Evolution of Digestive Enzymes and RNASE1 Provides Insights into Dietary Switch of Cetaceans
Although cetaceans (whales, porpoises, and dolphins) have multi-chambered stomachs, feeding habits of modern cetaceans have dramatically changed from herbivorous to carnivorous. However, the genetic basis underlying this dietary switch remains unexplored. Here, we present the first systematic investigation of 10 digestive enzymes genes (i.e., CYP7A1, CTRC, LIPC, LIPF, PNLIP, PGC, PRSS1, SI, SLC5A1, and TMPRSS15) of representative cetaceans, and the evolutionary trajectory of RNASE1 in cetartiodactylans. Positive selections were detected with proteinases (i.e., CTRC, PRSS1, and TMPRSS15) and lipases (i.e., CYP7A1, LIPF, and...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Wang, Z., Xu, S., Du, K., Huang, F., Chen, Z., Zhou, K., Ren, W., Yang, G. Tags: Discoveries Source Type: research
Dynamic Convergent Evolution Drives the Passage Adaptation across 48 Years History of H3N2 Influenza Evolution
Influenza viruses are often propagated in a diverse set of culturing media and additional substitutions known as passage adaptation can cause extra evolution in the target strain, leading to ineffective vaccines. Using 25,482 H3N2 HA1 sequences curated from Global Initiative on Sharing All Influenza Data and National Center for Biotechnology Information databases, we found that passage adaptation is a very dynamic process that changes over time and evolves in a seesaw like pattern. After crossing the species boundary from bird to human in 1968, the influenza H3N2 virus evolves to be better adapted to the human environment ...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Chen, H., Deng, Q., Ng, S. H., Lee, R. T. C., Maurer-Stroh, S., Zhai, W. Tags: Discoveries Source Type: research
Evolutionary Dynamics of Abundant Stop Codon Readthrough
Translational stop codon readthrough emerged as a major regulatory mechanism affecting hundreds of genes in animal genomes, based on recent comparative genomics and ribosomal profiling evidence, but its evolutionary properties remain unknown. Here, we leverage comparative genomic evidence across 21 Anopheles mosquitoes to systematically annotate readthrough genes in the malaria vector Anopheles gambiae, and to provide the first study of abundant readthrough evolution, by comparison with 20 Drosophila species. Using improved comparative genomics methods for detecting readthrough, we identify evolutionary signatures of conse...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Jungreis, I., Chan, C. S., Waterhouse, R. M., Fields, G., Lin, M. F., Kellis, M. Tags: Discoveries Source Type: research
The X to Autosome Expression Ratio in Haploid and Diploid Human Embryonic Stem Cells
Ohno proposed that the expression levels of X-linked genes have been doubled to compensate the degeneration of Y-linked homologs during the evolution of mammalian sex chromosomes, but RNA sequencing in human somatic tissues showed no such upregulation for the vast majority of X-linked genes. Here we report that the X to autosome expression ratio equals ~1 in haploid human parthenogenetic embryonic stem (pES) cells and ~0.5 in diploidized pES cells, both with one active X chromosome. Although we confirmed the upregulation of ~5% of X-linked genes encoding members of large protein complexes in diploids, these genes are also ...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Chen, X., Zhang, J. Tags: Discoveries Source Type: research
Evolutionary History of the Nesophontidae, the Last Unplaced Recent Mammal Family
The mammalian evolutionary tree has lost several major clades through recent human-caused extinctions. This process of historical biodiversity loss has particularly affected tropical island regions such as the Caribbean, an area of great evolutionary diversification but poor molecular preservation. The most enigmatic of the recently extinct endemic Caribbean mammals are the Nesophontidae, a family of morphologically plesiomorphic lipotyphlan insectivores with no consensus on their evolutionary affinities, and which constitute the only major recent mammal clade to lack any molecular information on their phylogenetic placeme...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Brace, S., Thomas, J. A., Dalen, L., Burger, J., MacPhee, R. D. E., Barnes, I., Turvey, S. T. Tags: Discoveries Source Type: research
Is Genome Complexity a Consequence of Inefficient Selection? Evidence from Intron Creation in Nonrecombining Regions
