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Molecular Biology and Evolution

Zhichao Yan, Gongyin Ye, John H Werren
The mitochondrion is a pivotal organelle for energy production, and includes components encoded by both the mitochondrial and nuclear genomes. Functional and evolutionary interactions are expected between the nuclear and mitochondrial encoded components. The topic is of broad interest in biology, with implications to genetics, evolution, and medicine. Here we compare the evolutionary rates of mitochondrial proteins and ribosomal RNAs to rates of mitochondria-associated nuclear-encoded proteins, across the major orders of holometabolous insects...
February 20, 2019: Molecular Biology and Evolution
Flora Jay, Simon Boitard, Frédéric Austerlitz
Species generally undergo a complex demographic history consisting, in particular, of multiple changes in population size. Genome-wide sequencing data are potentially highly informative for reconstructing this demographic history. A crucial point is to extract the relevant information from these very large datasets. Here we design an approach for inferring past demographic events from a moderate number of fully sequenced genomes. Our new approach uses Approximate Bayesian Computation (ABC), a simulation-based statistical framework that allows (i) identifying the best demographic scenario among several competing scenarios, and (ii) estimating the best-fitting parameters under the chosen scenario...
February 20, 2019: Molecular Biology and Evolution
Katherine H Shaw, Travis K Johnson, Alisha Anderson, Marien de Bruyne, Coral G Warr
Insect odorant receptor (Or) genes determine the responses of sensory neurons that mediate critical behaviours. The Drosophila melanogaster Or22 locus represents an interesting example of molecular evolution, with high levels of sequence divergence and copy number variation between D. melanogaster and other Drosophila species, and a corresponding high level of variability in the responses of the neuron it controls, ab3A. However, the link between Or22 molecular and functional diversity has not been established...
February 15, 2019: Molecular Biology and Evolution
Beth L Dumont
Mutation provides the ultimate source of all new alleles in populations, including variants that cause disease and fuel adaptation. Recent whole genome sequencing studies have uncovered variation in the mutation rate among individuals and differences in the relative frequency of specific nucleotide changes (the mutation spectrum) between populations. Although parental age is a major driver of differences in overall mutation rate among individuals, the causes of variation in the mutation spectrum remain less well understood...
February 11, 2019: Molecular Biology and Evolution
Rachael C Aikens, Kelsey E Johnson, Benjamin F Voight
Our understanding of the human mutation rate helps us build evolutionary models and interpret patterns of genetic variation observed in human populations. Recent work indicates that the frequencies of specific polymorphism types have been elevated in Europe, and that many more, subtler signatures of global polymorphism variation may yet remain unidentified. Here, we present an analysis of the 1,000 Genomes Project supported by analysis in the Simons Genome Diversity Panel, suggesting additional putative signatures of mutation rate variation across populations and the extent to which they are shaped by local sequence context...
February 7, 2019: Molecular Biology and Evolution
Timothy Q DuBuc, Joseph Ryan, Mark Q Martindale
Placozoa are a morphologically simplistic group of marine animals found globally in tropical and subtropical environments. They consist of two named species, Trichoplax adhaerens and more recently Hoilungia hongkongensis, both with roughly six morphologically distinct cell types. With a sequenced genome, a limited number of cell-types, and a simple flattened morphology, Trichoplax is an ideal model organism from which to explore the biology of an animal with a cellular complexity analagous to that of the earliest animals...
February 6, 2019: Molecular Biology and Evolution
Michail Rovatsos, Ivan Rehák, Petr Velenský, Lukáš Kratochvíl
Sex determination in varanids, Gila monsters, beaded lizards and other anguimorphan lizards is still poorly understood. Sex chromosomes were reported only in a few species based solely on cytogenetics, which precluded assessment of their homology. We uncovered Z-chromosome specific genes in varanids from their transcriptomes. Comparison of differences in gene copy numbers between sexes across anguimorphan lizards and outgroups revealed that homologous differentiated ZZ/ZW sex chromosomes are present in Gila monsters, beaded lizards, alligator lizards and a wide phylogenetic spectrum of varanids...
