Biogeography of the Pistia Clade (Araceae): Based on Chloroplast and Mitochondrial DNA Sequences and Bayesian Divergence Time Inference

Pinellia genus: A systematic review of active ingredients, pharmacological effects and action mechanism, toxicological evaluation, and multi-omics application

The dried tuber of Pinellia ternata (Thunb.) Breit, Pinelliae Rhizoma (PR, also named 'Banxia' in Chinese), is widely used in traditional medicine. This review aims to provide detail summary of active ingredients, pharmacological effects, toxic ingredients, detoxification strategies, and omic researches, etc. Pharmacological ingredients from PR are mainly classified into six categories: alkaloids, amino acids, polysaccharides, phenylpropanoids, essential oils, and glucocerebrosides. Diversity of chemical composition determines the broad-spectrum efficacy and gives a foundation for the comprehensive utilization of P. ternata germplasm resources. The pharmacological compounds are involved in inhibition of cancer cells by targeting various pathways, including activation of immune system, inhibition of proliferation and cycle, induction of apoptosis, and inhibition of angiogenesis. The pharmacological components of PR act on nervous system by targeting neurotransmitters, activating immune system, decreasing apoptosis, and increasing redox system. Lectins, one major class of the toxic ingredients extracted from raw PR, possess significant toxic effects on human cells. Inflammatory factors, cytochrome P450 proteins (CYP) family enzymes, mammalian target of rapamycin (mTOR) signaling factors, transforming growth factor-β (TGF-β) signaling factors, and nervous system, are considered to be the target sites of lectins. Recently, omic analysis is widely applied in Pinellia genus studies. Plastome genome-based molecular markers are deeply used for identifying and resolving phylogeny of Pinellia genus plants. Various omic works revealed and functional identified a series of environmental stress responsive factors and active component biosynthesis-related genes. Our review summarizes the recent progress in active and toxic ingredient evaluation, pharmacological effects, detoxification strategies, and functional gene identification and accelerates efficient utilization of this traditional herb.

Target sequence data shed new light on the infrafamilial classification of Araceae

PREMISE

Recent phylogenetic studies of the Araceae have confirmed the position of the duckweeds nested within the aroids, and the monophyly of a clade containing all the unisexual flowered aroids plus the bisexual-flowered Calla palustris. The main objective of the present study was to better resolve the deep phylogenetic relationships among the main lineages within the family, particularly the relationships between the eight currently recognized subfamilies. We also aimed to confirm the phylogenetic position of the enigmatic genus Calla in relation to the long-debated evolutionary transition between bisexual and unisexual flowers in the family.

METHODS

Nuclear DNA sequence data were generated for 128 species across 111 genera (78%) of Araceae using target sequence capture and the Angiosperms 353 universal probe set.

RESULTS

The phylogenomic data confirmed the monophyly of the eight Araceae subfamilies, but the phylogenetic position of subfamily Lasioideae remains uncertain. The genus Calla is included in subfamily Aroideae, which has also been expanded to include Zamioculcadoideae. The tribe Aglaonemateae is newly defined to include the genera Aglaonema and Boycea.

CONCLUSIONS

Our results strongly suggest that new research on African genera (Callopsis, Nephthytis, and Anubias) and Calla will be important for understanding the early evolution of the Aroideae. Also of particular interest are the phylogenetic positions of the isolated genera Montrichardia, Zantedeschia, and Anchomanes, which remain only moderately supported here.

Comparative chloroplast genomes and phylogenetic analyses of Pinellia

Background

Pinellia Tenore (Araceae) is a genus of perennial herbaceous plants, all of which have medicinal value. The chloroplast (cp) genome data of Pinellia are scarce, and the phylogenetic relationship and gene evolution remain unclear.

