Phylogenetic systematics of the nymphaeales

A cladistic analysis was applied to reveal the phylogenetic relationships among the Nymphaeales. Seventeen out of twenty three characters in gross morphology, anatomy and palynology were analyzed, for their evolutionary polarities. From the results of the present analysis, the phylogenetic status of each genus and their relationships were clarified: 1)Nelumbo is a distinct taxon and is presumed to have originated from an ancestral stock of the Nymphaeales; 2)Ceratophyllum has a close phylogenetic relationship withCabomba; and 3) in the Nymphaeaceaesensu stricto, Nuphar and the remaining genral constitute a monophyletic group. A conclusion obtained from the present analysis was that the following three families should be recognized in the Nymphaeales; Nelumbonaceae Nymphaeaceae, and Ceratophyllaceae. The generaBrasenia andCabomba are traditionally classified in the Nymphaeaceae or in the independent family Cabombaceae. However, they should be included in the family Ceratophyllaceae.     

Phylogenetic systematics of microorganisms inhabiting thermal environments

Thermal habitats harbor specialized communities of thermophilic microorganisms, primarily prokaryotes. This review considers modern systematics of prokaryotes and the place of thermophilic archaea and bacteria in it. Among the existing hierarchical classifications of prokaryotes, the bulk of attention is given to the one accepted in the current second edition of "Bergey's Manual of Systematic Bacteriology", which is primarily based on 16S rRNA phylogeny and phenotypic properties of the organisms. Analysis of the genomics data shows that they on the whole agree with the 16S rRNA-based system, although revealing the significance of the evolutionary role of lateral transfer, duplication, and loss of genes. According to the classification elaborated in the current edition of "Bergey's Manual", the prokaryotes currently culturable under laboratory conditions are distributed among 26 phyla, two of which belong to the domain Archaea and 24 to the domain Bacteria. Six phyla contain exclusively thermophiles, and eleven phyla contain thermophiles along with mesophiles, thermophiles being usually separated phylogenetically and representing high-level taxa (classes, orders). In light of the data on the topology of the 16S rRNA-based phylogenetic tree and some other data, this review discusses the probable hyperthermophilic nature of the universal common ancestor.     

BRCA2 in meiosis: turning over a new leaf

Although originally thought to be confined to mammals, putative orthologues of the breast cancer susceptibility gene BRCA2 have now been found in a wide range of evolutionarily diverse taxa. These include the smut fungus Ustilago maydis, intracellular parasites, flies and vertebrates. A recent article demonstrates that two BRCA2-like genes in the plant Arabidopsis thaliana have a key role in meiosis. Investigating BRCA2 in distantly related organisms is likely to help to elucidate how the dysfunction of this gene leads to tumourigenesis.     

Phylogenetic systematics and biomecha cs in ecomorphology

Synopsis Research in all fields of biology increasingly uses phylogenetic systematics to interpret biological data in an evolutionary context. It is becoming widely accepted that comparative studies of the correlation of biological features, such as ecomorphological studies, must frame their analyses within the context of a phylogenetic hierarchy rather than treating each taxonomic unit as an independent replicate. Recent methods for the interpretation of ecological and functional data in the framework of a phylogeny can reveal the degree to which ecomorphological characters are correlated with one another, and are congruent with hierarchical cladistic groups. An example of the ecomorphology of labrid fishes is used here to illustrate the application of several of these methods. The structural design and mechanics of the jaws of labrids are tested for ecomorphological associations with the natural diets of these fishes. Methods for analysis of the correlated evolution of both discrete and continuous quantitative characters within a phylogeny are practiced on a single ecomorphological data set. Techniques used include character coding, character mapping, phylogenetic autocorrelation, independent contrasts, and squared change parsimony. These approaches to diverse biological data allow the study of ecomorphology to account for patterns of phylogenetic ancestry. Biomechanics or functional morphology also plays a vital role in the determination of ecomorphological relationships by clarifying the mechanisms by which morphologies can perform behaviors important to the organism's ecology. The synthesis of systematics with biomechanics is an example of interdisciplinary study in which information exchange can elucidate patterns of evolution in ecomorphology.     

Phylogenetic information and experimental design in molecular systematics.

Despite the widespread perception that evolutionary inference from molecular sequences is a statistical problem, there has been very little attention paid to questions of experimental design. Previous consideration of this topic has led to little more than an empirical folklore regarding the choice of suitable genes for analysis, and to dispute over the best choice of taxa for inclusion in data sets. I introduce what I believe are new methods that permit the quantification of phylogenetic information in a sequence alignment. The methods use likelihood calculations based on Markov-process models of nucleotide substitution allied with phylogenetic trees, and allow a general approach to optimal experimental design. Two examples are given, illustrating realistic problems in experimental design in molecular phylogenetics and suggesting more general conclusions about the choice of genomic regions, sequence lengths and taxa for evolutionary studies.     

