Angiosperm Phylogeny Research Articles

Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Three Arcto-Tertiary Relicts: Camptotheca acuminata, Davidia involucrata, and Nyssa sinensis.

The Arcto-Tertiary relict genera, Camptotheca, Davidia, and Nyssa represent deep lineages in the asterid order Cornales. Recent phylogenetic studies suggested that these genera should be placed in a newly circumscribed family, Nyssaceae. However, because these analyses were based upon a few genes, it is prudent and necessary to examine further evidence before adopting this taxonomic treatment. In this study, we determined the complete chloroplast (cp) genomes of Camptotheca acuminata, Davidia involucrata, and Nyssa sinensis. Their cp genomes ranged from 156,672 to 158,409 bp, which included 115 genes, and their genome features were highly similar to those of other species within the order Cornales. The phylogenetic relationships among the genera Camptotheca, Davidia, Nyssa, and 23 related taxa in the asterids were analyzed based on 73 protein-coding genes from the cp genomes. All of the previously recognized major clades (namely Cornales, Ericales, Campanulids, and Lamiids) in the asterids, as well as their relationships, were recovered with robust support. A clade including the genera Davidia, Nyssa, Camptotheca, and Diplopanax, was resolved as a well-supported monophyletic group, which was fully separated from the family Cornaceae by the family Hydrangeaceae. Our results provide novel evidence to support the acceptance of the family Nyssaceae outlined by the updated Angiosperm Phylogeny Group.

The ancestral flower of angiosperms and its early diversification

Recent advances in molecular phylogenetics and a series of important palaeobotanical discoveries have revolutionized our understanding of angiosperm diversification. Yet, the origin and early evolution of their most characteristic feature, the flower, remains poorly understood. In particular, the structure of the ancestral flower of all living angiosperms is still uncertain. Here we report model-based reconstructions for ancestral flowers at the deepest nodes in the phylogeny of angiosperms, using the largest data set of floral traits ever assembled. We reconstruct the ancestral angiosperm flower as bisexual and radially symmetric, with more than two whorls of three separate perianth organs each (undifferentiated tepals), more than two whorls of three separate stamens each, and more than five spirally arranged separate carpels. Although uncertainty remains for some of the characters, our reconstruction allows us to propose a new plausible scenario for the early diversification of flowers, leading to new testable hypotheses for future research on angiosperms.

Updated angiosperm family tree for analyzing phylogenetic diversity and community structure

ABSTRACT The computation of phylogenetic diversity and phylogenetic community structure demands an accurately calibrated, high-resolution phylogeny, which reflects current knowledge regarding diversification within the group of interest. Herein we present the angiosperm phylogeny R20160415.new, which is based on the topology proposed by the Angiosperm Phylogeny Group IV, a recently released compilation of angiosperm diversification. R20160415.new is calibratable by different sets of recently published estimates of mean node ages. Its application for the computation of phylogenetic diversity and/or phylogenetic community structure is straightforward and ensures the inclusion of up-to-date information in user specific applications, as long as users are familiar with the pitfalls of such hand-made supertrees.

PHYTOCHEMISTRY AND ETHNOPHARMACOLOGY OF THE SEA GRASS CYMODOCEACEA FAMILY– A REVIEW

Cymodoceaceae is a family of flowering plants, sometimes known as the “manatee-grass family,” the family Cymodoceaceae includes only marine species. The angiosperm phylogeny II system, of 2003 (unchanged from the APG system, of 1998), does recognize Cymodoceaceae and places it in the order Alismatales, in the clade monocots. They are marine hydrophytes that grow and complete their life cycle in a submerged condition, in a saline environment. Like terrestrial plant they obtain their energy from light through photosynthesis thus, they grow only in clear and shallow water, and at the suitable condition, they form beds or meadows. The family includes five genera, totalling 16 species of marine plants occurring in tropical seas and oceans (so-called seagrasses). Cymodoceaceae consist of five genera such as Amphibolis, Cymodocea, Halodule, Syringodium, and Thalassodendron. In this genera Cymodocea rotundata Ehrenb. and Hempr. Ex Asch. Cymodocea serrulata, (R.Br.) Asch. and Magnus, Halodule pinifolia (Miki) Hartog, Halodule uninervis (Forssk.) Asch and Syringodium isoetifolium (Asch.) are the species mostly adopted in Indian coastal region. These seagrass species have unique nature and wide application to the environment including human being. In this article botanical aspects, phytochemistry and ethnopharmacology of these five seagrass species belong to Cymodoceaceae family will be discussed.