Methods and results

We sequenced and annotated the Pinellia pedatisecta cp genome and combined it with previously published genomes for other Pinellia species. We used bioinformatics methods to analyse the genomic structure, repetitive sequences, interspecific variation, divergence hotspots, phylogenetic relationships, divergence time estimation and selective pressure of four Pinellia plastomes. Results showed that the cp genomes of Pinellia varied in length between 168,178 (P. pedatisecta MN046890) and 164,013 bp (P. ternata KR270823). A total of 68–111 SSR loci were identified as candidate molecular markers for further genetic diversity study. Eight mutational hotspot regions were determined, including psbI-trnG-UCC, psbM-rpoB, ndhJ-trnT-UGU, trnP-UGG-trnW-CCA, ndhF-trnN-GUU, ndhG-ndhE, ycf1-rps15 and trnR-ycf1. Gene selection pressure suggested that four genes were subjected to positive selection. Phylogenetic inferences based on the complete cp genomes revealed a sister relationship between Pinellia and Arisaema plants whose divergence was estimated to occur around 22.48 million years ago. All Pinellia species formed a monophyletic evolutionary clade in which P. peltata, rather than P. pedatisecta, earlier diverged, indicating that P. pedatisecta is not the basal taxon of Pinellia but P. peltata may be.

Conclusions

The cp genomes of Pinellia will provide valuable information for species classification, identification, molecular breeding and evolutionary exploration of the genus Pinellia.

Supplementary Information

The online version of this article (10.1007/s11033-022-07617-5) contains supplementary material, which is available to authorized users.

Complete chloroplast genome sequences of three aroideae species (Araceae): lights into selective pressure, marker development and phylogenetic relationships

Background

Colocasia gigantea, Caladium bicolor and Xanthosoma sagittifolium are three worldwide famous ornamental and/or vegetable plants in the Araceae family, these species in the subfamily Aroideae are phylogenetically perplexing due to shared interspecific morphological traits and variation.

Result

This study, for the first time ever, assembled and analyzed complete chloroplast genomes of C. gigantea, C. bicolor and X. sagittifolium with genome sizes of 165,906 bp, 153,149 bp and 165,169 bp in length, respectively. The genomes were composed of conserved quadripartite circular structures with a total of 131 annotated genes, including 8 rRNA, 37 tRNA and 86 protein-coding genes. A comparison within Aroideae showed seven protein-coding genes (accD, ndhF, ndhK, rbcL, rpoC1, rpoC2 and matK) linked to environmental adaptation. Phylogenetic analysis confirmed a close relationship of C. gigantea with C. esculenta and S. colocasiifolia, and the C. bicolor with X. sagittifolium. Furthermore, three DNA barcodes (atpH-atpI + psaC-ndhE, atpH-atpI + trnS-trnG, atpH-atpI + psaC-ndhE + trnS-trnG) harbored highly variable regions to distinguish species in Aroideae subfamily.

Conclusion

These results would be beneficial for species identification, phylogenetic relationship, genetic diversity, and potential of germplasm resources in Aroideae.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08400-3.

The Ribosomal DNA Loci of the Ancient Monocot Pistia stratiotes L. (Araceae) Contain Different Variants of the 35S and 5S Ribosomal RNA Gene Units

The freshwater plant water lettuce (Pistia stratiotes L.) grows in warm climatic zones and is used for phytoremediation and biomass production. P. stratiotes belongs to the Araceae, an ecologically and structurally diverse early monocot family, but the phylogenetic relationships among Araceae members are poorly understood. Ribosomal DNAs (rDNAs), including the 35S and 5S rDNA, encode the RNA components of ribosomes and are widely used in phylogenetic and evolutionary studies of various plant taxa. Here, we comprehensively characterized the chromosomal locations and molecular organization of 35S and 5S rDNA genes in water lettuce using karyological and molecular methods. Fluorescence in situ hybridization revealed a single location for the 35S and 5S rDNA loci, each on a different pair of the species' 28 chromosomes. Molecular cloning and nucleotide sequencing of 35S rDNA of P. stratiotes, the first representative Araceae sensu stricto in which such a study was performed, displayed typical structural characteristics. The full-length repeat showed high sequence conservation of the regions producing the 18S, 5.8S, and 25S rRNAs and divergence of the internal transcribed spacers ITS1 and ITS2 as well as the large intergenic spacer (IGS). Alignments of the deduced sequence of 18S rDNA with the sequences available for other Araceae and representatives of other clades were used for phylogenetic analysis. Examination of 11 IGS sequences revealed significant intra-genomic length variability due to variation in subrepeat number, with four types of units detected within the 35S rDNA locus of the P. stratiotes genome (estimated size 407 Mb/1C). Similarly, the 5S rDNA locus harbors gene units comprising a conserved 119-bp sequence encoding 5S rRNA and two types of non-transcribed spacer (NTS) sequences. Type I was classified into four subtypes, which apparently originated via progressive loss of subrepeats within the duplicated NTS region containing the 3' part of the 5S rRNA gene. The minor Type II NTS is shorter than Type I and differs in nucleotide composition. Some DNA clones containing two or three consecutive 5S rDNA repeats harbored 5S rDNA genes with different types of NTSs, confirming the mosaic composition of the 5S rDNA locus.

