overall growth as well as prey spectrum. There was significantly lower growth in prey-eliminated plants than those utilising prey. This finding, although initially unsurprising, is actually contrary to the consensus that seedlings (traps < 5 mm) do not catch prey. Furthermore, flytrap was shown to have prey specificity at its different growth stages; the dominant prey size for seedlings did not trigger mature traps. Seedlings are capturing and utilising prey for nutrients to increase their overall trap size. These novel findings show Venus flytrap to have a much more complex evolutionary ecology than previously thought.

Adaxial-abaxial polarity: the developmental basis of leaf shape diversity

Leaves of flowering plants are diverse in shape. Part of this morphological diversity can be attributed to differences in spatiotemporal regulation of polarity in the upper (adaxial) and lower (abaxial) sides of developing leaves. In a leaf primordium, antagonistic interactions between polarity determinants specify the adaxial and abaxial domains in a mutually exclusive manner. The patterning of those domains is critical for leaf morphogenesis. In this review, we first summarize the gene networks regulating adaxial-abaxial polarity in conventional bifacial leaves and then discuss how patterning is modified in different leaf type categories.

Disproportional plastome-wide increase of substitution rates and relaxed purifying selection in genes of carnivorous Lentibulariaceae

Carnivorous Lentibulariaceae exhibit the most sophisticated implementation of the carnivorous syndrome in plants. Their unusual lifestyle coincides with distinct genomic peculiarities such as the smallest angiosperm nuclear genomes and extremely high nucleotide substitution rates across all genomic compartments. Here, we report the complete plastid genomes from each of the three genera Pinguicula, Utricularia, and Genlisea, and investigate plastome-wide changes in their molecular evolution as the carnivorous syndrome unfolds. We observe a size reduction by up to 9% mostly due to the independent loss of genes for the plastid NAD(P)H dehydrogenase and altered proportions of plastid repeat DNA, as well as a significant plastome-wide increase of substitution rates and microstructural changes. Protein-coding genes across all gene classes show a disproportional elevation of nonsynonymous substitutions, particularly in Utricularia and Genlisea. Significant relaxation of purifying selection relative to noncarnivores occurs in the plastid-encoded fraction of the photosynthesis ATP synthase complex, the photosystem I, and in several other photosynthesis and metabolic genes. Shifts in selective regimes also affect housekeeping genes including the plastid-encoded polymerase, for which evidence for relaxed purifying selection was found once during the transition to carnivory, and a second time during the diversification of the family. Lentibulariaceae significantly exhibit enhanced rates of nucleotide substitution in most of the 130 noncoding regions. Various factors may underlie the observed patterns of relaxation of purifying selection and substitution rate increases, such as reduced net photosynthesis rates, alternative paths of nutrient uptake (including organic carbon), and impaired DNA repair mechanisms.

S-like ribonuclease gene expression in carnivorous plants

Functions of S-like ribonucleases (RNases) differ considerably from those of S-RNases that function in self-incompatibility. Expression of S-like RNases is usually induced by low nutrition, vermin damage or senescence. However, interestingly, an Australian carnivorous plant Drosera adelae (a sundew), which traps prey with a sticky digestive liquid, abundantly secretes an S-like RNase DA-I in the digestive liquid even in ordinary states. Here, using D. adelae, Dionaea muscipula (Venus flytrap) and Cephalotus follicularis (Australian pitcher plant), we show that carnivorous plants use S-like RNases for carnivory: the gene da-I encoding DA-I and its ortholog cf-I of C. follicularis are highly expressed and constitutively active in each trap/digestion organ, while the ortholog dm-I of D. muscipula becomes highly active after trapping insects. The da-I promoter is unmethylated only in its trap/digestion organ, glandular tentacles (which comprise a small percentage of the weight of the whole plant), but methylated in other organs, which explains the glandular tentacles-specific expression of the gene and indicates a very rare gene regulation system. In contrast, the promoters of dm-I, which shows induced expression, and cf-I, which has constitutive expression, were not methylated in any organs examined. Thus, it seems that the regulatory mechanisms of the da-I, dm-I and cf-I genes differ from each other and do not correlate with the phylogenetic relationship. The current study suggests that under environmental pressure in specific habitats carnivorous plants have managed to evolve their S-like RNase genes to function in carnivory.

Green synthesis of silver nanoparticles, their characterization, application and antibacterial activity

Our research focused on the production, characterization and application of silver nanoparticles (AgNPs), which can be utilized in biomedical research and environmental cleaning applications. We used an environmentally friendly extracellular biosynthetic technique for the production of the AgNPs. The reducing agents used to produce the nanoparticles were from aqueous extracts made from the leaves of various plants. Synthesis of colloidal AgNPs was monitored by UV-Visible spectroscopy. The UV-Visible spectrum showed a peak between 417 and 425 nm corresponding to the Plasmon absorbance of the AgNPs. The characterization of the AgNPs such as their size and shape was performed by Atom Force Microscopy (AFM), and Transmission Electron Microscopy (TEM) techniques which indicated a size range of 3 to 15 nm. The anti-bacterial activity of AgNPs was investigated at concentrations between 2 and 15 ppm for Gram-negative and Gram-positive bacteria. Staphylococcus aureus and Kocuria rhizophila, Bacillus thuringiensis (Gram-positive organisms); Escherichia coli, Pseudomonas aeruginosa, and Salmonella typhimurium (Gram-negative organisms) were exposed to AgNPs using Bioscreen C. The results indicated that AgNPs at a concentration of 2 and 4 ppm, inhibited bacterial growth. Preliminary evaluation of cytotoxicity of biosynthesized silver nanoparticles was accomplished using the InQ™ Cell Research System instrument with HEK 293 cells. This investigation demonstrated that silver nanoparticles with a concentration of 2 ppm and 4 ppm were not toxic for human healthy cells, but inhibit bacterial growth.

