Was the ANITA rooting of the angiosperm phylogeny affected by long-branch attraction? Amborella, Nymphaeales, Illiciales, Trimeniaceae, and Austrobaileya

Five groups of basal angiosperms, Amborella, Nymphaeales, Illiciales, Trimeniaceae, and Austrobaileya (ANITA), were identified in several recent studies as representing a series of the earliest-diverging lineages of the angiosperm phylogeny. All of these studies except one employed a multigene analysis approach and used gymnosperms as the outgroup to determine the ingroup topology. The high level of divergence between gymnosperms and angiosperms, however, has long been implicated in the difficulty of reconstructing relationships at the base of angiosperm phylogeny using DNA sequences, for fear of long-branch attraction (LBA). In this study, we replaced the gymnosperm sequences from the five-gene matrix (mitochondrial atp1 and matR, plastid atpB and rbcL, and nuclear 18S rDNA) used in our earlier study with four categories of divergent sequences--random sequences with equal base frequencies or equally AT- and GC-rich contents, homopolymers and heteropolymers, misaligned gymnosperm sequences, and aligned lycopod and bryophyte sequences--to evaluate whether the gymnosperms were an appropriate outgroup to angiosperms in our earlier study that identified the ANITA rooting. All 24 analyses performed rooted the angiosperm phylogeny at either Acorus or Alisma (or Alisma-Triglochin-Potamogeton in one case due to use of a slightly different alignment) and placed the monocots as a basal grade, producing genuine LBA results. These analyses demonstrate that the identification of ANITA as the basalmost extant angiosperms was based on historical signals preserved in the gymnosperm sequences and that the gymnosperms were an appropriate outgroup with which to root the angiosperm phylogeny in the multigene sequence analysis. This strategy of evaluating the appropriateness of an outgroup using artificial sequences and a series of outgroups with increments of divergence levels can be applied to investigations of phylogenetic patterns at the bases of other major clades, such as land plants, animals, and eukaryotes.     

POLLEN WALL ULTRASTRUCTURE OF SELECTED DISPERSED MONOSULCATE POLLEN FROM THE CENOMANIAN,DAKOTA FORMATION,OF CENTRAL USA

Seven dispersed monosulcate pollen taxa from the Dakota Formation of Minnesota, Nebraska, and Kansas were examined ultrastructurally. Rugubivesiculites rugosus has gymnosperm affinities based on its anasulcate aperture and the presence and nature of the formation of sacci. Stellatopollis sp. has exine sculpturing restricted to taxa with angiosperm affinities and is monosulcate. The affinities of the other five monosulcate taxa are uncertain and the exines are tectategranular. The sulcus in many of the remaining five taxa are flanked by small flange-like sacci. These five taxa have features found in gymnosperms and also some features of primitive extant angiosperms. The combination of characters of the pollen types presented here does not entirely agree with our current concept of primitive pollen characters as understood from extant ranalean angiosperms.     

Leaf energy balance modelling as a tool to infer habitat preference in the early angiosperms

Despite more than a century of research, some key aspects of habitat preference and ecology of the earliest angiosperms remain poorly constrained. Proposed growth ecology has varied from opportunistic weedy species growing in full sun to slow-growing species limited to the shaded understorey of gymnosperm forests. Evidence suggests that the earliest angiosperms possessed low transpiration rates: gas exchange rates for extant basal angiosperms are low, as are the reconstructed gas exchange rates for the oldest known angiosperm leaf fossils. Leaves with low transpirational capacity are vulnerable to overheating in full sun, favouring the hypothesis that early angiosperms were limited to the shaded understorey. Here, modelled leaf temperatures are used to examine the thermal tolerance of some of the earliest angiosperms. Our results indicate that small leaf size could have mitigated the low transpirational cooling capacity of many early angiosperms, enabling many species to survive in full sun. We propose that during the earliest phases of the angiosperm leaf record, angiosperms may not have been limited to the understorey, and that some species were able to compete with ferns and gymnosperms in both shaded and sunny habitats, especially in the absence of competition from more rapidly growing and transpiring advanced lineages of angiosperms.     