Mitogenome of Tolypocladium guangdongense

Tolypocladium guangdongense is a high-value edible fungus with various medicinal and food safety properties. However, its evolutionary and genetic information is still limited. Mitochondrial genomes are potential models for molecular evolution and phylogenetic studies. In this study, we sequenced the complete mitogenome of T. guangdongense, demonstrating circular sequence of 46,102 bp, containing 14 standard protein-coding genes (PCGs), 2 ribosomal RNA subunit genes, and 28 tRNA genes. Phylogenetic analysis based on mitochondrial genes indicated that T. guangdongense was clustered into the Tolypocladium genus with high support value, based on the core PCG dataset. In addition, rps3 is also a suitable marker in the phylogenetic analysis in Hypocreales. Gene rearrangement analysis indicated that the gene order of PCGs was highly consistent in Hypocreales, and tRNA rearrangement events occurred in most species of Hypocreales; however, the rearrangement rates were not taxonomically correlated. Divergence time estimation based on the old fossil record and previous reports revealed that T. guangdongense originated approximately in the middle Cenozoic (42 Mya, 95% highest posterior density interval: 43-116) with the Tolypocladium genus differentiation. Our results provided more mitogenomic information of T. guangdongense and shed new insights into evolution of the Tolypocladium genus. KEY POINTS: • The general and unique features of T. guangdongense mitogenome are firstly reported. • Phylogenetic analysis further verified the taxonomic status of T. guangdongense. • Divergence time estimation provides more evolutionary information of T. guangdongense.

Characterization of the complete chloroplast genome sequence of Pistia stratiotes (Araceae) and its phylogenetic implications

Pistia stratiotes is an invasive aquatic weed in South China. In this study, the first complete chloroplast (cp) genome of P. stratiotes was reported and phylogenetic analysis was conducted with Araceae species based on the cp genome sequences. The genome is a circular molecule of 164,551 bp in length with 36.00% average GC content and includes a large single-copy region (90,705 bp), a small single-copy region (21,886 bp), and two inverted repeat regions (25,980 bp). It contains a total of 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The maximum likelihood tree indicated that P. stratiotes is related to the genus of Alocasia. The cp genome will provide useful molecular data for further phylogenetic and evolutionary analysis of P. stratiotes.

Morphological phylogenetic analysis confirms the monophyly of Rhysophora Cresson (Diptera: Ephydridae) and provides a framework for a revision of the genus

With discovery of four new Neotropical species, the New World shore-fly genus Rhysophora Cresson, 1924 is revised, including a phylogenetic reassessment of some generic relationships within Discomyzini and of species within Rhysophora. The reconstructed phylogenetic relationships are based on 43 adult morphological characters and resulted in the following discoveries, mostly based on the well-supported cladogram: (1) the monophyly of Rhysophora is corroborated; (2) its sister group is Helaeomyia Cresson, not Guttipsilopa Wirth, as previously proposed; (3) three species groups within Rhysophora are recognized; and (4) greater species diversity is in South America, where there is also greater diversity in host plants. We hypothesise that the two Nearctic species, R. robusta and R. laffooni, resulted from two independent dispersal and speciation events when their water lettuce and pickerel weed hosts also dispersed there from the Neotropics. All of these flies are associated with aquatic plants of the families Pontederiaceae (Pontederia, Eichhornia) and Araceae (Pistia stratiotes), with the exception of R. griseola. All species are redescribed and an identification key, distribution maps and illustrations of male terminalia are provided to assist identification of these species.

