An updated classification of the class Magnoliopsida (“Angiospermae”)

The present classification of extant flowering plants (Magnoliopsida) updates and revises those presented previously by bringing together the vast majority of new information published since 1999. The extant members of Magnoliopsida are subdivided into 12 subclasses, 35 superorders, 87 orders, 40 suborders, 472 families, and 400 subfamilies. The number of genera and species for each accepted taxon is indicated, along with a statement of the taxonomic confidence that the taxon is worthy of recognition as outlined. Authorships and year of publication are provided for each accepted name and cited synonym. A rule change adopted in 2005 at the Vienna Botanical Congress has fundamentally altered authorships and valid places of publication for hundreds of names, and the full extent of the changes is unknown at present. Newly proposed names include subclass Malvidae; superorder Berberidopsidanae and Huerteanae; suborders Aralidiineae, Asphodelineae, Chloranthineae, Eriocaulineae, Hamamelidineae, Juglandineae, Myricineae, Papaverineae, and Xyridineae; and subfamilies Circaeasteroideae, Dampieroideae, Dasypogonoideae, Davidsonioideae, Ebenoideae, Goetzeoideae, Hesperocallidoideae, Hortonioideae, Isophysidoideae, Kingdonioideae, Laxmannioideae, Ledocarpoideae, Lilaeoideae, Lomandroideae, Morkillioideae, Octoknemoideae, Petunioideae, Phormioideae, Rhynchothecoideae, Sargentodoxoideae, Sclerophylacoideae, Siparunoideae, Sparattanthelioideae, Styloceratoideae, Tribeloideae, Tricyrtidoideae, and Xanthoceroideae.     

Angiosperm classification and phylogeny: a rectifying comment

A commentary is given on the criticism of Dahlgren's recent classification of angiosperms by Corner ( Botanical Journal of the Linnean Society, 82: 81–87 (1981)). In his dissatisfaction with the current, (almost) generally accepted nomenclatural concepts he has chosen to use my classification as a target. It is agreed that nomenclature is not 'fair' to plant groups playing the most important role in building up the biosphere, and that nomenclatural constructions do not reflect the consideration given to various parts of the plant. Corner does not seem to be familiar with the fact that his so-called 'pseudons' are common to all current systems of classification, nor that the termination '-florae' has been used by Thorne (1968) and in a number of publications since. This suffix does not imply that the botanists using it neglect vegetative characters, nor characters from fruits and seeds. Other misunderstandings are also pointed out. In no case has it been satisfactorily demonstrated by Corner that my orders or superorders are unnatural entities (even though a number of them most likely are).     

Host Plant Specialization and Species Turnover of Caterpillars Among Hosts in the Brazilian Cerrado

Decrease in the species composition similarity of herbivore assemblages with increasing phylogenetic distance between host plants is a widespread pattern. Here we used data for caterpillars in the Brazilian Cerrado to investigate how the similarity in caterpillar species composition decreases as the taxonomic level and genetic distance (GD) of their host plants increases. In addition, we elucidate the plant taxonomic level that provides the greatest contribution to turnover in the caterpillar species composition among host taxa. Adult Lepidoptera were reared from caterpillars collected from 52 plants over 13 yr in the same area, with each host plant sampled for 1 yr. Most species were specialists, with 66 percent of genus specialists among the nonsingleton species. The similarity in caterpillar species composition across plant taxa decreased from host species to genera, and from host genera to orders. Above this level, the similarity was consistently low. The GD between plants explained 82 percent of the variation in the similarity of caterpillar species composition. The contribution of caterpillar species turnover among host orders from the same superorder and among host superorders from the same subclass explained 70 percent of the caterpillar species richness as a whole. Our results lend support to the view that most tropical caterpillars are host specialists. Our findings further indicate that the number of orders and superorders of plants provide the greatest contribution to the total caterpillar richness compared with all of the other host taxonomic levels combined. Abstract in Portuguese is available at http://www.blackwell‐synergy.com/loi/btp .     

