The closest relatives of cacti: insights from phylogenetic analyses of chloroplast and mitochondrial sequences with special emphasis on relationships in the tribe Anacampseroteae

Recent molecular and morphological systematic investigations revealed that the cacti are most closely related to Anacampseroteae, Portulaca and Talinum of the family Portulacaceae (ACPT clade of suborder Portulacineae). A combined analysis of ndhF, matK, and nad1 sequence data from the chloroplast and the mitochondrial genomes indicates that the tribe Anacampseroteae is the sister group of the family Cactaceae. This clade, together with Portulaca, is well characterized by the presence of axillary hairs or scales. Relationships within Anacampseroteae are characterized by a grade of five species of Grahamia s.l. from North and South America, and Grahamia australiana is found to be sister to the genera Anacampseros and Avonia. A comparison of vegetative characteristics indicates an evolutionary transition from woody subshrubs to dwarf perennial and highly succulent herbs during the diversification of Anacampseroteae. Available evidence from the present investigation as well as from previously published studies suggests that a revised classification of Portulacineae on the basis of inferred phylogenetic relationships might consist of a superfamily that includes Cactaceae and the three genera Anacampseros s.l. (including Avonia and Grahamia s.l.), Portulaca, and Talinum (including Talinella), either referred to three monogeneric families or to a paraphyletic family Portulacaceae*.     

Crassulacean acid metabolism photosynthesis in Bromeliaceae: an evolutionary key innovation

Crassulacean acid metabolism (CAM) is a photosynthetic pathway that significantly increases water use efficiency in plants. It has been proposed that CAM photosynthesis, which evolved from the ancestral C3 pathway, has played a role in the diversification of some prominent plant groups because it may have allowed them to colonize and successfully spread into arid or semi‐arid environments. However, the hypothesis that CAM photosynthesis constitutes an evolutionary key innovation, thereby enhancing diversification rates of the clades possessing it, has not been evaluated quantitatively. We tested whether CAM photosynthesis is a key innovation in the Bromeliaceae, a large and highly diversified plant family that has successfully colonized arid environments. We identified five pairs of sister groups with and without the CAM feature, including 31 genera and over 2000 species. In all five cases, the clades with CAM photosynthesis were more diverse than their C3 counterparts. We provide quantitative evidence that the evolution of CAM photosynthesis is significantly associated with increased diversification in Bromeliaceae and thus constitutes an evolutionary key innovation. We also found preliminary evidence of an association between the CAM pathway and growth habit in bromeliads, with terrestrial species being more likely to show CAM photosynthesis than epiphytic species. To our knowledge, this is the first case of a physiological attribute shown to be a key innovation in plants. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 480–486.     

Evolutionary physiology: the extent of C4 and CAM photosynthesis in the genera Anacampseros and Grahamia of the Portulacaceae

The Portulacaceae is one of the few terrestrial plant families known to have both C(4) and Crassulacean acid metabolism (CAM) species. There may be multiple origins of the evolution of CAM within the Portulacaceae but the only clear evidence of C(4) photosynthesis is found in members of the genus Portulaca. In the Portulaca, CAM succulent tissue is overlaid with the C(4) tissue in a unique fashion where both pathways are operating simultaneously. Earlier reports have shown that the clade containing the genera Anacampseros and Grahamia may also contain C(4) photosynthetic species similar to the Portulaca, which would indicate multiple origins of C(4) photosynthesis within the family. The aim of the present study was to ascertain the true photosynthetic nature of these genera. An initial survey of the carbon isotope composition of the Anacampseros ranged from -12.6 per thousand to -24.0 per thousand, indicating very little CAM activity in some species, with other values close to the C(4) range. Anacampseros (=Grahamia) australiana which had been previously identified as a C(4) species had a carbon isotope composition value of -24.0 per thousand, which is more indicative of a C(3) species with a slight contribution of CAM activity. Other Anacampseros species with C(4)-like values have been shown to be CAM plants. The initial isotope analysis of the Grahamia species gave values in the range of -27.1 per thousand to -23.6 per thousand, placing the Grahamia species well towards the C(3) photosynthetic range. Further physiological studies indicated increased night-time CO(2) uptake with imposition of water stress, associated with a large diurnal acid fluctuation and a marked increased phosphoenolpyruvate carboxylase activity. This showed that the Grahamia species are actually facultative CAM plants despite their C(3)-like carbon isotope values. The results indicate that the Grahamia and Anacampseros species do not utilize the C(4) photosynthetic pathway. This is the first to identify that the Grahamia species are facultative CAM plants where CAM can be induced by water stress. This work supports earlier physiological work that indicates that this clade containing Anacampseros and Grahamia species comprises predominantly facultative CAM plants. This report suggests there may be only one clade which contains C(4) photosynthetic members with CAM-like characteristics.     

