Phylogenetic analysis of the formin homology 2 domain

Formin proteins are key regulators of eukaryotic actin filament assembly and elongation, and many species possess multiple formin isoforms. A nomenclature system based on fundamental features would be desirable, to aid the rapid identification and characterization of novel formins. In this article, we attempt to systematize the formin family by performing phylogenetic analyses of the formin homology 2 (FH2) domain, an independently folding region common to all formins, which alone can influence actin dynamics. Through database searches, we identify 101 FH2 domains from 26 eukaryotic species, including 15 in mice. Sequence alignments reveal a highly conserved yeast-specific insert in the "knob loop" region of the FH2 domain, with unknown functional consequences. Phylogenetic analysis using minimum evolution (ME), maximum parsimony (MP), and maximum likelihood (ML) algorithms strongly supports the existence of seven metazoan groups. Yeast FH2 domains segregate from all other eukaryotes, including metazoans, other fungi, plants, and protists. Sequence comparisons of non-FH2 regions support relationships between three metazoan groups (Dia, DAAM, and FRL) and examine previously identified coiled-coil and Diaphanous auto-regulatory domain sequences. This analysis allows for a formin nomenclature system based on sequence relationships, as well as suggesting strategies for the determination of biochemical and cellular activities of these proteins.     

Phylogenetic analysis of fungal centromere H3 proteins

Centromere H3 proteins (CenH3's) are variants of histone H3 specialized for packaging centromere DNA. Unlike canonical H3, which is among the most conserved of eukaryotic proteins, CenH3's are rapidly evolving, raising questions about orthology and conservation of function across species. To gain insight on CenH3 evolution and function, a phylogenetic analysis was undertaken on CenH3 proteins drawn from a single, ancient lineage, the Fungi. Using maximum-likelihood methods, a credible phylogeny was derived for the conserved histone fold domain (HFD) of 25 fungal CenH3's. The collection consisted mostly of hemiascomycetous yeasts, but also included basidiomycetes, euascomycetes, and an archaeascomycete. The HFD phylogeny closely recapitulated known evolutionary relationships between the species, supporting CenH3 orthology. The fungal CenH3's lacked significant homology in their N termini except for those of the Saccharomyces/Kluyveromyces clade that all contained a region homologous to the essential N-terminal domain found in Saccharomyces cerevisiae Cse4. The ability of several heterologous CenH3's to function in S. cerevisiae was tested and found to correlate with evolutionary distance. Domain swapping between S. cerevisiae Cse4 and the noncomplementing Pichia angusta ortholog showed that species specificity could not be explained by the presence or absence of any recognized secondary structural element of the HFD.     

Phylogenetic classification and the definition of taxon names

Taxon names should be founded on phylogenetic relationships. and the names defined on the basis of common ancestry. Definitions based on evolutionary relationships relate the names to a phylogeny, and while the inclusiveness of the name may change with changing hypotheses of monophyly, the actual name remains unaltered. The limits of the name arc fixed by pointing to a monophyletic clade, where group membership is determined by the relationship to this clade. and not to subjective decisions of taxon delineations. Since phylogenetic definitions unambiguously connect the name to a specified clade, and not to a type, the conventional type concept becomes superfluous. We furthermore consider the Linnean categories poorly suited to convey the information in evolutionary trees, and suggest that these categories are abandoned.     

Phylogenetic and trait-based assembly of arbuscular mycorrhizal fungal communities

Both competition and environmental filtering are expected to influence the community structure of microbes, but there are few tests of the relative importance of these processes because trait data on these organisms is often difficult to obtain. Using phylogenetic and functional trait information, we tested whether arbuscular mycorrhizal (AM) fungal community composition in an old field was influenced by competitive exclusion and/or environmental filtering. Communities at the site were dominated by species from the most speciose family of AM fungi, the Glomeraceae, though species from two other lineages, the Acaulosporaceae and Gigasporaceae were also found. Despite the dominance of species from a single family, AM fungal species most frequently co-existed when they were distantly related and when they differed in the ability to colonize root space on host plants. The ability of AM fungal species to colonize soil did not influence co-existence. These results suggest that competition between closely related and functionally similar species for space on plant roots influences community assembly. Nevertheless, in a substantial minority of cases communities were phylogenetically clustered, indicating that closely related species could also co-occur, as would be expected if i) the environment restricted community membership to single functional type or ii) competition among functionally similar species was weak. Our results therefore also suggest that competition for niche space between closely related fungi is not the sole influence of mycorrhizal community structure in field situations, but may be of greater relative importance than other ecological mechanisms.     

