Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers

Estimating phylogenetic relationships among closely related species can be extremely difficult when there is incongruence among gene trees and between the gene trees and the species tree. Here we show that incorporating a model of the stochastic loss of gene lineages by genetic drift into the phylogenetic estimation procedure can provide a robust estimate of species relationships, despite widespread incomplete sorting of ancestral polymorphism. This approach is applied to a group of montane Melanoplus grasshoppers for which genealogical discordance among loci and incomplete lineage sorting obscures any obvious phylogenetic relationships among species. Unlike traditional treatments where gene trees estimated using standard phylogenetic methods are implicitly equated with the species tree, with the coalescent-based approach the species tree is modeled probabilistically from the estimated gene trees. The estimated species phylogeny (the ESP) is calculated for the grasshoppers from multiple gene trees reconstructed for nuclear loci and a mitochondrial gene. This empirical application is coupled with a simulation study to explore the performance of the coalescent-based approach. Specifically, we test the accuracy of the ESP given the data based on analyses of simulated data matching the multilocus data collected in Melanoplus (i.e., data were simulated for each locus with the same number of base pairs and locus-specific mutational models). The results of the study show that ESPs can be computed using the coalescent-based approach long before reciprocal monophyly has been achieved, and that these statistical estimates are accurate. This contrasts with analyses of the empirical data collected in Melanoplus and simulated data based on concatenation of multiple loci, for which the incomplete lineage sorting of recently diverged species posed significant problems. The strengths and potential challenges associated with incorporating an explicit model of gene-lineage coalescence into the phylogenetic procedure to obtain an ESP, as illustrated by application to Melanoplus, versus concatenation and consensus approaches are discussed. This study represents a fundamental shift in how species relationships are estimated - the relationship between the gene trees and the species phylogeny is modeled probabilistically rather than equating gene trees with a species tree.     

Molecular phylogeny and biogeography of an ancient Holarctic lineage of mygalomorph spiders (Araneae: Antrodiaetidae: Antrodiaetus)

The mygalomorph spider genera Antrodiaetus and Atypoides (Antrodiaetidae) belong to an ancient lineage that has persisted since at least the Cretaceous. These spiders display a classic disjunct Holarctic distribution with species in the eastern Palaearctic plus the western and eastern Nearctic. Prior phylogenetic analyses of this group have been proposed on the basis of morphology, but lack strong support and independent corroboration. Here we present the first phylogenetic analysis of species-level relationships based on molecular data obtained from the mitochondrial (cytochrome c oxidase subunit I) and nuclear (18S and 28S rRNA) genomes. Analyses corroborate earlier findings that Atypoides forms a paraphyletic grade with respect to Antrodiaetus, and consequently, that genus is formally synonymized under Antrodiaetus. In addition, our results support the relatively early divergence of Antrodiaetus roretzi. Antrodiaetus pacificus is "paraphyletic" with respect to the A. lincolnianus group and is likely an assemblage of numerous species. The final topology based on a combined molecular dataset, in conjunction with two different molecular dating techniques (penalized likelihood plus a Bayesian approach) and ancestral distribution reconstructions, was used to infer the historical biogeography of these spiders. Trans-Beringian and trans-Atlantic routes appear to account for the present-day distribution of Antrodiaetus in Japan and North America. Future studies on Antrodiaetus phylogeny will be used to address questions regarding morphological stasis and the evolution of quantitative morphological characters.     

A new lineage of lichenized basidiomycetes inferred from a two-gene phylogeny: The Lepidostromataceae with three species from the tropics

The lichen habit has apparently evolved independently in at least five major clades of mushroom-forming basidiomycetes (Agaricomycetes). Tracing the origin of lichenization in these groups depends on a clearer understanding of the phylogenetic relationships of basidiolichens to other fungi. We describe here a new family of basidiolichens made up of tropical, soil-inhabiting fungi that form lichenized, scale-like squamules and erect, coral-like fruiting structures. These structures are common to two basidiolichen genera, Multiclavula and Lepidostroma. Molecular studies have confirmed the phylogenetic position of Multiclavula species in the Cantharellales, but Lepidostroma species have never been sequenced. We obtained nuclear small and large subunit ribosomal sequences from specimens of L. calocerum collected in Costa Rica and Mexico and also from specimens of two Multiclavula spp. recently described from Rwanda. The phylogenetic placement of these fungi within the Agaricomycetes was investigated using likelihood and Bayesian analyses. Our results indicate that L. calocerum and the Rwandan species form a natural group unrelated to Multiclavula and sister to the Atheliales, members of which are neither lichen-forming nor clavarioid. The independent evolution of morphologically similar forms in so many groups of basidiomycetes is a remarkable example of convergence, indicating similar pathways to lichenization in these fungi.     