Anatomical variation in Cactaceae and relatives: Trait lability and evolutionary innovation

The cacti have undergone extensive specialization in their evolutionary history, providing an excellent system in which to address large-scale questions of morphological and physiological adaptation. Recent molecular phylogenetic studies suggest that (1) Pereskia, the leafy genus long interpreted as the sister group of all other cacti, is likely paraphyletic, and (2) Cactaceae are nested within a paraphyletic Portulacaceae as a member of the "ACPT" clade (Anacampseroteae, Cactaceae, Portulaca, and Talinum). We collected new data on the vegetative anatomy of the ACPT clade and relatives to evaluate whether patterns in the distributions of traits may provide insight into early events in the evolutionary transition to the cactus life form. Many traits had high levels of homoplasy and were mostly equivocal with regard to infraclade relationships of ACPT, although several characters do lend further support to a paraphyletic Pereskia. These include a thick stem cuticle, prominent stem mucilage cells, and hypodermal calcium oxalate druses, all of which are likely to be important traits for stem water storage and photosynthesis. We hypothesize that high lability of many putative "precursor" traits may have been critical in generating the organismal context necessary for the evolution of an efficient and integrated photosynthetic stem.     

Seed germination in Gactaceae

The mode of germination of representatives of 89 genera of the Cactaceae, 4 genera of Portulacaceae and 1 genus of Phytolaccaceae was studied. Most of the species of the Cactaceae germinate by means of a seed lid (operculum). In the Cactaceae studied 11 kinds of germination could be distinguished, 3 of which were with, and 8 without, operculum formation.
Opercula are restricted in their occurrence to the subfamilies Cactoideae (Cereoideae) and Pereskioideae and are not found in the subfamily Opuntioideae. Within the subfamily Cactoideae operculum formation was found to occur in all tribes and in all investigated subtribes. Opercula were also found in two genera of the related family of the Portulacaceae. In the Phytolaccaceae no operculum formation was observed.     

How prevalent is crassulacean acid metabolism among vascular epiphytes?

The occurrence of crassulacean acid metabolism (CAM) in the epiphyte community of a lowland forest of the Atlantic slope of Panama was investigated. I hypothesized that CAM is mostly found in orchids, of which many species are relatively small and/or rare. Thus, the relative proportion of species with CAM should not be a good indicator for the prevalence of this photosynthetic pathway in a community when expressed on an individual or a biomass basis. In 0.4 ha of forest, 103 species of vascular epiphytes with 13,099 individuals were found. As judged from the C isotope ratios and the absence of Kranz anatomy, CAM was detected in 20 species (19.4% of the total), which were members of the families Orchidaceae, Bromeliaceae, and Cactaceae. As predicted, the contribution of CAM epiphytes to the total number of individuals and to total biomass (69.6 kg ha^-1) was considerably lower (3.6% or 466 individuals and, respectively, 3.0% or 2.1 kg ha^-1).     