The rhizosheath – a potential trait for future agricultural sustainability occurs in orders throughout the angiosperms

The rhizosheath is defined as the weight of soil adhering strongly to roots on excavation, and current interest in this trait as a potential tolerance mechanism to abiotic stress has prompted us to explore the extent of its occurrence throughout the angiosperm phylogeny. Here we describe a robust, novel method which was used to screen species for the presence/absence and strength of a rhizosheath. We correlate the latter with root hair length to provide insight into some of the factors affecting its formation. We go on to compare experimental data with previous observations in the literature. Results of a glasshouse screen demonstrate that rhizosheaths exist in species from many angiosperm orders, and the frequency of their occurrence and their strength and size are related. No correlation between root hair length and rhizosheath size was found, except when root hairs were extremely short, but the presence of root hairs was required for rhizosheath formation. The rhizosheath is present in species from many angiosperm orders. Potential to enhance the trait is likely to exist in a range of crop species and could help contribute to future agricultural sustainability.

Phylogenetic analysis of 25 plant species representing 19 angiosperm families and one gymnosperm family based on 390 orthologous genes

High-throughput sequencing is fundamentally altering traditional phylogenetic classifications. While the Angiosperm Phylogeny Group (APG) III system based on chloroplast sequences has opened up a new era of angiosperm molecular classification, the use of nuclear genome sequences is more helpful for a precise phylogenetic analysis. However, such attempts have so far been applied to only a very limited number of angiosperm plant families. We constructed a phylogenetic tree of 25 plant species with well assembled genome sequences representing 19 angiosperm families and one gymnosperm family (as out group) using 390 orthologous genes. Our results strongly support the moving of Rhamnaceae to order Rosales from Rhamnales, abolishing Rhamnales, and establishing the new order Malpighiales in the APG III system. Our data also showed some characteristics inconsistent with the APG III classification and provided a reinterpretation of phylogeny for some of the families involved. We propose that Malpighiales should be placed in Malvids, not Fabids. The four monocot species representing four families were clustered together, indicating that monocot is a natural taxon. In summary, our results support almost all the APGIII treatments of the orders involved in this study and provided some surprising reinterpretations at levels beyond order.

Evolutionary history of a keystone pollinator parallels the biome occupancy of angiosperms in the Greater Cape Floristic Region

The Greater Cape Floristic Region (GCFR) in South Africa has been extensively investigated for its phenomenal angiosperm diversity. A key emergent pattern is the occurrence of older plant lineages in the southern Fynbos biome and younger lineages in the northern Succulent Karoo biome. We know practically nothing, however, about the evolutionary history of the animals that pollinate this often highly-specialized flora. In this study, we explore the evolutionary history of an important GCFR fly pollinator, Megapalpus capensis, and ask whether it exhibits broadly congruent genetic structuring and timing of diversification to flowering plants within these biomes. We find that the oldest M. capensis lineages originated in Fynbos during the Miocene, while younger Succulent Karoo lineages diverged in the Pliocene and correspond to the proposed age of this recent biome. A strong signature of population expansion is also recovered for flies in this arid biome, consistent with recent colonization. Our first investigation into the evolutionary history of GCFR pollinators thus supports a recent origin of the SK biome, as inferred from angiosperm phylogenies, and suggests that plants and pollinators may have co-diverged within this remarkable area.

Database on Chromosome Counts of Plants of Acharya Jagadish Chandra Bose Indian Botanic Garden, Howrah, India

The chromosome numbers of the extant and extinct plants play a significant role in determining the phylogenetic interrelation of different groups. In the post Angiosperm Phylogeny Group system of plant classification era more and more attentions were given in molecular based studies, evidences on plant breeding, intraspecific variation, origin and taxonomic relationship studies of diverse plant group. Exhaustive online database on chromosomal counts have already been developed from various sources. Still, there are many species and genera of plants for which no chromosome count is known. There are countries from which very few counts have been reported. Therefore, there is still a great deal of traditional cytotaxonomic work to be done. The present communication presents 519 records belonging to 343 species, 265 genera and 85 families of Angiosperms of Acharya Jagadish Chandra Bose Indian Botanic Garden, Howrah. The paper also reports 60 plant species with new chromosome counts, which were hitherto not reported either in the Chromosome Counts Database (CCDB) or Chromosome Atlas of Flowering Plants of the Indian Subcontinent.