Phylogenetic classification of protozoa based on the structure of the linker domain in the bifunctional enzyme, dihydrofolate reductase-thymidylate synthase

We have determined the crystal structure of dihydrofolate reductase-thymidylate synthase (DHFR-TS) from Cryptosporidium hominis, revealing a unique linker domain containing an 11-residue alpha-helix that has extensive interactions with the opposite DHFR-TS monomer of the homodimeric enzyme. Analysis of the structure of DHFR-TS from C. hominis and of previously solved structures of DHFR-TS from Plasmodium falciparum and Leishmania major reveals that the linker domain primarily controls the relative orientation of the DHFR and TS domains. Using the tertiary structure of the linker domains, we have been able to place a number of protozoa in two distinct and dissimilar structural families corresponding to two evolutionary families and provide the first structural evidence validating the use of DHFR-TS as a tool of phylogenetic classification. Furthermore, the structure of C. hominis DHFR-TS calls into question surface electrostatic channeling as the universal means of dihydrofolate transport between TS and DHFR in the bifunctional enzyme.     

Phylogenetic classification of short environmental DNA fragments

Metagenomics is providing striking insights into the ecology of microbial communities. The recently developed massively parallel 454 pyrosequencing technique gives the opportunity to rapidly obtain metagenomic sequences at a low cost and without cloning bias. However, the phylogenetic analysis of the short reads produced represents a significant computational challenge. The phylogenetic algorithm CARMA for predicting the source organisms of environmental 454 reads is described. The algorithm searches for conserved Pfam domain and protein families in the unassembled reads of a sample. These gene fragments (environmental gene tags, EGTs), are classified into a higher-order taxonomy based on the reconstruction of a phylogenetic tree of each matching Pfam family. The method exhibits high accuracy for a wide range of taxonomic groups, and EGTs as short as 27 amino acids can be phylogenetically classified up to the rank of genus. The algorithm was applied in a comparative study of three aquatic microbial samples obtained by 454 pyrosequencing. Profound differences in the taxonomic composition of these samples could be clearly revealed.     

Phylogenetic determinants of potential host shifts in fungal pathogens

Understanding what determines the host range of pathogens and the potential for host shifts is of critical importance to controlling their introductions into new environments. The phylogeny of the hosts has been shown to be important: pathogens are more likely to be infectious on hosts closely related to their host‐of‐origin because of the similar host environments that is shared by descent. The importance of pathogen phylogenies for predicting host range has never been investigated, although a pathogen should also be able to exploit a new host that its close relative can infect. We performed cross‐inoculations using a plant–fungal association and showed that both host and pathogen phylogenies were significant predictors of host range, with at least partly independent effects. Furthermore, we showed that some pathogens were better at infecting novel hosts. Our results should have implications in the context of biological invasions and emergences of new diseases due to globalization.     

Phylogenetic analysis of the Cnidaria

The recent members of the phylum Cnidaria were analyzed with phylogenetic methodology and the help of the PAUP Computer program. The Cnidaria are established as a monophylum by their cnidocysts, planula larva, and a polyp stage. The Ctenophora were seen as the most probable sister group of the Cnidaria. Arguments for the monophyly of the cnidarian classes Anthozoa, Scyphozoa, Cubozoa, and Hydrozoa were providea. For the ground plan of the Cnidaria the following characters were postulated: triphasic life cycle consisting of a planula larva, a benthic polyp stage, and a sexually propagating medusa like stage. For the polyp a radial symmetry, lack of septae, and hollow tentacles were assumed. The original medusa probably was tetraradial and developed from the polyp stage by a total metamorphosis. Twelve polarized characters were used to generate cladograms. The most parsimonious one showed the Anthozoa as the first offshoot of the tree with the united Scyphozoa, Cubozoa and Hydrozoa forming its sister group. Within this sister group the Scyphozoa and Cubozoa were seen as sistergroups to each other. Both groups united are then the sistergroup of the Hydrozoa. A bootstrap analysis yielded the same tree with high probabilities for the internal nodes. Despite assuming a planktonic origin of the Cnidaria in this investigation, the resulting cladogram is also compatible with an evolution of the medusa stage within the Cnidaria after the splitting-off of the Anthozoa. The possible loss of the medusa stage in the Anthozoa is discussed.     