A revised evolutionary history of Poales: origins and diversification

Poales represents more than one‐third of all monocotyledons (c. 20 000 species in 16 families) and constitutes a microcosm of the angiosperms. The extreme variation in species richness among the families of Poales is still not understood: Poaceae includes ～10 000 species, whereas six families have fewer than ten species. Here, using the largest phylogenetic analysis of Poales to date, molecular dating, ancestral reconstructions and diversification analyses, we develop a macro‐evolutionary and macro‐ecological approach to seek correlates for changing diversification patterns. We show that the poalean families diverged in the Late Cretaceous, a time of high levels of CO₂ and high rainfall. Our habitat reconstructions indicate that Poales inhabited open and dry habitats in this environment. We also demonstrate that lineages with CO₂‐concentrating mechanisms inhabiting dry and open environments exhibited higher diversification rates than C₃, shade and wet lineages. CO₂‐concentrating mechanisms counteract the effects of low atmospheric CO₂ and reduce phototranspiration. It is believed that the parallel evolution of C₄ and CAM (Crassulacean acid metabolism) photosynthesis in Poaceae, Cyperaceae and Bromeliaceae is an adaptation to changes in atmospheric CO₂ concentrations. Combinations of extrinsic and intrinsic factors might have played a role in shifts in diversification rates and may explain the variation in species richness in Poales. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 175 , 4–16.     

Flavonols and C-Glycosylflavonoids of the caryophyllales

A survey of 112 species of the Caryophyllales showed the presence of flavonols in all eleven families and of C-glycosylflavonoids in nine families, being absent from the Aizoaceae and Cactaceae. 18% of the species contained both classes of compound. C-glycosylflavonoids are reported for the first time in the Amaranthaceae, Basellaceae, Didieraceae, Nyctaginaceae, Phytolaccaceae, Portulacaceae and Molluginaceae. The Caryophyllaceae contained prodominantly C-glycosylflavonoids, suggesting they are the most advanced family in the order.     

C3 photosynthesis in Aristida longifolia: Implication for photosynthetic diversification in Aristidoideae (Poaceae)

Only a small percentage of plant species undergo C(4) photosynthesis. Despite its rarity, the C(4) pathway has evolved numerous times from C(3) ancestors, with as many as 18 independent origins in grasses alone. We report non-Kranz (C(3)) anatomy in Aristida longifolia, a species in a genus of ca. 300 species previously thought to possess only Kranz (C(4)) anatomy. Leaf blade transections of A. longifolia show widely spaced vascular bundles, nonradiate chlorenchyma, and few or no chloroplasts in cells of the sheaths surrounding the vascular bundle, all features indicative of C(3) photosynthesis. Carbon isotope ratios range from -27.68 to -29.71%, likewise indicative of C(3) photosynthesis. We also reconstruct the phylogeny of Aristidoideae, comprising Aristida, Sartidia (C(3)), and Stipagrostis (C(4)), using a sample of 11 species, including A. longifolia, and DNA sequences of the nuclear ribosomal internal transcribed spacer region and the chloroplast rpl16 intron and trnL-trnF region. Sartidia and Stipagrostis resolve as sisters, and sister to this clade is Aristida. Aristida longifolia resolves as sister to the remaining species in the genus. C(3) photosynthesis is hypothesized to be ancestral in Aristidoideae, which means the C(4) pathway evolved twice in the subfamily-in Stipagrostis and early in the diversification of the Aristida clade.     

Basal cactus phylogeny: implications of Pereskia (Cactaceae) paraphyly for the transition to the cactus life form

The cacti are well-known desert plants, widely recognized by their specialized growth form and essentially leafless condition. Pereskia, a group of 17 species with regular leaf development and function, is generally viewed as representing the "ancestral cactus," although its placement within Cactaceae has remained uncertain. Here we present a new hypothesis of phylogenetic relationships at the base of the Cactaceae, inferred from DNA sequence data from five gene regions representing all three plant genomes. Our data support a basal split in Cactaceae between a clade of eight Pereskia species, centered around the Caribbean basin, and all other cacti. Two other Pereskia clades, distributed mostly in the southern half of South America, are part of a major clade comprising Maihuenia plus Cactoideae, and Opuntioideae. This result highlights several events in the early evolution of the cacti. First, during the transition to stem-based photosynthesis, the evolution of stem stomata and delayed bark formation preceded the evolution of the stem cortex into a specialized photosynthetic tissue system. Second, the basal split in cacti separates a northern from an initially southern cactus clade, and the major cactus lineages probably originated in southern or west-central South America.     