The stem species of our species: a place for the archaic human cranium from Ceprano, Italy

One of the present challenges in the study of human evolution is to recognize the hominin taxon that was ancestral to Homo sapiens. Some researchers regard H. heidelbergensis as the stem species involved in the evolutionary divergence leading to the emergence of H. sapiens in Africa, and to the evolution of the Neandertals in Europe. Nevertheless, the diagnosis and hypodigm of H. heidelbergensis still remain to be clarified. Here we evaluate the morphology of the incomplete cranium (calvarium) known as Ceprano whose age has been recently revised to the mid of the Middle Pleistocene, so as to test whether this specimen may be included in H. heidelbergensis. The analyses were performed according to a phenetic routine including geometric morphometrics and the evaluation of diagnostic discrete traits. The results strongly support the uniqueness of H. heidelbergensis on a wide geographical horizon, including both Eurasia and Africa. In this framework, the Ceprano calvarium--with its peculiar combination of archaic and derived traits--may represent, better than other penecontemporaneous specimens, an appropriate ancestral stock of this species, preceding the appearance of regional autapomorphic features.     

Differentiation profile of brain tumor stem cells： a comparative study with neural stem cells

Understanding of the differentiation profile of brain tumor stem cells （BTSCs）, the key ones among tumor cell population, through comparison with neural stem cells （NSCs） would lend insight into the origin of glioma and ultimately yield new approaches to fight this intractable disease. Here, we cultured and purified BTSCs from surgical glioma specimens and NSCs from human fetal brain tissue, and further analyzed their cellular biological behaviors, especially their differentiation property. As expected, NSCs differentiated into mature neural phenotypes. In the same differentiation condition, however, BTSCs exhibited distinguished differences. Morphologically, cells grew flattened and attached for the first week, but gradually aggregated and reformed floating tumor sphere thereafter. During the corresponding period, the expression rate of undifferentiated cell marker CD 133 and nestin in BTSCs kept decreasing, but 1 week later, they regained ascending tendency. Interestingly, the differentiated cell markers GFAP and β-tubulinlII showed an expression change inverse to that of undifferentiated cell markers. Taken together, BTSCs were revealed to possess a capacity to resist differentiation, which actually represents the malignant behaviors of glioma.     

Platelet membrane molecular organization: relationship with membrane bound calcium

The fatty acid spin label 5 nitroxide stearate has been used to determine the membrane organization changes induced by platelet aggregation. A decrease in order is observed with thrombin, even in the presence of EDTA, when aggregation is inhibited. Conversely, after aggregation by the calcium ionophore A23187 the rigidity of the phospholipids is not modified. These effects are discussed in relation to the release of membrane bound calcium induced by thrombin.     

Brain tumour stem cells: the undercurrents of human brain cancer and their relationship to neural stem cells

Conceptual and technical advances in neural stem cell biology are being applied to the study of human brain tumours. These studies suggest that human brain tumours are organized as a hierarchy and are maintained by a small number of tumour cells that have stem cell properties. Most of the bulk population of human brain tumours comprise cells that have lost the ability to initiate and maintain tumour growth. Although the cell of origin for human brain tumours is uncertain, recent evidence points towards the brain's known proliferative zones. The identification of brain tumour stem cells has important implications for understanding brain tumour biology and these cells may be critical cellular targets for curative therapy.     