Glucan-rich diet is digested and taken up by the carnivorous sundew (Drosera rotundifolia L.): implication for a novel role of plant β-1,3-glucanases

Carnivory in plants evolved as an adaptation strategy to nutrient-poor environments. Thanks to specialized traps, carnivorous plants can gain nutrients from various heterotrophic sources such as small insects. Digestion in traps requires a coordinated action of several hydrolytic enzymes that break down complex substances into simple absorbable nutrients. Among these, several pathogenesis-related proteins including β-1,3-glucanases have previously been identified in digestive fluid of some carnivorous species. Here we show that a single acidic endo-β-1,3-glucanase of ~50 kDa is present in the digestive fluid of the flypaper-trapped sundew (Drosera rotundifolia L.). The enzyme is inducible with a complex plant β-glucan laminarin from which it releases simple saccharides when supplied to leaves as a substrate. Moreover, thin-layer chromatography of digestive exudates showed that the simplest degradation products (especially glucose) are taken up by the leaves. These results for the first time point on involvement of β-1,3-glucanases in digestion of carnivorous plants and demonstrate the uptake of saccharide-based compounds by traps. Such a strategy could enable the plant to utilize other types of nutritional sources e.g., pollen grains, fungal spores or detritus from environment. Possible multiple roles of β-1,3-glucanases in the digestive fluid of carnivorous sundew are also discussed.

A comprehensive review on Nymphaea stellata: A traditionally used bitter

Nymphaea stellata Willd. (Syn. Nymphaea nouchali Burman f.) (Nymphaeaceae) is an important and well-known medicinal plant, widely used in the Ayurveda and Siddha systems of medicines for the treatment of diabetes, inflammation, liver disorders, urinary disorders, menorrhagia, blenorrhagia, menstruation problem, as an aphrodisiac, and as a bitter tonic. There seems to be an agreement between the traditional use and experimental observations, such as, hepatoprotective, anti-inflammatory, and particularly antidiabetic activity. Nymphayol, a steroid isolated from the flowers has been scientifically proved to be responsible for the traditionally claimed antidiabetic activity; it reverses the damaged endocrine tissue and stimulates secretion of insulin in the β-cells. However, taking into account the magnitude of its traditional uses, the studies conducted are still negligible. This review is an attempt to provide the pharmaceutical prospective of Nymphaea stellata.

Can phylogeny predict chemical diversity and potential medicinal activity of plants? A case study of Amaryllidaceae

BACKGROUND

During evolution, plants and other organisms have developed a diversity of chemical defences, leading to the evolution of various groups of specialized metabolites selected for their endogenous biological function. A correlation between phylogeny and biosynthetic pathways could offer a predictive approach enabling more efficient selection of plants for the development of traditional medicine and lead discovery. However, this relationship has rarely been rigorously tested and the potential predictive power is consequently unknown.

RESULTS

We produced a phylogenetic hypothesis for the medicinally important plant subfamily Amaryllidoideae (Amaryllidaceae) based on parsimony and Bayesian analysis of nuclear, plastid, and mitochondrial DNA sequences of over 100 species. We tested if alkaloid diversity and activity in bioassays related to the central nervous system are significantly correlated with phylogeny and found evidence for a significant phylogenetic signal in these traits, although the effect is not strong.

CONCLUSIONS

Several genera are non-monophyletic emphasizing the importance of using phylogeny for interpretation of character distribution. Alkaloid diversity and in vitro inhibition of acetylcholinesterase (AChE) and binding to the serotonin reuptake transporter (SERT) are significantly correlated with phylogeny. This has implications for the use of phylogenies to interpret chemical evolution and biosynthetic pathways, to select candidate taxa for lead discovery, and to make recommendations for policies regarding traditional use and conservation priorities.

Phylogeny and biogeography of the carnivorous plant family Sarraceniaceae

The carnivorous plant family Sarraceniaceae comprises three genera of wetland-inhabiting pitcher plants: Darlingtonia in the northwestern United States, Sarracenia in eastern North America, and Heliamphora in northern South America. Hypotheses concerning the biogeographic history leading to this unusual disjunct distribution are controversial, in part because genus- and species-level phylogenies have not been clearly resolved. Here, we present a robust, species-rich phylogeny of Sarraceniaceae based on seven mitochondrial, nuclear, and plastid loci, which we use to illuminate this family's phylogenetic and biogeographic history. The family and genera are monophyletic: Darlingtonia is sister to a clade consisting of Heliamphora+Sarracenia. Within Sarracenia, two clades were strongly supported: one consisting of S. purpurea, its subspecies, and S. rosea; the other consisting of nine species endemic to the southeastern United States. Divergence time estimates revealed that stem group Sarraceniaceae likely originated in South America 44–53 million years ago (Mya) (highest posterior density [HPD] estimate = 47 Mya). By 25–44 (HPD = 35) Mya, crown-group Sarraceniaceae appears to have been widespread across North and South America, and Darlingtonia (western North America) had diverged from Heliamphora+Sarracenia (eastern North America+South America). This disjunction and apparent range contraction is consistent with late Eocene cooling and aridification, which may have severed the continuity of Sarraceniaceae across much of North America. Sarracenia and Heliamphora subsequently diverged in the late Oligocene, 14–32 (HPD = 23) Mya, perhaps when direct overland continuity between North and South America became reduced. Initial diversification of South American Heliamphora began at least 8 Mya, but diversification of Sarracenia was more recent (2–7, HPD = 4 Mya); the bulk of southeastern United States Sarracenia originated co-incident with Pleistocene glaciation, <3 Mya. Overall, these results suggest climatic change at different temporal and spatial scales in part shaped the distribution and diversity of this carnivorous plant clade.

