Major clades of Agaricales: a multilocus phylogenetic overview

An overview of the phylogeny of the Agaricales is presented based on a multilocus analysis of a six-gene region supermatrix. Bayesian analyses of 5611 nucleotide characters of rpb1, rpb1-intron 2, rpb2 and 18S, 25S, and 5.8S ribosomal RNA genes recovered six major clades, which are recognized informally and labeled the Agaricoid, Tricholomatoid, Marasmioid, Pluteoid, Hygrophoroid and Plicaturopsidoid clades. Each clade is discussed in terms of key morphological and ecological traits. At least 11 origins of the ectomycorrhizal habit appear to have evolved in the Agaricales, with possibly as many as nine origins in the Agaricoid plus Tricholomatoid clade alone. A family-based phylogenetic classification is sketched for the Agaricales, in which 30 families, four unplaced tribes and two informally named clades are recognized.     

小鼠属(Mus)与田鼠属(Microtus)的系统发生关系研究概述

在啮齿动物的生存竞争中, 鼠类是最成功的一类。尤其是小鼠, 一直以来受到生物学专家的广泛关注。因为对小鼠的研究最为透彻, 致使它在实验室中有多方面应用, 同时小鼠是研究其他生物的好材料。文章综合现代遗传学的各种遗传标记(蛋白质、mtDNA、rDNA等), 更深入地探讨了小鼠属和田鼠属物种间的系统发生, 并进一步阐述了这2个属物种的分类和进化问题, 同时指出这2个属中某些物种的分类和系统发生地位仍需进一步的研究。     

系统比较方法的原理及应用

物种的大部分性状与其系统进化过程相联系,亲缘关系近的物种,其性状差异通常较小.因此在种间或更高分类单元层次研究性状之间的关系,或性状与环境间关系时需要考虑系统进化的影响,以满足常规统计分析对于样本独立性的要求.自20世纪80年代以来国际上已经陆续推出一系列的系统比较方法,其共同原理是:在推断物种间系统关系的基础上,在种间水平上比较,将原本不符合样本独立性的物种性状或环境变量数据,将其转化为适用于常规统计分析方法的彼此独立的数据,然后运用常规统计方法分析,得到排除了系统进化历史影响的物种性状间或者物种性状与环境变量间的关系.首先简单介绍了运用系统比较方法之前的建立系统关系和数据诊断这两个步骤,在此基础上阐述简单独立对比分析、Felsenstein的独立比较方法和自回归方法这3种常用的系统比较方法的基本原理、各自的特点以及它们在生态学、进化生物学等领域的应用.系统比较方法已经获得广泛的应用和认可,发现了应用常规统计分析所没有能发现的问题和规律,但在构建准确反映系统进化过程的系统关系、进化模型的选择等方面仍具有一定的局限性;而生物信息学、生物系统学的发展,以及各种相关软件的开发为系统比较方法的进一步完善发展和更为广泛的应用创造了条件.     

A phylogenetic overview of the family Pyronemataceae (Ascomycota, Pezizales)

Partial sequences of nuLSU rDNA were obtained to investigate the phylogenetic relationships of Pyronemataceae, the largest and least studied family of Pezizales. The dataset includes sequences for 162 species from 51 genera of Pyronemataceae, and 39 species from an additional 13 families of Pezizales. Parsimony, ML, and Bayesian analyses suggest that Pyronemataceae is not monophyletic as it is currently circumscribed. Ascodesmidaceae is nested within Pyronemataceae, and several pyronemataceous taxa are resolved outside the family. Glaziellaceae forms the sister group to Pyronemataceae in ML analyses, but this relationship, as well as those of Pyronemataceae to the other members of the lineage, are not resolved with support. Fourteen clades of pyronemataceous taxa are well supported and/or present in all recovered trees. Several pyronemataceous genera are suggested to be non-monophyletic, including Anthracobia, Cheilymenia, Geopyxis, Humaria, Lasiobolidium, Neottiella, Octospora, Pulvinula, Stephensia, Tricharina, and Trichophaea. Cleistothecial and truffle or truffle-like ascomata forms appear to have evolved independently multiple times within Pyronemataceae. Results of these analyses do not support previous classifications of Pyronemataceae, and suggest that morphological characters traditionally used to segregate the family into subfamilial groups are not phylogenetically informative above the genus level.     