Out of Africa: Miocene dispersal, vicariance, and extinction within Hyacinthaceae subfamily Urgineoideae

Disjunct distribution patterns in plant lineages are usually explained according to three hypotheses: vicariance, geodispersal, and long-distance dispersal. The role of these hypotheses is tested in Urgineoideae (Hyacinthaceae), a subfamily disjunctly distributed in Africa, Madagascar, India, and the Mediterranean region. The potential ancestral range, dispersal routes, and factors responsible for the current distribution in Urgineoideae are investigated using divergence time estimations. Urgineoideae originated in Southern Africa approximately 48.9 Mya. Two independent dispersal events in the Western Mediterranean region possibly occurred during Early Oligocene and Miocene (29.9-8.5 Mya) via Eastern and Northwestern Africa. A dispersal from Northwestern Africa to India could have occurred between 16.3 and 7.6 Mya. Vicariance and extinction events occurred approximately 21.6 Mya. Colonization of Madagascar occurred between 30.6 and 16.6 Mya, after a single transoceanic dispersal event from Southern Africa. The current disjunct distributions of Urgineoideae are not satisfactorily explained by Gondwana fragmentation or dispersal via boreotropical forests, due to the younger divergence time estimates. The flattened winged seeds of Urgineoideae could have played an important role in long-distance dispersal by strong winds and big storms, whereas geodispersal could have also occurred from Southern Africa to Asia and the Mediterranean region via the so-called arid and high-altitude corridors.

Reconstructing the origin and elaboration of insect-trapping inflorescences in the Araceae

PREMISE OF THE STUDY

Floral traps are among the most sophisticated devices that have evolved in angiosperms in the context of pollination, but the evolution of trap pollination has not yet been studied in a phylogenetic context. We aim to determine the evolutionary history of morphological traits that facilitate trap pollination and to elucidate the impact of pollinators on the evolution of inflorescence traps in the family Araceae. •

METHODS

Inflorescence morphology was investigated to determine the presence of trapping devices and to classify functional types of traps. We inferred phylogenetic relationships in the family using maximum likelihood and Bayesian methods. Character evolution of trapping devices, trap types, and pollinator types was then assessed with maximum parsimony and Bayesian methods. We also tested for an association of trap pollination with specific pollinator types. •

KEY RESULTS

Inflorescence traps have evolved independently at least 10 times within the Araceae. Trapping devices were found in 27 genera. On the basis of different combinations of trapping devices, six functional types of traps were identified. Trap pollination in Araceae is correlated with pollination by flies. •

CONCLUSIONS

Trap pollination in the Araceae is more common than was previously thought. Preadaptations such as papillate cells or elongated sterile flowers facilitated the evolution of inflorescence traps. In some clades, imperfect traps served as a precursor for the evolution of more elaborate traps. Traps that evolved in association with fly pollination were most probably derived from mutualistic ancestors, offering a brood-site to their pollinators.

Global history of the ancient monocot family Araceae inferred with models accounting for past continental positions and previous ranges based on fossils

The family Araceae (3790 species, 117 genera) has one of the oldest fossil records among angiosperms. Ecologically, members of this family range from free-floating aquatics (Pistia and Lemna) to tropical epiphytes. Here, we infer some of the macroevolutionary processes that have led to the worldwide range of this family and test how the inclusion of fossil (formerly occupied) geographical ranges affects biogeographical reconstructions. Using a complete genus-level phylogeny from plastid sequences and outgroups representing the 13 other Alismatales families, we estimate divergence times by applying different clock models and reconstruct range shifts under different models of past continental connectivity, with or without the incorporation of fossil locations. Araceae began to diversify in the Early Cretaceous (when the breakup of Pangea was in its final stages), and all eight subfamilies existed before the K/T boundary. Early lineages persist in Laurasia, with several relatively recent entries into Africa, South America, South-East Asia and Australia. Water-associated habitats appear to be ancestral in the family, and DNA substitution rates are especially high in free-floating Araceae. Past distributions inferred when fossils are included differ in nontrivial ways from those without fossils. Our complete genus-level time-scale for the Araceae may prove to be useful for ecological and physiological studies.

Is Remusatia (araceae) monophyletic? Evidence from three plastid regions

The genus Remusatia (Araceae) includes four species distributed in the tropical and subtropical Old World. The phylogeny of Remusatia was constructed using parsimony and Bayesian analyses of sequence data from three plastid regions (the rbcL gene, the trnL-trnF intergenic spacer, and the rps16 intron). Phylogenetic analyses of the concatenated plastid data suggested that the monophyly of Remusatia was not supported because R. hookeriana did not form a clade with the other three species R. vivipara, R. yunnanensis, and R. pumila. Nevertheless, the topology of the analysis constraining Remusatia to monophyly was congruent with the topology of the unconstrained analysis. The results confirmed the inclusion of the previously separate genus Gonatanthus within Remusatia and disagreed with the current infrageneric classification of the genus.