Carnivorous pitcher plants: insights in an old topic

Plant insect interactions are usually recognized as a scenario where herbivorous insects feed on a host plant. However, also the opposite situation is known, where plants feed on insects. Carnivorous pitcher plants of the genus Nepenthes as well as other pitcher plants obtain many nutrients from caught insect prey. Special features of the pitcher traps' surface are responsible for attraction and trapping insects. Once caught, the prey is digested in the fluid of the pitchers to release nutrients and make them available for the plant. Nutrients are taken up by special glands localized on the inner surface of the pitchers. These glands also secrete the hydrolyzing enzymes into the digestion fluid. Although this is known for more than 100 years, our knowledge of the pitcher fluid composition is still limited. Only in recent years some enzymes have been purified from the pitcher fluid and their corresponding genes could be identified. Among them, many pathogenesis-related proteins have been identified, most of which exhibiting hydrolytic activities. The role of these proteins as well as the role of secondary metabolites, which have been identified in the pitcher fluid, is discussed in general and in the context of further studies on carnivorous plants that might give answers to basic questions in plant biology.

Contrasting patterns of the 5S and 45S rDNA evolutions in the Byblis liniflora complex (Byblidaceae)

To clarify the evolutionary dynamics of ribosomal RNA genes (rDNAs) in the Byblis liniflora complex (Byblidaceae), we investigated the 5S and 45S rDNA genes through (1) chromosomal physical mapping by fluorescence in situ hybridization (FISH) and (2) phylogenetic analyses using the nontranscribed spacer of 5S rDNA (5S-NTS) and the internal transcribed spacer of 45S rDNA (ITS). In addition, we performed phylogenetic analyses based on rbcL and trnK intron. The complex was divided into 2 clades: B. aquatica-B. filifolia and B. guehoi-B. liniflora-B. rorida. Although members of the complex had conservative symmetric karyotypes, they were clearly differentiated on chromosomal rDNA distribution patterns. The sequence data indicated that ITS was almost homogeneous in all taxa in which two or four 45S rDNA arrays were frequently found at distal regions of chromosomes in the somatic karyotype. ITS homogenization could have been prompted by relatively distal 45S rDNA positions. In contrast, 2-12 5S rDNA arrays were mapped onto proximal/interstitial regions of chromosomes, and some paralogous 5S-NTS were found in the genomes harboring 4 or more arrays. 5S-NTS sequence type-specific FISH analysis showed sequence heterogeneity within and between some 5S rDNA arrays. Interlocus homogenization may have been hampered by their proximal location on chromosomes. Chromosomal location may have affected the contrasting evolutionary dynamics of rDNAs in the B. liniflora complex.

Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences

BACKGROUND

In the large angiosperm order Lamiales, a diverse array of highly specialized life strategies such as carnivory, parasitism, epiphytism, and desiccation tolerance occur, and some lineages possess drastically accelerated DNA substitutional rates or miniaturized genomes. However, understanding the evolution of these phenomena in the order, and clarifying borders of and relationships among lamialean families, has been hindered by largely unresolved trees in the past.

RESULTS

Our analysis of the rapidly evolving trnK/matK, trnL-F and rps16 chloroplast regions enabled us to infer more precise phylogenetic hypotheses for the Lamiales. Relationships among the nine first-branching families in the Lamiales tree are now resolved with very strong support. Subsequent to Plocospermataceae, a clade consisting of Carlemanniaceae plus Oleaceae branches, followed by Tetrachondraceae and a newly inferred clade composed of Gesneriaceae plus Calceolariaceae, which is also supported by morphological characters. Plantaginaceae (incl. Gratioleae) and Scrophulariaceae are well separated in the backbone grade; Lamiaceae and Verbenaceae appear in distant clades, while the recently described Linderniaceae are confirmed to be monophyletic and in an isolated position.

CONCLUSIONS

Confidence about deep nodes of the Lamiales tree is an important step towards understanding the evolutionary diversification of a major clade of flowering plants. The degree of resolution obtained here now provides a first opportunity to discuss the evolution of morphological and biochemical traits in Lamiales. The multiple independent evolution of the carnivorous syndrome, once in Lentibulariaceae and a second time in Byblidaceae, is strongly supported by all analyses and topological tests. The evolution of selected morphological characters such as flower symmetry is discussed. The addition of further sequence data from introns and spacers holds promise to eventually obtain a fully resolved plastid tree of Lamiales.

