Phylogeny of the Asparagales based on three plastid and two mitochondrial genes

The gynostemium: More than the sum of its parts with emerging floral complexities

Partial or complete floral organ fusion, which occurs in most angiosperm lineages, promotes integration of whorls leading to specialization and complexity. One of the most remarkable floral organ fusions occurs in the gynostemium, a highly specialized structure formed by the congenital fusion of the androecium and the upper portion of the gynoecium. Here we review the gynostemia evolution across flowering plants, the morphological requirements for the synorganization of the two fertile floral whorls, and the molecular basis most likely responsible for such intimate fusion process.

Young evolutionary origins of dioecy in the genus Asparagus

PREMISE

Dioecy (separate sexes) has independently evolved numerous times across the angiosperm phylogeny and is recently derived in many lineages. However, our understanding is limited regarding the evolutionary mechanisms that drive the origins of dioecy in plants. The recent and repeated evolution of dioecy across angiosperms offers an opportunity to make strong inferences about the ecological, developmental, and molecular factors influencing the evolution of dioecy, and thus sex chromosomes. The genus Asparagus (Asparagaceae) is an emerging model taxon for studying dioecy and sex chromosome evolution, yet estimates for the age and origin of dioecy in the genus are lacking.

METHODS

We use plastome sequences and fossil time calibrations in phylogenetic analyses to investigate the age and origin of dioecy in the genus Asparagus. We also review the diversity of sexual systems present across the genus to address contradicting reports in the literature.

RESULTS

We estimate that dioecy evolved once or twice approximately 2.78-3.78 million years ago in Asparagus, of which roughly 27% of the species are dioecious and the remaining are hermaphroditic with monoclinous flowers.

CONCLUSIONS

Our findings support previous work implicating a young age and the possibility of two origins of dioecy in Asparagus, which appear to be associated with rapid radiations and range expansion out of Africa. Lastly, we speculate that paleoclimatic oscillations throughout northern Africa may have helped set the stage for the origin(s) of dioecy in Asparagus approximately 2.78-3.78 million years ago.

Comprehensive Comparative Analyses of Aspidistra Chloroplast Genomes: Insights into Interspecific Plastid Diversity and Phylogeny

Limestone karsts are renowned for extremely high species richness and endemism. Aspidistra (Asparagaceae) is among the highly diversified genera distributed in karst areas, making it an ideal group for studying the evolutionary mechanisms of karst plants. The taxonomy and identification of Aspidistra species are mainly based on their specialized and diverse floral structures. Aspidistra plants have inconspicuous flowers, and the similarity in vegetative morphology often leads to difficulties in species discrimination. Chloroplast genomes possess variable genetic information and offer the potential for interspecies identification. However, as yet there is little information about the interspecific diversity and evolution of the plastid genomes of Aspidistra. In this study, we reported chloroplast (cp) genomes of seven Aspidistra species (A. crassifila, A. dolichanthera, A. erecta, A. longgangensis, A. minutiflora, A. nankunshanensis, and A. retusa). These seven highly-conserved plastid genomes all have a typical quartile structure and include a total of 113 unique genes, comprising 79 protein-coding genes, 4 rRNA genes and 30 tRNA genes. Additionally, we conducted a comprehensive comparative analysis of Aspidistra cp genomes. We identified eight divergent hotspot regions (trnC-GCA-petN, trnE-UUC-psbD, accD-psaI, petA-psbJ, rpl20-rps12, rpl36-rps8, ccsA-ndhD and rps15-ycf1) that serve as potential molecular markers. Our newly generated Aspidistra plastomes enrich the resources of plastid genomes of karst plants, and an investigation into the plastome diversity offers novel perspectives on the taxonomy, phylogeny and evolution of Aspidistra species.

Phylogeny and evolution of Asparagaceae subfamily Nolinoideae: new insights from plastid phylogenomics

BACKGROUND AND AIMS

Asparagaceae subfamily Nolinoideae is an economically important plant group, but the deep relationships and evolutionary history of the lineage remain poorly understood. Based on a large data set including 37 newly sequenced samples and publicly available plastomes, this study aims to better resolve the inter-tribal relationships of Nolinoideae, and to rigorously examine the tribe-level monophyly of Convallarieae, Ophiopogoneae and Polygonateae.

METHODS

Maximum likelihood (ML) and Bayesian inference (BI) methods were used to infer phylogenetic relationships of Nolinoideae at the genus level and above. The diversification history of Nolinoideae was explored using molecular dating.