An overview of the phylogenetic relationships of the suborder Trachinoidei (Acanthomorpha: Perciformes)

The phylogenetic relationships of the perciform suborder Trachinoidei, currently including 11 families (Cheimarrichthyidae, Pinguipedidae, Percophidae, Trichonotidae, Creediidae, Champsodontidae, Chiasmodontidae, Leptoscopidae, Ammodytidae, Trachinidae and Uranoscopidae) are reviewed from an historical perspective. The previously questioned monophyly of the suborder and familial limitations remain unclear because of conflicting evidence and differing phylogenetic proposals resulting from morphological and molecular perspectives.     

A phylogenetic study of the Plantaginaceae

In a study based on morphological, embryological and chemical data of the Plantaginaceae, within the subclass Sympetalae or Asteridae, the superorder Lamianae is shown to be monophyletic. However, it was not possible to reconstruct the phylogeny within Lamianae or to find a sister-group for the monophyletic Plantaginaceae – Hydrostachyaceae for the latter is rejected. Three or rarely four genera have previously been recognized within Plantaginaceae, but in both cases Plantago appears as polyphyletic, which is considered unacceptable. Six clades are recognized as subgenera within Plantago: subgen. Plantago (c. 131 species), subgen. Coronopus (c. 11 species), subgen. Littorella (three species), subgen. Psyllium (c. 16 species), subgen. Bougueria (one species), and subgen. Albicans (51 species). Within P. subgen. Plantago, the paraphyletic sect. Plantago (c. 42 species) is found in all parts of the world except South America, New Zealand, Australia, and New Guinea, where sect. Oliganthos and sect. Mesembryniae vicariate. It is not possible to infer the phylogeny within sect. Plantago, for example between the endemic species from distant Pacific Islands; their common ancestor might be a species that once had a very wide distribution. Keys to genera, subgenera, sections and series are given. Only one genus, Plantago L., is recognized. The following proposals are made in the Appendix: P. ser. Oliganthos Rahn, ser. nov.; P. ser. Carpophorae (Rahn) Rahn, stat. nov. (= sect. C.); P. ser. Microcalyx (Pilg.) Rahn, stat. nov. (= sect. M.); P. unibrackteata Rahn, nom. nov. (=P. uniflora Hook.f. non L.); P. subgen. Littorella (P. J. Bergius) Rahn, stat. nov. (=Littorella P. J. Bergius); P. araucana Rahn, nom. nov. (=Littorella australis Griseb. non Plantago australis Lam.); P. americana (Fernald) Rahn, comb. nov.(=Littorella a.); P. subgen. Bougueria (Decne.) Rahn, stat. nov. (=Bougueria Decne.); P. nubicola (Decne.) Rahn, comb. nov. (=Bougueria n. Decne.); P. subgen. Albicans Rahn, subgen. nov. Ten lectotypes are selected.     

Molecular phylogenetics of the Gloeophyllales and relative ages of clades of Agaricomycotina producing a brown rot

The Gloeophyllales is a recently described order of Agaricomycotina containing a morphologically diverse array of polypores (Gloeophyllum), agarics (Neolentinus, Heliocybe) and resupinate fungi (Veluti-Veluticeps, Boreostereum, Chaetodermella), most of which have been demonstrated to produce a brown-rot mode of wood decay and are found preferentially on coniferous substrates. Multiple phylogenetic studies have included taxa of Gloeophyllales, but none have sampled the order thoroughly, and so far only ribosomal RNA genes have been used. Consequently the limits and higher level placement of the Gloeophyllales are obscure. We obtained sequence data for three protein-coding genes (rpb2, atp6, tef1) and three rRNA regions (nuc-ssu, nuc-lsu, 5.8S) in 19 species of Gloeophyllales representing seven genera and analyzed them together with a diverse set of Agaricomycotina, emphasizing Polyporales. Boreostereum, which is suspected to produce a white rot, is the sister group of the rest of the Gloeophyllales, all of which produce a brown rot. Gloeophyllum contains at least two independent clades, one of which might correspond to the genus Osmoporus. White rot and resupinate fruiting bodies appear to be plesiomorphic in Gloeophyllales. Relaxed molecular clock analyses suggest that the Gloeophyllales arose in the Cretaceous, after the origin of Pinaceae.     