Diversity of Mesozoic gnetophytes and the first angiosperms

A provisionary system of gnetophytes is proposed, including recently discovered Mesozoic members. The following principal characters are used, in descending order of significance: strobilar structure of ovulate organs (eugnetophytes) as opposed to flowerlike cupules and their aggregates (anthognetophytes), radial vs. bilateral symmetry of seed cupules, and morphological distinctions in the pollen organs, pollen micromorphology and exine ultrastructure. The fossil members show mosaic associations of morphological traits, which attests to different evolution rates of their ovulate and pollinate structures. The system includes two superorders and eight orders, several of which are new. A dichotomous key is provided to differentiate between genera of fossil gnetophytes based on ovulate structures. Two stages in evolution of gnetophyte morphological diversity are recognized: first in the Triassic and then in the Early Cretaceous, the latter was associated with the origin of new type herbaceous wetland communities. Angiosperms or some of them might have originated as elements of gnetophyte diversity in such communities.     

Comparative aspects of trophoblast development and placentation

Based on the number of tissues separating maternal from fetal blood, placentas are classified as epitheliochorial, endotheliochorial or hemochorial. We review the occurrence of these placental types in the various orders of eutherian mammals within the framework of the four superorders identified by the techniques of molecular phylogenetics. The superorder Afrotheria diversified in ancient Africa and its living representatives include elephants, sea cows, hyraxes, aardvark, elephant shrews and tenrecs. Xenarthra, comprising armadillos, anteaters and sloths, diversified in South America. All placentas examined from members of these two oldest superorders are either endotheliochorial or hemochorial. The superorder Euarchontoglires includes two sister groups, Glires and Euarchonta. The former comprises rodents and lagomorphs, which typically have hemochorial placentas. The most primitive members of Euarchonta, the tree shrews, have endotheliochorial placentation. Flying lemurs and all higher primates have hemochorial placentas. However, the lemurs and lorises are exceptional among primates in having epitheliochorial placentation. Laurasiatheria, the last superorder to arise, includes several orders with epitheliochorial placentation. These comprise whales, camels, pigs, ruminants, horses and pangolins. In contrast, nearly all carnivores have endotheliochorial placentation, whilst bats have endotheliochorial or hemochorial placentas. Also included in Laurasiatheria are a number of insectivores that have many conserved morphological characters; none of these has epitheliochorial placentation. Consideration of placental type in relation to the findings of molecular phylogenetics suggests that the likely path of evolution in Afrotheria was from endotheliochorial to hemochorial placentation. This is also a likely scenario for Xenarthra and the bats. We argue that a definitive epitheliochorial placenta is a secondary specialization and that it evolved twice, once in the Laurasiatheria and once in the lemurs and lorises.     

An ultracentrifugation analysis of two hundred fish genomes

The goal of this study was to provide a comprehensive view of the compositional characteristics of fish genomes. We therefore expanded the number of fish species that we had explored so far in their DNAs by analytical ultracentrifugation in CsCl density gradient from 122 to 201. This study included representatives from three out of nine orders of Elasmobranchs (sharks and rays), both orders of dipnoan lungfishes, and both orders of chondrosteans (sturgeons and bichirs). We also studied 19 out of 38 teleostean orders, which represent all but four (minor) superorders of the subdivision Teleostei, a group comprising about 23,600 species (96% of all extant fishes). This leaves for further studies two subclasses, Holocephali (chimaeras), and Coelacanthimorpha (gombessas). In spite of this substantial increase in the number of species and orders analysed, all average properties (the modal buoyant density, rho(0), the average buoyant density, , the CsCl profile asymmetry, A, and the compositional heterogeneity, H), and all their ranges were unchanged compared to a previous study [J. Mol. Evol. 31 (1990) 265]. This suggests that, in all likelihood, the properties reported in the present paper can be considered as generally valid for all fish genomes.     

The mitochondrial nad2 gene as a novel marker locus for phylogenetic analysis of early land plants: a comparative analysis in mosses