KEY RESULTS

Both ML and BI analyses identically recovered five clades within Nolinoideae, respectively corresponding to Dracaeneae + Rusceae, Polygonateae + Theropogon, Ophiopogoneae, Nolineae, and Convallarieae excluding Theropogon, and most deep nodes were well supported. As Theropogon was embedded in Polygonateae, the plastome phylogeny failed to resolve Convallarieae and Polygonateae as reciprocally monophyletic. Divergence time estimation showed that the origins of most Nolinoideae genera were dated to the Miocene and Pliocene. The youthfulness of Nolinoideae genera is well represented in the three herbaceous tribes (Convallarieae, Ophiopogoneae and Polygonateae) chiefly distributed in temperate areas of the Northern Hemisphere, as the median stem ages of all 14 genera currently belonging to them were estimated at <12.37 Ma.

CONCLUSIONS

This study recovered a robust backbone phylogeny, providing new insights for better understanding the evolution and classification of Nolinoideae. Compared with the deep relationships recovered by a previous study based on transcriptomic data, our data suggest that ancient hybridization or incomplete lineage sorting may have occurred in the early diversification of Nolinoideae. Our findings will provide important reference for further study of the evolutionary complexity of Nolinoideae using nuclear genomic data. The recent origin of these herbaceous genera currently belonging to Convallarieae, Ophiopogoneae and Polygonateae provides new evidence to support the hypothesis that the global expansion of temperate habitats caused by the climate cooling over the past 15 million years may have dramatically driven lineage diversification and speciation in the Northern Hemisphere temperate flora.

Evolutionary Comparison of the Complete Chloroplast Genomes in Convallaria Species and Phylogenetic Study of Asparagaceae

The genus Convallaria (Asparagaceae) comprises three herbaceous perennial species that are widely distributed in the understory of temperate deciduous forests in the Northern Hemisphere. Although Convallaria species have high medicinal and horticultural values, studies related to the phylogenetic analysis of this genus are few. In the present study, we assembled and reported five complete chloroplast (cp) sequences of three Convallaria species (two of C. keiskei Miq., two of C. majalis L., and one of C. montana Raf.) using Illumina paired-end sequencing data. The cp genomes were highly similar in overall size (161,365–162,972 bp), and all consisted of a pair of inverted repeats (IR) regions (29,140–29,486 bp) separated by a large single-copy (LSC) (85,183–85,521 bp) and a small single-copy (SSC) region (17,877–18,502 bp). Each cp genome contained the same 113 unique genes, including 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Gene content, gene order, AT content and IR/SC boundary structure were nearly identical among all of the Convallaria cp genomes. However, their lengths varied due to contraction/expansion at the IR/LSC borders. Simple sequence repeat (SSR) analyses indicated that the richest SSRs are A/T mononucleotides. Three highly variable regions (petA-psbJ, psbI-trnS and ccsA-ndhD) were identified as valuable molecular markers. Phylogenetic analysis of the family Asparagaceae using 48 cp genome sequences supported the monophyly of Convallaria, which formed a sister clade to the genus Rohdea. Our study provides a robust phylogeny of the Asparagaceae family. The complete cp genome sequences will contribute to further studies in the molecular identification, genetic diversity, and phylogeny of Convallaria.

Comparative Plastome Analysis of Three Amaryllidaceae Subfamilies: Insights into Variation of Genome Characteristics, Phylogeny, and Adaptive Evolution

In the latest APG IV classification system, Amaryllidaceae is placed under the order of Asparagus and includes three subfamilies: Agapanthoideae, Allioideae, and Amaryllidoideae, which include many economically important crops. With the development of molecular phylogeny, research on the phylogenetic relationship of Amaryllidaceae has become more convenient. However, the current comparative analysis of Amaryllidaceae at the whole chloroplast genome level is still lacking. In this study, we sequenced 18 Allioideae plastomes and combined them with publicly available data (a total of 41 plastomes), including 21 Allioideae species, 1 Agapanthoideae species, 14 Amaryllidoideae species, and 5 Asparagaceae species. Comparative analyses were performed including basic characteristics of genome structure, codon usage, repeat elements, IR boundary, and genome divergence. Phylogenetic relationships were detected using single-copy genes (SCGs) and ribosomal internal transcribed spacer sequences (ITS), and the branch-site model was also employed to conduct the positive selection analysis. The results indicated that all Amaryllidaceae species showed a highly conserved typical tetrad structure. The GC content and five codon usage indexes in Allioideae species were lower than those in the other two subfamilies. Comparison analysis of Bayesian and ML phylogeny based on SCGs strongly supports the monophyly of three subfamilies and the sisterhood among them. Besides, positively selected genes (PSGs) were detected in each of the three subfamilies. Almost all genes with significant posterior probabilities for codon sites were associated with self-replication and photosynthesis. Our study investigated the three subfamilies of Amaryllidaceae at the whole chloroplast genome level and suggested the key role of selective pressure in the adaptation and evolution of Amaryllidaceae.