Molecular phylogenetics of Prescottiinae s.l. and their close allies (Orchidaceae, Cranichideae) inferred from plastid and nuclear ribosomal DNA sequences

The Andes are a cradle of orchid evolution, but most phylogenetic studies of Orchidaceae in this biodiversity hotspot have dealt with epiphytic epidendroid lineages. Here we present a study on neotropical, terrestrial, orchidoid taxa of Prescottiinae s.l. (8 genera, ∼100 species), which are adapted to some of the highest elevation habitats on earth that support orchids. They are currently included within an expanded concept of Cranichidinae in the tribe Cranichideae, but DNA sequence data show that neither Prescottiinae s.l. nor Cranichidinae s.s. are monophyletic. Prescottiinae s.l. consist of two strongly supported lineages: the Altensteinia and Prescottia clades, which have closer affinities to Spiranthinae than to Cranichidinae. The Prescottia clade comprises two well-supported subclades, one including most sampled species of Prescottia and a second one with Pseudocranichis thysanochila sister to Prescottia tubulosa. As a group, they are sister to Spiranthinae. Sister to this pair is the Altensteinia clade comprised of six genera, whose intergeneric relationships are well resolved. Finally, Cranichidinae s.s. is sister to all three of these clades. Morphological and ecological features distinguishing the major groups are discussed, as are potential synapomorphies to define them. The reconstructed phylogeny indicates that the classification of Cranichideae needs to be reexamined.

Energetics and the evolution of carnivorous plants--Darwin's 'most wonderful plants in the world'

Carnivory has evolved independently at least six times in five angiosperm orders. In spite of these independent origins, there is a remarkable morphological convergence of carnivorous plant traps and physiological convergence of mechanisms for digesting and assimilating prey. These convergent traits have made carnivorous plants model systems for addressing questions in plant molecular genetics, physiology, and evolutionary ecology. New data show that carnivorous plant genera with morphologically complex traps have higher relative rates of gene substitutions than do those with simple sticky traps. This observation suggests two alternative mechanisms for the evolution and diversification of carnivorous plant lineages. The 'energetics hypothesis' posits rapid morphological evolution resulting from a few changes in regulatory genes responsible for meeting the high energetic demands of active traps. The 'predictable prey capture hypothesis' further posits that complex traps yield more predictable and frequent prey captures. To evaluate these hypotheses, available data on the tempo and mode of carnivorous plant evolution were reviewed; patterns of prey capture by carnivorous plants were analysed; and the energetic costs and benefits of botanical carnivory were re-evaluated. Collectively, the data are more supportive of the energetics hypothesis than the predictable prey capture hypothesis. The energetics hypothesis is consistent with a phenomenological cost-benefit model for the evolution of botanical carnivory, and also accounts for data suggesting that carnivorous plants have leaf construction costs and scaling relationships among leaf traits that are substantially different from those of non-carnivorous plants.

A viscoelastic deadly fluid in carnivorous pitcher plants

BACKGROUND

The carnivorous plants of the genus Nepenthes, widely distributed in the Asian tropics, rely mostly on nutrients derived from arthropods trapped in their pitcher-shaped leaves and digested by their enzymatic fluid. The genus exhibits a great diversity of prey and pitcher forms and its mechanism of trapping has long intrigued scientists. The slippery inner surfaces of the pitchers, which can be waxy or highly wettable, have so far been considered as the key trapping devices. However, the occurrence of species lacking such epidermal specializations but still effective at trapping insects suggests the possible implication of other mechanisms.

METHODOLOGY/PRINCIPAL FINDINGS

Using a combination of insect bioassays, high-speed video and rheological measurements, we show that the digestive fluid of Nepenthes rafflesiana is highly viscoelastic and that this physical property is crucial for the retention of insects in its traps. Trapping efficiency is shown to remain strong even when the fluid is highly diluted by water, as long as the elastic relaxation time of the fluid is higher than the typical time scale of insect movements.

CONCLUSIONS/SIGNIFICANCE

This finding challenges the common classification of Nepenthes pitchers as simple passive traps and is of great adaptive significance for these tropical plants, which are often submitted to high rainfalls and variations in fluid concentration. The viscoelastic trap constitutes a cryptic but potentially widespread adaptation of Nepenthes species and could be a homologous trait shared through common ancestry with the sundew (Drosera) flypaper plants. Such large production of a highly viscoelastic biopolymer fluid in permanent pools is nevertheless unique in the plant kingdom and suggests novel applications for pest control.

Proteome analysis of leaves from the resurrection plant Boea hygrometrica in response to dehydration and rehydration

Resurrection plants differ from other species in their unique ability to survive desiccation. In order to understand the mechanisms of desiccation tolerance, proteome studies were carried out using leaves of the resurrection plant Boea hygrometrica to reveal proteins that were differentially expressed in response to changes in relative water content. This opportunity was afforded by the rare ability of excised B. hygrometrica leaves to survive and resume metabolism following desiccation in a manner similar to intact plants. From a total of 223 proteins that were reproducibly detected and analyzed, 35% showed increased abundance in dehydrated leaves, 5% were induced in rehydrated leaves and 60% showed decreased or unchanged abundance in dehydrated and rehydrated leaves. Since the induction kinetics fall into clearly defined patterns, we suggest that programmed regulation of protein expression triggered by changes of water status. Fourteen dehydration responsive proteins were analyzed by mass spectrometry. Eight proteins were classified as playing a role in reactive oxygen species scavenging, photosynthesis and energy metabolism. In agreement with these findings, glutathione content and polyphenol oxidase activity were found to increase upon dehydration and rapid recovery of photosynthesis was observed.

