SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes
Model-based phylogenetic reconstructions increasingly consider spatial or phenotypic traits in conjunction with sequence data to study evolutionary processes. Alongside parameter estimation, visualization of ancestral reconstructions represents an integral part of these analyses. Here, we present a complete overhaul of the spatial phylogenetic reconstruction of evolutionary dynamics software, now called SpreaD3 to emphasize the use of data-driven documents, as an analysis and visualization package that primarily complements Bayesian inference in BEAST (http://beast.bio.ed.ac.uk, last accessed 9 May 2016). The integration o...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Bielejec, F., Baele, G., Vrancken, B., Suchard, M. A., Rambaut, A., Lemey, P. Tags: Resources Source Type: research
Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web
Phylogenetic trees are pervasively used to depict evolutionary relationships. Increasingly, researchers need to visualize large trees and compare multiple large trees inferred for the same set of taxa (reflecting uncertainty in the tree inference or genuine discordance among the loci analyzed). Existing tree visualization tools are however not well suited to these tasks. In particular, side-by-side comparison of trees can prove challenging beyond a few dozen taxa. Here, we introduce Phylo.io, a web application to visualize and compare phylogenetic trees side-by-side. Its distinctive features are: highlighting of similariti...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Robinson, O., Dylus, D., Dessimoz, C. Tags: Resources Source Type: research
TriLoNet: Piecing Together Small Networks to Reconstruct Reticulate Evolutionary Histories
Phylogenetic networks are a generalization of evolutionary trees that can be used to represent reticulate processes such as hybridization and recombination. Here, we introduce a new approach called TriLoNet (Trinet Level- one Network algorithm) to construct such networks directly from sequence alignments which works by piecing together smaller phylogenetic networks. More specifically, using a bottom up approach similar to Neighbor-Joining, TriLoNet constructs level-1 networks (networks that are somewhat more general than trees) from smaller level-1 networks on three taxa. In simulations, we show that TriLoNet compares well...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Oldman, J., Wu, T., van Iersel, L., Moulton, V. Tags: Resources Source Type: research
Controlling for Phylogenetic Relatedness and Evolutionary Rates Improves the Discovery of Associations Between Species Phenotypic and Genomic Differences
The growing number of sequenced genomes allows us now to address a key question in genetics and evolutionary biology: which genomic changes underlie particular phenotypic changes between species? Previously, we developed a computational framework called Forward Genomics that associates phenotypic to genomic differences by focusing on phenotypes that are independently lost in different lineages. However, our previous implementation had three main limitations. Here, we present two new Forward Genomics methods that overcome these limitations by (1) directly controlling for phylogenetic relatedness, (2) controlling for differe...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Prudent, X., Parra, G., Schwede, P., Roscito, J. G., Hiller, M. Tags: Methods Source Type: research
A New Orthology Assessment Method for Phylogenomic Data: Unrooted Phylogenetic Orthology
We describe a procedure to detect and document the phylogenetic distribution of orthologs allowing researchers to use this information to guide selection of loci best suited to test specific evolutionary questions. At the core of this pipeline is a new phylogenetic orthology method that is neither affected by the position of the root nor requires explicit assignment of outgroups. We discuss the properties of this new orthology assessment method and exemplify its utility for phylogenomics using a small insects dataset. In addition, we exemplify the pipeline to identify and document stable orthologs for the group of orb-weav...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Ballesteros, J. A., Hormiga, G. Tags: Methods Source Type: research
Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data
When viruses spread, outbreaks can be spawned in previously unaffected regions. Depending on the time and mode of introduction, each regional outbreak can have its own epidemic dynamics. The migration and phylodynamic processes are often intertwined and need to be taken into account when analyzing temporally and spatially structured virus data. In this article, we present a fully probabilistic approach for the joint reconstruction of phylodynamic history in structured populations (such as geographic structure) based on a multitype birth–death process. This approach can be used to quantify the spread of a pathogen in ...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Kühnert, D., Stadler, T., Vaughan, T. G., Drummond, A. J. Tags: Methods Source Type: research
The Footprint of Polygenic Adaptation on Stress-Responsive Cis-Regulatory Divergence in the Arabidopsis Genus
Adaptation of a complex trait often requires the accumulation of many modifications to finely tune its underpinning molecular components to novel environmental requirements. The investigation of cis-acting regulatory modifications can be used to pinpoint molecular systems partaking in such complex adaptations. Here, we identify cis-acting modifications with the help of an interspecific crossing scheme designed to distinguish modifications derived in each of the two sister species, Arabidopsis halleri and A. lyrata. Allele-specific expression levels were assessed in three environmental conditions chosen to reflect interspec...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: He, F., Arce, A. L., Schmitz, G., Koornneef, M., Novikova, P., Beyer, A., de Meaux, J. Tags: Discoveries Source Type: research
Evolution of Vertebrate Phototransduction: Cascade Activation