The complete plastome of the South African species, Amaryllis belladonna L. (Amaryllidaceae)

The complete plastome sequence of Amaryllis belladonna L. is assembled and annotated. This is the type species of Amaryllis and therefore the type of the family Amaryllidaceae and as such, is important to document the phylogenetic position of the family. The plastome sequence has a length of 158,145 bp, with the large single copy (LSC) regions comprising 85,963 bp, the small single copy (SSC) 18634 bp and two identical inverted repeats (IR) regions each of 26,774 bp. Phylogenetic analysis fully resolved Amaryllis in a clade with Crinum L. in the Amaryllidoideae, as expected, with the Allioideae as a sister group. Agapanthus (Agapanthoideae) is a sister to the other two subfamilies in the Amaryllidaceae. The phylogenetic tree produced corresponds to previous topologies based on plastome molecular markers including matK, ndhF and rbcL. This is the first paper reporting the whole plastome comparison of the type genera of all three subfamilies in the Amaryllidaceae.

Comparative plastomics of Amaryllidaceae: inverted repeat expansion and the degradation of the ndh genes in Strumaria truncata Jacq

Amaryllidaceae is a widespread and distinctive plant family contributing both food and ornamental plants. Here we present an initial survey of plastomes across the family and report on both structural rearrangements and gene losses. Most plastomes in the family are of similar gene arrangement and content however some taxa have shown gains in plastome length while in several taxa there is evidence of gene loss. Strumaria truncata shows a substantial loss of ndh family genes while three other taxa show loss of cemA, which has been reported only rarely. Our sparse sampling of the family has detected sufficient variation to suggest further sampling across the family could be a rich source of new information on plastome variation and evolution.

Comparative flower morphology of Agapanthus africanus and A. praecox (Amaryllidaceae)

The structure of Agapanthus africanus and A. praecox flowers was studied on permanent cross-sectional and longitudinal sections using a light microscope. The genus Agapanthus belongs to the subfamily Agapanthoideae, the family Amaryllidaceae, which is characterized by the presence of the upper ovary, septal nectaries and fruit – fleshy capsule. Micromorphological studies of the flower are considered as a way for detection of unknown plant features, adjustment of plants to specialized ways of pollination and determining the first stages of morphogenesis of fruit, and further use these features in taxonomy. 10 flowers of A. africanus and A. praecox were sectioned using standard methods of Paraplast embedding and serial sectioning at 20 micron thickness. Sections were stained with Safranin and Astra Blau and mounted in Eukitt. It was found that in the studied species the tepals have single-bundle traces. The vascular system of the superior ovary consists of a three bundle dorsal vein, of the ventral roots complex, which are reorganized into paired ventral bundles of the carpel, which form traces to ovules. For the first time, the following gynoecium zones were detected in A. africanus: a synascidiate structural zone with a height of about 560 μm and a fertile symplicate structural zone with a height of about 380 μm and a hemisymplicate zone of 2580 μm. In A. praecox gynoecium, there is a synascidiate structural zone with a height of 200 μm and a symplicate structural zone of 600 μm and a hemisymplicate zone of 620 μm. Septal nectaries appear in the hemisymplicate zone and open with nectar fissures at the base of the column, with a total septal nectar height of 2880 μm in A. africanus and 820 μm in A. praecox. The ovary roof is 300 µm in A. africanus and 200 µm in A. praecox. Triple dorsal bundles of carpels in A. africanus have been identified, which could be considered as adaptation of different stages of morphogenesis of fruit to dehiscence. The new data obtained by the vascular anatomy of the flower and the presence of different ovary zones significantly add to the information about anatomical and morphological features of the studied species, which can be further used in the taxonomy of the family Amaryllidaceae.

The complete chloroplast genome sequence of Heteropolygonatum ginfushanicum (Asparagaceae) and phylogenetic analysis

Heteropolygonatum ginfushanicum is an endemic epiphytic herb in China. The complete chloroplast (cp) genome of H. ginfushanicum is reported in this study. The total length of the cp genome is 155,508 bp with a typical quadripartite structure consisting of a large single copy region (LSC) of 84,552 bp and a small single copy region (SSC) of 18,528 bp, separated by a pair of 26,214 bp inverted repeats (IRs). It encodes a total of 113 unique genes, including 79 protein-coding, 30 tRNA, and four rRNA genes. Phylogenetic analysis indicated that H. ginfushanicum is sister to Heteropolygonatum marmoratum within subfamily Nolinoideae.

