PHYLOGENETIC RELATIONSHIPS IN SEED PLANTS

Abstract— The phylogenetic relationships of nineteen extant and fossil seed plants are considered. Analysis of 31 characters produced ten topologically similar and equally parsimonious cladograms. A strict consensus tree derived from these cladograms places Lyginopteris as the sister taxon to the other seed plants included. Within this clade all the taxa considered, except medullosans and cycads, form a single monophyletic group defined by the presence of flattened seeds and saccate pollen ("platy-sperms"). Relationships between medullosans, cycads, and "platysperms" were not resolved, but within the "platysperm" clade conifers and cordaites ( Cordaixylon, Mesoxylon ) + Ginkgo form a monophyletic group ("coniferophytes"). The "higher platysperms" (glossopterids, Caytonia , corystosperms, Bennettitales, Pentoxylon , Gnetales, and angiosperms) are also monophyletic, but their relationship to "coniferophytes," peltasperms, and Callistophyton is unresolved. Pentoxylon is placed as sister taxon to the Bennettitales, and together they form the sister group to a clade in which Gnetales and angiosperm are sister taxa. The Bennettitales + Pentoxylon + Gnetales + angiosperms ("anthophytes") form a monophyletic sister group to the corystosperms. This analysis is compared with current classifications of seed plants. It does not support a close relationship between Bennettitales and cycads, it provides no evidence for seed plant polyphyly, and it strongly suggests that the current concept of seed ferns has little value in a phylogenetic context.     

Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae)

We have determined the complete chloroplast genome sequences of four early-diverging lineages of angiosperms, Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae), to examine the organization and evolution of plastid genomes and to estimate phylogenetic relationships among angiosperms. For the most part, the organization of these plastid genomes is quite similar to the ancestral angiosperm plastid genome with a few notable exceptions. Dioscorea has lost one protein-coding gene, rps16; this gene loss has also happened independently in four other land plant lineages, liverworts, conifers, Populus, and legumes. There has also been a small expansion of the inverted repeat (IR) in Dioscorea that has duplicated trnH-GUG. This event has also occurred multiple times in angiosperms, including in monocots, and in the two basal angiosperms Nuphar and Drimys. The Illicium chloroplast genome is unusual by having a 10 kb contraction of the IR. The four taxa sequenced represent key groups in resolving phylogenetic relationships among angiosperms. Illicium is one of the basal angiosperms in the Austrobaileyales, Chloranthus (Chloranthales) remains unplaced in angiosperm classifications, and Buxus and Dioscorea are early-diverging eudicots and monocots, respectively. We have used sequences for 61 shared protein-coding genes from these four genomes and combined them with sequences from 35 other genomes to estimate phylogenetic relationships using parsimony, likelihood, and Bayesian methods. There is strong congruence among the trees generated by the three methods, and most nodes have high levels of support. The results indicate that Amborella alone is sister to the remaining angiosperms; the Nymphaeales represent the next-diverging clade followed by Illicium; Chloranthus is sister to the magnoliids and together this group is sister to a large clade that includes eudicots and monocots; and Dioscorea represents an early-diverging lineage of monocots just internal to Acorus.     