Phylogenetic similarity and structure of Agaricomycotina communities across a forested landscape

The Agaricomycotina are a phylogenetically diverse group of fungi that includes both saprotrophic and mycorrhizal species, and that form species – rich communities in forest ecosystems. Most species are infrequently observed, and this hampers assessment of the role that environmental heterogeneity plays in determining local community composition and in driving β‐diversity. We used a combination of phenetic (TRFLP) and phylogenetic approaches [Unifrac and Net Relatedness Index (NRI)] to examine the compositional and phylogenetic similarity of Agaricomycotina communities in forest floor and surface soil of three widely distributed temperate upland forest ecosystems (one, xeric oak – dominated and two, mesic sugar maple dominated). Generally, forest floor and soil communities had similar phylogenetic diversity, but there was little overlap of species or evolutionary lineages between these two horizons. Forest floor communities were dominated by saprotrophic species, and were compositionally and phylogenetically similar in all three ecosystems. Mycorrhizal species represented 30% to 90% of soil community diversity, and these communities differed compositionally and phylogenetically between ecosystems. Estimates of NRI revealed significant phylogenetic clustering in both the forest floor and soil communities of only the xeric oak‐dominated forest ecosystem, and may indicate that this ecosystem acts as a habitat filter. Our results suggest that environmental heterogeneity strongly influences the phylogenetic β‐diversity of soil inhabiting Agaricomycotina communities, but has only a small influence on forest floor β‐diversity. Moreover, our results suggest that the strength of community assembly processes, such as habitat filtering, may differ between temperate forest ecosystems.     

A phylogenetic study of the genus Cookeina

Cookeina, with seven recognized species, is one of the commonly encountered genera of the Sarcoscyphaceae (Pezizales) in tropical and subtropical areas around the world. Morphologically the species are distinguished by combinations of several features including ascospore shape and surface relief, presence and origin of apothecial hairs and presence or absence of gelatinous material within the cortical layer of the excipular tissue. Color of the hymenium, attributed to carotenoid pigments, is particularly variable in some collections especially those referred to as C. speciosa. In this study phylogenetic analyses were carried out using rDNA ITS and rDNA LSU sequences. Forty-four collections were studied which included a broad sampling of color variants of C. speciosa from a field site in Venezuela. The genus was shown to be monophyletic with several well-supported lineages. These analyses generally support the established, morphologically distinguished taxa within a monophyletic genus Cookeina. Collections referred to as C. speciosa segregate within a clade in which hymenial color differences are associated with groups within the clade. Cookeina sinensis is sister to C. tricholoma but is distinct from it; C. indica fails to resolve with any of the major clades. The placement of C. insititia is ambiguous but it falls within Cookeina and thus is considered in the genus Cookeina rather than in a separate genus, Boedijnopeziza.     

A phylogenetic test of the calcichordate scenario

The calcichordate scenario of Jefferies and colleagues purports to explain the origin and early evolution of the phyla Echinodermata and Chordata. Calcichordate proponents have argued that echinoderms are the sister group of the chordates and urochordates are the sister group of the craniates. These phylogenetic hypotheses, which differ from the traditional groupings, are derived primarily from morphological interpretations of carpoids (solutes, cornutes, and mitrates), an enigmatic fossil group usually held to be primitive stem-group echinoderms. Although the scenario has received only limited support, it has yet to be falsified. The difficulty with falsifying the calcichordate scenario is proving that the morphological interpretations, for example, that carpoids possessed notochords, dorsal hollow nerve cords, and other typical chordate or craniate characters, are incorrect. Here, rather than argue over the interpretation of fossils, the phylogenetic hypotheses embedded within the scenario are tested. It is found that the calcichordate scenario fails such a test, even if both the Recent and fossils forms are coded according to the calcichordate scenario. It is argued that: (1) the erection of scenarios must follow the construction of a cladogram; and (2) fossils are unable to dictate the relationships among phyla. □ Calcichordate scenario, Carpoidea, Deuterostomia, Echinodermata, Chordata, phylogeny, cladistics.     