Biogeography of the monocotyledon astelioid clade (Asparagales): A history of long-distance dispersal and diversification with emerging habitats

The astelioid families (Asteliaceae, Blandfordiaceae, Boryaceae, Hypoxidaceae, and Lanariaceae) have centers of diversity in Australasia and temperate Africa, with secondary centers of diversity in Afromontane Africa, Asia, and Pacific Islands. The global distribution of these families makes this an excellent lineage to test if current distribution patterns are the result of vicariance or long-distance dispersal and to evaluate the roles of Tertiary climatic and geological drivers in lineage diversification. Sequence data were generated from five chloroplast regions (petL-psbE, rbcL, rps16-trnK, trnL-trnLF, trnS-trnSG) for 104 ingroup species sampled across global diversity. The astelioid phylogeny was inferred using maximum parsimony, maximum likelihood, and Bayesian inference methods. Divergence dates were estimated with a relaxed clock applied in BEAST. Ancestral ranges were reconstructed in the R package 'BioGeoBEARS' applying the corrected Akaike information criterion to test for the best-fit biogeographic model. Diversification rates were estimated in Bayesian Analysis of Macroevolutionary Mixtures (BAMM). Astelioid relationships were inferred as Boryaceae(Blandfordiaceae(Asteliaceae(Hypoxidaceae plus Lanariaceae))). The crown astelioid node was dated to the Late Cretaceous (75.2 million years; 95% highest posterior density interval 61.0-90.0 million years) and an Antarctic-Australasian origin was inferred. Astelioid speciation events have not been shaped by Gondwanan vicariance. Rather long-distance dispersal since the Eocene is inferred to account for current distributions. Crown Asteliaceae and Boryaceae have Australian ancestral ranges and diversified since the Eocene. In Hypoxidaceae, Empodium, Hypoxis, and Pauridia have African ancestral ranges, while Curculigo and Molineria have an Asian ancestral range. Diversification of Pauridia and the Curculigo clade occurred steadily, while diversification of Astelia and Hypoxis was punctuated over time. Diversification of Hypoxis and Astelia coincided temporally with the expansion of the habitat types occupied by extant taxa, e.g., grassland habitat in Africa during the Late Miocene and alpine habitat in New Zealand during the Pliocene, respectively.

The Deep Evolutionary Relationships of the Morphologically Heterogeneous Nolinoideae (Asparagaceae) Revealed by Transcriptome Data

The subfamily Nolinoideae of Asparagaceae is an extremely morphologically heterogeneous group, which is comprised of seven lineages, formerly known as Eriospermaceae, Polygonateae, Ophiopogoneae, Convallarieae, Ruscaceae s.s., Dracaenaceae, and Nolinaceae from different families or even orders. Their drastically divergent morphologies and low level of molecular resolution have hindered our understanding on their evolutionary history. To resolve reliable and clear phylogenetic relationships of the Nolinoideae, a phylogenetic study was conducted based on transcriptomic sequencing of 15 species representing all the seven lineages. A dataset containing up to 2,850,331 sites across 2,126 genes was analyzed using both concatenated and coalescent methods. Except for Eriospermum as outgroup, the transcriptomic data strongly resolved the remaining six lineages into two groups, one is a paraphyletic grade including the woody lineages of dracaenoids, ruscoids, and nolinoids and a monophyletic herbaceous clade. Within the herbaceous group, the Ophiopogoneae + Theropogon is sister to a clade that is composed of Convallarieae and the monophyletic Polygonateae. Our work provides a first robust deep relationship of the highly heterogeneous Nolinoideae and paves the way for further investigations of its complex evolution.

Evolution of Lomandroideae: Multiple origins of polyploidy and biome occupancy in Australia

Asparagaceae: Lomandroideae are a species-rich and economically important subfamily in the monocot order Asparagales, with a center of diversity in Australia. Lomandroideae are ecologically diverse, occupying mesic and arid biomes in Australia and possessing an array of key traits, including sexual dimorphism, storage organs and polyploidy that are potentially adaptive for survival in seasonally arid and fire-dependent habitats. The Lomandroideae phylogeny was reconstructed using maximum likelihood and Bayesian inference criteria, based on plastome data from genome-skimming to infer relationships. A fossil-calibrated chronogram provided a temporal framework for understanding trait transitions. Ancestral state reconstructions and phylogenetic comparative trait correlation analyses provided insights into the evolutionary and ecological drivers associated with Lomandroideae diversification. Lomandroideae diverged from the other Asparagaceae ca. 56.61 million years ago (95% highest posterior density values 70.31-45.34 million years) and the major lineages diversified since the Oligocene. The most recent common ancestor of the clade likely occupied the mesic biome, was hermaphroditic and geophytic. Biome occupancy transitions were correlated with polyploidy and the presence of storage roots. Polyploidy potentially serves as an "enabler" trait, generating novel phenotypes, which may confer tolerance to climatic ranges and soil conditions putatively required for expansion into and occupation of new arid biomes. Storage roots, as a key factor driving biome transitions, may have been associated with fire rather than with aridification events in the Australian flora. This study contributes significantly to our understanding of biome evolution by identifying polyploidy and storage organs as key factors associated with transitions in biome occupancy in this lineage.

