Transcriptomes of Plant Gametophytes Have a Higher Proportion of Rapidly Evolving and Young Genes than Sporophytes
Reproductive traits in plants tend to evolve rapidly due to various causes that include plant-pollinator coevolution and pollen competition, but the genomic basis of reproductive trait evolution is still largely unknown. To characterize evolutionary patterns of genome wide gene expression in reproductive tissues in the gametophyte and to compare them to developmental stages of the sporophyte, we analyzed evolutionary conservation and genetic diversity of protein-coding genes using microarray-based transcriptome data from three plant species, Arabidopsis thaliana, rice (Oryza sativa), and soybean (Glycine max). In all three...
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Gossmann, T. I., Saleh, D., Schmid, M. W., Spence, M. A., Schmid, K. J. Tags: Discoveries Source Type: research
Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
Species tree reconstruction is complicated by effects of incomplete lineage sorting, commonly modeled by the multi-species coalescent model (MSC). While there has been substantial progress in developing methods that estimate a species tree given a collection of gene trees, less attention has been paid to fast and accurate methods of quantifying support. In this article, we propose a fast algorithm to compute quartet-based support for each branch of a given species tree with regard to a given set of gene trees. We then show how the quartet support can be used in the context of the MSC to compute (1) the local posterior prob...
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Sayyari, E., Mirarab, S. Tags: Fast Track Source Type: research
Recurrent Gene Duplication Diversifies Genome Defense Repertoire in Drosophila
Transposable elements (TEs) comprise large fractions of many eukaryotic genomes and imperil host genome integrity. The host genome combats these challenges by encoding proteins that silence TE activity. Both the introduction of new TEs via horizontal transfer and TE sequence evolution requires constant innovation of host-encoded TE silencing machinery to keep pace with TEs. One form of host innovation is the adaptation of existing, single-copy host genes. Indeed, host suppressors of TE replication often harbor signatures of positive selection. Such signatures are especially evident in genes encoding the piwi-interacting-RN...
Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Authors: Levine, M. T., Vander Wende, H. M., Hsieh, E., Baker, E. P., Malik, H. S. Tags: Fast Track Source Type: research
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Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Tags: Cover / standing material Source Type: research
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Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Tags: Cover / standing material Source Type: research
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Source: Molecular Biology and Evolution - June 20, 2016 Category: Molecular Biology Tags: Cover / standing material Source Type: research
When Silent Mutations Provide Evolutionary Advantages
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
Adaptation Helps Fish Thrive in Toxic Environments
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including ...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Huerta-Cepas, J., Serra, F., Bork, P. Tags: Resource Source Type: research
LS3: A Method for Improving Phylogenomic Inferences When Evolutionary Rates Are Heterogeneous among Taxa
Phylogenetic inference artifacts can occur when sequence evolution deviates from assumptions made by the models used to analyze them. The combination of strong model assumption violations and highly heterogeneous lineage evolutionary rates can become problematic in phylogenetic inference, and lead to the well-described long-branch attraction (LBA) artifact. Here, we define an objective criterion for assessing lineage evolutionary rate heterogeneity among predefined lineages: the result of a likelihood ratio test between a model in which the lineages evolve at the same rate (homogeneous model) and a model in which different...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Rivera-Rivera, C. J., Montoya-Burgos, J. I. Tags: Methods Source Type: research
Efficiencies of the NJp, Maximum Likelihood, and Bayesian Methods of Phylogenetic Construction for Compositional and Noncompositional Genes
At the present time it is often stated that the maximum likelihood or the Bayesian method of phylogenetic construction is more accurate than the neighbor joining (NJ) method. Our computer simulations, however, have shown that the converse is true if we use p distance in the NJ procedure and the criterion of obtaining the true tree (Pc expressed as a percentage) or the combined quantity (c) of a value of Pc and a value of Robinson–Foulds’ average topological error index (dT). This c is given by Pc (1 – dT/dTmax) = Pc (m – 3 – dT/2)/(m – 3), where m is the number of taxa used and dTmax is ...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Yoshida, R., Nei, M. Tags: Methods Source Type: research
Computing the Internode Certainty and Related Measures from Partial Gene Trees
We present, implement, and evaluate an approach to calculate the internode certainty (IC) and tree certainty (TC) on a given reference tree from a collection of partial gene trees. Previously, the calculation of these values was only possible from a collection of gene trees with exactly the same taxon set as the reference tree. An application to sets of partial gene trees requires mathematical corrections in the IC and TC calculations. We implement our methods in RAxML and test them on empirical datasets. These tests imply that the inclusion of partial trees does matter. However, in order to provide meaningful measurements...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Kobert, K., Salichos, L., Rokas, A., Stamatakis, A. Tags: Methods Source Type: research
Clustering Genes of Common Evolutionary History
Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent—due to events such as incomplete lineage sorting or horizontal gene transfer—it can be misleading to infer a single tree. To address this, many previous contributions have taken a mechanistic approach, by modeling specific processes. Alternatively, one can cluster loci without assuming how these incongruencies might arise. Such "process-agnostic" approaches typically infer a tree for each locus and cluster these. There are, however, many possible combinations of tree distance...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Gori, K., Suchan, T., Alvarez, N., Goldman, N., Dessimoz, C. Tags: Methods Source Type: research
Codon Usage Selection Can Bias Estimation of the Fraction of Adaptive Amino Acid Fixations
A growing number of molecular evolutionary studies are estimating the proportion of adaptive amino acid substitutions (α) from comparisons of ratios of polymorphic and fixed DNA mutations. Here, we examine how violations of two of the model assumptions, neutral evolution of synonymous mutations and stationary base composition, affect α estimation. We simulated the evolution of coding sequences assuming weak selection on synonymous codon usage bias and neutral protein evolution, α = 0. We show that weak selection on synonymous mutations can give polymorphism/divergence ratios that yield α-hat (estima...
Source: Molecular Biology and Evolution - May 15, 2016 Category: Molecular Biology Authors: Matsumoto, T., John, A., Baeza-Centurion, P., Li, B., Akashi, H. Tags: Methods Source Type: research