A phylogenetic dissection of the family micrococcaceae

A comparative analysis of 16S ribosomal RNA sequences in the Micrococcaceae shows the family not to be a phylogenetically coherent unit. In fact, at least two of its three genera are themselves not valid phylogenetic units. Species, of the genusMicrococcus are phylogenetically inseparable from those ofArthrobacter. The genusPlanococcus groups specifically with certain members ofBacillus, andStaphylococcus is also related to the genusBacillus, though more peripherally. These findings question the validity of spherical shape as a valid indicator of phylogenetic relationships on all but the lowest levels.     

A phylogenetic study of the free-living amoeba

Immunological distances were determined for four strains of the free-living amoeba classified as Amoeba proteus, two strains classified as Polychaos dubia and a single strain classified as Chaos carolinensis. The data show that the _ShP strain does not belong to the proteus group; that A. proteus is more closely related to C. carolinensis and is derived from Chaos as is the _ShP strain; that P. dubia and C. carolinensis are the more distantly related species and appear to be the first of the above to have diverged from a common ancestor; and that the amoebae have a long evolutionary history. The accuracy of the phylogenetic tree and the distance Wagner network was discussed. Since the amoebae may be polyphyletic in origin, the latter was assumed to be a more accurate representation of the immunological distance data.     

A phylogenetic analysis of the land plants

Phylogenetic systematics (cladistics) is a theory of phylogeny reconstruction and classification widely used in zoology. Taxa are grouped hierarchically by the sharing of derived (advanced) characters. The information is expressed in a cladogram, a best estimate of a phylogeny. Plant systematists generally use a phenetic system, grouping taxa on overall similarity which results in many groups being formed, at least in part, on the basis of shared primitive characters.
The methods of phylogenetic systematics are used to create a preliminary cladogram of land plants. The current classification of land plants is criticized for its inclusion of many groups which are not monophyletic.
Objections to the use of phylogenetic systematics in botany, apparent convergences within major groups and frequent hybridization, are shown to be invalid. It is concluded that cladistic analysis presents the best estimate of die natural hierarchy of organisms, and should be adopted by plant systematists in their assessment of plant interrelationships.     

A phylogenetic analysis of the family Dermatophilaceae

The comparative analysis of the 16S ribosomal ribonucleic acid (rRNA) of Geodermatophilus obscurus DSM 43060 and Dermatophilus congolensis DSM 43037 revealed that these members of the family Dermatophilaceae were only remotely related. While G. obscurus represented an individual and separate line of descent within the phylogenetically defined order Actinomycetales, D. congolensis was closely related to representatives of Arthrobacter, Micrococcus, Cellulomonas, Brevibacterium, Promicromonospora and Microbacterium.     

A phylogenetic analysis of the allometry of diving

The oxygen store/usage hypothesis suggests that larger animals are able to dive for longer and hence deeper because oxygen storage scales isometrically with body mass, whereas oxygen usage scales allometrically with an exponent <1 (typically 0.67-0.75). Previous tests of the allometry of diving tend to reject this hypothesis, but they are based on restricted data sets or invalid statistical analyses (which assume that every species provides independent information). Here we apply information-theoretic statistical methods that are phylogenetically informed to a large data set on diving variables for birds and mammals to describe the allometry of diving. Body mass is strongly related to all dive variables except dive:pause ratio. We demonstrate that many diving variables covary strongly with body mass and that they have allometric exponents close to 0.33. Thus, our results fail to falsify the oxygen store/usage hypothesis. The allometric relationships for most diving variables are statistically indistinguishable for birds and mammals, but birds tend to dive deeper than mammals of equivalent mass. The allometric relationships for all diving variables except mean dive duration are also statistically indistinguishable for all major taxonomic groups of divers within birds and mammals, with the exception of the procellariiforms, which, strictly speaking, are not true divers.     

A phylogenetic analysis of Legionella

Four species of Legionella, L. pneumophila NCTC 11192, L. bozemanii NCTC 11368, L. micdadei NCTC 11371 and L. jordanis ATCC 33623 have been characterized by oligonucleotide cataloguing of their 16S ribosomal RNA. All four species are phylogenetically closely related, while no specific relationship could be detected with any other group of organisms investigated so far with respect to this method. At a low level of relationship legionellae are members of the broad group of purple photosynthetic bacteria and their non-phototrophic relatives, in which Legionella form an independent line of descent.     