February 5, 2019: Molecular Biology and Evolution
Theresa L Cole, Daniel T Ksepka, Kieren J Mitchell, Alan J D Tennyson, Daniel B Thomas, Hailin Pan, Guojie Zhang, Nicolas J Rawlence, Jamie R Wood, Pere Bover, Juan L Bouzat, Alan Cooper, Steven Fiddaman, Tom Hart, Gary Miller, Peter G Ryan, Lara D Shepherd, Janet M Wilmshurst, Jonathan M Waters
The emergence of islands has been linked to spectacular radiations of diverse organisms. Although penguins spend much of their lives at sea, they rely on land for nesting, and a high proportion of extant species are endemic to geologically-young islands. Islands may thus have been crucial to the evolutionary diversification of penguins. We test this hypothesis using a fossil-calibrated phylogeny of mitochondrial genomes (mitogenomes) from all extant and recently extinct penguin taxa. Our temporal analysis demonstrates that numerous recent island-endemic penguin taxa diverged following the formation of their islands during the Plio-Pleistocene, including the Galápagos (Galápagos Islands), northern rockhopper (Gough Island), erect-crested (Antipodes Islands), Snares crested (Snares) and royal (Macquarie Island) penguins...
February 5, 2019: Molecular Biology and Evolution
Jeffrey I Boucher, Troy W Whitfield, Ann Dauphin, Gily Nachum, Carl Hollins, Konstantin B Zeldovich, Ronald Swanstrom, Celia A Schiffer, Jeremy Luban, Daniel N A Bolon
The evolution of HIV-1 protein sequences should be governed by a combination of factors including nucleotide mutational probabilities, the genetic code, and fitness. The impact of these factors on protein sequence evolution are interdependent, making it challenging to infer the individual contribution of each factor from phylogenetic analyses alone. We investigated the protein sequence evolution of HIV-1 by determining an experimental fitness landscape of all individual amino acid changes in protease. We compared our experimental results to the frequency of protease variants in a publicly available dataset of 32,163 sequenced isolates from drug-naïve individuals...
February 4, 2019: Molecular Biology and Evolution
Tung Dang, Hirohisa Kishino
The pattern of molecular evolution varies among gene sites and genes in a genome. By taking into account the complex heterogeneity of evolutionary processes among sites in a genome, Bayesian infinite mixture models of genomic evolution enable robust phylogenetic inference. With large modern data sets, however, the computational burden of Markov chain Monte Carlo sampling techniques becomes prohibitive. Here, we have developed a variational Bayesian procedure to speed up the widely used PhyloBayes MPI program, which deals with the heterogeneity of amino acid profiles...
February 1, 2019: Molecular Biology and Evolution
Hanna M Heidel-Fischer, Roy Kirsch, Michael Reichelt, Seung-Joon Ahn, Natalie Wielsch, Simon W Baxter, David G Heckel, Heiko Vogel, Juergen Kroymann
Antagonistic chemical interactions between herbivorous insects and their host plants are often thought to co-evolve in a stepwise process, with an evolutionary innovation on one side being countered by a corresponding advance on the other. Glucosinolate sulfatase (GSS) enzyme activity is essential for the Diamondback moth (DBM), Plutella xylostella, to overcome a highly diversified secondary metabolite-based host defense system in the Brassicales. GSS genes are located in an ancient cluster of arylsulfatase-like genes, but the exact roles of gene copies and their evolutionary trajectories are unknown...
February 1, 2019: Molecular Biology and Evolution
Joseph Caspermeyer
No abstract text is available yet for this article.
January 31, 2019: Molecular Biology and Evolution
Celine Scornavacca, Khalid Belkhir, Jimmy Lopez, Rémy Dernat, Frédéric Delsuc, Emmanuel J P Douzery, Vincent Ranwez
We present version 10 of OrthoMaM, a database of orthologous mammalian markers. OrthoMaM is already 11 years old and since the outset it has kept on improving, providing alignments and phylogenetic trees of high quality computed with state-of-the-art methods on up-to-date data. The main contribution of this version is the increase in the number of taxa: 116 mammalian genomes for 14,509 one-to-one orthologous genes. This has been made possible by the combination of genomic data deposited in Ensembl complemented by additional good-quality genomes only available in NCBI...