Wide-band tracheids in genera of Portulacaceae: novel, non-xylary tracheids possibly evolved as an adaptation to water stress

Wide-band tracheids (WBTs) are novel tracheids with wide, lignified secondary walls that intrude deeply into the cell lumen when viewed in transverse sections. These tracheids are found in a few genera in related families in the order Caryophyllales: Aizoaceae, Cactaceae, and Portulacaceae. WBTs in these three families vary in (1) systematic occurrence (found in more highly derived genera in each family), (2) location in plant organs, and (3) structure and dimensions. In addition, an analysis was conducted of WBT cell walls to test the hypothesis that WBTs evolved as an adaptation to water stress (i.e., the wide secondary walls should prevent collapse of the primary wall during water stress). The cell wall data show that primary cell walls in WBTs cannot inwardly collapse to occlusion, thus providing support for the water stress hypothesis of WBT evolution. With consideration of their systematic occurrence, the molecular phylogenetic data, and data here showing support for a water stress adaptive origin, it is logical to assume that WBTs evolved in genera that were adapting to environments undergoing a rapid trend toward aridification.     

Dynamic diversification history with rate upshifts in Holarctic bell‐flowers (Campanula and allies)

Campanula s.l. is one of the most speciose flowering plant lineages of the Holarctic (ca. 600 species). In the present study we sequenced three regions of the plastid genome (petD, rpl16 and trnK/matK) across a broad sample of Campanula s.l., which markedly improved phylogenetic resolution and statistical support compared to previous studies. Based on this robust phylogenetic hypothesis we estimated divergence times using BEAST, diversification rate shifts using Bayesian Analysis of Macroevolutionary Mixture (BAMM) and TreePar, and ancestral ranges using Biogeography with Bayesian (and likelihood) Evolutionary Analyses in R. Campanula s.l. is estimated to have originated during the Early Eocene but the major diversification events occurred between the Late Oligocene and Middle Miocene. Two upward diversification rate shifts were revealed by BAMM, specific to the crown nodes of two Campanula clades: CAM17, a mostly South European‐SW Asian lineage originating during the Middle Miocene and containing nearly half of all known Campanula species; and CAM15B, a SW Asian–Sino‐Himalayan lineage of nine species originating in the early Pleistocene. The dynamic diversification history of Campanula and the inferred rate shifts are discussed in a geo‐historical context.     

Crassulacean acid metabolism photosynthesis: `working the night shift'

Crassulacean acid metabolism (CAM) can be traced from Roman times through persons who noted a morning acid taste of some common house plants. From India in 1815, Benjamin-Heyne described a `daily acid taste cycle' with some succulent garden plants. Recent work has shown that the nocturnally formed acid is decarboxylated during the day to become the CO₂ for photosynthesis. Thus, CAM photosynthesis extends over a 24-hour day using several daily interlocking cycles. To understand CAM photosynthesis, several landmark discoveries were made at the following times: daily reciprocal acid and carbohydrate cycles were found during 1870 to 1887; their precise identification, as malic acid and starch, and accurate quantification occurred from 1940 to 1954; diffusive gas resistance methods were introduced in the early 1960s that led to understanding the powerful stomatal control of daily gas exchanges; C₄ photosynthesis in two different types of cells was discovered from 1965 to ∼1974 and the resultant information was used to elucidate the day and night portions of CAM photosynthesis in one cell; and exceptionally high internal green tissue CO₂ levels, 0.2 to 2.5%, upon the daytime decarboxylation of malic acid, were discovered in 1979. These discoveries then were combined with related information from C₃ and C₄ photosynthesis, carbon biochemistry, cellular anatomy, and ecological physiology. Therefore by ∼1980, CAM photosynthesis finally was rigorously outlined. In a nutshell, 24-hour CAM occurs by phosphoenol pyruvate (PEP) carboxylase fixing CO₂(HCO₃ ⁻) over the night to form malic acid that is stored in plant cell vacuoles. While stomata are tightly closed the following day, malic acid is decarboxylated releasing CO₂ for C₃ photosynthesis via ribulose bisphosphate carboxylase oxygenase (Rubisco). The CO₂ acceptor, PEP, is formed via glycolysis at night from starch or other stored carbohydrates and after decarboxylation the three carbons are restored each day. In mid to late afternoon the stomata can open and mostly C₃ photosynthesis occurs until darkness. CAM photo-synthesis can be both inducible and constitutive and is known in 33 families with an estimated 15 to 20 000 species. CAM plants express the most plastic and tenacious photosynthesis known in that they can switch photosynthesis pathways and they can live and conduct photosynthesis for years even in the virtual absence of external H₂O and CO₂, i.e., CAM tenaciously protects its photosynthesis from both H₂O and CO₂ stresses. This revised version was published online in August 2006 with corrections to the Cover Date.     