Contributions of plant molecular systematics to studies of molecular evolution

Dobzhansky stated that nothing in biology makes sense except in the light of evolution. A close corollary, and the central theme of this paper, is that everything makes a lot more sense in the light of phylogeny. Systematics is in the midst of a renaissance, heralded by the widespread application of new analytical approaches and the introduction of molecular techniques. Molecular phylogenetic analyses are now commonplace, and they have provided unparalleled insights into relationships at all levels of plant phylogeny. At deep levels, molecular studies have revealed that charophyte green algae are the closest relatives of the land plants and suggested that liverworts are sister to all other extant land plants. Other studies have suggested that lycopods are sister to all other vascular plants and clarified relationships among the ferns. The impact of molecular phylogenetics on the angiosperms has been particularly dramatic – some of the largest phylogenetic analyses yet conducted have involved the angiosperms. Inferences from three genes (rbcL, atpB, 18S rDNA) agree in the major features of angiosperm phylogeny and have resulted in a reclassification of the angiosperms. This ordinal-level reclassification is perhaps the most dramatic and important change in higher-level angiosperm taxonomy in the past 200 years. At lower taxonomic levels, phylogenetic analyses have revealed the closest relatives of many crops and model organisms for studies of molecular genetics, concomitantly pointing to possible relatives for use in comparative studies and plant breeding. Furthermore, phylogenetic information has contributed to new perspectives on the evolution of polyploid genomes. The phylogenetic trees now available at all levels of the taxonomic hierarchy for angiosperms and other green plants should play a pivotal role in comparative studies in diverse fields from ecology to molecular evolution and comparative genetics.     

A phylogenetic classification of the land plants to accompany APG III

A formal classification of the land plants that is compatible with the APG III classification is proposed. Previous classifications inflated taxonomic ranks, particularly of the angiosperms. If the major clades of green algae are recognized as classes, then all land plants, the embryophytes, should be included in a single class, here recognized as Equisitopsida. Accordingly, the 16 major clades of land plants, including the angiosperms, should all be recognized as subclasses, the angiosperms as Magnoliidae. Major clades within the angiosperms are then recognized as superorders. This classification still uses a few informal categories (e.g. eudicots, lamiids, etc.) within the angiosperms because this is convenient. Two new names are established: Amborellanae and Austrobaileyanae. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 161 , 122–127.     

Introduction and Notes to R. Dahlgren's System of Classification of the Angiosperms

The present paper aims at introducting Dahlgren’s system of classification of the angiosperms. Phenetic and phylogenetic classifications are discussed. The basic principles and methods used by Dahlgren are explained. Dahlgren’s opinions on some important problems, such as the origin of angiosperms, the flowers of primitive angiosperms, the relation between the dicotyledons and monocotyledons, the origin of the monocotyledons, the treatment of the “Amentiferae” and of the orders of the “Sympetalae”, are all expressed. A brief comparison between Dahlgren’s system and three other current systems, viz. those of Takhtajan, Cronquist and Thorne is also given.     

Molecular data place Hydnoraceae with Aristolochiaceae

Utilization of molecular phylogenetic information over the past decade has resulted in clarification of the position of most angiosperms. In contrast, the position of the holoparasitic family Hydnoraceae has remained controversial. To address the question of phylogenetic position of Hydnoraceae among angiosperms, nuclear SSU and LSU rDNA and mitochondrial atp1 and matR sequences were obtained for Hydnora and Prosopanche. These sequences were used in combined analyses that included the above four genes as well as chloroplast rbcL and atpB (these plastid genes are missing in Hydnoraceae and were hence coded as missing). Three data sets were analyzed using maximum parsimony: (1) three genes with 461 taxa; (2) five genes with 77 taxa; and (3) six genes with 38 taxa. Analyses of separate and combined data partitions support the monophyly of Hydnoraceae and the association of that clade with Aristolochiaceae sensu lato (s.l.) (including Lactoridaceae). The latter clade is sister to Piperaceae and Saururaceae. Despite over 11 kilobases (kb) of sequence data, relationships within Aristolochiaceae s.l. remain unresolved, thus it cannot yet be determined whether Aristolochiaceae, Hydnoraceae, and Lactoridaceae should be classified as distinct families. In contrast to most traditional classifications, molecular phylogenetic analyses do not suggest a close relationship between Hydnoraceae and Rafflesiaceae. A number of morphological features is shared by Hydnoraceae and Aristolochiaceae; however, a more resolved phylogeny is required to determine whether these represent synapomorphies or independent acquisitions.     

