Cover
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - April 20, 2016 Category: Molecular Biology Tags: Cover / standing material Source Type: research
Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization
Wasabi is an open source, web-based environment for evolutionary sequence analysis. Wasabi visualizes sequence data together with a phylogenetic tree within a modern, user-friendly interface: The interface hides extraneous options, supports context sensitive menus, drag-and-drop editing, and displays additional information, such as ancestral sequences, associated with specific tree nodes. The Wasabi environment supports reproducibility by automatically storing intermediate analysis steps and includes built-in functions to share data between users and publish analysis results. For computational analysis, Wasabi supports PRA...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Veidenberg, A., Medlar, A., Löytynoja, A. Tags: Resource Source Type: research
Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)
Production of massive DNA sequence data sets is transforming phylogenetic inference, but best practices for analyzing such data sets are not well established. One uncertainty is robustness to missing data, particularly in coalescent frameworks. To understand the effects of increasing matrix size and loci at the cost of increasing missing data, we produced a 90 taxon, 2.2 megabase, 4,800 locus sequence matrix of landfowl using target capture of ultraconserved elements. We then compared phylogenies estimated with concatenated maximum likelihood, quartet-based methods executed on concatenated matrices and gene tree reconcilia...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Hosner, P. A., Faircloth, B. C., Glenn, T. C., Braun, E. L., Kimball, R. T. Tags: Methods Source Type: research
VHICA, a New Method to Discriminate between Vertical and Horizontal Transposon Transfer: Application to the Mariner Family within Drosophila
Transposable elements (TEs) are genomic repeated sequences that display complex evolutionary patterns. They are usually inherited vertically, but can occasionally be transmitted between sexually independent species, through so-called horizontal transposon transfers (HTTs). Recurrent HTTs are supposed to be essential in life cycle of TEs, which are otherwise destined for eventual decay. HTTs also impact the host genome evolution. However, the extent of HTTs in eukaryotes is largely unknown, due to the lack of efficient, statistically supported methods that can be applied to multiple species sequence data sets. Here, we deve...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Wallau, G. L., Capy, P., Loreto, E., Le Rouzic, A., Hua-Van, A. Tags: Methods Source Type: research
Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data
To characterize natural selection, various analytical methods for detecting candidate genomic regions have been developed. We propose to perform genome-wide scans of natural selection using principal component analysis (PCA). We show that the common FST index of genetic differentiation between populations can be viewed as the proportion of variance explained by the principal components. Considering the correlations between genetic variants and each principal component provides a conceptual framework to detect genetic variants involved in local adaptation without any prior definition of populations. To validate the PCA-base...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Duforet-Frebourg, N., Luu, K., Laval, G., Bazin, E., Blum, M. G. B. Tags: Methods Source Type: research
Convergent Substitutions in a Sodium Channel Suggest Multiple Origins of Toxin Resistance in Poison Frogs
Complex phenotypes typically have a correspondingly multifaceted genetic component. However, the genotype–phenotype association between chemical defense and resistance is often simple: genetic changes in the binding site of a toxin alter how it affects its target. Some toxic organisms, such as poison frogs (Anura: Dendrobatidae), have defensive alkaloids that disrupt the function of ion channels, proteins that are crucial for nerve and muscle activity. Using protein-docking models, we predict that three major classes of poison frog alkaloids (histrionicotoxins, pumiliotoxins, and batrachotoxins) bind to similar sites...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Tarvin, R. D., Santos, J. C., O'Connell, L. A., Zakon, H. H., Cannatella, D. C. Tags: Discoveries Source Type: research
Cross-Study Comparison Reveals Common Genomic, Network, and Functional Signatures of Desiccation Resistance in Drosophila melanogaster
Repeated attempts to map the genomic basis of complex traits often yield different outcomes because of the influence of genetic background, gene-by-environment interactions, and/or statistical limitations. However, where repeatability is low at the level of individual genes, overlap often occurs in gene ontology categories, genetic pathways, and interaction networks. Here we report on the genomic overlap for natural desiccation resistance from a Pool-genome-wide association study experiment and a selection experiment in flies collected from the same region in southeastern Australia in different years. We identified over 60...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Telonis-Scott, M., Sgro, C. M., Hoffmann, A. A., Griffin, P. C. Tags: Discoveries Source Type: research
Laterally Transferred Gene Recruited as a Venom in Parasitoid Wasps
In this study, a GH19 chitinase LGT is described from the unicellular microsporidia/Rozella clade into parasitoid wasps of the superfamily Chalcidoidea, where it has become recruited as a venom protein. The GH19 chitinase is present in 15 species of chalcidoid wasps representing four families, and phylogenetic analysis indicates that it was laterally transferred near or before the origin of Chalcidoidea (~95 Ma). The GH19 chitinase gene is highly expressed in the venom gland of at least seven species, indicating a role in the complex host manipulations performed by parasitoid wasp venom. RNAi knockdown in the model parasit...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Martinson, E. O., Martinson, V. G., Edwards, R., Mrinalini, , Werren, J. H. Tags: Discoveries Source Type: research