Phylogenetic systematics of Archembiidae (Embiidina, Insecta)

Abstract. A cladistic analysis of the American genera of Embiidae is presented, using fifty‐seven representative taxa and ninety‐four morphological characters. The results support the elevation (and significant re‐delimitation) of the subfamily Archembiinae to family level; as delimited here, Archembiidae, revised status, includes the genera Ecuadembia n.gen., Calamoclostes Enderlein, Archembia Ross, Embolyntha Davis, Xiphosembia Ross, Ochrembia Ross, Dolonembia Ross, Conicercembia Ross, Neorhagadochir Ross, Pachylembia Ross, Rhagadochir Enderlein, Litosembia Ross, Navasiella Davis, Ambonembia Ross, Malacosembia Ross, Biguembia Szumik, Gibocercus Szumik and Pararhagadochir Davis. The results also indicate that some genera recently proposed are unjustified and therefore they are synonymized: Argocercembia Ross (a junior synonym of Embolyntha), Brachypterembia Ross (Neorhagadochir), Scelembia Ross (Rhagadochir), Ischnosembia Ross (Ambonembia) and Aphanembia Ross (Biguembia); all new synonymy. The new genus Ecuadembia is described (type species Archembia arida Ross). Ischnosembia surinamensis (Ross) is returned to the genus Pararhagadochir. The following species synonymies are established: Archembia lacombea Ross 1971 = Archembia kotzbaueri (Navas 1925), Archembia peruviana Ross 2001 = Archembia batesi (MacLachlan 1877), and Conicercembia septentrionalis (Mariño & Márquez 1988) = Conicercembia tepicensis Ross 1984; all new synonymy. The family Archembiidae, and all its constituent genera, are diagnosed and described. The genus Microembia Ross (originally described as an Embiidae) is transferred to Anisembiidae. Pachylembiinae, Scelembiinae, and Microembiinae proposed by Ross are unsupported by the present cladistic analysis. 1     

Phylogenetic systematics and character evolution in the angiosperm family Haloragaceae

The poorly known Haloragaceae R. Br. (Saxifragales) are highly diverse in habit (small trees to submerged aquatics) and labile in floral merosity (2-4), both uncommon among the core eudicots. This family has a cosmopolitan distribution, but taxonomic diversity is concentrated in Australia. An explicit phylogenetic approach has not previously been utilized to examine relationships or character evolution in this family. We used molecular evidence from nrDNA ITS and cpDNA trnK and matK regions under both Bayesian and parsimony analyses to address phylogenetic relationships. Combined molecular analyses defined a monophyletic Haloragaceae with the woody genera (Haloragodendron, Glischrocaryon) sister to the rest. Relationships among many genera were well resolved, with genera as currently delimited generally well supported, although there were notable exceptions; a new genus (Trihaloragis) is recognized, and the aquatic genus Meionectes is again distinct from Haloragis. Three new species combinations are also recognized. There are multiple (two or three) origins of the submerged aquatic habit in the family and potentially an intermediate reversal to the terrestrial habit, neither previously demonstrated in a core eudicot family using an explicit phylogenetic hypothesis. Ancestral character analyses suggest two origins of trimerous flowers and multiple reductions to dimerous flowers throughout Haloragaceae.     

Phylogenetic systematics of Pseudolebinthus, a new genus of Eneopterinae crickets (Orthoptera, Grylloidea, Eneopteridae) from south-east Africa

Abstract.  Within a framework of historical analysis of Eneopterinae crickets, the genus Pseudolebinthus Robillard gen.n. and two new species P. africanus Robillard, sp.n. and P. whellani Robillard, sp.n. , endemic from south-east Africa, are described. A cladistic analysis using 198 morphological characters and 47 terminals assessed the phylogenetic position of the new taxa within the subfamily. The resultant topologies support the previously proposed phylogeny for the subfamily and contained tribes. The monophyly of Pseudolebinthus is supported strongly as well as its sister relationship with Xenogryllus within the tribe Xenogryllini. A key to Eneopterinae tribes, Xenogryllini genera and Pseudolebinthus species is given. Taxonomic, evolutionary and acoustic issues raised by the recognition of Pseudolebinthus are discussed.     

Phylogenetic systematics of the genus Echinococcus (Cestoda: Taeniidae)

Echinococcosis is a serious helminthic zoonosis in humans, livestock and wildlife. The pathogenic organisms are members of the genus Echinococcus (Cestoda: Taeniidae). Life cycles of Echinococcus spp. are consistently dependent on predator–prey association between two obligate mammalian hosts. Carnivores (canids and felids) serve as definitive hosts for adult tapeworms and their herbivore prey (ungulates, rodents and lagomorphs) as intermediate hosts for metacestode larvae. Humans are involved as an accidental host for metacestode infections. The metacestodes develop in various internal organs, particularly in liver and lungs. Each metacestode of Echinococcus spp. has an organotropism and a characteristic form known as an unilocular (cystic), alveolar or polycystic hydatid. Recent molecular phylogenetic studies have demonstrated that the type species, Echinococcus granulosus, causing cystic echinococcosis is a cryptic species complex. Therefore, the orthodox taxonomy of Echinococcus established from morphological criteria has been revised from the standpoint of phylogenetic systematics. Nine valid species including newly resurrected taxa are recognised as a result of the revision. This review summarises the recent advances in the phylogenetic systematics of Echinococcus, together with the historical backgrounds and molecular epidemiological aspects of each species. A new phylogenetic tree inferred from the mitochondrial genomes of all valid Echinococcus spp. is also presented. The taxonomic nomenclature for Echinococcus oligarthrus is shown to be incorrect and this name should be replaced with Echinococcus oligarthra.     