Giant taro and its relatives: a phylogeny of the large genus Alocasia (Araceae) sheds light on Miocene floristic exchange in the Malesian region

Alocasia comprises over 113 species of rainforest understorey plants in Southeast Asia, the Malesian region, and Australia. Several species, including giant taro, Alocasia macrorrhizos, and Chinese taro, Alocasia cucullata, are important food plants or ornamentals. We investigated the biogeography of this genus using plastid and nuclear DNA sequences (5200 nucleotides) from 78 accessions representing 71 species, plus 25 species representing 16 genera of the Pistia clade to which Alocasia belongs. Divergence times were inferred under strict and relaxed clock models, and ancestral areas with Bayesian and maximum likelihood approaches. Alocasia is monophyletic and sister to Colocasiagigantea from the SE Asian mainland, whereas the type species of Colocasia groups with Steudnera and Remusatia, requiring taxonomic realignments. Nuclear and plastid trees show topological conflict, with the nuclear tree reflecting morphological similarities, the plastid tree species' geographic proximity, suggesting chloroplast capture. The ancestor of Alocasia diverged from its mainland sister group c. 24 million years ago, and Borneo then played a central role in the expansion of Alocasia: 11-13 of 18-19 inferred dispersal events originated on Borneo. The Philippines were reached from Borneo 4-5 times in the Late Miocene and Early Pliocene, and the Asian mainland 6-7 times in the Pliocene. Domesticated giant taro originated on the Philippines, Chinese taro on the Asian mainland.

Relationships within the Araceae: comparison of morphological patterns with molecular phylogenies

PREMISE OF THE STUDY

The first family-wide molecular phylogeny of the Araceae, a family of about 3800 published species in 120 genera, became available in 1995, followed by a cladistic analysis of morpho-anatomical data in 1997. The most recent and comprehensive family-wide molecular phylogeny was published in 2008 and included species from 102 genera. We reanalyzed the molecular data with a more complete genus sampling and compared the resulting phylogeny with morphological and anatomical data, with a view to contributing to a new formal classification of the Araceae.

METHODS

We analyzed 113 aroid genera and 4494 aligned nucleotides that resulted from adding 11 genera to the 2008 molecular matrix. We also analyzed 81 morphological characters in the context of the molecular phylogeny, using an extended version of the 1997 morpho-anatomical data set.

KEY RESULTS

The resulting maximum-likelihood phylogeny is well resolved and supported, and most of the 44 larger clades also have morphological or anatomical synapomorphies as well as ecological or geographic cohesion. Of the 44 clades, 16 are here newly circumscribed and informally named. However, some relationships remain poorly supported within the Aroideae subfamily. The most problematic placement is Calla within Aroideae, which conflicts with the distribution of morphological, anatomical, and palynological character states.

CONCLUSIONS

The comparison of the molecular analysis with morphological and anatomical data presented here represents an important basis for a new formal classification for the Araceae and for the understanding of the evolution of this ancient family, a monocot group known in the fossil record from the early Cretaceous.

Weevils associated with Pistia stratiotes L. (Araceae) in the Central Amazon Region, with new records for Argentinorhynchus Brèthes (Coleoptera, Curculionidae)

Data on the occurrence of ten weevils species associated with Pistia stratiotes L. (Araceae), from Ilha de Marchantaria, Manaus (Amazonas, Brazil) are presented for the first time. During the period from March to August 2005, 809 weevils specimens were sampled on P. stratiotes, distributed across nine species allocated in five genera of Stenopelmini, in addition to one unidentified species in the Cryptorhynchinae. Among the Stenopelmini, Argentinorhynchus breyeri Brèthes, 1910 (N = 665) was the dominant species, with the highest abundance in July (N = 189) and the lowest in August (N = 11), while Ochetina uniformis Pascoe, 1881 (N = 63), Neochetina bruchi Hustache, 1926 (N = 45), Neohydronomus pulchellus Hustache, 1926 (N = 15), Neohydronomus affinis Hustache, 1926 (N = 10), A. squamosus (Hustache, 1926) (N = 5), Neochetina eichhorniae Warner, 1970 (N = 4), A. minimus O'Brien & Wibmer, 1989b (N = 1), and Tanysphiroideus sp. (N = 1) had lower abundances. In addition, the co-occurrences of A. breyeri, A. minimus, and A. squamosus on P. stratiotes were recorded for Brazil and the first records of A. minimus and A. squamosus were observed for the State of Amazonas.