Systematics and evolution of lycophytes and ferns

Systematics and evolution of lycophytes and ferns

A review of the plants of the Princeton chert (Eocene, British Columbia, Canada)

The Princeton chert is one of the most completely studied permineralized floras of the Paleogene. Remains of over 30 plant taxa have been described in detail, along with a diverse assemblage of fungi that document a variety of ecological interactions with plants. As a flora of the Okanagan Highlands, the Princeton chert plants are an assemblage of higher elevation taxa of the latest early to earliest middle Eocene, with some components similar to those in the related compression floras. However, like the well-known floras of Clarno, Appian Way, the London Clay, and Messel, the Princeton chert provides an additional dimension of internal structure. In the present study, we outline the history of Princeton chert plant research, starting with Boneham and others, and extending into studies by Stockey and her students and colleagues. These studies were undertaken primarily at the University of Alberta, Edmonton. We then re-examine the individual elements of the Princeton chert flora, using the framework of the currently recognized Angiosperm Phylogeny Group (APG III) phylogeny and in light of recent fossil discoveries. We hope that this update will bring to mind new aspects of the significance of the Princeton chert flora to Paleogene paleobiology, biogeography, and plant evolution.

Revision of Icacinaceae from the Early Eocene London Clay flora based on X-ray micro-CT

The Early Eocene (Ypresian) London Clay Formation contains one of the most important fruit and seed assemblages from the Paleogene, including a large diversity of taxa (>350 spp.) preserved as pyrite permineralizations retaining 3D structure as well as anatomical detail. Despite the importance of the flora for understanding angiosperm biogeographic and evolutionary history, the majority of the fossil material has not been revisited since the original taxonomic treatments by E.M. Reid and M.E.J. Chandler. Given subsequent advances in our understanding of angiosperm phylogeny and fruit morphology, coupled with technological advances in imaging/visualizing fossil material, many of the taxa represented in the flora deserve further study. Here we present a revision of the pantropical family Icacinaceae using X-ray micro-computed tomography (micro-CT) images of 21 species from the flora. Based on the results, four new combinations are made, a new fossil-genus is established for a distinctive species with affinities to the Phytocreneae, and emended diagnoses are provided for eight taxa. Of the seven genera recognized from the flora, only one, Iodes Blume, is extant. This study offers important insights on the biogeographic and evolutionary history of Icacinaceae, which is one of the most abundant and diverse components of the flora from the London Clay Formation.

Fruits and frugivores of the Brazilian Cerrado: ecological and phylogenetic considerations

Knowing the morphological and phylogenetic patterns of fruits of a plant community may elucidate plant-frugivore interactions, and analysis of dispersal syndromes is a practical approach to understanding these mutualisms. We investigated different zoochorous fruits and frugivorous animals among Cerrado formations (forest, savanna and grassland), mapped dispersal syndromes on a Cerrado angiosperm phylogeny and tested for phylogenetic signal. For a core region in Cerrado, we found that, among almost a thousand fruit species and 258 fruit-eating vertebrates, 60% of the fruits had an ornithochorous syndrome and that 70% of the frugivores were birds. Most fruit and frugivorous species (~80%) inhabit forest formations, but many of them also occurred in more than one Cerrado formation. The zoochorous syndromes were found to have little phylogenetic signal, with many plant families exhibiting more than one fruit syndrome, and with ornithochory being widely distributed throughout the phylogeny. Our results suggest that plant-frugivore interactions tend to be evolutionarily labile in this Neotropical region, although birds have had a prominent role in fruit evolution. Furthermore, we found that all three Cerrado formations seem to be interrelated in maintaining functional stability of the plant-frugivore mutualisms in the Cerrado biome.

The Tree of Life: China project

The Tree of Life: China project

Tree of life for the genera of Chinese vascular plants

AbstractWe reconstructed a phylogenetic tree of Chinese vascular plants (Tracheophyta) using sequences of the chloroplast genes atpB, matK, ndhF, and rbcL and mitochondrial matR. We produced a matrix comprising 6098 species and including 13 695 DNA sequences, of which 1803 were newly generated. Our taxonomic sampling spanned 3114 genera representing 323 families of Chinese vascular plants, covering more than 93% of all genera known from China. The comprehensive large phylogeny supports most relationships among and within families recognized by recent molecular phylogenetic studies for lycophytes, ferns (monilophytes), gymnosperms, and angiosperms. For angiosperms, most families in Angiosperm Phylogeny Group IV are supported as monophyletic, except for a paraphyletic Dipterocarpaceae and Santalaceae. The infrafamilial relationships of several large families and monophyly of some large genera are well supported by our dense taxonomic sampling. Our results showed that two species of Eberhardtia are sister to a clade formed by all other taxa of Sapotaceae, except Sarcosperma. We have made our phylogeny of Chinese vascular plants publically available for the creation of subtrees via SoTree (http://www.darwintree.cn/flora/index.shtml), an automated phylogeny assembly tool for ecologists.