Genomes show remarkable variation in architecture and complexity across organisms, with large differences in genome size and in numbers of genes, gene duplicates, introns and transposable elements. These differences have important implications for transcriptome and regulatory complexity and ultimately for organismal complexity. Numbers of spliceosomal introns show particularly striking differences, ranging across organisms from zero to hundreds of thousands of introns per genome. The causes of these differences remain poorly understood. According to one influential perspective, differences across species reflect the differ...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Roy, S. W. Tags: Discoveries Source Type: research
The Evolution of Innate Immune Genes: Purifying and Balancing Selection on {beta}-Defensins in Waterfowl
In disease dynamics, high immune gene diversity can confer a selective advantage to hosts in the face of a rapidly evolving and diverse pathogen fauna. This is supported empirically for genes involved in pathogen recognition and signalling. In contrast, effector genes involved in pathogen clearance may be more constrained. β-Defensins are innate immune effector genes; their main mode of action is via disruption of microbial membranes. Here, five β-defensin genes were characterized in mallards (Anas platyrhynchos) and other waterfowl; key reservoir species for many zoonotic diseases. All five genes showed remarkab...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Chapman, J. R., Hellgren, O., Helin, A. S., Kraus, R. H. S., Cromie, R. L., Waldenström, J. Tags: Discoveries Source Type: research
Selective Sweeps across Twenty Millions Years of Primate Evolution
The contribution from selective sweeps to variation in genetic diversity has proven notoriously difficult to assess, in part because polymorphism data only allows detection of sweeps in the most recent few hundred thousand years. Here, we show how linked selection in ancestral species can be quantified across evolutionary timescales by analyzing patterns of incomplete lineage sorting (ILS) along the genomes of closely related species. We show that sweeps in the human–chimpanzee and human–orangutan ancestors can be identified as depletions of ILS in regions in excess of 100 kb in length. Sweeps predicted in each...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Munch, K., Nam, K., Schierup, M. H., Mailund, T. Tags: Fast Track Source Type: research
Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes
Two-component signaling (TCS) is the primary means by which bacteria sense and respond to the environment. TCS involves two partner proteins working in tandem, which interact to perform cellular functions whereas limiting interactions with non-partners (i.e., cross-talk). We construct a Potts model for TCS that can quantitatively predict how mutating amino acid identities affect the interaction between TCS partners and non-partners. The parameters of this model are inferred directly from protein sequence data. This approach drastically reduces the computational complexity of exploring the sequence-space of TCS proteins. As...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Cheng, R. R., Nordesjö, O., Hayes, R. L., Levine, H., Flores, S. C., Onuchic, J. N., Morcos, F. Tags: Fast Track Source Type: research
The Roles of Mutation, Selection, and Expression in Determining Relative Rates of Evolution in Mitochondrial versus Nuclear Genomes
Eukaryotes rely on proteins encoded by the nuclear and mitochondrial (mt) genomes, which interact within multisubunit complexes such as oxidative-phosphorylation enzymes. Although selection is thought to be less efficient on the asexual mt genome, in bilaterian animals the ratio of nonsynonymous to synonymous substitutions () is lower in mt- compared with nuclear-encoded OXPHOS subunits, suggesting stronger effects of purifying selection in the mt genome. Because high levels of gene expression constrain protein sequence evolution, one proposed resolution to this paradox is that mt genes are expressed more highly than nucle...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Havird, J. C., Sloan, D. B. Tags: Fast Track Source Type: research
Unusual Diversity of Myoglobin Genes in the Lungfish
Myoglobin is a respiratory protein that serves as a model system in a variety of biological fields. Its main function is to deliver and store O2 in the heart and skeletal muscles, but myoglobin is also instrumental in homeostasis of nitric oxide (NO) and detoxification of reactive oxygen species (ROS). Almost every vertebrate harbors a single myoglobin gene; only some cyprinid fishes have two recently duplicated myoglobin genes. Here we show that the West African lungfish Protopterus annectens has at least seven distinct myoglobin genes (PanMb1–7), which diverged early in the evolution of lungfish and showed an enhan...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Koch, J., Lüdemann, J., Spies, R., Last, M., Amemiya, C. T., Burmester, T. Tags: Fast Track Source Type: research
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