Polyploidy and angiosperm diversification

Polyploidy has long been recognized as a major force in angiosperm evolution. Recent genomic investigations not only indicate that polyploidy is ubiquitous among angiosperms, but also suggest several ancient genome-doubling events. These include ancient whole genome duplication (WGD) events in basal angiosperm lineages, as well as a proposed paleohexaploid event that may have occurred close to the eudicot divergence. However, there is currently no evidence for WGD in Amborella, the putative sister species to other extant angiosperms. The question is no longer "What proportion of angiosperms are polyploid?", but "How many episodes of polyploidy characterize any given lineage?" New algorithms provide promise that ancestral genomes can be reconstructed for deep divergences (e.g., it may be possible to reconstruct the ancestral eudicot or even the ancestral angiosperm genome). Comparisons of diversification rates suggest that genome doubling may have led to a dramatic increase in species richness in several angiosperm lineages, including Poaceae, Solanaceae, Fabaceae, and Brassicaceae. However, additional genomic studies are needed to pinpoint the exact phylogenetic placement of the ancient polyploidy events within these lineages and to determine when novel genes resulting from polyploidy have enabled adaptive radiations.     

Morphological and molecular phylogenetic context of the angiosperms: contrasting the 'top-down' and 'bottom-up' approaches used to infer the likely characteristics of the first flowers

Recent attempts to address the long-debated 'origin' of the angiosperms depend on a phylogenetic framework derived from a matrix of taxa versus characters; most assume that empirical rigour is proportional to the size of the matrix. Sequence-based genotypic approaches increase the number of characters (nucleotides and indels) in the matrix but are confined to the highly restricted spectrum of extant species, whereas morphology-based approaches increase the number of phylogenetically informative taxa (including fossils) at the expense of accessing only a restricted spectrum of phenotypic characters. The two approaches are currently delivering strongly contrasting hypotheses of relationship. Most molecular studies indicate that all extant gymnosperms form a natural group, suggesting surprisingly early divergence of the lineage that led to angiosperms, whereas morphology-only phylogenies indicate that a succession of (mostly extinct) gymnosperms preceded a later angiosperm origin. Causes of this conflict include: (i) the vast phenotypic and genotypic lacuna, largely reflecting pre-Cenozoic extinctions, that separates early-divergent living angiosperms from their closest relatives among the living gymnosperms; (ii) profound uncertainty regarding which (a) extant and (b) extinct angiosperms are most closely related to gymnosperms; and (iii) profound uncertainty regarding which (a) extant and (b) extinct gymnosperms are most closely related to angiosperms, and thus best serve as 'outgroups' dictating the perceived evolutionary polarity of character transitions among the early-divergent angiosperms. These factors still permit a remarkable range of contrasting, yet credible, hypotheses regarding the order of acquisition of the many phenotypic characters, reproductive and vegetative, that distinguish 'classic' angiospermy from 'classic' gymnospermy. The flower remains ill-defined and its mode (or modes) of origin remains hotly disputed; some definitions and hypotheses of evolutionary relationships preclude a role for the flower in delimiting the angiosperms. We advocate maintenance of parallel, reciprocally illuminating programmes of morphological and molecular phylogeny reconstruction, respectively supported by homology testing through additional taxa (especially fossils) and evolutionary-developmental genetic studies that explore genes potentially responsible for major phenotypic transitions.     

Cenozoic extinctions account for the low diversity of extant gymnosperms compared with angiosperms

We test the widely held notion that living gymnosperms are 'ancient' and 'living fossils' by comparing them with their sister group, the angiosperms. This perception derives partly from the lack of gross morphological differences between some Mesozoic gymnosperm fossils and their living relatives (e.g. Ginkgo, cycads and dawn redwood), suggesting that the rate of evolution of gymnosperms has been slow. We estimated the ages and diversification rates of gymnosperm lineages using Bayesian relaxed molecular clock dating calibrated with 21 fossils, based on the phylogenetic analysis of alignments of matK chloroplast DNA (cpDNA) and 26S nuclear ribosomal DNA (nrDNA) sequences, and compared these with published estimates for angiosperms. Gymnosperm crown groups of Cenozoic age are significantly younger than their angiosperm counterparts (median age: 32 Ma vs 50 Ma) and have long unbranched stems, indicating major extinctions in the Cenozoic, in contrast with angiosperms. Surviving gymnosperm genera have diversified more slowly than angiosperms during the Neogene as a result of their higher extinction rate. Compared with angiosperms, living gymnosperm groups are not ancient. The fossil record also indicates that gymnosperms suffered major extinctions when climate changed in the Oligocene and Miocene. Extant gymnosperm groups occupy diverse habitats and some probably survived after making adaptive shifts.     