热带爪蟾bHLH转录因子鉴定与进化分析

爪蟾是重要的生物医学模式动物。文章根据NCBI公布的热带爪蟾(Xenopus tropicalis)基因组数据,利用生物信息学方法提取和鉴定了爪蟾全基因组范围的碱性螺旋-环-螺旋(bHLH)基因信息,应用系统发生方法进行分类并做基因本体论(Gene Ontology,GO)功能富集分布分析,以期从整体上探讨爪蟾bHLH转录因子基因家族的分类及功能。结果表明,在热带爪蟾基因组数据库中发现了70个bHLH转录因子,其中69个可以分别归到6大组(A~F)的34个亚家族中,另一个为"孤儿因子"(Orphan)基因。GO富集分布统计发现有51个显著富集分布的GO注释语句,其中转录调控活性、转录调控、DNA结合、RNA代谢过程调控、DNA依赖的转录调控、转录和转录因子活性等出现频率很高,表明这些GO术语是爪蟾bHLH基因最常见的功能;许多bHLH转录因子在一些重要的发育或生理过程中发挥调控作用,如肌肉组织和器官(横纹肌、骨骼肌、眼部和咽部肌肉)的分化和发育、消化系统发育、咽部和感觉器官的发育、碱基和核苷及核酸的代谢调控、生物合成过程调控、DNA结合和蛋白质异聚化活性等。另外,还有一些重要信号通路(Signaling pathway)的GO术语显著地富集。文章还对Hes转录因子家族做了进化分析。这些结果为热带爪蟾bHLH基因的进一步研究打下了很好的基础。     

New fungal classification and their applications in medicine

Fungi are gaining importance with the increased incidence of invasive, often fatal mycoses, in immunocompromised patients. In addition, the increased number of emerging opportunistic pathogens has prompted interest in studies pertaining to fungal classification. The traditional methods of identification and classification of these microorganisms are based on the morphology of the sexual and asexual reproductive structures. Recently, this system of classification has been shown incongruent with approaches that better establish phylogenetic relationships among these organisms. Novel aspects of fungal reclassification are described as follows: 1) the position of fungi in the historical classification systems, 2) the recognition of their polyphyly, based on comparative studies of nucleic acid sequences and on analysis of descent lines and, 3) the contribution of molecular phylogeny to medical mycology, including identification of mycotic agents, their molecular epidemiology, prevention of infection and methods of diagnosis.     

Phylogenetic analysis of Allium subg. Melanocrommyum infers cryptic species and demands a new sectional classification

Allium subgenus Melanocrommyum (Alliaceae) from Eurasia comprises about 150 mostly diploid species adapted to arid conditions. The group is taxonomically complicated with different and contradictory taxonomic treatments, and was thought to include a considerable number of hybrid species, as the taxa show an admixture of assumed morphological key characters. We studied the phylogeny of the subgenus, covering all existing taxonomic groups and their entire geographic distribution. We analyzed sequences of the nuclear rDNA internal transcribed spacer region (ITS) for multiple individuals of more than 100 species. Phylogenetic analyses of cloned and directly sequenced PCR products confirmed the monophyly of the subgenus, while most sections were either para- or polyphyletic. The splits of the large sections are supported by differences in the anatomy of flower nectaries. ITS data (i) demand a new treatment at sectional level, (ii) do not support the hypotheses of frequent gene flow among species, (iii) indicate that multiple rapid radiations occurred within different monophyletic groups of the subgenus, and (iv) detected separately evolving lineages within three morphologically clearly defined species (cryptic species). In two cases these lineages were close relatives, while in Allium darwasicum they fall in quite different clades in the phylogenetic tree. Fingerprint markers show that this result is not due to ongoing introgression of rDNA (ITS capture) but that genome-wide differences between both lineages exist. Thus, we report one of the rare cases in plants where morphologically indistinguishable diploid species occurring in mixed populations are non-sister cryptic species.     