Fluorescence labelling of phosphatase activity in digestive glands of carnivorous plants

A new ELF (enzyme labelled fluorescence) assay was applied to detect phosphatase activity in glandular structures of 47 carnivorous plant species, especially Lentibulariaceae, in order to understand their digestive activities. We address the following questions: (1) Are phosphatases produced by the plants and/or by inhabitants of the traps? (2) Which type of hairs/glands is involved in the production of phosphatases? (3) Is this phosphatase production a common feature among carnivorous plants or is it restricted to evolutionarily advanced species? Our results showed activity of the phosphatases in glandular structures of the majority of the plants tested, both from the greenhouse and from sterile culture. In addition, extracellular phosphatases can also be produced by trap inhabitants. In Utricularia, activity of phosphatase was detected in internal glands of 27 species from both primitive and advanced sections and different ecological groups. Further positive reactions were found in Genlisea, Pinguicula, Aldrovanda, Dionaea, Drosera, Drosophyllum, Nepenthes, and Cephalotus. In Utricularia and Genlisea, enzymatic secretion was independent of stimulation by prey. Byblis and Roridula are usually considered as "proto-carnivores", lacking digestive enzymes. However, we found high activity of phosphatases in both species. Thus, they should be classified as true carnivores. We suggest that the inflorescence of Byblis and some Pinguicula species might also be an additional "carnivorous organ", which can trap a prey, digest it, and finally absorb available nutrients.

Nutrient limitation and stoichiometry of carnivorous plants

The cost-benefit model for the evolution of carnivorous plants posits a trade-off between photosynthetic costs associated with carnivorous structures and photosynthetic benefits accrued through additional nutrient acquisition. The model predicts that carnivory is expected to evolve if its marginal benefits exceed its marginal costs. Further, the model predicts that when nutrients are scarce but neither light nor water is limiting, carnivorous plants should have an energetic advantage in competition with non-carnivorous plants. Since the publication of the cost-benefit model over 20 years ago, marginal photosynthetic costs of carnivory have been demonstrated but marginal photosynthetic benefits have not. A review of published data and results of ongoing research show that nitrogen, phosphorus, and potassium often (co-)limit growth of carnivorous plants and that photosynthetic nutrient use efficiency is 20 - 50 % of that of non-carnivorous plants. Assessments of stoichiometric relationships among limiting nutrients, scaling of leaf mass with photosynthesis and nutrient content, and photosynthetic nutrient use efficiency all suggest that carnivorous plants are at an energetic disadvantage relative to non-carnivorous plants in similar habitats. Overall, current data support some of the predictions of the cost-benefit model, fail to support others, and still others remain untested and merit future research. Rather than being an optimal solution to an adaptive problem, botanical carnivory may represent a set of limited responses constrained by both phylogenetic history and environmental stress.

Recent progress in understanding the evolution of carnivorous lentibulariaceae (lamiales)

Carnivorous plants have emerged as model systems for addressing many ecological and evolutionary questions, and since Lentibulariaceae comprise more than half of all known carnivorous species (325 spp.), they are of particular interest. Studies using various molecular markers have established that Lentibulariaceae and their three genera are monophyletic with Pinguicula being sister to a Genlisea-Utricularia-clade, while the closest relatives of the family remain uncertain. Character states of the carnivorous syndrome in related proto-carnivorous lamialean families apparently emerged independently. In Utricularia, the terrestrial habit has been reconstructed as plesiomorphic, and an extension of subgenus Polypompholyx is warranted. In the protozoan-attracting Genlisea, subgenus Tayloria is revealed as basal lineage. In Pinguicula, the six major lineages found reflect radiations in clearly defined geographic regions, whereas most previously recognized subgeneric taxa are non-monophyletic. Genlisea and Utricularia exhibit substitutional rates that rank among the highest in angiosperms for the molecular markers analyzed. One possible explanation for this lies in selective constraints on a wide range of genomic regions that may have been lowered due to the use of an alternative mode of acquiring nutrients.

Molecular phylogeny and character evolution of carnivorous plant families in Caryophyllales--revisited

Recent phylogenetic analyses based on single gene and combined data sets have substantially increased our knowledge of the phylogeny of Caryophyllales s.l., indicating that additional carnivorous families are related to this alliance. In earlier contributions towards a reassessment of inter- and infrafamilial relationships slowly evolving genes had been preferred for phylogenetic inference. The resulting tree topologies based on rbcL and 18S rDNA, however, were characterized by limited resolution, low internal support and topological incongruence. Therefore genomic regions evolving more rapidly have been used in subsequent studies. Comparative sequencing of the matK gene and the flanking trnK intron region as well as combined analyses based on plastid matK, atpB, rbcL, and nuclear 18S rDNA have effectively improved resolution and internal support. Tree topologies revealed Caryophyllales s.l. as monophyletic group and indicated a clear division into two sister clades, the "core" and the "non-core" Caryophyllales (with Rhabdodendraceae and Simmondsiaceae with unclear affinities). Contrary to the "core" group (with Asteropeiaceae and Physenaceae as successive sister groups), which corresponds largely to the previous circumscription of the order, the monophyly of "non-core" Caryophyllales comprising Polygonaceae, Plumbaginaceae, Frankeniaceae, and Tamaricaceae along with the carnivorous families Droseraceae, Nepenthaceae, Drosophyllaceae, Dioncophyllaceae, and Ancistrocladaceae are a recent discovery. Based on reliable tree topologies it is hypothesized that pitfall traps of Nepenthes and snap traps typical for Aldrovanda and Dionaea were derived from a common ancestor with adhesive flypaper traps. With exception of Triphyophyllum carnivory was secondarily lost in the remaining Dioncophyllaceae (Dioncophyllum, Habropetalum) and all taxa of Ancistrocladaceae.