Floral anomalies in <i>Calotropis procera</i> (Aiton) Dryand – Nature’s Bizarre play

Not available.Bangladesh J. Plant Taxon. 23(1): 79-81, 2016 (June)

Using nuclear genes to reconstruct angiosperm phylogeny at the species level: A case study with Brassicaceae species

AbstractAngiosperm phylogeny has been investigated extensively using organellar sequences; recent efforts using nuclear genes have also been successful in reconstructing angiosperm phylogenies at family or deeper levels. However, it is not clear whether nuclear genes are also effective in understanding relationships between species in a genus. Here we present a case study of phylogeny at generic and specific levels with nuclear genes, using Brassicaceae taxa as examples. Brassicaceae includes various crops and the model plant Arabidopsis thaliana. A recent study showed that nuclear genes can provide well‐resolved relationships between tribes and larger lineages in Brassicaceae, but few species were included in any given genus. We present a phylogeny with multiple species in each of five genera within Brassicaceae for a total of 65 taxa, using three protein‐coding nuclear genes, MLH1, SMC2, and MCM5, with up to approximately 10 200 base pairs (in both exons and introns). Maximum likelihood and Bayesian analyses of the separate gene regions and combined data reveal high resolution at various phylogenetic depths. The relationships between genera here were largely congruent with previous results, with further resolution at the species level. Also, we report for the first time the affinity of Cardamine rockii with tribe Camelineae instead of other Cardamine members. In addition, we report sequence divergence at three levels: across angiosperms, among Brassicaceae species, and between Arabidopsis ecotypes. Our results provide a robust species‐level phylogeny for a number of Brassicaceae members and support an optimistic perspective on the phylogenetic utility of conserved nuclear data for relatively recent clades.

RNA-seq of Ranunculus sceleratus and Identification of Orthologous Genes among Four Ranunculus Species.

Ranunculus L. is an early diverging clade in the Angiosperm phylogeny. The split between terrestrial and aquatic/semi-aquatic lineages within the genus occurred within 20 Ma (Emadzade and Horandl, 2011), which is much younger than for some well-known aquatic lineages such as Ceratophyllum and Potamogeton. Ranunculus sceleratus Linn. is a semi-aquatic plant commonly found in paddy fields, streams and lakes in Asia, Europe and North America (eFlora of China, http://www.efloras.org/). The plant has also been studied for its unique toxicological and pharmacological properties (Prieto et al., 2003). Its karyotype is 2n = 32, x = 8 in mainland China (Yang, 2000). It usually roots in inundated soils, with stems and leaves emergent. The semi-aquatic R. sceleratus has been hypothesized to be an inter-mediate type in the transition from a terrestrial to aquatic habitat within the genus (Barrett et al., 1993; Prieto et al., 2003). In this study, we generated RNA-seq data of R. sceleratus and analyzed this in relation to the RNA-seq data of Ranunculus bungei Steud., Ranunculus cantoniensis DC., and Ranunculus brotherusii Freyn (Chen et al., 2015). Our aim was to generate RNA-seq data of R. sceleratus and identify the orthologous genes among the four species. Links to deposited data RNA-seq data of R. sceleratus was deposited at NCBI sequence Reads Archive (no. SRP072329). It is in SRA format. ITS sequence of R. sceleratus was deposited in GenBank (no. {type:entrez-nucleotide,attrs:{text:KT957621,term_id:949478889,term_text:KT957621}}KT957621). All the unigenes of R. sceleratus, data matrices of ITS and chloroplast DNA, sequences of the 3455 putative orthologous clusters identified using the program OrthoMCL, and 884 clusters after filters were deposited in figshare (https://figshare.com/s/f40d8f9bd8f894f2d630; sequences in fasta format). These data can be used for further transcriptome assembly, selective pressure estimation, phylogenetic analyses, etc.

Phylogenetic assemblage structure of North American trees is more strongly shaped by glacial-interglacial climate variability in gymnosperms than in angiosperms.

