Four-cluster analysis: a simple method to test phylogenetic hypotheses

A simple statistical test for comparing three alternative phylogenetic hypotheses for four monophyletic groups is presented. This test is based on the minimum-evolution principle, and it does not require any information regarding the branching order within each monophyletic group. It is computationally efficient and can be easily extended to five or more monophyletic groups.      

Variances of the average numbers of nucleotide substitutions within and between populations

Statistical methods for computing the variances of nucleotide diversity within populations and of nucleotide divergence between populations are developed. Both variances are computed by finding the phylogenetic relationships of the DNA sequences studied through the unweighted pair-group method or some other tree-making method. The methods developed are applicable to both DNA sequence and restriction-site map data.     

Global analysis of genes involved in freshwater adaptation in threespine sticklebacks (Gasterosteus aculeatus)

Examples of parallel evolution of phenotypic traits have been repeatedly demonstrated in threespine sticklebacks (Gasterosteus aculeatus) across their global distribution. Using these as a model, we performed a targeted genome scan--focusing on physiologically important genes potentially related to freshwater adaptation--to identify genetic signatures of parallel physiological evolution on a global scale. To this end, 50 microsatellite loci, including 26 loci within or close to (<6 kb) physiologically important genes, were screened in paired marine and freshwater populations from six locations across the Northern Hemisphere. Signatures of directional selection were detected in 24 loci, including 17 physiologically important genes, in at least one location. Although no loci showed consistent signatures of selection in all divergent population pairs, several outliers were common in multiple locations. In particular, seven physiologically important genes, as well as reference ectodysplasin gene (EDA), showed signatures of selection in three or more locations. Hence, although these results give some evidence for consistent parallel molecular evolution in response to freshwater colonization, they suggest that different evolutionary pathways may underlie physiological adaptation to freshwater habitats within the global distribution of the threespine stickleback.     

Probing the role of tryptophan-derived secondary metabolism in defense responses against Bipolaris oryzae infection in rice leaves by a suicide substrate of tryptophan decarboxylase

Tryptophan-derived secondary metabolites, including serotonin and its hydroxycinnamic acid amides, markedly accumulate in rice leaves in response to pathogen attack. These compounds have been implicated in the physical defense system against pathogen invasion by being deposited in cell walls. Serotonin is biosynthesized from tryptophan via tryptamine, and tryptophan decarboxylase (TDC) catalyzes the first committed reaction. In this study, (S)-α-(fluoromethyl)tryptophan (S-αFMT) was utilized to investigate the effects of the inhibition of TDC on the defense responses of rice leaves. S-αFMT, enantiospecifically synthesized from l-tryptophan, effectively inhibited TDC activity extracted from rice leaves infected by Bipolaris oryzae. The inhibition rate increased dependently on the incubation time, indicating that S-αFMT served as a suicide substrate. Treatment of rice seedlings with S-αFMT suppressed accumulation of serotonin, tryptamine, and hydroxycinnamic acid amides of serotonin in a dose-dependent manner in B. oryzae-inoculated leaves. The lesions formed on seedlings treated with S-αFMT lacked deposition of brown materials, and those leaves were severely damaged in comparison with leaves without S-αFMT treatment. Administrating tryptamine to S-αFMT-treated leaves restored accumulation of tryptophan-derived secondary metabolites as well as deposition of brown material. In addition, tryptamine administration reduced damage caused by fungal infection. Accordingly, the accumulation of tryptophan-derived secondary metabolites was suggested to be part of the effective defense mechanism of rice.     

MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.     

Species introduction promotes hybridization and introgression in Coregonus: is there sign of selection against hybrids?

Species introductions are considered one of the major drivers of biodiversity loss via ecological interactions and genetic admixture with local fauna. We examined two well-recognized fish species, native whitefish (Coregonus lavaretus) and introduced vendace (Coregonus albula), as well as their morphological hybrids in a single lake to test for selection against hybrids and backcrosses in the wild. A representative random subsample of 693 individuals (27.8%) was taken from the total catch of coregonids. This subsample was examined with the aim to select c. 50 individuals of pure whitefish (n = 52), pure vendace (n = 55) and putative hybrid (n = 19) for genetic analyses. The subsequent microsatellites and mitochondrial (mt) DNA analyses provided compelling evidence of hybridization and introgression. Of the 126 fish examined, four were found to be F(1) , 14 backcrosses to whitefish and seven backcrosses to vendace. The estimates of historical gene flow suggested higher rates from introduced vendace into native whitefish than vice versa, whereas estimates of contemporary gene flow were equal. Mitochondrial introgression was skewed, with 18 backcrosses having vendace mtDNA and only three with whitefish mtDNA. Hybrids and backcrosses had intermediate morphology and niche utilization compared with parental species. No evidence of selection against hybrids or backcrosses was apparent, as both hybrid and backcross growth rates and fecundities were high. Hybrids (F(1) ) were only detected in 2 year-classes, suggesting temporal variability in mating between vendace and whitefish. However, our data show that hybrids reached sexual maturity and reproduced actively, with backcrosses recorded from six consecutive year-classes, whereas no F(2) individuals were found. The results indicate widespread introgression, as 10.8% of coregonids were estimated to be backcrosses.     

Synthesis, structure, and biological activity of dumbbell-shaped nanocircular RNAs for RNA interference

RNA interference (RNAi) is one of the most promising new approaches for disease therapy. The design of a dumbbell-shaped nanocircular RNA allows it to act as a short interfering RNA (siRNA) precursor. To optimize the design, we studied the relationship between the nanostructure and RNAi activity by synthesizing various RNA dumbbells. An RNA dumbbell with a 23-bp stem and 9-nt loops was the most potent. Sequence analysis by mass spectrometry showed that Dicer could edit RNA dumbbells to siRNA species. The reaction offered the slow release of siRNA species, which conferred prolonged RNAi activity. Introduction of DNA into the loop position significantly stabilized the dumbbell in biological fluid without any loss of RNAi activity. In-depth pharmacological evaluation was performed by introducing dumbbells into HeLa cells that stably express the target luciferase gene. The dumbbells provided a rapid silencing effect and retained this effect for a longer time even at a lower concentration than that at which standard siRNA completely lost RNAi activity. We conclude that an RNA dumbbell with DNA loops is the most promising design for in vivo applications for RNA medicine.