A new model for the evolution of carnivory in the bladderwort plant (utricularia): adaptive changes in cytochrome C oxidase (COX) provide respiratory power

The evolution of carnivorous plants has been modeled as a selective tradeoff between photosynthetic costs and benefits in nutrient-poor habitats. Although possibly applicable for pitfall and flypaper trappers, more variables may be required for active trapping systems. Bladderwort (utricularia) suction traps react to prey stimuli with an extremely rapid release of elastic instability. Trap setting requires considerable energy to engage an active ion transport process whereby water is pumped out through the thin bladder walls to create negative internal pressure. Accordingly, empirical estimates have shown that respiratory rates in bladders are far greater than in leafy structures. Cytochrome C oxidase (COX) is a multi-subunit enzyme that catalyzes the respiratory reduction of oxygen to water and couples this reaction to translocation of protons, generating a transmembrane electrochemical gradient that is used for the synthesis of adenosine triphosphate (ATP). We have previously demonstrated that two contiguous cysteine residues in helix 3 of COX subunit I (COX I) have evolved under positive Darwinian selection. This motif, absent in approximately 99.9 % of databased COX I proteins from eukaryotes, Archaea, and Bacteria, lies directly at the docking point of COX I helix 3 and cytochrome C. Modeling of bovine COX I suggests the possibility that a vicinal disulfide bridge at this position could cause premature helix termination. The helix 3-4 loop makes crucial contacts with the active site of COX, and we postulate that the C-C motif might cause a conformational change that decouples (or partly decouples) electron transport from proton pumping. Such decoupling would permit bladderworts to optimize power output (which equals energy times rate) during times of need, albeit with a 20 % reduction in overall energy efficiency of the respiratory chain. A new model for the evolution of bladderwort carnivory is proposed that includes respiration as an additional tradeoff parameter.

Phylogeny of the Cucurbitales based on DNA sequences of nine loci from three genomes: Implications for morphological and sexual system evolution

The Cucurbitales are a clade of rosids with a worldwide distribution and a striking heterogeneity in species diversity among its seven family members: the Anisophylleaceae (29-40 species), Begoniaceae (1400 spp.), Coriariaceae (15 spp.), Corynocarpaceae (6 spp.), Cucurbitaceae (800 spp.), Datiscaceae (2 spp.), and Tetramelaceae (2 spp.). Most Cucurbitales have unisexual flowers, and species are monoecious, dioecious, andromonoecious, or androdioecious. To resolve interfamilial relationships within the order and to polarize morphological character evolution, especially of flower sexual systems, we sequenced nine plastids (atpB, matK, ndhF, rbcL, the trnL-F region, and the rpl20-rps12 spacer), nuclear (18S and 26S rDNA), and mitochondrial (nad1 b/c intron) genes (together approximately 12,000 bp) of 26 representatives of the seven families plus eight outgroup taxa from six other orders of the Eurosids I. Cucurbitales are strongly supported as monophyletic and are closest to Fagales, albeit with moderate support; both together are sister to Rosales. The deepest split in the Cucurbitales is that between the Anisophylleaceae and the remaining families; next is a clade of Corynocarpaceae and Coriariaceae, followed by Cucurbitaceae, which are sister to a clade of Begoniaceae, Datiscaceae, and Tetramelaceae. Based on this topology, stipulate leaves, inferior ovaries, parietal placentation, and one-seeded fruits are inferred as ancestral in Cucurbitales; exstipulate leaves, superior ovaries, apical placentation, and many-seeded fruits evolved within the order. Bisexual flowers are reconstructed as ancestral, but dioecy appears to have evolved already in the common ancestor of Begoniaceae, Cucurbitaceae, Datiscaceae, and Tetramelaceae, and then to have been lost repeatedly in Begoniaceae and Cucurbitaceae. Both instances of androdioecy (Datisca glomerata and Schizopepon bryoniifolius) evolved from dioecious ancestors, corroborating recent hypotheses about androdioecy often evolving from dioecy.

Asymmetrical introgression between two Morus species (M. alba, M. rubra) that differ in abundance

Asymmetrical introgression is an expected genetic consequence of hybridization when parental taxa differ in abundance; however, evidence for such effects in small populations is scarce. To test this prediction, we estimated the magnitude and direction of hybridization between red mulberry (Morus rubra L.), an endangered species in Canada, and the introduced and more abundant white mulberry (Morus alba L.) using nuclear (randomly amplified polymorphic DNA) and cytoplasmic (chloroplast DNA sequence) markers. Parentage of 184 trees (n = 42 using cpDNA) from four sympatric populations was estimated using a hybrid index and related to six morphological characters and population frequencies of the parental classes. Overall, the frequency of nuclear hybrids was 53.7% (n = 99) and ranged from 43% to 67% among populations. The parental and hybrid taxa differed with respect to all of the morphological traits. Sixty-seven percent of all hybrids contained more nuclear markers from M. alba than M. rubra (hybrid index x = 0.46); among populations, the degree of M. alba bias was correlated with the frequency of M. alba. In addition, the majority of hybrids (68%) contained the chloroplast genome of white mulberry. These results suggest that introgression is bidirectional but asymmetrical and is related, in part, to the relative frequency of parental taxa.

What’s in a character?