January 29, 2019: Molecular Biology and Evolution
Emmanuel Noutahi, Virginie Calderon, Mathieu Blanchette, Nadia El-Mabrouk, B Franz Lang
Genetic code deviations involving stop codons have been previously reported in mitochondrial genomes of several green plants (Viridiplantae), most notably chlorophyte algae (Chlorophyta). However, as changes in codon recognition from one amino acid to another are more difficult to infer, such changes might have gone unnoticed in particular lineages with high evolutionary rates that are otherwise prone to codon reassignments. To gain further insight into the evolution of the mitochondrial genetic code in green plants, we have conducted an in-depth study across mtDNAs from 51 green plants (32 chlorophytes and 19 streptophytes)...
January 29, 2019: Molecular Biology and Evolution
Walker Pett, Marcin Adamski, Maja Adamska, Warren R Francis, Michael Eitel, Davide Pisani, Gert Wörheide
Resolving the relationships of animals (Metazoa) is crucial to our understanding of, for example, the origin of key traits such as muscles, guts and nerves. However, a broadly accepted metazoan consensus phylogeny has yet to emerge. In part this is because the genomes of deeply-diverging and fast-evolving lineages may undergo significant gene turnover, reducing the number of orthologs shared with related phyla. This can limit the usefulness of traditional phylogenetic methods that rely on alignments of orthologous sequences...
January 28, 2019: Molecular Biology and Evolution
James Stimson, Jennifer Gardy, Barun Mathema, Valeriu Crudu, Ted Cohen, Caroline Colijn
Whole genome sequencing (WGS) is increasingly used to aid the understanding of pathogen transmission. A first step in analysing WGS data is usually to define" transmission clusters", sets of cases that are potentially linked by direct transmission. This is often done by including two cases in the same cluster if they are separated by fewer SNPs than a specified threshold. However, there is little agreement as to what an appropriate threshold should be. We propose a probabilistic alternative, suggesting that the key inferential target for transmission clusters is the number of transmissions separating cases...
January 25, 2019: Molecular Biology and Evolution
Nathanaëlle Saclier, Clémentine M François, Lara Konecny-Dupré, Nicolas Lartillot, Laurent Guéguen, Laurent Duret, Florian Malard, Christophe J Douady, Tristan Lefébure
No abstract text is available yet for this article.
January 23, 2019: Molecular Biology and Evolution
Qiqing Tao, Koichiro Tamura, Fabia Battistuzzi, Sudhir Kumar
New species arise from pre-existing species and inherit similar genomes and environments. This predicts greater similarity of the tempo of molecular evolution between direct ancestors and descendants, resulting in autocorrelation of evolutionary rates in the tree of life. Surprisingly, molecular sequence data have not confirmed this expectation, possibly because available methods lack the power to detect autocorrelated rates. Here we present a machine learning method, CorrTest, to detect the presence of rate autocorrelation in large phylogenies...
January 23, 2019: Molecular Biology and Evolution
Jorge Hernández-García, Asier Briones-Moreno, Renaud Dumas, Miguel A Blázquez
DELLA proteins are plant specific transcriptional regulators known to interact through their C-terminal GRAS domain with over 150 transcription factors in Arabidopsis thaliana. Besides, DELLAs from vascular plants can interact through the N-terminal domain with the gibberellin receptor encoded by GID1, through which gibberellins promote DELLA degradation. However, this regulation is absent in non-vascular land plants, which lack active gibberellins or a proper GID1 receptor. Current knowledge indicates that DELLAs are important pieces of the signalling machinery of vascular plants, especially angiosperms, but nothing is known about DELLA function during early land plant evolution or if they exist at all in charophytan algae...
January 22, 2019: Molecular Biology and Evolution
Sandra Backes, Sriram G Garg, Laura Becker, Valentina Peleh, Rudi Glockshuber, Sven B Gould, Johannes M Herrmann
The mitochondrial intermembrane space evolved from the bacterial periplasm. Presumably as a consequence of their common origin, most proteins of these compartments are stabilized by structural disulfide bonds. The molecular machineries that mediate oxidative protein folding in bacteria and mitochondria, however, appear to share no common ancestry. Here we tested whether the enzymes Erv1 and Mia40 of the yeast mitochondrial disulfide relay could be functionally replaced by corresponding components of other compartments...
January 22, 2019: Molecular Biology and Evolution
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