Evolution of Reproductive Organs in Land Plants

LEAFY gene is the positive regulator of the MADS-box genes in flower primordia. The number of MADS-box genes presumably increased by gene duplications before the divergence of ferns and seed plants. Most MADS-box genes in ferns are expressed similarly in both vegetative and reproductive organs, while in gymnosperms, some MADS-box genes are specifically expressed in reproductive organs. This suggests that (1) the increase in the number of MADS-box genes and (2) the subsequent recruitment of some MADS-box genes as homeotic selector genes were important for the evolution of complex reproductive organs. The phylogenetic tree including both angiosperm and gymnosperm MADS-box genes indicates the loss of the A-function genes in the gymnosperm lineage, which is presumably related to the absence of perianths in extant gymnosperms. Comparison of expression patterns of orthologous MADS-box genes in angiosperms, Gnetales, and conifers supports the sister relationship of Gnetales and conifers over that of Gnetales and angiosperms predicted by phylogenetic trees based on amino acid and nucleotide sequences. Received 30 July 1999/ Accepted in revised form 9 September 1999     

Molecular phylogenies in angiosperm evolution

We have cloned and sequenced cDNAs for the glyceraldehyde-3-phosphate dehydrogenase of glycolysis, gapC, from a bryophyte, a gymnosperm, and three angiosperms. Phylogenetic analyses are presented for these data in the context of other gapC sequences and in parallel with published nucleotide sequences for the chloroplast encoded gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL). Relative-rate tests were performed for these genes in order to assess variation in substitution rate for coding regions, along individual plant lineages studied. The results of both gene analyses suggest that the deepest dichotomy within the angiosperms separates not magnoliids from remaining angiosperms, but monocotyledons from dicotyledons, in sharp contrast to prediction from the Euanthial theory for angiosperm evolution. Furthermore, these chloroplast and nuclear sequence data taken together suggest that the separation of monocotyledonous and dicotyledonous lineages took place in late Carboniferous times [approximately 300 Myr before the present (Mybp)]. This date would exceed but be compatible with the late-Triassic (approximately 220 Mybp) occurrence of fossil reproductive structures of the primitive angiosperm Sanmiguelia lewisii.      

裸子植物5S rRNA基因序列变异及二级结构特征

在高等植物中,5SrRNA基因一级结构是高度保守的,二级结构也相当一致。通过比较18种裸子植物5SrRNA基因序列和二级结构变异,发现55％的核苷酸位点是可变的,这种变异有68％发生在干区（双链区）,其中一些变异,如双链的互补性核苷酸替代,GU配对等能够维系5SrRNA二级结构的稳定性。环区相对保守,这与5SrRNA三级结构折叠或在转录翻译过程中蛋白质、RNA的结合相关。另外,首次报道了松属环E区核苷酸的变异性,这可能与其他区域的变异一样,是假基因造成的结果。5SrRNA基因信息可反映大分类群的系统进化关系,但由于基因长度短,信息量小,其在近缘种系统分类的应用受到限制。     

The complete nucleotide sequence of the small-subunit ribosomal RNA coding region for the cycadZamia pumila: Phylogenetic implications

Summary The DNA sequence of the small-subunit ribosomal RNA coding region for the cycadZamia pumila L. was determined. TheZamia smallsubunit rRNA was found to be 1813 nucleotides in length and approximately 92% identical to published angiosperm small-subunit rRNA sequences. Conserved regions interspersed with variable regions are observed corresponding to those found in other eukaryotic small-subunit sequences. Using representatives from protist, fungal, plant, and animal groups, a distance matrix was constructed of average nucleotide substitution rates for pairs of organisms. Phylogenetic trees were inferred from similarities between sequences. The sequence ofZamia represents the earliest divergence from the higher plant lineage reported to date for small-subunit rRNA data. Inferred phylogenies also support a monophyletic origin for the angiosperms consistent with studies citing phenotypic characters.     

