Test a clade in phylogenetic trees

We develop a new method for testing a portion of a tree (called a clade) based on multiple tests of many 4-taxon trees in this paper. This is particularly useful when the phylogenetic tree constructed by other methods have a clade that is difficult to explain from a biological point of view. The statement about the test of the clade can be made through the multiple P values from these individual tests. By controlling the familywise error rate or the false discovery rate (FDR), 4 different tree test methods are evaluated through simulation methods. It shows that the combination of the approximately unbiased (AU) test and the FDR-controlling procedure provides strong power along with reasonable type I error rate and less heavy computation.     

Tripartitions do not always discriminate phylogenetic networks

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In a recent series of papers devoted to the study of reconstructibility of phylogenetic networks, Moret, Nakhleh, Warnow and collaborators introduced the so-called tripartition metric for phylogenetic networks. In this paper we show that, in fact, this tripartition metric does not satisfy the separation axiom of distances (zero distance means isomorphism, or, in a more relaxed version, zero distance means indistinguishability in some specific sense) in any of the subclasses of phylogenetic networks where it is claimed to do so. We also present a subclass of phylogenetic networks whose members can be singled out by means of their sets of tripartitions (or even clusters), and hence where the latter can be used to define a meaningful metric.     

Phylostat: a web-based tool to analyze paralogous clade divergence in phylogenetic trees

Phylogenetic trees are useful tools to infer evolutionary relationships between genetic entities. Phylogenetics enables not only evolution-based gene clustering but also the assignment of gene duplication and deletion events to the nodes when coupled with statistical approaches such as bootstrapping. However, extensive gene duplication and deletion events bring along a challenge in interpreting phylogenetic trees and require manual inference. In particular, there has been no robust method of determining whether one of the paralog clades systematically shows higher divergence following the gene duplication event as a sign of functional divergence. Here, we provide Phylostat, a graphical user interface that enables clade divergence analysis, visually and statistically. Phylostat is a web-based tool built on phylo.io to allow comparative clade divergence analysis, which is available at https://phylostat.adebalilab.org under an MIT open-source licence.     

Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees

Background  

In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking.     

Estimating errors and confidence intervals for branch lengths in phylogenetic trees by a bootstrap approach

A method, based on the bootstrap procedure, is proposed for the estimation of branch-length errors and confidence intervals in a phylogenetic tree for which equal rates of substitution among lineages do not necessarily hold. The method can be used to test whether an estimated internodal distance is significantly greater than zero. In the application of the method, any estimator of genetic distances, as well as any tree reconstruction procedure (based on distance matrices), can be used. Also the method is not limited by the number of species involved in the phylogenetic tree. An example of the application of the method in the reconstruction of the phylogenetic tree for the four hominoid species—human, chimpanzee, gorilla, and orangutan—is shown. Correspondence to: J. Dopazo     

Estimation of evolutionary parameters with phylogenetic trees

An important issue in the phylogenetic analysis of nucleotide sequence data using the maximum likelihood (ML) method is the underlying evolutionary model employed. We consider the problem of simultaneously estimating the tree topology and the parameters in the underlying substitution model and of obtaining estimates of the standard errors of these parameter estimates. Given a fixed tree topology and corresponding set of branch lengths, the ML estimates of standard evolutionary model parameters are asymptotically efficient, in the sense that their joint distribution is asymptotically normal with the variance–covariance matrix given by the inverse of the Fisher information matrix. We propose a new estimate of this conditional variance based on estimation of the expected information using a Monte Carlo sampling (MCS) method. Simulations are used to compare this conditional variance estimate to the standard technique of using the observed information under a variety of experimental conditions. In the case in which one wishes to estimate simultaneously the tree and parameters, we provide a bootstrapping approach that can be used in conjunction with the MCS method to estimate the unconditional standard error. The methods developed are applied to a real data set consisting of 30 papillomavirus sequences. This overall method is easily incorporated into standard bootstrapping procedures to allow for proper variance estimation.     