Euarchontan Opsin Variation Brings New Focus to Primate Origins
Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patterns and therefore selective ecological pressures. A problem with this approach is that opsin gene variation is incompletely known in the grandorder Euarchonta, that is, the orders Scandentia (treeshrews), Dermoptera (colugos), and Primates. The ancestral state of primate color vision is therefore uncertain. Her...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Melin, A. D., Wells, K., Moritz, G. L., Kistler, L., Orkin, J. D., Timm, R. M., Bernard, H., Lakim, M. B., Perry, G. H., Kawamura, S., Dominy, N. J. Tags: Discoveries Source Type: research
Evolutionary Transition of Promoter and Gene Body DNA Methylation across Invertebrate-Vertebrate Boundary
Genomes of invertebrates and vertebrates exhibit highly divergent patterns of DNA methylation. Invertebrate genomes tend to be sparsely methylated, and DNA methylation is mostly targeted to a subset of transcription units (gene bodies). In a drastic contrast, vertebrate genomes are generally globally and heavily methylated, punctuated by the limited local hypo-methylation of putative regulatory regions such as promoters. These genomic differences also translate into functional differences in DNA methylation and gene regulation. Although promoter DNA methylation is an important regulatory component of vertebrate gene expres...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Keller, T. E., Han, P., Yi, S. V. Tags: Discoveries Source Type: research
Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor
Mammals have evolved remarkably different sensory, reproductive, metabolic, and skeletal systems. To explore the genetic basis for these differences, we developed a comparative genomics approach to scan whole-genome multiple sequence alignments to identify regions that evolved rapidly in an ancestral lineage but are conserved within extant species. This pattern suggests that ancestral changes in function were maintained in descendants. After applying this test to therian mammals, we identified 4,797 accelerated regions, many of which are noncoding and located near developmental transcription factors. We then used mouse tra...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Holloway, A. K., Bruneau, B. G., Sukonnik, T., Rubenstein, J. L., Pollard, K. S. Tags: Discoveries Source Type: research
Selection on Mitochondrial Variants Occurs between and within Individuals in an Expanding Invasion
Mitochondria are critical for life, yet their underlying evolutionary biology is poorly understood. In particular, little is known about interaction between two levels of evolution: between individuals and within individuals (competition between cells, mitochondria or mitochondrial DNA molecules). Rapid evolution is suspected to occur frequently in mitochondrial DNA, whose maternal inheritance predisposes advantageous mutations to sweep rapidly though populations. Rapid evolution is also predicted in response to changed selection regimes after species invasion or removal of pathogens or competitors. Here, using empirical a...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Rollins, L. A., Woolnough, A. P., Fanson, B. G., Cummins, M. L., Crowley, T. M., Wilton, A. N., Sinclair, R., Butler, A., Sherwin, W. B. Tags: Discoveries Source Type: research
Strong Maternal Effects on Gene Expression in Arabidopsis lyrata Hybrids
Hybridization between populations or species can have pronounced fitness consequences. Yet little is known about how hybridization affects gene regulation. Three main models have been put forward to explain gene expression patterns in hybrids: additive, dominance, or parental effects. Here, we use high throughput RNA-sequencing to examine the extent to which hybrid gene expression follows predictions by each of the three models. We performed a reciprocal crossing experiment between two differentiated populations of the perennial herb Arabidopsis lyrata and sequenced RNA in rosette leaves of 12-week-old plants grown in gree...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Videvall, E., Sletvold, N., Hagenblad, J., Agren, J., Hansson, B. Tags: Discoveries Source Type: research
Evolutionary Origins of Rhizarian Parasites
The SAR group (Stramenopila, Alveolata, Rhizaria) is one of the largest clades in the tree of eukaryotes and includes a great number of parasitic lineages. Rhizarian parasites are obligate and have devastating effects on commercially important plants and animals but despite this fact, our knowledge of their biology and evolution is limited. Here, we present rhizarian transcriptomes from all major parasitic lineages in order to elucidate their evolutionary relationships using a phylogenomic approach. Our results suggest that Ascetosporea, parasites of marine invertebrates, are sister to the novel clade Apofilosa. The phytom...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Sierra, R., Canas-Duarte, S. J., Burki, F., Schwelm, A., Fogelqvist, J., Dixelius, C., Gonzalez-Garcia, L. N., Gile, G. H., Slamovits, C. H., Klopp, C., Restrepo, S., Arzul, I., Pawlowski, J. Tags: Discoveries Source Type: research
Evolution of a Catalytic Mechanism
The means by which superfamilies of specialized enzymes arise by gene duplication and functional divergence are poorly understood. The escape from adaptive conflict hypothesis, which posits multiple copies of a gene encoding a primitive inefficient and highly promiscuous generalist ancestor, receives support from experiments showing that resurrected ancestral enzymes are indeed more substrate-promiscuous than their modern descendants. Here, we provide evidence in support of an alternative model, the innovation–amplification–divergence hypothesis, which posits a single-copied ancestor as efficient and specific a...
Source: Molecular Biology and Evolution - March 3, 2016 Category: Molecular Biology Authors: Rauwerdink, A., Lunzer, M., Devamani, T., Jones, B., Mooney, J., Zhang, Z.-J., Xu, J.-H., Kazlauskas, R. J., Dean, A. M. Tags: Discoveries Source Type: research