The evolution of embryo size in angiosperms and other seed plants: implications for the evolution of seed dormancy

Abstract.— Seed dormancy plays an important role in germination ecology and seed plant evolution. Morphological seed dormancy is caused by an underdeveloped embryo that must mature prior to germination. It has been suggested that the presence of an underdeveloped embryo is plesiomorphic among seed plants and that parallel directional change in embryo morphology has occurred separately in gymnosperms and in angiosperms. We test these hypotheses using original data on embryo morphology of key basal taxa, a published dataset, and the generalized least squares (GLS) method of ancestral character state reconstruction. Reconstructions for embryo to seed ratio (E:S) using family means for 179 families showed that E:S has increased between the ancestral angiosperm and almost all extant angiosperm taxa. Species in the rosid clade have particularly large embryos relative to the angiosperm ancestor. Results for the gymnosperms show a similar but smaller increase. There were no statistically significant differences in E:S between basal taxa and any derived group due to extremely large standard errors produced by GLS models. However, differences between reconstructed values for the angiosperm ancestor and more highly nested nodes are large and these results are robust to topological and branch-length manipulations. Our analysis supports the idea that the underdeveloped embryo is primitive among seed plants and that there has been a directional change in E:S within both angiosperms and gymnosperms. Our analysis suggests that dormancy enforced by an underdeveloped embryo is plesiomorphic among angiosperms and that nondormancy and other dormancy types probably evolved within the angiosperms. The shift in E:S was likely a heterochronic change, and has important implications for the life history of seed plants.     

Patterns of gene duplication and functional evolution during the diversification of the AGAMOUS subfamily of MADS box genes in angiosperms

Members of the AGAMOUS (AG) subfamily of MIKC-type MADS-box genes appear to control the development of reproductive organs in both gymnosperms and angiosperms. To understand the evolution of this subfamily in the flowering plants, we have identified 26 new AG-like genes from 15 diverse angiosperm species. Phylogenetic analyses of these genes within a large data set of AG-like sequences show that ancient gene duplications were critical in shaping the evolution of the subfamily. Before the radiation of extant angiosperms, one event produced the ovule-specific D lineage and the well-characterized C lineage, whose members typically promote stamen and carpel identity as well as floral meristem determinacy. Subsequent duplications in the C lineage resulted in independent instances of paralog subfunctionalization and maintained functional redundancy. Most notably, the functional homologs AG from Arabidopsis and PLENA (PLE) from Antirrhinum are shown to be representatives of separate paralogous lineages rather than simple genetic orthologs. The multiple subfunctionalization events that have occurred in this subfamily highlight the potential for gene duplication to lead to dissociation among genetic modules, thereby allowing an increase in morphological diversity.     

The branching pattern of major groups of land plants inferred from parsimony analysis of ribosomal RNA sequences

The parsimony and bootstrap branching pattern of major groups of land plants derived from relevant 5S rRNA sequence trees have been discussed in the light of paleobotanical and morphological evidences. Although 5S rRNA sequence information is not useful for dileneating angiosperm relationships, it does capture the earlier phase of land plant evolution. The consensus branching pattern indicates an ancient split of bryophytes and vascular plants from the charophycean algal stem. Among the bryophytes,Marchantia andLophocolea appear to be phylogenetically close and together withPlagiomnium form a monophyletic group.Lycopodium andPsilotum arose early in vascular land plant evolution, independent of fem-sphenopsid branch. Gymnosperms are polyphyletic; conifers, Gnetales and cycads emerge in that order with ginkgo joiningCycas. Among the conifers,Metasequoia,Juniperus andTaxus emerge as a branch independent ofPinus which joins Gnetales. The phylogeny derived from the available ss-RNA sequences shows that angiosperms are monophyletic with monocots and dicots diverging from a common stem. The nucleotide replacements during angiosperm descent from the gymnosperm ancestor which presumably arose around 370 my ago indicates that monocots and dicots diverged around 180 my ago, which is compatible with the reported divergence estimate of around 200 my ago deduced from chloroplast DNA sequences. Since deceased.     

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.     

The origin of angiosperms

The claim of monophyletic origin of angiosperms arose from the confusion of phylogenetic and taxonomic concepts. Unpreconceived studies of extant angiosperms point to more than one archetype. Several lines of angiosperms have simultaneously entered the fossil record; the monocotyledons, proto-Hamamelidales, proto-Laurales and “proteophylls” (possibly ancestral to the Rosidae) are recognized among them. Three groups of Mesozoic seed plants — the Caytoniales, Czekanowskiales and Dirhopalostachyaceae — are distinguished as major sources of angiosperm characters (proangiosperms). Other Mesozoic lineages probably also contributed to the angiosperm character pool. Angiospermization is related to Mammalization and other processes involved in development of the Cenozoic lithosphere and biosphere.     