Golgi organization and the apical extension of fungal hyphae: an essential relationship

The Golgi apparatus performs crucial functions in the sorting and processing of proteins destined for secretion from eukaryotic cells. In filamentous fungi, organization of the Golgi apparatus reflects the unique challenges brought about by the highly polarized nature of hyphal growth. Recent results show that Golgi compartments are spatially segregated within hyphal tip cells in a manner that depends upon the integrity of the cytoskeleton. Moreover, loss of normal Golgi organization stops polarized hyphal extension and triggers de‐polarization of the hyphal tip. These results emphasize the point that a spatially organized and dynamic Golgi apparatus represents an adaptation that is as important for hyphal extension as is the presence of a Spitzenkörper. In addition, they also identify regulatory mechanisms that could enable controlled de‐polarization of hyphae during development or infection‐related morphogenesis.     

New insights on the phylogeny of Tectaria (Tectariaceae), with special reference to Polydictyum as a distinct lineage

The fern genus Tectaria (Tectariaceae) Cav. is morphologically diverse and difficult in terms of recognizing species and species groups. To infer the systematic positions of some species and identity-unknown collections with special morphological characters, we undertook phylogenetic analyses based on sequences of five plastid regions (atpB, ndhF + ndhF-trnL, rbcL, rps16-matK + matK, and trnL-F). Three analysis methods (maximum parsimony, maximum likelihood, and Bayesian inference) were used to reconstruct the phylogeny of Tectaria. The most surprising result is that T. menyanthidis (C. Presl) Copel., T. ternata (Baker) Copel., and T. variabilis Tardieu & Ching are revealed to represent a distinct lineage from Tectaria, which should be called Polydictyum C. Presl, and is supported as sister to Pteridrys C. Chr. & Ching. Other accessions of Tectaria are well resolved into four major clades, which is consistent with the results of previous studies. Of the four clades, Clade II (T. subtriphylla (Hook. & Arn.) Copel. group) is unpredictable, with morphologically very diverse species clustered there, and is supposed to be a minor evolutionary line within Tectaria in the Old World. In addition, the position of the climbing genus Arthropteris J. Sm. and the utility of molecular data in recognizing species of Tectaria are briefly discussed. As a conclusion, we formally reinstate the genus Polydictyum by providing diagnostic characters, key to species, nomenclature, and information of detailed distribution and habitat for the currently known three species.     

Multilocus phylogeny defines a new classification of Staphylininae (Coleoptera,Staphylinidae), a rove beetle group with high lineage diversity

We provide the first multilocus molecular phylogeny of a group corresponding to the former subfamily Staphylininae. Results are corroborated by the morphological, biogeographical and palaeobiological evidence to serve as a baseline for an updated suprageneric classification. The former subfamily Staphylininae is proven to be a lineage sister to the monophyletic Paederinae and reclassified according to a robust phylogeny resolving a number of long-standing controversies. The subfamily Xantholininae (revised status) is reinstated to contain the tribes Xantholinini, Othiini, Maorothiini and Diochini. Subfamily Platyprosopinae (revised status) is reinstated for the tribes Platyprosopinini, Arrowinini and †Thayeralinini. For a highly peculiar genus Coomania Cameron, formerly in Diochini, a new subfamily Coomaniinae subfam.n. is established and the composition of Diochini (revised status) is changed accordingly. The subfamily Staphylininae (revised status) is reduced to contain the former tribe Staphylinini only. Elevating this mega-diverse tribe to the subfamily rank opened up an opportunity for its more fractional classification by raising several subtribes to the tribal level as follows: Acylophorini, Afroquediini, Amblyopinini, Antimerini, †Baltognathini, Cyrtoquediini, Erichsoniini, Hyptiomini, Indoquediini, Quediini and Tanygnathinini (revised status for all). As a result, the most species-rich tribe Staphylinini (revised status) is reduced to the more homogeneous lineage containing the subtribes Algonina, Anisolinina, Philonthina, Philothalpina, Staphylinina and Xanthopygina. Morphological synapomorphies and diagnostic characters supporting all newly defined higher taxa are provided. This published work has been registered on ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:DED8B042-83C9-4D10-B0CB-B50372B067A9 .     