Phylogenetic and functional analysis of Aspergillus fumigatus MGTC, a fungal protein homologous to a bacterial virulence factor

MgtC is important for the survival of several bacterial pathogens in macrophages and for growth under magnesium limitation. Among eukaryotes, a gene homologous to mgtC was found only in the pathogenic fungus Aspergillus fumigatus. Our data show that the A. fumigatus MgtC (AfuMgtC) protein does not have the same function as the bacterial MgtC proteins.     

Phylogenetic analysis of four nuclear protein-encoding genes largely corroborates the traditional classification of Bivalvia (Mollusca)

Revived interest in molluscan phylogeny has resulted in a torrent of molecular sequence data from phylogenetic, mitogenomic, and phylogenomic studies. Despite recent progress, basal relationships of the class Bivalvia remain contentious, owing to conflicting morphological and molecular hypotheses. Marked incongruity of phylogenetic signal in datasets heavily represented by nuclear ribosomal genes versus mitochondrial genes has also impeded consensus on the type of molecular data best suited for investigating bivalve relationships. To arbitrate conflicting phylogenetic hypotheses, we evaluated the utility of four nuclear protein-encoding genes-ATP synthase β, elongation factor-1α, myosin heavy chain type II, and RNA polymerase II-for resolving the basal relationships of Bivalvia. We sampled all five major lineages of bivalves (Archiheterodonta, Euheterodonta [including Anomalodesmata], Palaeoheterodonta, Protobranchia, and Pteriomorphia) and inferred relationships using maximum likelihood and Bayesian approaches. To investigate the robustness of the phylogenetic signal embedded in the data, we implemented additional datasets wherein length variability and/or third codon positions were eliminated. Results obtained include (a) the clade (Nuculanida+Opponobranchia), i.e., the traditionally defined Protobranchia; (b) the monophyly of Pteriomorphia; (c) the clade (Archiheterodonta+Palaeoheterodonta); (d) the monophyly of the traditionally defined Euheterodonta (including Anomalodesmata); and (e) the monophyly of Heteroconchia, i.e., (Palaeoheterodonta+Archiheterodonta+Euheterodonta). The stability of the basal tree topology to dataset manipulation is indicative of signal robustness in these four genes. The inferred tree topology corresponds closely to those obtained by datasets dominated by nuclear ribosomal genes (18S rRNA and 28S rRNA), controverting recent taxonomic actions based solely upon mitochondrial gene phylogenies.     

Phylogenetic relationships and classification of the Vespinae (Hymenoptera: Vespidae)

Abstract. The phylogenetic relationships of the genera, subgenera and species-groups of the Vespinae are analysed using cladistic techniques. The results are used as the basis for a natural classification of these wasps. The cladogram for the four genera recognized is: Vespa + (Provespa + (Dolichovespula + Vespula)). No subgenera are recognized; all those previously described are synonymized with the appropriate genus. The synonymies of Nyctovespa with Vespa and Rugovespula with Vespula are new.     

Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins

Sirtuins (Sir2-like proteins) are present in prokaryotes and eukaryotes. Here, two new human sirtuins (SIRT6 and SIRT7) are found to be similar to a particular subset of insect, nematode, plant, and protozoan sirtuins. Molecular phylogenetic analysis of 60 sirtuin conserved core domain sequences from a diverse array of organisms (including archaeans, bacteria, yeasts, plants, protozoans, and metazoans) shows that eukaryotic Sir2-like proteins group into four main branches designated here as classes I-IV. Prokaryotic sirtuins include members of classes II and III. A fifth class of sirtuin is present in gram positive bacteria and Thermotoga maritima. Saccharomyces cerevisiae has five class I sirtuins. Caenorhabditis elegans and Drosophila melanogaster have sirtuin genes from classes I, II, and IV. The seven human sirtuin genes include all four classes: SIRT1, SIRT2, and SIRT3 are class I, SIRT4 is class II, SIRT5 is class III, and SIRT6 and SIRT7 are class IV.