Complete chloroplast genome of Reineckia carnea and its implications for the phylogenetic position within Nolinoideae (Asparagaceae)

Reineckia carnea is an important horticultural and medicinal plant in East Asia. Here, we determined the first complete chloroplast genome of R. carnea using genome skimming approach. The cp genome was 157,059 bp long, with a large single-copy region (LSC) of 85,474 bp and a small single-copy region (SSC) of 18,535 bp separated by a pair of inverted repeats (IRs) of 26,525 bp. It encodes 132 genes, including 86 protein-coding genes, 38 tRNA genes, and eight ribosomal RNA genes. The phylogenetic analysis indicated that R. carnea is close related to Rohdea chinensis.

Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales)

Astelia pumila (G.Forst.) Gaudich. (Asteliaceae, Asparagales) is a major element of West Patagonian cushion peat bog vegetation. With the aim to identify appropriate chloroplast markers for the use in a phylogeographic study, the complete chloroplast genomes of five A. pumila accessions from almost the entire geographical range of the species were assembled and screened for variable positions. The chloroplast genome sequence was obtained via a mapping approach, using Eustrephus latifolius (Asparagaceae) as a reference. The chloroplast genome of A. pumila varies in length from 158,215 bp to 158,221 bp, containing a large single copy region of 85,981–85,983 bp, a small single copy region of 18,182–18,186 bp and two inverted repeats of 27,026 bp. Genome annotation predicted a total of 113 genes, including 30 tRNA and four rRNA genes. Sequence comparisons revealed a very low degree of intraspecific genetic variability, as only 37 variable sites (18 indels, 18 single nucleotide polymorphisms, one 3-bp mutation)—most of them autapomorphies—were found among the five assembled chloroplast genomes. A Maximum Likelihood analysis, based on whole chloroplast genome sequences of several Asparagales accessions representing six of the currently recognized 14 families (sensu APG IV), confirmed the phylogenetic position of A. pumila. The chloroplast genome of A. pumila is the first to be reported for a member of the astelioid clade (14 genera with c. 215 species), a basally branching group within Asparagales.

The complete chloroplast genome of Narcissus poeticus L. (Amaryllidaceae: Amaryllidoideae)

The first complete chloroplast genome sequence for Narcissus is assembled and annotated in this study. The total length of the N. poeticus chloroplast genome is 160,099 bp and comprises the large single copy (LSC) spanning 86,445 bp, the small single copy (SSC) spanning 16,434 bp, and two inverted repeat regions each of 28,610 bp length. The truncated copy of ycf1 before the junction between IR_B and SSC was 1277–2428 bp longer than in other included Asparagales samples. A potential pseudogene, cemA, was also identified. This is the first reported plastome for Amaryllidaceae subfamily Amaryllidoideae.

Timing of rapid diversification and convergent origins of active pollination within Agavoideae (Asparagaceae)

PREMISE OF THE STUDY

Yucca species are ideal candidates for the study of coevolution due to the obligate mutualism they form with yucca moth pollinators (genera Tegeticula and Parategeticula). Yuccas are not the only species to exhibit a mutualism with yucca moths; the genus Hesperoyucca is pollinated by the California yucca moth (Tegeticula maculata). Relationships among yuccas, Hesperoyucca, and other members of subfamily Agavoideae are necessary to understand the evolution of this unique pollination syndrome. Here, we investigate evolutionary relationships of yuccas and closely related genera looking at the timing and origin of yucca moth pollination.

METHODS

In this study, we sequenced the chloroplast genomes of 20 species in the subfamily Agavoideae (Asparagaceae) and three confamilial outgroup taxa to resolve intergeneric phylogenetic relationships of Agavoideae. We estimated divergence times using protein-coding genes from 67 chloroplast genomes sampled across monocots to determine the timing of the yucca moth pollination origin.

KEY RESULTS

We confidently resolved intergeneric relationships in Agavoideae, demonstrating the origin of the yucca-yucca moth mutualism on two distinct lineages that diverged 27 million years ago. Comparisons of Yucca and Hesperoyucca divergence time to those of yucca moths (Tegeticula and Parategeticula, Prodoxidae) indicate overlapping ages for the origin of pollinating behavior in the moths and pollination by yucca moths in the two plant lineages.

CONCLUSION

Whereas pollinating yucca moths have been shown to have a single origin within the Prodoxidae, there were independent acquisitions of active pollination on lineages leading to Yucca and Hesperoyucca within the Agavoideae.