Phylogenetic systematics of the reptantian Decapoda (Crustacea, Malacostraca)

Although the biology of the reptantian Decapoda has been much studied, the last comprehensive review of reptantian systematics was published more than 80 years ago. We have used cladistic methods to reconstruct the phylogenetic system of the reptantian Decapoda. We can show that the Reptantia represent a monophyletic taxon. The classical groups, the 'Palinura', 'Astacura' and 'Anomura' are paraphyletic assemblages. The Polychelida is the sister-group of all other reptantians. The Astacida is not closely related to the Homarida, but is part of a large monophyletic taxon which also includes the Thalassinida, Anomala and Brachyura. The Anomala and Brachyura are sister-groups and the Thalassinida is the sister-group of both of them. Based on our reconstruction of the sister-group relationships within the Reptantia, we discuss alternative hypotheses of reptantian interrelationships, the systematic position of the Reptantia within the decapods, and draw some conclusions concerning the habits and appearance of the reptantian stem species.     

Phylogenetic systematics of leaffishes (Teleostei: Polycentridae,Nandidae)

The Asian (nandid) and Afro‐Neotropical (polycentrid) leaffishes represent two superficially similar, but historically poorly diagnosed families – a situation resulting in a convoluted systematic history. Here, and including for the first time in a molecular study all leaffish genera, we generate a hypothesis of the phylogenetic history of both groups. We analyse a multilocus molecular data set encompassing 257 acanthomorph taxa, carry out a survey and assessment of selected osteological characters for the polycentrid leaffishes and also provide a reanalysis of previously published morphological data. Our results confirm: (1) that the Polycentridae and Nandidae are only remotely related, and hence, the classic leaffishes are diphyletic; (2) that the Polycentridae is monophyletic, with new skeletal synapomorphies being congruent with molecular data in placing the enigmatic Afronandus – a taxon that thus far has never been included in any molecular study – as sistergroup to the remaining genera; (3) the monophyly of the Nandidae + Badidae and their inclusion into a larger monophyletic group – along with the Pristolepididae, Anabantoidei and Channoidei – comprising the Labyrinthici sensu Rosen & Patterson. We also review the morphological and molecular evidence for both the conflicting placement of Pristolepis and the putative sistergroup relationship between the labyrinth fishes (Anabantoidei) and snakeheads (Channoidei).     

Phylogenetic systematics of Erythronium (Liliaceae): morphological and molecular analyses

For a nearly complete set of species of Erythronium (Liliaceae), we examined two plastid loci (the rps16 intron and the 5′ trnK intron, excluding the matK exon), one nuclear locus (nrITS) and morphology to evaluate species relationships and that of Erythronium to Amana, the putatively most closely allied genus. A matrix of morphological characters was developed through observation of around 900 living and herbarium specimens; evolution of these was examined using character optimization on the combined (total‐evidence) tree. Parsimony methods were used to examine the morphological and molecular data sets produced, both separately and in combination, with Bayesian methods also used on the molecular data sets. These established that the genus is probably sister to Amana (although most analyses placed Amana inside Erythronium) and that Tulipa is sister to the pair of Erythronium and Amana. Within Erythronium, there are three strongly supported geographically distinct clades: (1) Eurasian and (2) eastern and (3) western North American. Separation of species in these three clades is less clear, particularly among the western North American taxa. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ●●, ●●–●●.     

Phylogenetic and population systematics of the Mangabeys (primates: Cercopithecoidea)

On the basis of original craniological studies, it is concluded that recently published claims based on blood proteins that the Mangabeys are diphletic are valid, and it is proposed to divide them into two distinct genera:Cercocebus (with three species:torquatus (includingatys),agilis, andgaleritus), which belongs to the Cercocebini but has a somewhat isolated position in this tribe, andLophocebus (with one species,albigena: includingaterrimus as a subspecies), which is closer toPapio. The inter-relationships within each genus are discussed, with particular reference to the problem of subspeciesvs. allopatric species. A new subspecies is named and described,Lophocebus albigena osmani, and the anomalous position of the poorly-known subspeciesL.a. opdenboschi is extensively discussed.     

线粒体DNA序列特点与昆虫系统学研究

昆虫线粒体DNA是昆虫分子系统学研究中应用最为广泛的遗传物质之一。线粒体DNA具有进化速率较核DNA快 ,遗传过程不发生基因重组、倒位、易位等突变 ,并且遵守严格的母系遗传方式等特点。本文概述了mtDNA中的rRNA、tRNA、蛋白编码基因和非编码区的一般属性 ,分析了它们在昆虫分子系统学研究中的应用价值 ,以及应用DNA序列数据来推导分类阶 (单 )元的系统发育关系时 ,基因或DNA片段选择的重要性