Phylogenetic relationships of the Santalales and relatives

Summary Determining relationships among parasitic angiosperms has often been difficult owing to frequent morphological reductions in floral and vegetative features. We report 18S (small-subunit) rRNA sequences for representative genera of three families within the Santalales (Olacaceae, Santalaceae, and Viscaceae) and six outgroup dicot families (Celastraceae, Cornaceae, Nyssaceae, Buxaceae, Apiaceae, and Araliaceae). Using Wagner parsimony analysis, one most parsimonius tree resulted that shows the Santalales to be a holophyletic taxon most closely related toEuronymus (Celastraceae). The santalalean taxa showed approximately 13% more transitional mutations than the group of seven other dicot species. This suggests a higher fixation rate for mutations in these organisms, possibly owing to a relaxation of selection pressures at the molecular level in parasitic vs nonparasitic plants. Outgroup relationships are generally in accord with current taxonomic classifications, such as the grouping of Nyssaceae and Cornaceae together (Cornales) and the grouping of Araliaceae with Apiaceae (Apiales). These data provide the first nucleotide sequences for any parasitic flowering plant and support the contention that rRNA sequence analysis can result in robust phylogenetic comparisons at the family level and above.     

Darwin's second 'abominable mystery': Why are there so many angiosperm species?

The rapid diversification and ecological dominance of the flowering plants beg the question "Why are there so many angiosperm species and why are they so successful?" A number of equally plausible hypotheses have been advanced in response to this question, among which the most widely accepted highlights the mutually beneficial animal-plant relationships that are nowhere better developed nor more widespread than among angiosperm species and their biotic vectors for pollination and dispersal. Nevertheless, consensus acknowledges that there are many other attributes unique to or characteristic of the flowering plants. In addition, the remarkable coevolution of the angiosperms and pollination/dispersal animal agents could be an effect of the intrinsic adaptability of the flowering plants rather than a primary cause of their success, suggesting that the search for underlying causes should focus on an exploration of the genetic and epigenetic mechanisms that might facilitate adaptive evolution and speciation. Here, we explore angiosperm diversity promoting attributes in their general form and draw particular attention to those that, either individually or collectively, have been shown empirically to favor high speciation rates, low extinction rates, or broad ecological tolerances. Among these are the annual growth form, homeotic gene effects, asexual/sexual reproduction, a propensity for hybrid polyploidy, and apparent "resistance" to extinction. Our survey of the literature suggests that no single vegetative, reproductive, or ecological feature taken in isolation can account for the evolutionary success of the angiosperms. Rather, we believe that the answer to Darwin's second "abominable mystery" lies in a confluence of features that collectively make the angiosperms unique among the land plants.     

Flavonoids and phylogenetic reconstruction

Flavonoids have been used successfully for interpreting evolutionary relationships in many groups of angiosperms. These interpretations often have been presented in narrative fashion without specific indications of the kinds of relationships expressed. In this paper a method of phylogeny reconstruction with flavonoid data showing cladistic, patristic, and phenetic relationships is presented. Such a phylogram contains maximal information about flavonoid evolution. As an example, relationships in the North American species ofCoreopsis (Compositae), containing 46 species in 11 sections, are analyzed by this approach. A phylogeny of sections of the genus from previous morphological, chromosomal and hybridization data is compared with that from data on anthochlors (chalcones and aurones). Strong correspondence of these evolutionary interpretations gives support to the hypothesized evolutionary trends within the group.     

被子植物系统发育深层关系研究: 进展与挑战

被子植物系统发育学是研究被子植物及其各类群间亲缘关系与进化历史的学科。从20世纪90年代起, 核苷酸和氨基酸序列等分子数据开始被广泛运用于被子植物系统发育研究, 经过20多年的发展, 从使用单个或联合少数几个细胞器基因, 到近期应用整个叶绿体基因组来重建被子植物的系统发育关系, 目、科水平上的被子植物系统发育框架已被广泛接受。在这个框架中, 基部类群、主要的5个分支(即真双子叶植物、单子叶植物、木兰类、金粟兰目和金鱼藻目)、每个分支所包含的目以及几个大分支包括的核心类群等都具有高度支持。与此同时, 细胞器基因还存在一些固有的问题, 例如单亲遗传、系统发育信息量有限等, 因此近年来双亲遗传的核基因在被子植物系统发育研究中的重要性逐渐得到关注, 并在不同分类阶元的研究中都取得了一定进展。但是, 被子植物系统发育中仍然存在一些难以确定的关系, 例如被子植物5个分支之间的关系、真双子叶植物内部某些类群的位置等。本文简述了20多年来被子植物系统发育深层关系的主要研究进展, 讨论了被子植物系统发育学常用的细胞器基因和核基因的选用, 已经确定和尚未确定系统发育位置的主要类群, 以及研究中尚存在的问题和可能的解决方法。     