Seasonal variation in crassulacean acid metabolism by the aquatic isoetid Littorella uniflora

The seasonal temperature acclimation in crassulacean acid metabolism (CAM) and photosynthetic performance were investigated in the aquatic isoetid, Littorella uniflora. Plants were collected monthly from January to September, and CAM capacity and photosynthesis rates were measured at 5, 10, 15, and 20?°C. Seasonal acclimation was observed for CAM (Q (10) range: 0.6-1.8), and CAM was optimised close to ambient temperature throughout the season. Thus, in winter acclimated L. uniflora, the short-term response to raised temperature resulted in a decline in CAM capacity. Even though the ambient CAM increased from winter to spring/summer, CAM was present in cold acclimated plants, thus indicating an ecophysiological role for CAM even in winter. Similar to CAM, seasonal acclimation was observed in the light and carbon-saturated photosynthesis (Q (10) values ranged from 1.4 to 2.3), and the photosynthetic capacity was generally higher during the winter at all temperatures, indicating compensatory investments in the photosynthetic apparatus. Thus, L. uniflora displayed seasonal temperature acclimation with respect to both CAM and photosynthesis. The estimated in situ contribution of CAM to the carbon budget in L. uniflora was independent of season and varied from 23 to 46?%. A positive correlation between photosynthetic capacity and CAM capacity (both measured in the lab at temperature close to ambient temperature) was found, and the ratio of CAM activity to photosynthetic capacity was higher in summer compared with winter plants. Overall, the results from the present study support the suggested role of CAM as a carbon conserving mechanism of importance for survival in a carbon-limited habitat.     

Molecular systematics of the suborder Trogiomorpha (Insecta: Psocodea: 'Psocoptera')

Phylogenetic relationships among extant families in the suborder Trogiomorpha (Insecta: Psocodea: 'Psocoptera') were inferred from partial sequences of the nuclear 18S rDNA and Histone 3 and mitochondrial 16S rDNA genes. Analyses of these data produced trees that largely supported the traditional classification; however, monophyly of the infraorder Psocathropetae (= Psyllipsocidae + Prionoglarididae) was not recovered. Instead, the family Psyllipsocidae was recovered as the sister taxon to the infraorder Atropetae (= Lepidopsocidae + Trogiidae + Psoquillidae), and the Prionoglarididae was recovered as sister to all other families in the suborder. Character states previously used to diagnose Psocathropetae are shown to be plesiomorphic. The sister group relationship between Psyllipsocidae and Atropetae was supported by two morphological apomorphies: the presence of a paraproctal anal spine and an anteriorly opened phallosome. Based on these sequence data and morphological observations, we propose a new classification scheme for the Trogiomorpha as follows: infraorder Prionoglaridetae (Prionoglarididae), infraorder Psyllipsocetae (Psyllipsocidae), infraorder Atropetae (Lepidopsocidae, Trogiidae, Psoquillidae).  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 146 , 287–299.     

Environmental regulation of carbon isotope composition and crassulacean acid metabolism in three plant communities along a water availability gradient