Evolution of Asparagus L. (Asparagaceae): Out-of-South-Africa and multiple origins of sexual dimorphism

In the most comprehensive study to date we explored the phylogeny and evolution of the genus Asparagus, with emphasis on the southern African species. We included 211 accessions, representing 77 (92%) of the southern African, 6 (17%) of the tropical African, 10 (56%) of the strictly European and 6 (9%) of the Eurasian species. We analyzed DNA sequences from three plastid regions (trnH-psbA, trnD-T, ndhF) and from the nuclear region phytochrome C (PHYC) with parsimony and maximum likelihood methods, and recovered a monophyletic Asparagus. The phylogeny conflicts with all previous infra-generic classifications. It has many strongly supported clades, corroborated by morphological characters, which may provide a basis for a revised taxonomy. Additionally, the phylogeny indicates that many of the current species delimitations are problematic. Using biogeographic analyses that account for phylogenetic uncertainty (S-DIVA) and take into account relative branch lengths (Lagrange) we confirm the origin of Asparagus in southern Africa, and find no evidence that the dispersal of Asparagus follow the Rand flora pattern. We find that all truly dioecious species of Asparagus share a common origin, but that sexual dimorphism has arisen independently several times.

Lateral Meristems Responsible for Secondary Growth of the Monocotyledons: A Survey of the State of the Art

This review highlights key historical works and the recent research on the monocot lateral meristems. It discusses the terminological issues (elucidating the terminological inconsistency found in the literature concerned), origination of secondary meristems, their morphology and characteristic features of the derivative tissues. Also the monocot cambium response to hormonal and gravitational stimuli is discussed. The summarized inputs in the present note are believed to renew interest in this field, which is important for a more comprehensive understanding of the abnormal secondary growth in the monocotyledons.

Clock model makes a large difference to age estimates of long-stemmed clades with no internal calibration: a test using Australian grasstrees

BACKGROUND

Estimating divergence times in phylogenies using a molecular clock depends on accurate modeling of nucleotide substitution rates in DNA sequences. Rate heterogeneity among lineages is likely to affect estimates, especially in lineages with long stems and short crowns ("broom" clades) and no internal calibration. We evaluate the performance of the random local clocks model (RLC) and the more routinely employed uncorrelated lognormal relaxed clock model (UCLN) in situations in which a significant rate shift occurs on the stem branch of a broom clade. We compare the results of simulations to empirical results from analyses of a real rate-heterogeneous taxon - Australian grass trees (Xanthorrhoea) - whose substitution rate is slower than in its sister groups, as determined by relative rate tests.

RESULTS

In the simulated datasets, the RLC model performed much better than UCLN: RLC correctly estimated the age of the crown node of slow-rate broom clades, whereas UCLN estimates were consistently too young. Similarly, in the Xanthorrhoea dataset, UCLN returned significantly younger crown ages than RLC (mean estimates respectively 3-6 Ma versus 25-35 Ma). In both real and simulated datasets, Bayes Factor tests strongly favored the RLC model over the UCLN model.

CONCLUSIONS

The choice of an unsuitable molecular clock model can strongly bias divergence time estimates. In particular, for data predicted to have more rate variation among than within clades, dating with RLC is much more likely to be accurate than with UCLN. The choice of clocks should be informed by the biology of the study group (e.g., life-form) or assessed with relative rate tests and post-hoc model comparisons.

Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?

BACKGROUND AND AIMS

Zingiberales comprise a clade of eight tropical monocot families including approx. 2500 species and are hypothesized to have undergone an ancient, rapid radiation during the Cretaceous. Zingiberales display substantial variation in floral morphology, and several members are ecologically and economically important. Deep phylogenetic relationships among primary lineages of Zingiberales have proved difficult to resolve in previous studies, representing a key region of uncertainty in the monocot tree of life.

METHODS

Next-generation sequencing was used to construct complete plastid gene sets for nine taxa of Zingiberales, which were added to five previously sequenced sets in an attempt to resolve deep relationships among families in the order. Variation in taxon sampling, process partition inclusion and partition model parameters were examined to assess their effects on topology and support.

KEY RESULTS

Codon-based likelihood analysis identified a strongly supported clade of ((Cannaceae, Marantaceae), (Costaceae, Zingiberaceae)), sister to (Musaceae, (Lowiaceae, Strelitziaceae)), collectively sister to Heliconiaceae. However, the deepest divergences in this phylogenetic analysis comprised short branches with weak support. Additionally, manipulation of matrices resulted in differing deep topologies in an unpredictable fashion. Alternative topology testing allowed statistical rejection of some of the topologies. Saturation fails to explain observed topological uncertainty and low support at the base of Zingiberales. Evidence for conflict among the plastid data was based on a support metric that accounts for conflicting resampled topologies.

CONCLUSIONS

Many relationships were resolved with robust support, but the paucity of character information supporting the deepest nodes and the existence of conflict suggest that plastid coding regions are insufficient to resolve and support the earliest divergences among families of Zingiberales. Whole plastomes will continue to be highly useful in plant phylogenetics, but the current study adds to a growing body of literature suggesting that they may not provide enough character information for resolving ancient, rapid radiations.