Effects of sequence diversity and recombination on the accuracy of phylogenetic trees estimated by kSNP

kSNP v2 is a powerful tool for single nucleotide polymorphism (SNP) identification from complete microbial genomes and for estimating phylogenetic trees from the identified SNPs. kSNP can analyse finished genomes, genome assemblies, raw reads or any combination of those and does not require either genome alignment or reference genomes. This study uses sequence evolution simulations to evaluate the topological accuracy of kSNP trees and to assess the effects of diversity and recombination on that accuracy. The accuracies of kSNP trees are strongly affected by increasing diversity, with parsimony accuracy > maximum‐likelihood accuracy > neighbour‐joining accuracy. Accuracy is also strongly influenced by recombination; as recombination increases accuracy decreases. Reliable trees are arbitrarily defined as those that have ≥ 90% topological accuracy. It is determined that the best predictor of topological accuracy is the ratio of r/m, a measure of the effect of recombination, to FCK (the fraction of core kmers), a measure of diversity. Tools are available to allow investigators to determine both r/m and FCK, and the relationship between topological accuracy and the ratio of r/m to FCK is determined. The practical implication of this study is that kSNP is an effective tool for estimating phylogenetic trees from microbial genome sequences provided that both recombination and sequence diversity are within acceptable ranges.     

Aspergillus niger cyclic AMP levels are not influenced by manganese deficiency and do not correlate with citric acid accumulation

Summary The role of intracellular levels of cyclic AMP in the control of citic acid accumulation by Aspergillus niger has been investigated. For this purpose, A. niger was grown in media containing either high (14%, w/v) or low (2%, w/v) concentrations of sucrose, supplemented with 10 M Mn²⁺ (manganese-sufficient) or not (manganese-deficient), to obtain conditions leading to variable citrate accumulation. Citric acid accumulation was only observed in high-sugar, manganese-deficient medium. Intracellular levels of cyclic AMP were significantly higher in mycelia grown on low-sugar media, but were not significantly influenced by the absence of manganese ions. When sucrose in the high-sugar medium was substituted by other mono- or disaccharides, similar intracellular concentrations of cyclic AMP were observed. However, citric acid accumulation was only significant with sucrose, glucose and fructose. It is thus concluded that the intracellular level of cyclic AMP is not causally related to the accumulation of citric acid by the fungus, and —noteworthy — is not affected by manganese deficiency (despite adenylate cyclase reputed to be a manganese-requiring enzyme).Offprint requests to: C. P. Kubicek     

Monophyly of clade III nematodes is not supported by phylogenetic analysis of complete mitochondrial genome sequences

Background

The orders Ascaridida, Oxyurida, and Spirurida represent major components of zooparasitic nematode diversity, including many species of veterinary and medical importance. Phylum-wide nematode phylogenetic hypotheses have mainly been based on nuclear rDNA sequences, but more recently complete mitochondrial (mtDNA) gene sequences have provided another source of molecular information to evaluate relationships. Although there is much agreement between nuclear rDNA and mtDNA phylogenies, relationships among certain major clades are different. In this study we report that mtDNA sequences do not support the monophyly of Ascaridida, Oxyurida and Spirurida (clade III) in contrast to results for nuclear rDNA. Results from mtDNA genomes show promise as an additional independently evolving genome for developing phylogenetic hypotheses for nematodes, although substantially increased taxon sampling is needed for enhanced comparative value with nuclear rDNA. Ultimately, topological incongruence (and congruence) between nuclear rDNA and mtDNA phylogenetic hypotheses will need to be tested relative to additional independent loci that provide appropriate levels of resolution.

Results

For this comparative phylogenetic study, we determined the complete mitochondrial genome sequences of three nematode species, Cucullanus robustus (13,972 bp) representing Ascaridida, Wellcomia siamensis (14,128 bp) representing Oxyurida, and Heliconema longissimum (13,610 bp) representing Spirurida. These new sequences were used along with 33 published nematode mitochondrial genomes to investigate phylogenetic relationships among chromadorean orders. Phylogenetic analyses of both nucleotide and amino acid sequence datasets support the hypothesis that Ascaridida is nested within Rhabditida. The position of Oxyurida within Chromadorea varies among analyses; in most analyses this order is sister to the Ascaridida plus Rhabditida clade, with representative Spirurida forming a distinct clade, however, in one case Oxyurida is sister to Spirurida. Ascaridida, Oxyurida, and Spirurida (the sampled clade III taxa) do not form a monophyletic group based on complete mitochondrial DNA sequences. Tree topology tests revealed that constraining clade III taxa to be monophyletic, given the mtDNA datasets analyzed, was a significantly worse result.