Systematic analyses are included as integral parts of bioinformatic analysis. The use of phenetic and phylogenetic trees in many of the newer areas of biology create a need for bioinformaticists to understand more completely the nuances of systematic analysis. Any description in comparative biology, universally begins with what information to use in the comparative endeavor. Phylogenetic approaches are no different. The diversity of approaches and phylogenetic questions in systematics have sometimes hindered a precise understanding of what primary data should be collected to perform such analyses. In addition, one should always keep in mind that the objective of systematic organization of entities in nature not only strives to organize those entities in an objective, repeatable and operational way, but also to organize the attributes of the entities in a similar hierarchical context. This paper attempts to describe characters as the basis of all comparative analysis, to describe the diverse kinds of primary data that exist today in biology, genomics, and bioinformatics, and to place these kinds of primary data in the context of the established approaches to tree building.

First nuclear DNA C-values for 18 eudicot families

BACKGROUND AND AIMS

A key target set at the second Plant Genome Size Workshop, held at the Royal Botanic Gardens, Kew in 2003, was to produce first DNA C-value data for an additional 1 % of angiosperm species, and, within this, to achieve 75 % familial coverage overall (up from approx. 50 %) by 2009. The present study targeted eudicot families for which representation in 2003 (42.5 %) was much lower than monocot (72.8 %) and basal angiosperm (69.0 %) families.

METHODS

Flow cytometry or Feulgen microdensitometry were used to estimate nuclear DNA C-values, and chromosome counts were obtained where possible.

KEY RESULTS

First nuclear DNA C-values are reported for 20 angiosperm families, including 18 eudicots. This substantially increases familial representation to 55.2 % for angiosperms and 48.5 % for eudicots.

CONCLUSIONS

The importance of targeting specific plant families to improve familial nuclear DNA C-value representation is reconfirmed. International collaboration will be increasingly essential to locate and obtain material of unsampled plant families, if the target set by the second Plant Genome Size Workshop is to be met.

Convergent evolution: floral guides, stingless bee nest entrances, and insectivorous pitchers

Several recent hypotheses, including sensory drive and sensory exploitation, suggest that receiver biases may drive selection of biological signals in the context of sexual selection. Here we suggest that a similar mechanism may have led to convergence of patterns in flowers, stingless bee nest entrances, and pitchers of insectivorous plants. A survey of these non-related visual stimuli shows that they share features such as stripes, dark centre, and peripheral dots. Next, we experimentally show that in stingless bees the close-up approach to a flower is guided by dark centre preference. Moreover, in the approach towards their nest entrance, they have a spontaneous preference for entrance patterns containing a dark centre and disrupted ornamentation. Together with existing empirical evidence on the honeybee's and other insects' orientation to flowers, this suggests that the signal receivers of the natural patterns we examined, mainly Hymenoptera, have spontaneous preferences for radiating stripes, dark centres, and peripheral dots. These receiver biases may have evolved in other behavioural contexts in the ancestors of Hymenoptera, but our findings suggest that they have triggered the convergent evolution of visual stimuli in floral guides, stingless bee nest entrances, and insectivorous pitchers.

CALIBRATION OF MOLECULAR CLOCKS AND THE BIOGEOGRAPHIC HISTORY OF CRYPTERONIACEAE

A recent molecular clock analysis concluded that Gondwanan vicariance and out-of-India dispersal best explained the distribution of Crypteroniaceae and its allies (Conti et al. 2002). A reanalysis of their data using a different molecular dating technique and calibration point is congruent with an alternative hypothesis, namely dispersal between India, Africa, and South America long after the initial break-up of Gondwana.

Evolution of carnivory in Lentibulariaceae and the Lamiales

As a basis for analysing the evolution of the carnivorous syndrome in Lentibulariaceae (Lamiales), phylogenetic reconstructions were conducted based on coding and non-coding chloroplast DNA (matK gene and flanking trnK intron sequences, totalling about 2.4 kb). A dense taxon sampling including all other major lineages of Lamiales was needed since the closest relatives of Lentibulariaceae and the position of "proto-carnivores" were unknown. Tree inference using maximum parsimony, maximum likelihood, and Bayesian approaches resulted in fully congruent topologies within Lentibulariaceae, whereas relationships among the different lineages of Lamiales were only congruent between likelihood and Bayesian optimizations. Lentibulariaceae and their three genera (Pinguicula, Genlisea, and Utricularia) are monophyletic, with Pinguicula being sister to a Genlisea-Utricularia clade. Likelihood and Bayesian trees converge on Bignoniaceae as sister to Lentibulariaceae, albeit lacking good support. The "proto-carnivores" (Byblidaceae, Martyniaceae) are found in different positions among other Lamiales but not as sister to the carnivorous Lentibulariaceae, which is also supported by Khishino-Hasegawa tests. This implies that carnivory and its preliminary stages ("proto-carnivores") independently evolved more than once among Lamiales. Ancestral states of structural characters connected to the carnivorous syndrome are reconstructed using the molecular tree, and a hypothesis on the evolutionary pathway of the carnivorous syndrome in Lentibulariaceae is presented. Extreme DNA mutational rates found in Utricularia and Genlisea are shown to correspond to their unusual nutritional specialization, thereby hinting at a marked degree of carnivory in these two genera.