We applied high-throughput sequencing to eye tissue from several species of basal vertebrates (a hagfish, two species of lamprey, and five species of gnathostome fish), and we analyzed the mRNA sequences for the proteins underlying activation of the phototransduction cascade. The molecular phylogenies that we constructed from these sequences are consistent with the 2R WGD model of two rounds of whole genome duplication. Our analysis suggests that agnathans retain an additional representative (that has been lost in gnathostomes) in each of the gene families we studied; the evidence is strong for the G-protein α subuni...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Lamb, T. D., Patel, H., Chuah, A., Natoli, R. C., Davies, W. I. L., Hart, N. S., Collin, S. P., Hunt, D. M. Tags: Discoveries Source Type: research
Expanded Genetic Codes Create New Mutational Routes to Rifampicin Resistance in Escherichia coli
Until recently, evolutionary questions surrounding the nature of the genetic code have been mostly limited to the realm of conjecture, modeling, and simulation due to the difficulty of altering this fundamental property of living organisms. Concerted genome and protein engineering efforts now make it possible to experimentally study the impact of alternative genetic codes on the evolution of biological systems. We explored how Escherichia coli strains that incorporate a 21st nonstandard amino acid (nsAA) at the recoded amber (TAG) stop codon evolve resistance to the antibiotic rifampicin. Resistance to rifampicin arises fr...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Hammerling, M. J., Gollihar, J., Mortensen, C., Alnahhas, R. N., Ellington, A. D., Barrick, J. E. Tags: Discoveries Source Type: research
Insertion DNA Accelerates Meiotic Interchromosomal Recombination in Arabidopsis thaliana
Nucleotide insertions/deletions are ubiquitous in eukaryotic genomes, and the resulting hemizygous (unpaired) DNA has significant, heritable effects on adjacent DNA. However, little is known about the genetic behavior of insertion DNA. Here, we describe a binary transgenic system to study the behavior of insertion DNA during meiosis. Transgenic Arabidopsis lines were generated to carry two different defective reporter genes on nonhomologous chromosomes, designated as "recipient" and "donor" lines. Double hemizygous plants (harboring unpaired DNA) were produced by crossing between the recipient and the donor, and double hom...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Sun, X.-Q., Li, D.-H., Xue, J.-Y., Yang, S.-H., Zhang, Y.-M., Li, M.-M., Hang, Y.-Y. Tags: Discoveries Source Type: research
Regulatory Differences in Natal Down Development between Altricial Zebra Finch and Precocial Chicken
Birds can be classified into altricial and precocial. The hatchlings of altricial birds are almost naked, whereas those of precocial birds are covered with natal down. This regulatory divergence is thought to reflect environmental adaptation, but the molecular basis of the divergence is unclear. To address this issue, we chose the altricial zebra finch and the precocial chicken as the model animals. We noted that zebra finch hatchlings show natal down growth suppressed anterior dorsal (AD) skin but partially down-covered posterior dorsal (PD) skin. Comparing the transcriptomes of AD and PD skins, we found that the feather ...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Chen, C.-K., Ng, C. S., Wu, S.-M., Chen, J.-J., Cheng, P.-L., Wu, P., Lu, M.-Y. J., Chen, D.-R., Chuong, C.-M., Cheng, H.-C., Ting, C.-T., Li, W.-H. Tags: Discoveries Source Type: research
Characterization of the Cadherin-Catenin Complex of the Sea Anemone Nematostella vectensis and Implications for the Evolution of Metazoan Cell-Cell Adhesion
The cadherin–catenin complex (CCC) mediates cell–cell adhesion in bilaterian animals by linking extracellular cadherin-based adhesions to the actin cytoskeleton. However, it is unknown whether the basic organization of the complex is conserved across all metazoans. We tested whether protein interactions and actin-binding properties of the CCC are conserved in a nonbilaterian animal, the sea anemone Nematostella vectensis. We demonstrated that N. vectensis has a complete repertoire of cadherin–catenin proteins, including two classical cadherins, one α-catenin, and one β-catenin. Using size-exclu...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Clarke, D. N., Miller, P. W., Lowe, C. J., Weis, W. I., Nelson, W. J. Tags: Discoveries Source Type: research
A Recent Whole-Genome Duplication Divides Populations of a Globally Distributed Microsporidian
This study reveals ongoing dramatic reorganization of genome structure and the evolution of new gene functions in modern microsporidians despite extensive genomic streamlining in their common ancestor. (Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Williams, T. A., Nakjang, S., Campbell, S. E., Freeman, M. A., Eydal, M., Moore, K., Hirt, R. P., Embley, T. M., Williams, B. A. P. Tags: Discoveries Source Type: research
Sperm Bindin Divergence under Sexual Selection and Concerted Evolution in Sea Stars
Selection associated with competition among males or sexual conflict between mates can create positive selection for high rates of molecular evolution of gamete recognition genes and lead to reproductive isolation between species. We analyzed coding sequence and repetitive domain variation in the gene encoding the sperm acrosomal protein bindin in 13 diverse sea star species. We found that bindin has a conserved coding sequence domain structure in all 13 species, with several repeated motifs in a large central region that is similar among all sea stars in organization but highly divergent among genera in nucleotide and pre...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Patino, S., Keever, C. C., Sunday, J. M., Popovic, I., Byrne, M., Hart, M. W. Tags: Discoveries Source Type: research
Dynamic Evolution of Nitric Oxide Detoxifying Flavohemoglobins, a Family of Single-Protein Metabolic Modules in Bacteria and Eukaryotes
Due to their functional independence, proteins that comprise standalone metabolic units, which we name single-protein metabolic modules, may be particularly prone to gene duplication (GD) and horizontal gene transfer (HGT). Flavohemoglobins (flavoHbs) are prime examples of single-protein metabolic modules, detoxifying nitric oxide (NO), a ubiquitous toxin whose antimicrobial properties many life forms exploit, to nitrate, a common source of nitrogen for organisms. FlavoHbs appear widespread in bacteria and have been identified in a handful of microbial eukaryotes, but how the distribution of this ecologically and biomedica...
Source: Molecular Biology and Evolution - July 17, 2016 Category: Molecular Biology Authors: Wisecaver, J. H., Alexander, W. G., King, S. B., Todd Hittinger, C., Rokas, A. Tags: Discoveries Source Type: research