Functional brain organization of global and local visual perception: an ERP study

Adult subjects were asked to recognize a hierarchical visual stimulus (a letter) while their attention was drawn to either the global or local level of the stimulus. Event-related potentials (ERP) and psychophysical indices (reaction time and percentage of correct responses) were measured. An analysis of psychophysical indices showed the global level precedence effect, i.e., the increase in a small letter recognition time when this letter is a part of incongruent stimulus. An analysis of ERP components showed level-related (global vs. local) differences in the timing and topography of the brain organization of perceptual processing and regulatory mechanisms of attention. Visual recognition at the local level was accompanied by (1) stronger activation of the visual associative areas (Pz and T6) at the stage of sensory features analysis (P1 ERP component), (2) involvement mainly of inferior temporal cortices of the right hemisphere (T6) at the stage of sensory categorization (P2 ERP component), and (3) involvement of prefrontal cortex of the right hemisphere at the stage of the selection of the relevant features of the target (N2 ERP component). Visual recognition at the global level was accompanied by (1) pronounced involvement of mechanisms of early sensory selection (N1 ERP component), (2) prevailing activation of parietal cortex of the right hemisphere (P4) at the stage of sensory categorization (P2 ERP component) as well as at the stage of the target stimulus identification (P3 ERP component). It is suggested that perception at the global level of the hierarchical stimulus is related primarily to the analysis of the spatial features of the stimulus in the dorsal visual system whereas the perception at the local level primarily involves an analysis of the object-related features in the ventral visual system.     

Mycobacteriophage Marvin: a new singleton phage with an unusual genome organization

Mycobacteriophages represent a genetically diverse group of viruses that infect mycobacterial hosts. Although more than 80 genomes have been sequenced, these still poorly represent the likely diversity of the broader population of phages that can infect the host, Mycobacterium smegmatis mc(2)155. We describe here a newly discovered phage, Marvin, which is a singleton phage, having no previously identified close relatives. The 65,100-bp genome contains 107 predicted protein-coding genes arranged in a noncanonical genomic architecture in which a subset of the minor tail protein genes are displaced about 20 kbp from their typical location, situated among nonstructural genes anticipated to be expressed early in lytic growth. Marvin is not temperate, and stable lysogens cannot be recovered from infections, although the presence of a putative xis gene suggests that Marvin could be a relatively recent derivative of a temperate parent. The Marvin genome is replete with novel genes not present in other mycobacteriophage genomes, and although most are of unknown function, the presence of amidoligase and glutamine amidotransferase genes suggests intriguing possibilities for the interactions of Marvin with its mycobacterial hosts.     

Identification of a second 16-hydroxytabersonine-O-methyltransferase suggests an evolutionary relationship between alkaloid and flavonoid metabolisms in Catharanthus roseus

Protoplasma - The medicinal plant Catharanthus roseus biosynthesizes many important drugs for human health, including the anticancer monoterpene indole alkaloids (MIAs) vinblastine and vincristine....     

McrA and 16S rRNA gene analysis suggests a novel lineage of Archaea phylogenetically affiliated with Thermoplasmatales in human subgingival plaque

Based on the molecular analysis of human subgingival plaque samples from 30 periodontitis patients a novel lineage of Archaea within the phylogenetic radiation of Thermoplasmatales was identified in 10% of cases. Co-occurrence of unique 16S rRNA gene and mcrA gene sequences suggests that this lineage corresponds to a hitherto unknown group of methanogens.     

A novel amphioxus cadherin that localizes to epithelial adherens junctions has an unusual domain organization with implications for chordate phylogeny

Although data are available from only vertebrates, urochordates, and three nonchordate animals, there are definite differences in the structures of classic cadherins between vertebrates plus urochordates and nonchordates. In this study we examined structural diversity of classic cadherins among bilaterian animals by obtaining new data from an amphioxus (Cephalochordata, Chordata), an acorn worm (Hemichordata), a sea star (Echinodermata), and an oyster (Mollusca). The structures of newly identified nonchordate cadherins are grouped together with those of the known sea urchin and Drosophila cadherins, whereas the structure of an amphioxus (Branchiostoma belcheri) cadherin, designated BbC, is differently categorized from those of other known chordate cadherins. BbC is identified as a cadherin by its cytoplasmic domain whose sequence is highly related to the cytoplasmic sequences of all known classic cadherins, but it lacks all of the five repeats constituting the extracellular homophilic-binding domain of other chordate cadherins. The ectodomains of BbC match the ectodomains found in nonchordate cadherins but not present in other chordate cadherins. We show that the BbC functions as a cell-cell adhesion molecule when expressed in Drosophila S2 cells and localizes to adherens junctions in the ectodermal epithelia in amphioxus embryos. We argue that BbC is the amphioxus homologue of the classic cadherins involved in the formation of epithelial adherens junctions. The structural relationships of the cadherin molecules allow us to propose a possibility that cephalochordates might be basal to the sister-groups vertebrates and urochordates.     