Phytosynergy in some Hypoxis species and pharmacological properties of a Hypoxis-based phytopharmaceutical formula

ETHNOPHARMACOLOGY RELEVANCE

Hypoxis species are used extensively in traditional medicine in southern Africa for several ailments including tuberculosis, chest infections, and nervous and urinary disorders. Several other claims have been made for extracts emanating from Hypoxis species and have led to the production of several commercial products used as immunostimulants mostly for people living with HIV/AIDS and cancer. This study was aimed at investigating the biological activity of four Hypoxis species and a commercial herbal product, 'African potato extract' (APE).

MATERIALS AND METHODS

Antibacterial, antifungal, cyclooxygenase (COX) and acetylcholineasterase (AChE) inhibitory activities of four Hypoxis species (H. acuminata, H. colchicifolia, H. hemerocallidea and H. rigidula) and a popular Hypoxis-based herbal preparation, APE were tested. The phytoconstituents of the mixture were also profiled using TLC methods. Several combinations of the Hypoxis species were prepared and their synergism, additive, autonomic and antagonism effects investigated. As a quality control measure, batch to batch comparison in the phytoconstituents and biological activity of APE was carried out.

RESULTS

The results confirmed H. colchicifolia and H. hemerocallidea as the phytoconstituents of APE. The extracts showed a broad spectrum of activities against the bacterial and fungal strains used. Of particular interest were the activities exhibited by the APE and combinations of H. colchicifolia and H. hemerocallidea. The APE mixture exhibited good antibacterial activity (MIC values of 0.78mg/ml each) in all the tested batches against the bacterial strains used. The water extracts of all four Hypoxis species, three batches of APE and the combination (water extracts) of H. colchicifolia and H. hemerocallidea exhibited high COX-1 and moderate COX-2 inhibitory activity except for H. acuminata which showed low activity against COX-2. All the extract, batches of APE and combinations showed low to moderate AChE inhibitory activity. These results provided some evidence of phytosynergy in some extracts of H. hemerocallidea and H. colchicifolia except for a few extracts which act as additive, autonomous and antagonistic when used to inhibit some bacterial and fungal strains. However, this was not the case for COX and AChE inhibition, as only acetone extracts acted in a synergistic way to reduce the activity of the enzyme.

CONCLUSION

Even though the results give an indication of a positive interaction between some extracts of H. hemerocallidea and H. colchicifolia, the study was carried out on 1:1 v/v combinations only. It is therefore important to carry out isobologram studies, which considers more than one ratio of the combinations.

Networks in a large-scale phylogenetic analysis: reconstructing evolutionary history of Asparagales (Lilianae) based on four plastid genes

Phylogenetic analysis aims to produce a bifurcating tree, which disregards conflicting signals and displays only those that are present in a large proportion of the data. However, any character (or tree) conflict in a dataset allows the exploration of support for various evolutionary hypotheses. Although data-display network approaches exist, biologists cannot easily and routinely use them to compute rooted phylogenetic networks on real datasets containing hundreds of taxa. Here, we constructed an original neighbour-net for a large dataset of Asparagales to highlight the aspects of the resulting network that will be important for interpreting phylogeny. The analyses were largely conducted with new data collected for the same loci as in previous studies, but from different species accessions and greater sampling in many cases than in published analyses. The network tree summarised the majority data pattern in the characters of plastid sequences before tree building, which largely confirmed the currently recognised phylogenetic relationships. Most conflicting signals are at the base of each group along the Asparagales backbone, which helps us to establish the expectancy and advance our understanding of some difficult taxa relationships and their phylogeny. The network method should play a greater role in phylogenetic analyses than it has in the past. To advance the understanding of evolutionary history of the largest order of monocots Asparagales, absolute diversification times were estimated for family-level clades using relaxed molecular clock analyses.

Networks in a large-scale phylogenetic analysis: reconstructing evolutionary history of Asparagales (Lilianae) based on four plastid genes

Phylogenetic analysis aims to produce a bifurcating tree, which disregards conflicting signals and displays only those that are present in a large proportion of the data. However, any character (or tree) conflict in a dataset allows the exploration of support for various evolutionary hypotheses. Although data-display network approaches exist, biologists cannot easily and routinely use them to compute rooted phylogenetic networks on real datasets containing hundreds of taxa. Here, we constructed an original neighbour-net for a large dataset of Asparagales to highlight the aspects of the resulting network that will be important for interpreting phylogeny. The analyses were largely conducted with new data collected for the same loci as in previous studies, but from different species accessions and greater sampling in many cases than in published analyses. The network tree summarised the majority data pattern in the characters of plastid sequences before tree building, which largely confirmed the currently recognised phylogenetic relationships. Most conflicting signals are at the base of each group along the Asparagales backbone, which helps us to establish the expectancy and advance our understanding of some difficult taxa relationships and their phylogeny. The network method should play a greater role in phylogenetic analyses than it has in the past. To advance the understanding of evolutionary history of the largest order of monocots Asparagales, absolute diversification times were estimated for family-level clades using relaxed molecular clock analyses.