Conclusion

The phylogenetic hypotheses from comparative analysis of the complete mitochondrial genome data (analysis of nucleotide and amino acid datasets, and nucleotide data excluding 3^rd positions) indicates that nematodes representing Ascaridida, Oxyurida and Spirurida do not share an exclusive most recent common ancestor, in contrast to published results based on nuclear ribosomal DNA. Overall, mtDNA genome data provides reliable support for nematode relationships that often corroborates findings based on nuclear rDNA. It is anticipated that additional taxonomic sampling will provide a wealth of information on mitochondrial genome evolution and sequence data for developing phylogenetic hypotheses for the phylum Nematoda.

     

The immunogenic properties of drug-resistant murine tumor cells do not correlate with expression of the MDR phenotype

Alterations in the immunogenic properties of tumor cells frequently accompany selection for multipledrug-resistant (MDR) variants. Therefore, studies were performed to examine the hypothesis that overexpression of membrane P-glycoprotein, commonly observed in MDR tumor cells, is associated with enhanced immunogenic properties. Immunogenicity was determined by (a) the ability of drug-sensitive parental UV2237M fibrosarcoma cells and drug-resistant UV2237M variant cells to immunize normal mice against rechallenge with parental tumor cells and (b) the ability of normal syngeneic mice to reject cell inocula that caused progressive tumor growth in immunocompromised mice. Variant UV2237M cell lines included subpopulations selected for a six- to ten-fold increase in mRNA for P-glycoprotein and expression of the MDR phenotype (resistance to doxorubicin) and cells sensitive to doxorubicin (and no expression of MDR properties) but resistant to ouabain. All UV2237M drug-resistant cells were highly immunogenic in immunocompetent mice, regardless of their MDR phenotype. Additional studies showed that CT-26 murine adenocarcinoma cells, sensitive or resistant to doxorubicin (expressing high levels of P-glycoprotein), injected into normal syngeneic Balb/c mice produced rapidly growing tumors. The data do not demonstrate a correlation between the immunogenic properties of drug-resistant tumor cells and the expression of P-glycoprotein.Supported in part by core grant CA-16672 R35-CA42 107 from the National Cancer Institute, and postdoctoral fellowship grant PF-3446 from the American Cancer Society (R. R.)     

Evolutionary models of phylogenetic trees

The most widely used evolutionary model for phylogenetic trees is the equal-rates Markov (ERM) model. A problem is that the ERM model predicts less imbalance than observed for trees inferred from real data; in fact, the observed imbalance tends to fall between the values predicted by the ERM model and those predicted by the proportional-to-distinguishable-arrangements (PDA) model. Here, a continuous multi-rate (MR) family of evolutionary models is presented which contains entire subfamilies corresponding to both the PDA and ERM models. Furthermore, this MR family covers an entire range from 'completely balanced' to 'completely unbalanced' models. In particular, the MR family contains other known evolutionary models. The MR family is very versatile and virtually free of assumptions on the character of evolution; yet it is highly susceptible to rigorous analyses. In particular, such analyses help to uncover adaptability, quasi-stabilization and prolonged stasis as major possible causes of the imbalance. However, the MR model is functionally simple and requires only three parameters to reproduce the observed imbalance.     

Carbon dioxide baited trap catches do not correlate with human landing collections of Anopheles aquasalis in Suriname

Three types of carbon dioxide-baited traps, i.e., the Centers for Disease Control Miniature Light Trap without light, the BioGents (BG) Sentinel Mosquito Trap (BG-Sentinel) and the Mosquito Magnet? Liberty Plus were compared with human landing collections in their efficiency in collecting Anopheles (Nyssorhynchus) aquasalis mosquitoes. Of 13,549 total mosquitoes collected, 1,019 (7.52%) were An. aquasalis. Large numbers of Culex spp were also collected, in particular with the (BG-Sentinel). The majority of An. aquasalis (83.8%) were collected by the human landing collection (HLC). None of the trap catches correlated with HLC in the number of An. aquasalis captured over time. The high efficiency of the HLC method indicates that this malaria vector was anthropophilic at this site, especially as carbon dioxide was insufficiently attractive as stand-alone bait. Traps using carbon dioxide in combination with human odorants may provide better results.