The mitochondrial nad2 gene is established as a novel marker locus for phylogenetic analyses among early land plants. The potential of this gene for phylogenetic resolution was checked with a broad taxon sampling of 42 mosses (Bryopsida, including the enigmatic genus Takakia) to allow both a comparative analysis with the recently explored nad5 gene and the fusion of independent data sets. The mitochondrial gene sequences provide valuable phylogenetic information on the relationships of classically defined orders and their respective monophylies. The more rapidly diverging sequences of a group I intron in nad5 and of a group II intron in nad2 add information for fine resolution. Although both genes provide phylogenetic information in the same taxonomic range (above family level), the combined sequence alignment results in an approximate doubling in the number of nodes with significant bootstrap support (>90). According to our data, Buxbaumiales are a paraphyletic taxon in a key position between the earliest branching taxa (Sphagnales, Takakiales, Andreaeales, Polytrichales, and Tetraphidales) and all other orders, possibly to be placed in the subclass Bryidae. A dichotomy in the latter recalls two previously suggested superorders Hypnanae and Dicrananae. Both genes independently question the monophyly of the orders Dicranales and Neckerales and reject the inclusion of the genera Schistostega, Timmia, and Encalypta among Eubryales.     

Phylogenetic relationships of elopomorph fishes inferred from mitochondrial ribosomal DNA sequences

The superorder Elopomorpha, a grouping which includes all teleost fishes that possess a specialized leptocephalous larva [true eels (Anguilliformes), gulpers and bobtail snipe eels (Saccopharyngiformes), bonefishes, spiny eels, and halosaurs (Albuliformes, including Notacanthiformes), ladyfishes and tarpons (Elopiformes, including Megalopiformes)] comprises >800 species for which phylogenetic relationships are poorly understood. In the present study, we analyzed mitochondrial DNA sequences in segments of the 12S and 16S rRNA genes in 33 elopomorph taxa encompassing all of the previously proposed orders, and 9 of the 15 currently recognized families of the Anguilliformes, as well as outgroup representatives from the superorders Osteoglossomorpha (nine species) and Clupeomorpha (three species), to develop phylogenetic hypotheses based on distance and parsimony methods. Both methods failed to support the monophyly of the Elopomorpha, casting doubt on the validity of the leptocephalus as an elopomorph synapomorphy. The orders Elopiformes, Albuliformes, and Anguilliformes, however, were resolved as monophyletic assemblages. Parsimony analysis supported the separation of the Anguilliformes into two groups (primitive and advanced) based on the presence of divided versus fused frontal bones. In addition, the molecular data indicated a close affinity of the anguilliform Thalassenchelys coheni (incertae sedis), known only from the leptocephalus, with the family Serrivomeridae. The implications of these data as regards the evolution of the elopomorph assemblage are discussed.     

Alkaloid evolution and angiosperm systematics

The correlation of biosynthetic steps leading to the primary precursors of the shikimate pathway with the distribution of derived alkaloids on dahlgren's system of classification of angiosperm orders suggests that evolution paralleled gradual blocking of these steps. Phenylalanine-derived alkaloids, with the centre of radiation situated in the magnoliales, are of widespread occurrence in angiosperms, an indication of the antiquity of the character. Anthranilic acid-derived alkaloids, with the centre of radiotion in the rutales, are less widespread. Orders in which such alkaloids co-occur with the former biogenetic group are considered to be of more recent origin. Finally, mevalonate-derived iridoid alkaloids, with the centre of radiation in the gentianales, are even less widespread. Orders in which such alkaloids co-occur with the former biogenetic groups should thus be of still more recent origin. These concepts are summarized bg a phylogenetic tree, which illustrates the divergence of three major groups of angiosperm superorders.     

中国古生代化石昆虫研究回顾

自林启彬先生1978年命名了我国第一个古生代昆虫至今, 中国学者共发表20余篇分类学论著, 描述鉴定我国古生代昆虫共61种, 归属于9目（总目）。这些标本分布于西北、 西南、 华东等9省区, 其中石炭纪47种, 二叠纪14种。本文统计了我国已发现的古生代化石昆虫属种名录以及它们的分布和地质年代, 总结了国内古生代化石昆虫当前的研究状况和发展趋势, 并分析了研究中存在的问题。其中关于化石昆虫普遍存在的脉序差异问题需给予足够的重视, 高级阶元的建立应更加慎重。研究表明我国古生代昆虫已经高度分异, 古翅类、 新翅类均已出现, 且代表着有翅昆虫辐射演化的重要阶段。     

Mitochondrial genomics of ostariophysan fishes: perspectives on phylogeny and biogeography