Expression of crassulacean acid metabolism (CAM) is characterized by extreme variability within and between taxa and its sensitivity to environmental variation. In this study, we determined seasonal fluctuations in CAM photosynthesis with measurements of nocturnal tissue acidification and carbon isotopic composition (δ¹³C) of bulk tissue and extracted sugars in three plant communities along a precipitation gradient (500, 700, and 1,000 mm year⁻¹) on the Yucatan Peninsula. We also related the degree of CAM to light habitat and relative abundance of species in the three sites. For all species, the greatest tissue acid accumulation occurred during the rainy season. In the 500 mm site, tissue acidification was greater for the species growing at 30% of daily total photon flux density (PFD) than species growing at 80% PFD. Whereas in the two wetter sites, the species growing at 80% total PFD had greater tissue acidification. All species had values of bulk tissue δ¹³C less negative than −20‰, indicating strong CAM activity. The bulk tissue δ¹³C values in plants from the 500 mm site were 2‰ less negative than in plants from the wetter sites, and the only species growing in the three communities, Acanthocereus tetragonus (Cactaceae), showed a significant negative relationship between both bulk tissue and sugar δ¹³C values and annual rainfall, consistent with greater CO₂ assimilation through the CAM pathway with decreasing water availability. Overall, variation in the use of CAM photosynthesis was related to water and light availability and CAM appeared to be more ecologically important in the tropical dry forests than in the coastal dune.     

Photosynthetic flexibility and ecophysiological plasticity: questions and lessons from Clusia, the only CAM tree, in the neotropics

The discovery of crassulacean acid metabolism (CAM) in the trees of Clusia: arrival in the limelight of international research 8 II. Phylogeny 8 III. Photosynthetic physiotypes 10 IV. Metabolic flexibility: organic acid variations 12 V. The environmental control of photosynthetic flexibility 13 VI. Phenotypic plasticity: physiotypes and morphotypes 16 VII. Ecological amplitude and habitat impact 16 VIII. Conclusions and outlook 21 Acknowledgements 22 References 22 Summary It is the aim of this review to present a monographic survey of the neotropical genus Clusia on scaling levels from molecular phylogeny, metabolism, photosynthesis and autecological environmental responses to ecological amplitude and synecological habitat impact. Clusia is the only dicotyledonous genus with real trees performing crassulacean acid metabolism (CAM). By way of introduction, a brief historical reminiscence describes the discovery of CAM in Clusia and the consequent increase in interest in studying this particular genus of tropical shrubs and trees. The molecular phylogeny of CAM in the genus is compared with that in Kalancho? and the Bromeliaceae. At the level of metabolism and photosynthesis, the great plasticity of expression of photosynthetic physiotypes, i.e. (i) C(3) photosynthesis, (ii) CAM including CAM idling, (iii) CAM cycling and (iv) C(3)/CAM-intermediate behaviour, as well as metabolic flexibility in Clusia is illustrated. At the level of autecology, the factors water, irradiance and temperature, which control photosynthetic flexibility, are assessed. The phenotypic plasticity of physiotypes and morphotypes is described. At the level of synecology, the ecological amplitude of Clusia in the tropics and the relations to habitat are surveyed.     

Origins and relationships of the Pleuronectoidei: Molecular and morphological analysis of living and fossil taxa

Flatfishes (Pleuronectiformes) are a species‐rich and distinct group of fishes characterized by cranial asymmetry. Flatfishes occupy a wide diversity of habitats, including the tropical deep‐sea and freshwaters, and often are small‐bodied fishes. Most scientific effort, however, has been focused on large‐bodied temperate marine species important in fisheries. Phylogenetic study of flatfishes has also long been limited in scope and focused on the placement and monophyly of flatfishes. As a result, several questions in systematic biology have persisted that molecular phylogenetic study can answer. We examine the Pleuronectoidei, the largest suborder of Pleuronectiformes with >99% of species diversity of the order, in detail with a multilocus nuclear and mitochondrial data set of 57 pleuronectoids from 13 families covering a wide range of habitats. We combine the molecular data with a morphological matrix to construct a total evidence phylogeny that places fossil flatfishes among extant lineages. Utilizing a time‐calibrated phylogeny, we examine the timing of diversification, area of origin and ancestral temperature preference of Pleuronectoidei. We find polyphyly or paraphyly of two flatfish families, the Paralichthyidae and the Rhombosoleidae, and support the creation of two additional families—Cyclopsettidae and Oncopteridae—to resolve their non‐monophyletic status. Our findings also support the distinctiveness of Paralichthodidae and refine the placement of that lineage. Despite a core fossil record in Europe, the observed recent diversity of pleuronectoids in the Indo‐West Pacific is most likely a result of the Indo‐West Pacific being the area of origin for pleuronectoids and the ancestral temperature preference of flatfishes is most likely tropical.