Function of epidermal surfaces in the trapping efficiency of Nepenthes alata pitchers

•   Several epidermal microstructures characterize surfaces of pitcher plants and are presumably involved in their trapping function. Here we report the effects of Nepenthes alata surfaces on insect locomotion and trapping efficiency. •   The architectural designs of pitcher surfaces were characterized using scanning electron microscopy. Two insect species - fruitfly (Drosophila melanogaster) and ant (Iridomyrmex humilis) - were tested for their ability to remain and walk on them. The relative contributions of various epidermal structures to trapping ability were quantified. •   Pitchers were very effective traps for both insect species. They were slightly more efficient in capturing the ants, but slightly more effective in retaining captured flies. Trapping efficiency was attributed to the combined effects of several surfaces displaying different functions. The waxy zone played a key role in the slippery syndrome: in addition to the wax itself, the subjacent layer of convex lunate cells interfered considerably with insect locomotion. The unsubmersed glandular zone displayed an important retentive effect and secretions of the digestive glands are suspected to be adhesive. •   Pad performances of the hairy and smooth system of attachment are discussed to explain the differences between the two insect species. This study aims to encourage biomechanical studies of plant-insect surface mechanisms.

Phylogenetics of asterids based on 3 coding and 3 non-coding chloroplast DNA markers and the utility of non-coding DNA at higher taxonomic levels

Asterids comprise 1/4-1/3 of all flowering plants and are classified in 10 orders and >100 families. The phylogeny of asterids is here explored with jackknife parsimony analysis of chloroplast DNA from 132 genera representing 103 families and all higher groups of asterids. Six different markers were used, three of the markers represent protein coding genes, rbcL, ndhF, and matK, and three other represent non-coding DNA; a region including trnL exons and the intron and intergenic spacers between trnT (UGU) to trnF (GAA); another region including trnV exons and intron, trnM and intergenic spacers between trnV (UAC) and atpE, and the rps16 intron. The three non-coding markers proved almost equally useful as the three coding genes in phylogenetic reconstruction at the high level of orders and families in asterids, and in relation to the number of aligned positions the non-coding markers were even more effective. Basal interrelationships among Cornales, Ericales, lamiids (new name replacing euasterids I), and campanulids (new name replacing euasterids II) are resolved with strong support. Family interrelationships are fully or almost fully resolved with medium to strong support in Cornales, Garryales, Gentianales, Solanales, Aquifoliales, Apiales, and Dipsacales. Within the three large orders Ericales, Lamiales, and Asterales, family interrelationships remain partly unclear. The analysis has contributed to reclassification of several families, e.g., Tetrameristaceae, Ebenaceae, Styracaceae, Montiniaceae, Orobanchaceae, and Scrophulariaceae (by inclusion of Pellicieraceae, Lissocarpaceae, Halesiaceae, Kaliphoraceae, Cyclocheilaceae, and Myoporaceae+Buddlejaceae, respectively), and to the placement of families that were unplaced in the APG-system, e.g., Sladeniaceae, Pentaphylacaceae, Plocospermataceae, Cardiopteridaceae, and Adoxaceae (in Ericales, Ericales, Lamiales, Aquifoliales, and Dipsacales, respectively), and Paracryphiaceae among campanulids. Several families of euasterids remain unclassified to order.

Phylogenetic relationships of Theaceae inferred from chloroplast DNA sequence data

Tribal and generic relationships within Theaceae were investigated using cladistic analyses of chloroplast-encoded rbcL and matK + flanking intergenic spacer region data. Molecular data were employed because recent morphological and anatomical studies of tea (Camellia sinensis) and related plant species provide conflicting support for tribal and generic relationships within the family. Parsimony analyses of separate and combined data consistently identify three strongly supported lineages: Theeae, Stewartieae, and Gordonieae. These data support the broad generic circumscription of Camellia and Stewartia but do not support the recognition of Gordonia sensu lato. Gordonia lasianthus and Gordonia brandegeei are the basal clade in Gordonieae, a position far removed from all other representatives of Gordonia sensu lato (Polyspora and Laplacea) included in this study. This phylogeny most closely mirrors Airy-Shaw's tribe Camellieae [= Theeae] and his two subtribes Stewartiinae and Gordoniinae, first published in 1936. We recognize all three major lineages at the tribal level, although there is weak statistical support for a sister relationship between Gordonieae and Theeae. We also find statistical support for the recognition of the two former subfamilies Theoideae and Ternstroemioideae as two separate families, Theaceae and Ternstroemiaceae.

Phylogenetic relationships within the Gentianales based on NDHF and RBCL sequences, with particular reference to the Loganiaceae

Phylogenetic relationships in the Gentianales with focus on Loganiaceae sensu lato are evaluated using parsimony analyses of nucleotide sequence data from the plastid genes rbcL and ndhF. Inter- and intrafamilial relationships in the Gentianales, which consist of the families Apocynaceae (including Asclepiadaceae), Gelsemiaceae, Gentianaceae, Loganiaceae, and Rubiaceae, are studied and receive increased support from the combination of rbcL and ndhF data, which indicate that the family Rubiaceae forms the sister group to the successively nested Gentianaceae, Apocynaceae, and Loganiaceae, all of which are well supported. The family Gelsemiaceae forms a distinct, supported group sister to Apocynaceae. The Loganiaceae sensu stricto form a strongly supported group consisting of 13 genera: Antonia, Bonyunia, Gardneria, Geniostoma, Labordia, Logania, Mitrasacme, Mitreola, Neuburgia, Norrisia, Spigelia, Strychnos, and Usteria. These genera form two well-supported lineages. Several members of Loganiaceae sensu Leeuwenberg and Leenhouts, i.e., Androya, Peltanthera, Plocosperma, Polypremum, and Sanango are clearly not members of the Gentianales. The earlier exclusion of Buddlejaceae (including Buddleja, Emorya, Gomphostigma, and Nicodemia) as well as the reclassification of the genera Nuxia and Retzia to Stilbaceae of the Lamiales are all well supported.