Abstract Ostariophysi is the second largest superorder within Teleostei. It contains five orders: Gonorynchiformes, Cypriniformes, Characiformes, Siluriformes, and Gymnotiformes. Resolving the higher-level relationships among ostariophysan and related fishes will aid in resolving basal teleostean divergence and provide basis to historical biogeographic analysis of major freshwater fish groups. In this study, we report the complete mitochondrial (mt) DNA sequences for eleven ostariophysan fishes and the results of phylogenetic analyses including these species plus four other ostariophysan and nine non-ostariophysan teleostean fishes. Maximum likelihood and maximum parsimony analyses reconfirmed clupeiforms as the closest relatives of ostariophysans. However, gonorynchiforms were closer to clupeiforms than to otophysans (ostariophysan groups excluding gonorynchiforms), thus raising a question over the current definition of Ostariophysi. The lack of clarity in otocephalan (ostariophysans + clupeiforms) basal relationships implies that such divergence took place over a short period of time. The monophyly of cypriniforms, characiphysans (characiforms, siluriforms, and gymnotiforms), and orders or superorders outside the ostariophysans examined here were conceivably reconstructed. The phylogenetic hypothesis suggests a Pangean origin of otophysans. Within characiphysans, gymnotiforms and siluriforms have independent evolutionary origins and evolutionary histories comparable to or older than that of characiforms. This helps to explain the present geographic distribution of characiphysans.     

Use of a cytogenetic whole-genome comparison to resolve phylogenetic relationships among three species: implications for mammalian systematics and conservation biology

The objective was to apply a novel modification of a genome-wide, comparative cytogenetic technique (comparative genomic hybridization, comparative genomic hybridization (CGH)), to study species belonging to the myrmecophagous (ant/termite eating) mammalian orders/superorders (Pholidota, Tubulidentata, Carnivora, and Xenarthra), as a model for other applications in mammalian systematics and conservation biology. In this study, CGH was applied to high-quality metaphase spreads of pangolin (Pholidota), using probes of sloth and canine (Xenarthra and Carnivora, respectively) genomic DNA labeled with different fluorophores, thereby facilitating analysis of the visible color spectrum on pangolin karyotypes. Our results posited that pholidotes are closer to carnivores than to xenarthrans, which confirmed the current consensus that myrmecophagy in these mammalian lineages was more likely because of homoplasy (convergent evolution) than being an ancestral character. Since the modified CGH technique used is genome-wide, has chromosome-level resolution, and does not need full genome sequencing, it has considerable potential in systematics and other fields.     

The crustacean lacinia mobilis: a reconsideration of its origin, function and phylogenetic implications

The lacinia mobilis of the Crustacea Malacostraca is a more or less spine-like movable appendage of the medial mandibular edge, inserted near the base of the incisor process. It occurs in two or possibly three eumalacostracan superorders but is retained in the adult stage only in the Peracarida. The lacinia has been interpreted as the distal member of the spine-row found in many adult Malacostraca and/or their larvae, or alternatively as a derivative of a certain cusp ('cusp b') of the biting edge of the primitive lophogastrids. The distribution, ontogeny and function of the lacinia were studied in a variety of Eumalacostraca. There is great variability in the guiding and locking mechanisms involved in biting, within the subclass and even within single orders. A lacinia-based guiding and locking system is likely to function only in weak mandibles. New evidence is produced in favour of derivation of the lacinia from the spine-row, and the 'cusp b' derivation hypothesis is rejected, 'cusp b' being only a highly specialized lacinia. Doubt is cast upon the unity of the superorder Peracarida mainly because the place of the order Amphipoda within it is regarded as insecure.     

Molecular phylogeny of the prickly shark, Echinorhinus cookei, based on a nuclear (18S rRNA) and a mitochondrial (cytochrome b) gene.

The classification of the sharks is unclear. This is particularly true for the superorder Squalomorphii. The relationships between the squalomorphs and other superorders of sharks and the relationships between the different orders within the squalomorphs are a matter of debate. Here, we report a molecular phylogeny for a little known member of this superorder, the genus Echinorhinus. Echinorhinus is most commonly classified in either the family Echinorhinidae (Squaliformes) or the family Squalidae (Squaliformes). However, some authors have suggested a closer relationship to the order Hexanchiformes. In an attempt to shed light on this controversy, we have cloned, sequenced, and compared two genes widely used in molecular phylogeny studies, the cytochrome b and the 18S rRNA from the rare prickly shark, Echinorhinus cookei, and two potential relatives, the spiny dogfish Squalus acanthias (Squaliformes), and the sevengill shark, Notorynchus cepedianus (Hexanchiformes). The sequences of these genes for the prickly shark, the dogfish, and the sevengill shark were found to be equally divergent, suggesting that the prickly shark is no closer to the order Squaliformes than to the order Hexanchiformes.     