Molecular and morphological phylogenetics of weevils (coleoptera,curculionoidea): do niche shifts accompany diversification?

The main goals of this study were to provide a robust phylogeny for the families of the superfamily Curculionoidea, to discover relationships and major natural groups within the family Curculionidae, and to clarify the evolution of larval habits and host-plant associations in weevils to analyze their role in weevil diversification. Phylogenetic relationships among the weevils (Curculionoidea) were inferred from analysis of nucleotide sequences of 18S ribosomal DNA (rDNA; approximately 2,000 bases) and 115 morphological characters of larval and adult stages. A worldwide sample of 100 species was compiled to maximize representation of weevil morphological and ecological diversity. All families and the main subfamilies of Curculionoidea were represented. The family Curculionidae sensu lato was represented by about 80 species in 30 "subfamilies" of traditional classifications. Phylogenetic reconstruction was accomplished by parsimony analysis of separate and combined molecular and morphological data matrices and Bayesian analysis of the molecular data; tree topology support was evaluated. Results of the combined analysis of 18S rDNA and morphological data indicate that monophyly of and relationships among each of the weevil families are well supported with the topology ((Nemonychidae, Anthribidae) (Belidae (Attelabidae (Caridae (Brentidae, Curculionidae))))). Within the clade Curculionidae sensu lato, the basal positions are occupied by mostly monocot-associated taxa with the primitive type of male genitalia followed by the Curculionidae sensu stricto, which is made up of groups with the derived type of male genitalia. High support values were found for the monophyly of some distinct curculionid groups such as Dryophthorinae (several tribes represented) and Platypodinae (Tesserocerini plus Platypodini), among others. However, the subfamilial relationships in Curculionidae are unresolved or weakly supported. The phylogeny estimate based on combined 18S rDNA and morphological data suggests that diversification in weevils was accompanied by niche shifts in host-plant associations and larval habits. Pronounced conservatism is evident in larval feeding habits, particularly in the host tissue consumed. Multiple shifts to use of angiosperms in Curculionoidea were identified, each time associated with increases in weevil diversity and subsequent shifts back to gymnosperms, particularly in the Curculionidae.     

Cretaceous diversification of angiosperms in the western part of the Iberian Peninsula

The classic leaf fossil floras from the Cretaceous of the Lusitanian Basin, Portugal, which were first described more than one hundred years ago, have played an important role in the development of ideas on the early evolution of angiosperms. Insights into the nature of vegetational change in the Lusitanian Basin through the Cretaceous have also come from studies of fossil pollen and spores, but the discovery of a series of mesofossil floras containing well-preserved angiosperm reproductive structures has provided a new basis for understanding the systematic relationships and biology of angiosperms at several stratigraphic levels through the Cretaceous. In the earliest mesofossil floras from the Torres Vedras locality, which are of probable Late Barremian-Early Aptian age, angiosperms are surprisingly diverse with about 50 different taxa. In slightly later mesofossil floras, which are of probable Late Aptian-Early Albian age, the diversity of angiosperms is still more substantial with more than hundred different kinds of angiosperm reproductive structures recognized from the Famalicão locality alone. However, this early diversity is largely among angiosperm lineages that produced monoaperturate pollen (e.g., Chloranthaceae, Nymphaeales) and early diverging monocots (Alismatales). Eudicots are rare in these Early Cretaceous mesofossil floras, but already by the Late Cenomanian the vegetation of the western Iberian Peninsula is dominated by angiosperms belonging to various groups of core eudicots. The Normapolles complex is a particularly conspicuous element in both mesofossil floras and in palynological assemblages. In the Late Cretaceous mesofossil floras from Esgueira and Mira, which are of Campanian-Maastrichtian age, core eudicots are also floristically dominant and flowers show great organisational similarity to fossil flowers from other Late Cretaceous floras described from other localities in Asia, Europe and North America.     

Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids

Background  

The Vitaceae (grape) is an economically important family of angiosperms whose phylogenetic placement is currently unresolved. Recent phylogenetic analyses based on one to several genes have suggested several alternative placements of this family, including sister to Caryophyllales, asterids, Saxifragales, Dilleniaceae or to rest of rosids, though support for these different results has been weak. There has been a recent interest in using complete chloroplast genome sequences for resolving phylogenetic relationships among angiosperms. These studies have clarified relationships among several major lineages but they have also emphasized the importance of taxon sampling and the effects of different phylogenetic methods for obtaining accurate phylogenies. We sequenced the complete chloroplast genome of Vitis vinifera and used these data to assess relationships among 27 angiosperms, including nine taxa of rosids.     

毛茛科分子系统发育研究进展

毛茛科(Ranunculaceae)在被子植物的系统演化中占有十分重要的地位,其系统位置和科下演化关系一直备受争议。近20多年的分子系统学研究表明,以往基于形态学的分类系统与分子系统学研究结果存在巨大差异。通过形态学性状界定的绝大多数亚科都没有得到分子系统学支持。此外,通过形态学确定的一些属如升麻属(Cimicifuga)、黄三七属(Souliea)、獐耳细辛属(Hepatica)、白头翁属(Pulsatilla)和水毛茛属(Batrachium)等,根据分子系统学研究均应予以归并。而分子系统学研究也确立了一些类群的属级地位,如露蕊乌头属(Gymnaconitum)等。以中国分布的毛茛科植物为例,通过以往分子系统学研究,共有10个属被归并,2个属新被确立。然而,毛茛科分子系统学研究对于科下许多类群之间的关系目前仍然没有得到很好的解决,如毛茛亚科和翠雀族等类群的系统发育关系仍需要进行深入研究后方能确定。该文对近年来国内外有关毛茛科的分子系统学研究进展进行了综述,并对该科尚存的一些问题和未来的研究方向进行了讨论。     

A theory on the ancestry of angiosperms

Summary By inferences from fossil records and circumstantial evidences, it is now generally postulated that angiosperms have a much longer history than hitherto believed and that they have already existed probably in Jurassic time. Studies in vascular tissues and reproductive, structures have negated the possibility of originating angiosperms from various gymnosperm groups. Chronologically, this derivation will be also an impossibility.From a consideration of various aspects in the life history of angiosperms, a hypothesis is here presented postulating that protangiosperms originated in an aquatic or subaquatic environment from an algal ancestry. The enclosure of ovules in the ovary is interpretated as a means of protection necessitated for the transmigration from an aquatic to an aerial habitat for the developing reproductive parts in the bud underwater. Trimery is suggested as a primitive condition, one that affords maximum efficiency in carrying out the purpose under the conditions.In the life history of angiosperms, the endosperm is of great significance in phylogeny. From morphological, physiological, cytological as well as genetical considerations, the endosperm should be regarded as of equal status with the gametophytic and sporophytic generations. There is no comparable structure in the gymnosperm groups and the ferns and fern-allies, while more or less similar conditions are present in the thallophytes. In the long life histories of many red algae, however, there is an especially notable resemblance to angiosperms, with certain details approaching the unique and characteristic features of the endosperms.Land plants are presumably all evolved from aquatic ancestors but instead of the usual concept of a monophyletic origin and lineal development of all vascular plants, a more plausible suggestion is the multiple and recurrent derivation of such plants from various algal ancestral groups. The angiosperms probably represent one of such major lines that originated more or less directly from a thallophytic ancestry.     