Phylogenetic origin of Phyllolobium with a further implication for diversification of Astragalus in China

Astragalus is a species-rich genus occurring in the western arid habitats in China and its diversification and infrageneric relationships in this region remain unclear. In the present study, based on molecular data, we aim to (i) test whether Phyllolobium (previously treated as a subgenus Pogonophace in Astragalus) should be warranted; and (ii) date the origin of Phyllolobium and probable diversification of Astragalus sensu stricto (s.s.). We sequenced five species from Phyllolobium first and collected all related sequences from the genus, Astragalus s.s and their close relatives (Oxytropis and Caragana etc.). Our phylogenetic analyses suggested that all species of Phyllolobium comprise a monophyletic sister-group to genera of the subtribe Coluteinae. Molecular dating suggested that Phyllolobium and Astragalus s.s. originated around 8 and 10 million years ago. These two estimates are highly consistent with the intense uplifts of the Qinghai-Tibetan Plateau inferred from geological evidence. In addition, one section of Pogonophace (Sect. Robusti) was estimated to originate 2.5 million years ago and this section with a tendency for dry habitats seems to be evidence of Asian intensified aridity resulting from the intense uplift of the Qinghai-Tibetan Plateau.

Island biogeography of Galápagos lava lizards (Tropiduridae: Microlophus): species diversity and colonization of the archipelago

The "lava lizards" (Microlophus) are distributed throughout the Galápagos Archipelago, and consist of radiations derived from two independent colonizations. The "Eastern Radiation" includes M. bivittatus and M. habeli endemic to San Cristobal and Marchena Islands. The "Western Radiation" includes five to seven historically recognized species distributed across almost the entire Archipelago. We combine dense geographic sampling and multilocus sequence data to estimate a phylogenetic hypothesis for the Western Radiation, to delimit species boundaries in this radiation, and to estimate a time frame for colonization events. Our phylogenetic hypothesis rejects two earlier topologies for the Western Radiation and paraphyly of M. albemarlensis, while providing strong support for single colonizations on each island. The colonization history implied by our phylogeny is consistent with general expectations of an east-to-west route predicted by the putative age of island groups, and prevailing ocean currents in the Archipelago. Additionally, combined evidence suggests that M. indefatigabilis from Santa Fe should be recognized as a full species. Finally, molecular divergence estimates suggest that the two colonization events likely occurred on the oldest existing islands, and the Western Radiation represents a recent radiation that, in most cases, has produced species that are considerably younger than the islands they inhabit.

Dating dispersal and radiation in the gymnosperm Gnetum (Gnetales)--clock calibration when outgroup relationships are uncertain

Most implementations of molecular clocks require resolved topologies. However, one of the Bayesian relaxed clock approaches accepts input topologies that include polytomies. We explored the effects of resolved and polytomous input topologies in a rate-heterogeneous sequence data set for Gnetum, a member of the seed plant lineage Gnetales. Gnetum has 10 species in South America, 1 in tropical West Africa, and 20 to 25 in tropical Asia, and explanations for the ages of these disjunctions involve long-distance dispersal and/or the breakup of Gondwana. To resolve relationships within Gnetum, we sequenced most of its species for six loci from the chloroplast (rbcL, matK, and the trnT-trnF region), the nucleus (rITS/5.8S and the LEAFY gene second intron), and the mitochondrion (nad1 gene second intron). Because Gnetum has no fossil record, we relied on fossils from other Gnetales and from the seed plant lineages conifers, Ginkgo, cycads, and angiosperms to constrain a molecular clock and obtain absolute times for within-Gnetum divergence events. Relationships among Gnetales and the other seed plant lineages are still unresolved, and we therefore used differently resolved topologies, including one that contained a basal polytomy among gymnosperms. For a small set of Gnetales exemplars (n = 13) in which rbcL and matK satisfied the clock assumption, we also obtained time estimates from a strict clock, calibrated with one outgroup fossil. The changing hierarchical relationships among seed plants (and accordingly changing placements of distant fossils) resulted in small changes of within-Gnetum estimates because topologically closest constraints overrode more distant constraints. Regardless of the seed plant topology assumed, relaxed clock estimates suggest that the extant clades of Gnetum began diverging from each other during the Upper Oligocene. Strict clock estimates imply a mid-Miocene divergence. These estimates, together with the phylogeny for Gnetum from the six combined data sets, imply that the single African species of Gnetum is not a remnant of a once Gondwanan distribution. Miocene and Pliocene range expansions are inferred for the Asian subclades of Gnetum, which stem from an ancestor that arrived from Africa. These findings fit with seed dispersal by water in several species of Gnetum, morphological similarities among apparently young species, and incomplete concerted evolution in the nuclear ITS region.