Spatio-temporal history of the disjunct family Tecophilaeaceae: a tale involving the colonization of three Mediterranean-type ecosystems

BACKGROUND AND AIMS

Tecophilaeaceae (27 species distributed in eight genera) have a disjunct distribution in California, Chile and southern and tropical mainland Africa. Moreover, although the family mainly occurs in arid ecosystems, it has colonized three Mediterranean-type ecosystems. In this study, the spatio-temporal history of the family is examined using DNA sequence data from six plastid regions.

METHODS

Modern methods in divergence time estimation (BEAST), diversification (LTT and GeoSSE) and biogeography (LAGRANGE) are applied to infer the evolutionary history of Tecophilaeaceae. To take into account dating and phylogenetic uncertainty, the biogeographical inferences were run over a set of dated Bayesian trees and the analyses were constrained according to palaeogeographical evidence.

KEY RESULTS

The analyses showed that the current distribution and diversification of the family were influenced primarily by the break up of Gondwana, separating the family into two main clades, and the establishment of a Mediterranean climate in Chile, coinciding with the radiation of Conanthera. Finally, unlike many other groups, no shifts in diversification rates were observed associated with the dispersals in the Cape region of South Africa.

CONCLUSIONS

Although modest in size, Tecophilaeaceae have a complex spatio-temporal history. The family is now most diverse in arid ecosystems in southern Africa, but is expected to have originated in sub-tropical Africa. It has subsequently colonized Mediterranean-type ecosystems in both the Northern and Southern Hemispheres, but well before the onset of the Mediterranean climate in these regions. Only one lineage, genus Conanthera, has apparently diversified to any extent under the impetus of a Mediterranean climate.

A new day dawning: Hemerocallis (daylily) as a future model organism

Genetic model organisms have revolutionized science, and today, with the rapid advances in technology, there is significant potential to launch many more plant species towards model status. However, these new model organisms will have to be carefully selected. Here, we argue that Hemerocallis (daylily) satisfies multiple criteria for selection and deserves serious consideration as a subject of intensive biological investigation. Several attributes of the genus are of great biological interest. These include the strict control of flower opening and, within a short period, the precisely regulated floral death by a programmed cell death system. The self-incompatibility system in Hemerocallis is also noteworthy and deserves more attention. Importantly, the genus is widely cultivated for food, medicinal value and ornamental interest. Hemerocallis has considerable potential as a 'nutraceutical' food plant and the source of new compounds with biomedical activity. The genus has also been embraced by ornamental plant breeders and the extraordinary morphological diversity of hybrid cultivars, produced within a relatively short time by amateur enthusiasts, is an exceptional resource for botanical and genetic studies. We explore these points in detail, explaining the reasons why this genus has considerable value-both academic and socio-economic-and deserves new resources devoted to its exploration as a model. Its impact as a future model will be enhanced by its amenability to cultivation in laboratory and field conditions. In addition, established methods for various tissue and cell culture systems as well as transformation will permit maximum exploitation of this genus by science.

Cell longevity and sustained primary growth in palm stems

Longevity, or organismal life span, is determined largely by the period over which constituent cells can function metabolically. Plants, with modular organization (the ability continually to develop new organs and tissues) differ from animals, with unitary organization (a fixed body plan), and this difference is reflected in their respective life spans, potentially much longer in plants than animals. We draw attention to the observation that palm trees, as a group of monocotyledons without secondary growth comparable to that of lignophytes (plants with secondary growth from a bifacial cambium), retain by means of sustained primary growth living cells in their trunks throughout their organismal life span. Does this make palms the longest-lived trees because they can grow as individuals for several centuries? No conventional lignophyte retains living metabolically active differentiated cell types in its trunk for this length of time, even though the tree as a whole can exist for millennia. Does this contrast also imply that the long-lived cells in a palm trunk have exceptional properties, which allows this seeming immortality? We document the long-life of many tall palm species and their inherent long-lived stem cell properties, comparing such plants to conventional trees. We provide a summary of aspects of cell age and life span in animals and plants. Cell replacement is a feature of animal function, whereas conventional trees rely on active growth centers (meristems) to sustain organismal development. However, the long persistence of living cells in palm trunks is seen not as evidence for unique metabolic processes that sustain longevity, but is a consequence of unique constructional features. This conclusion suggests that the life span of plant cells is not necessarily genetically determined.