Mesozoic plants and the problem of angiosperm ancestry

Krassilov, V.: Mesozoic plants and the problem of angiosperm ancestry.
Trends leading to the foliar and floral structures of angiosperms may be deduced by comparison with Mesozoic gymnosperms. The Debeya-Fontainea group of Cretaceous angiosperms closely resembles the Early Mesozoic Scoresbya group of pteridosperms with regard to leaf characters. The bivalved capsules of Jurassic Leptostrobus , with stigmatic bands, are regarded as the forerunners of certain types of angiosperm carpels. The angiospermous characters arose in several lineages of gymnosperms and were probably accumulated by non-sexual transfer of genetic material. The earliest angiosperm mega- and microfossils have been reported from the Middle and Upper Jurassic of the northern hemisphere. Most of these angiosperms were confined to chaparral-like communities dominated by shrubby conifers and cycadophytes. The rise of angiosperms was promoted by the climatic changes and the simultaneous rise of mammals.     

Morphological and molecular data on the origin of angiosperms: on a way to a synthesis

Molecular phylogenetic data have drastically changed the views on the phylogeny of higher plants. All the extant gymnosperms were asserted as a monophyletic group opposed to the highly isolated angiosperms. The 'Anthophyte Theory' was thus rejected. The identification and analysis of gymnosperm orthologues of genes regulating flower development in angiosperms resulted in the formulation of the 'Mostly Male Theory' of the evolutionary origin of flower; this theory does not contradict the concept of monophyly of all the extant gymnosperms. The Mostly Male Theory assumes that the origin of angiosperms was caused by a loss of the Needle family gene that effected ovuliferous (female) organs and the translocation of the ovules onto the adaxial side of some of the (male) leafy microsporangiophores. Having acquired ovules, the former microsporangiophores started evolving into the carpels. The prerequisite bisexual design of the ancestral fructification thus becomes unnecessary. Indeed, this assumption suggests the deriving of Angiosperms from any gymnosperm plant with leafy microsporangiophores. The problem of carpel origin has subsequently changed to some degree into the problem of the origin of the bitegmic anatropous ovule presumably inherent in ancestral Angiosperms. The Mostly Male Theory consideredeither Corystospermataceae (= Umkomasiaceae) or Caytoniaceae to be the forerunners of such an ovule. Yet the capsules of Corystospermataceae distinctly differ from angiosperm ovules in the locations of their adaxial/abaxial sides, while Caytoniaceae had no leafy microsporangiophores. This inconsistency suggests that functions of the Needle family regulatory genes in Gymnosperms should be much better understood to appraise properly both the possibilities and the consequences of their hypothetical loss by the emerging angiosperms. Moreover, the extant gymnosperm groups are actually held as monophyletic and contrasted to Angiosperms on the basis of analysing the unrepresentative scant remnants of these, mostly extinct, taxa. Therefore, traditional botanical and paleobotanical data should not be rejected. In any case, Meyen's idea angiosperms origin from Bennettitales is worth being retained as a hypothesis to be tested with new results of both paleobotany and molecular biology.     

Phylogenetic tree of vascular plants reveals the origins of aquatic angiosperms

Although aquatic plants are discussed as a unified biological group, they are phylogenetically well dispersed across the angiosperms. In this study, we annotated the aquatic taxa on the tree of vascular plants, and extracted the topology of these aquatic lineages to construct the tree of aquatic angiosperms. We also reconstructed the ancestral areas of aquatic families. We found that aquatic angiosperms could be divided into two different categories: the four aquatic orders and the aquatic taxa in terrestrial orders. Aquatic lineages evolved early in the radiation of angiosperms, both in the orders Nymphaeales and Ceratophyllales and among basal monocots (Acorales and Alismatales). These aquatic orders do not have any extant terrestrial relatives. They originated from aquatic habitats during the Early Cretaceous. Asia would have been one of the centers for early diversification of aquatic angiosperms. The aquatic families within terrestrial orders may originate from other areas besides Asia, such as America or Australia. The lineages leading to extant angiosperms diversified early in underexploited freshwater habitats. The four extant aquatic orders were relicts of an early radiation of angiosperm in aquatic environments. Their extinct ancestors might be aquatic early angiosperms.