Relaxed molecular clocks for dating historical plant dispersal events

Age estimation from molecular sequences has emerged as a powerful tool for inferring when a plant lineage arrived in a particular area. Knowing the tenure of lineages within a region is key to understanding the evolution of traits, the evolution of biotic interactions, and the evolution of floras. New analytical methods model change in substitution rates along individual branches of a phylogenetic tree by combining molecular data with time constraints, usually from fossils. These "relaxed clock" approaches can be applied to several gene regions that need not all have the same substitution rates, and they can also incorporate multiple simultaneous fossil calibrations. Since 1995, at least 100 plant biogeographic studies have used molecular-clock dating, and about a fifth has used relaxed clocks. Many of these report evidence of long-distance dispersal. Meta-analyses of studies from the same geographic region can identify directional biases because of prevailing wind or water currents and the relative position and size of landmasses.

When Earth started blooming: insights from the fossil record

Recent palaeobotanical studies have greatly increased the quantity and quality of information available about the structure and relationships of Cretaceous angiosperms. Discoveries of extremely well preserved Cretaceous flowers have been especially informative and, combined with results from phylogenetic analyses of extant angiosperms (based mainly on molecular sequence data), have greatly clarified important aspects of early angiosperm diversification. Nevertheless, many questions still persist. The phylogenetic origin of the group itself remains as enigmatic as ever and, in some cases, newly introduced techniques from molecular biology have given confusing results. In particular, relationships between the five groups of extant seed plants remain uncertain, and it has sometimes proved difficult to reconcile estimates of the time of divergence between extant lineages made using a 'molecular clock' with the fossil record. One result, however, is becoming increasingly clear: a great deal of angiosperm diversity is extinct. Some groups of angiosperms were evidently more diverse in the past than they are today. In other cases, fossils defy assignment to extant groups at the family level or below. This raises the possibility that evolutionary conclusions based solely upon extant taxa that are merely relics of groups that were once much more diverse might be misled by the effects of extinction. It also introduces the possibility that some early enigmatic fossils might represent lineages that diverged from the main line of angiosperm evolution below the most recent common ancestor of all extant taxa. These, and other questions, are among those that need to be addressed by future palaeobotanical research.

Araceae from the Early Cretaceous of Portugal: evidence on the emergence of monocotyledons

A new species (Mayoa portugallica genus novum species novum) of highly characteristic inaperturate, striate fossil pollen is described from the Early Cretaceous (Barremian-Aptian) of Torres Vedras in the Western Portuguese Basin. Based on comparison with extant taxa, Mayoa is assigned to the tribe Spathiphylleae (subfamily Monsteroideae) of the extant monocotyledonous family Araceae. Recognition of Araceae in the Early Cretaceous is consistent with the position of this family and other Alismatales as the sister group to all other monocots except Acorus. The early occurrence is also consistent with the position of Spathiphylleae with respect to the bulk of aroid diversity. Mayoa occurs in the earliest fossil floras (from circa 110 to 120 million years ago) that contain angiosperm flowers, carpels, and stamens. The new fossil provides unequivocal evidence of monocots in early angiosperm assemblages that also include a variety of key "magnoliid" lineages (e.g., Chloranthaceae) but only a limited diversity of eudicots.