Molecules, Morphology, Fossils, and the Relationship of Angiosperms and Gnetales

Morphological analyses of seed plant phylogeny agree that Gnetales are the closest living relatives of angiosperms, but some studies indicate that both groups are monophyletic, while others indicate that angiosperms are nested within Gnetales. Molecular analyses of several genes agree that both groups are monophyletic, but differ on whether they are related. Conflicts among morphological trees depend on the interpretation of certain characters; when these are analyzed critically, both groups are found to be monophyletic. Conflicts among molecular trees may reflect the rapid Paleozoic radiation of seed plant lines, aggravated by the long branches leading to extant taxa. Trees in which angiosperms are not related to Gnetales conflict more with the stratigraphic record. Even if molecular data resolve the relationships among living seed plant groups, understanding of the origin of angiosperm organs will require integration of fossil taxa, necessarily using morphology.     

General aspects of angiosperm evolution and macrosystematics

Taxonomy makes increasing use of significant results from many fields of research including the rapidly developing fields of micro– and macromolecular chemistry, ultrastructure and micromorphology in combination with macromorphology, anatomy, embryology, cytology, paleontology, biological interaction and distribution. Some of these results have contributed to make the current systems of classifications more concordant. Recent studies on Cretaceous fossils are related to present–day angiosperms and their floral types. It is concluded that pleiomerous flowers with helically arranged parts (corresponding to the Magnolia type, though probably less elaborate), on the basis of recent evidence can still be regarded as the probably earliest floral type in angiosperms. But the trimerous flowers must also have appeared very early, at least in the Albian. There is also evidence that the monocotyledons had differentiated as a separate group at that time. Similarities between certain extant monocotyledons and certain dicotyledons, in particular between some Dios–coreales and some Annonales–Aristolochiales, indicate that the monocotyledons had their roots in early Cretaceous pro–Magnoliiflorae. Fossil petaliferous flowers from Cenomanian layers, and later of a variety of flower types, such as the obdiplostemo–nous, petaliferous, epigynous Scandianthus (similar to extant saxifragaceous genera), or flowers with secondarily pleiomerous androecia of the theaceous type are discussed in relation to the distribution of corresponding floral types in extant dicotyledons. The main features of the author's classification of angiosperms are outlined with notes on important, though often neglected, aspects and critical problems. Finally, an updated table of classification down to family rank is presented.     

Phylogeny of the Botryosphaeriaceae reveals patterns of host association

Three anamorph genera of the Botryosphaeriaceae namely Diplodia, Lasiodiplodia and Dothiorella have typically dark, ovoid conidia with thick walls, and are consequently difficult to distinguish from each other. These genera are well-known pathogens of especially pine species. We generated a multiple gene genealogy to resolve the phylogenetic relationships of Botryosphaeriaceae with dark conidial anamorphs, and mapped host associations based on this phylogeny. The multiple gene genealogy separated Diplodia, Lasiodiplodia and Dothiorella and it revealed trends in the patterns of host association. The data set was expanded to include more lineages of the Botryosphaeriaceae, and included all isolates from different host species for which ITS sequence data are available. Results indicate that Diplodia species occur mainly on gymnosperms, with a few species on both gymnosperms and angiosperms. Lasiodiplodia species occur equally on both gymnosperms and angiosperms, Dothiorella species are restricted to angiosperms and Neofusicoccum species occur mainly on angiosperms with rare reports on Southern Hemisphere gymnosperms. Botryosphaeria species with Fusicoccum anamorphs occur mostly on angiosperms with rare reports on gymnosperms. Ancestral state reconstruction suggests that a putative ancestor of the Botryosphaeriaceae most likely evolved on the angiosperms. Another interesting observation was that both host generalist and specialist species were observed in all the lineages of the Botryosphaeriaceae, with little evidence of host associated co-evolution.