Hybrid insulin genes reveal a developmental lineage for pancreatic endocrine cells and imply a relationship with neurons

Insulin appears in the developing mouse pancreas at embryonic day 12 (e12). Transgenic mice harboring three distinct hybrid genes utilizing insulin gene regulatory information first express the transgene product two days earlier, at e10, in a few cells of the pancreatic bud. Throughout development and postnatal life, all of the insulin-producing (beta) cells coexpress the hybrid insulin gene. In addition, islet cells containing glucagon, somatostatin, pancreatic polypeptide, and the neuronal enzyme tyrosine hydroxylase coexpress the transgene when they first arise. Similarly, coexpression of these normally distinct islet cell markers occurs during differentiation of the four endocrine cell types. The transgene product also appears transiently during embryogenesis in cells of the neural tube and in neural crest. The results suggest a common precursor for the endocrine cells of the pancreas. Moreover, they imply a relationship between neural and pancreatic endocrine tissue.     

Evidence for a conserved relationship between an acceptor stem and a tRNA for aminoacylation.

The anticodon-independent aminoacylation of RNA hairpin helices that reconstruct tRNA acceptor stems has been demonstrated for at least 10 aminoacyl-tRNA synthetases. For Escherichia coli cysteine tRNA synthetase, the specificity of aminoacylation of the acceptor stem is determined by the U73 nucleotide adjacent to the amino acid attachment site. Because U73 is present in all known cysteine tRNAs, we investigated the ability of the E. coli cystein enzyme to aminoacylate a heterologous acceptor stem. We show here that a minihelixCys based on the acceptor-T psi C stem of yeast tRNACys is a substrate for the E. coli enzyme, and that aminoacylation of this minihelix is dependent on U73. Additionally, we identify two base pairs in the acceptor stem that quantitatively convert the E. coli acceptor stem to the yeast acceptor stem. The influence of U73 and these two base pairs is completely retained in the full-length tRNA. This suggests a conserved relationship between the acceptor stem alone and the acceptor stem in the context of a tRNA for aminoacylation with cysteine. However, the primary determinant in the species-specific aminoacylation of the E. coli and yeast cysteine tRNAs is a tertiary base pair at position 15:48 outside of the acceptor stem. Although E. coli tRNACys has an unusual G15:G48 tertiary base pair, yeast tRNACys has a more common G15:C48 that prevents efficient aminoacylation of yeast tRNACys by the E. coli enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)     

Molecular phylogeny suggests a single origin of insect symbiosis in the Pucciniomycetes with support for some relationships within the genus Septobasidium

In the Pucciniomycetes, a class of fungi that includes the plant pathogenic rust fungi, insect parasitism is restricted to a single family, the Septobasidiaceae. The Septobasidiaceae form a variety of symbioses with scale insects and have remained largely unstudied since the 1930s. Transitions between plant and animal parasitism and between mutualism and parasitism cannot be fully addressed in the Basidiomycota without a clear phylogenetic hypothesis for the Septobasidiales. Here, molecular phylogenetic methods were applied to understand the origin of scale insect parasitism, test the monophyly of the order Septobasidiales, and evaluate the infrageneric concepts in the largest genus of scale insect parasites, Septobasidium. DNA sequence data from rRNA genes were used to infer higher-level relationships within the Pucciniomycetes, and data from translation elongation factor 1-alpha (tef1) were added for phylogenetic inference within the Septobasidiaceae. Data from tef1 revealed different intron arrangements within Septobasidium, but the molecule did not provide much additional phylogenetically informative data. Likelihood-model-based phylogenetic analyses of 44 Pucciniomycotina taxa provided moderate support for a single origin of insect parasitism. Within the Septobasidiaceae, there was little or no support for a monophyletic Septobasidium, and well-resolved subclades of Septobasidium species contradict previous morphological delimitations of groups within the genus.