Specification of phylogenetic interrelations between skate-rays and sharks

There are several hypotheses concerning phylogenetic interrelations of the ray-skate other also called batoid elasmobranches with other orders of elasmobranchs. Most of these studies are based on morphological studies; however, none of them include the skate itself. Without skate the concept of interrelations of the Batoids will be incomplete. This work deals with a molecular study of ribosomal ITS1-2 regions by the maximum parsimony (MP) and neighbor joining (NJ) methods of analysis, including skate. It is important for understanding the phylogenetic interrelations of the Batoids. The complex of all combined ITS1-2 data with use of the both analyses disagrees with the definition of phylogenesis of the recent Elasmobranchs, which has been put forward by Compagno [1]. On the contrary, results of the ITS1 MP analysis confirm the definition of superorders Squalea and Galeomorphii, which was proposed by Compagno [1]. Mine Dosay-Akbulut, 2006, published in Russian in Zhurnal Evolyutsionnoi Biokhimii i Fiziologii, 2006, Vol. 42, No. 2, pp. 105–109.     

Trends in the evolution of dicotyledonous seeds based on character associations, with special reference to pachychalazy and recalcitrance

VON TEICHMAN, I. & VAN WYK, A. E., 1991. Trends in the evolution of dicotyledonous seeds based on character associations, with special reference to pachychalazy and recalcitrance. The possible evolutionary status of the endothelium, hypostase, pachychalaza and the recalcitrant viability behaviour of seeds is considered in relation to bitegmy/unitegmy, crassinucellate/tenuinucellate ovules, nuclear/cellular endosperm development, large/small seed size, woody/herbaceous habit and tropical/temperate habitat. The presence of the endothelium, hypostase, pachychalaza and recalcitrance in dicotyledonous families is plotted against Dahlgren's system of classification. Results are compared with Sporne's advancement index for the various families. An endothelium is considered derived since it occurs more often in highly evolved superorders and is significantly associated with derived ovule and endosperm character states as well as with smaller seed size. A hypostase appears to be relatively ancestral and is significantly associated with pachychalazy and recalcitrance. The endothelium and hypostase have developed independently in many taxa and could be interpreted as being structurally and functionally analogous. Pachychalazy and recalcitrance are significantly associated with ancestral ovule character states and, at the species level, with large seed size (overgrown seed), woody habit and tropical habitat. The presence of pachychalazy, recalcitrance and associated large seed size are therefore regarded as ancestral character states of the dicotyledons. Consideration of currently accepted dicta on seed character state polarity, suggests a reversal in the evolutionary status of pachychalazy and large seed size.     

应用非序列联配方法对哺乳动物系统发育关系的探讨

非序列联配的序列分析方法,将序列中特定寡聚核苷酸的kmer统计频率作为特征,在序列间按特征进行比较和分析。这种方法综合考虑了所有变异类型对序列整体特征的影响,因而在组学数据分析上有独特的优势。但是,这类方法在复杂多细胞生物基因组系统发育中的适用性仍然有待检验。在本文中,我们使用基于非序列联配方法的CVTree软件,以45种哺乳动物的蛋白质组数据建立了系统发育关系NJ树,并据此探讨了哺乳动物系统发育的若干问题。在广受关注的真兽下纲四个总目的关系问题上,CVTree支持形态学的普遍结论即上兽类(Epitheria)假说。这与基于序列联配方法支持的外非洲胎盘类(Exafro-placentalia )假说不同。在哺乳动物内部目的层次上,CVTree树的结论与分子和形态所普遍接受的系统发育关系基本一致。但是在目的内部,CVTree树会有较多的差异。研究结果初步显示非序列联配方法在使用复杂多细胞生物的组学数据进行系统发育关系分析中的可行性。对非序列联配方法自身的改进及其与传统基于取代的序列联配方法之间的比较仍有待深入研究。