A phylogenetic analysis of the globins in fungi

Background

All globins belong to one of three families: the F (flavohemoglobin) and S (sensor) families that exhibit the canonical 3/3 α-helical fold, and the T (truncated 3/3 fold) globins characterized by a shortened 2/2 α-helical fold. All eukaryote 3/3 hemoglobins are related to the bacterial single domain F globins. It is known that Fungi contain flavohemoglobins and single domain S globins. Our aims are to provide a census of fungal globins and to examine their relationships to bacterial globins.

Results

Examination of 165 genomes revealed that globins are present in >90% of Ascomycota and ∼60% of Basidiomycota genomes. The S globins occur in Blastocladiomycota and Chytridiomycota in addition to the phyla that have FHbs. Unexpectedly, group 1 T globins were found in one Blastocladiomycota and one Chytridiomycota genome. Phylogenetic analyses were carried out on the fungal globins, alone and aligned with representative bacterial globins. The Saccharomycetes and Sordariomycetes with two FHbs form two widely divergent clusters separated by the remaining fungal sequences. One of the Saccharomycete groups represents a new subfamily of FHbs, comprising a previously unknown N-terminal and a FHb missing the C-terminal moiety of its reductase domain. The two Saccharomycete groups also form two clusters in the presence of bacterial FHbs; the surrounding bacterial sequences are dominated by Proteobacteria and Bacilli (Firmicutes). The remaining fungal FHbs cluster with Proteobacteria and Actinobacteria. The Sgbs cluster separately from their bacterial counterparts, except for the intercalation of two Planctomycetes and a Proteobacterium between the Fungi incertae sedis and the Blastocladiomycota and Chytridiomycota.

Conclusion

Our results are compatible with a model of globin evolution put forward earlier, which proposed that eukaryote F, S and T globins originated via horizontal gene transfer of their bacterial counterparts to the eukaryote ancestor, resulting from the endosymbiotic events responsible for the origin of mitochondria and chloroplasts.     

A phylogenetic analysis of the lipocalin protein family

The lipocalins are a family of extracellular proteins that bind and transport small hydrophobic molecules. They are found in eubacteria and a great variety of eukaryotic cells, in which they play diverse physiological roles. We report here the detection of two new eukaryotic lipocalins and a phylogenetic analysis of 113 lipocalin family members performed with maximum-likelihood and parsimony methods on their amino acid sequences. Lipocalins segregate into 13 monophyletic clades, some of which are grouped in well-supported superclades. An examination of the G + C content of the bacterial lipocalin genes and the detection of four new conceptual lipocalins in other eubacterial species argue against a recent horizontal transfer as the origin of prokaryotic lipocalins. Therefore, we rooted our lipocalin tree using the clade containing the prokaryotic lipocalins. The topology of the rooted lipocalin tree is in general agreement with the currently accepted view of the organismal phylogeny of arthropods and chordates. The rooted tree allows us to assign polarity to character changes and suggests a plausible scenario for the evolution of important lipocalin properties. More recently evolved lipocalins tend to (1) show greater rates of amino acid substitutions, (2) have more flexible protein structures, (3) bind smaller hydrophobic ligands, and (4) increase the efficiency of their ligand-binding contacts. Finally, we found that the family of fatty-acid-binding proteins originated from the more derived lipocalins and therefore cannot be considered a sister group of the lipocalin family.     

A phylogenetic analysis of the purple photosynthetic bacteria

It is proposed that gliding motility in bacteria is based on rotary assemblies located in the cell envelope and that these assemblies may be analogous to basal regions of bacterial flagella. This proposal rests on the following evidence: (i) Structures resembling flagellar basal regions have been demonstrated in cells ofCytophaga johnsonae andFlexibacter columnaris, and such structures are absent from one nonmotile mutant ofF. columnaris. (ii) The effects of inhibitors of energy metabolism on gliding motility are identical with their effects on prokaryotic fiagellar motility. (iii) The active movement of latex spheres along surfaces of gliding bacteria appears to depend on mechanisms responsible for motility and can be explained by the presence of rotary surface assemblies.