How fast does biodiversity respond to climate change? The relationship of past and current climate with phylogenetic assemblage structure helps us to understand this question. Studies of angiosperm tree diversity in North America have already suggested effects of current water–energy balance and tropical niche conservatism. However, the role of glacial–interglacial climate variability remains to be determined, and little is known about any of these relationships for gymnosperms. Moreover, phylogenetic endemism, the concentration of unique lineages in restricted ranges, may also be related to glacial–interglacial climate variability and needs more attention. We used a refined phylogeny of both angiosperms and gymnosperms to map phylogenetic diversity, clustering and endemism of North American trees in 100‐km grid cells, and climate change velocity since Last Glacial Maximum together with postglacial accessibility to recolonization to quantify glacial–interglacial climate variability. We found: (1) Current climate is the dominant factor explaining the overall patterns, with more clustered angiosperm assemblages toward lower temperature, consistent with tropical niche conservatism. (2) Long‐term climate stability is associated with higher angiosperm endemism, while higher postglacial accessibility is linked to to more phylogenetic clustering and endemism in gymnosperms. (3) Factors linked to glacial–interglacial climate change have stronger effects on gymnosperms than on angiosperms. These results suggest that paleoclimate legacies supplement current climate in shaping phylogenetic patterns in North American trees, and especially so for gymnosperms.

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV

A revised and updated classification for the families of the flowering plants is provided. Newly adopted orders include Austrobaileyales, Canellales, Gunnerales, Crossosomatales and Celastrales. Pertinent literature published since the first APG classification is included, such that many additional families are now placed in the phylogenetic scheme. Among these are Hydnoraceae (Piperales), Nartheciaceae (Dioscoreales), Corsiaceae (Liliales), Triuridaceae (Pandanales), Hanguanaceae (Commelinales), Bromeliacae, Mayacaceae and Rapateaceae (all Poales), Barbeuiaceae and Gisekiaceae (both Caryophyllales), Geissolomataceae, Strasburgeriaceae and Vitaceae (unplaced to order, but included in the rosids), Zygophyllaceae (unplaced to order, but included in eurosids I), Bonnetiaceae, Ctenolophonaceae, Elatinaceae, Ixonanthaceae, Lophopyxidaceae, Podostemaceae (Malpighiales), Paracryphiaceae (unplaced in euasterid II), Sladeniaceae, Pentaphylacaceae (Ericales) and Cardiopteridaceae (Aquifoliales). Several major families are recircumscribed. Salicaceae are expanded to include a large part of Flacourtiaceae, including the type genus of that family; another portion of former Flacourtiaceae is assigned to an expanded circumscription of Achariaceae. Euphorbiaceae are restricted to the uniovulate subfamilies; Phyllanthoideae are recognized as Phyllanthaceae and Oldfieldioideae as Picrodendraceae. Scrophulariaceae are recircumscribed to include Buddlejaceae and Myoporaceae and exclude several former members; these are assigned to Calceolariaceae, Orobanchaceae and Plantaginaceae. We expand the use of bracketing families that could be included optionally in broader circumscriptions with other related families; these include Agapanthaceae and Amaryllidaceae in Alliaceae s.l. , Agavaceae, Hyacinthaceae and Ruscaceae (among many other Asparagales) in Asparagaceae s.l. , Dichapetalaceae in Chrysobalanaceae, Turneraceae in Passifloraceae, Erythroxylaceae in Rhizophoraceae, and Diervillaceae, Dipsacaceae, Linnaeaceae, Morinaceae and Valerianaceae in Caprifoliaceae s.l. © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 141 , 399‐436.

Evolutionary patterns of volatile terpene emissions across 202 tropical tree species

Plant responses to natural enemies include formation of secondary metabolites acting as direct or indirect defenses. Volatile terpenes represent one of the most diverse groups of secondary metabolites. We aimed to explore evolutionary patterns of volatile terpene emission. We measured the composition of damage‐induced volatile terpenes from 202 Amazonian tree species, spanning the angiosperm phylogeny. Volatile terpenes were extracted with solid‐phase micro extraction and desorbed in a gas chromatography–mass spectrometry for compound identification. The chemical diversity of the terpene blend showed a strong phylogenetic signal as closely related species emitted a similar number of compounds. Closely related species also tended to have compositionally similar blends, although this relationship was weak. Meanwhile, the ability to emit a given compound showed no significant phylogenetic signal for 200 of 286 compounds, indicating a high rate of diversification in terpene synthesis and/or great variability in their expression. Three lineages (Magnoliales, Laurales, and Sapindales) showed exceptionally high rates of terpene diversification. Of the 70 compounds found in >10% of their species, 69 displayed significant correlated evolution with at least one other compound. These results provide insights into the complex evolutionary history of volatile terpenes in angiosperms, while highlighting the need for further research into this important class of compounds.