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Journal of Molecular Evolution

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https://www.readbyqxmd.com/read/28669113/efficient-heritable-gene-expression-readily-evolves-in-rna-pools
#1
Michael Yarus
Heritable gene expression arises readily in a simple non-genetic system employing known small-RNA biochemistry. Pooled cross-templating ribonucleotides show varied chemical competence on which selection acts, even calculating only minimal effects. Evolution can be quick-computed progress toward encoded gene expression can require only days or weeks for two millimolar, partly activated complementary 5' ribonucleotides. After only one product selection cycle, early templating can become prevailing pool behavior...
July 1, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28664404/chemical-evolution-and-the-evolutionary-definition-of-life
#2
Paul G Higgs
Darwinian evolution requires a mechanism for generation of diversity in a population, and selective differences between individuals that influence reproduction. In biology, diversity is generated by mutations and selective differences arise because of the encoded functions of the sequences (e.g., ribozymes or proteins). Here, I draw attention to a process that I will call chemical evolution, in which the diversity is generated by random chemical synthesis instead of (or in addition to) mutation, and selection acts on physicochemical properties, such as hydrolysis, photolysis, solubility, or surface binding...
June 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28660301/evolution-of-gstd1-in-cactophilic-drosophila
#3
Karina López-Olmos, Therese Ann Markow, Carlos A Machado
GSTD1 is an insect glutathione S-transferase that has received considerable attention because of its role in detoxification of xenobiotic compounds, specifically pesticides and plant allelochemicals involved in detoxification, or in the use of some substrates as a nutritional source. GSTD1 has been implicated in the adaptation to a new cactus host in Drosophila mojavensis and thus constitutes an interesting candidate to study ecological genetics of adaptation in Drosophila. We conducted population genetic and molecular evolution analyses of the GstD1 gene in the context of association with different cactus hosts (Opuntia sp...
June 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28646326/transposable-elements-mediate-adaptive-debilitation-of-flagella-in-experimental-escherichia-coli-populations
#4
Gordon R Plague, Krystal S Boodram, Kevin M Dougherty, Sandar Bregg, Daniel P Gilbert, Hira Bakshi, Daniel Costa
Although insertion sequence (IS) elements are generally considered genomic parasites, they can mediate adaptive genetic changes in bacterial genomes. We discovered that among 12 laboratory-evolved Escherichia coli populations, three had experienced at least six different IS1-mediated deletions of flagellar genes. These deletions all involved the master flagellar regulator flhDC, and as such completely incapacitate motility. Two lines of evidence strongly suggest that these deletions were adaptive in our evolution experiment: (1) parallel evolution in three independent populations is highly unlikely just by chance, and (2) one of these deletion mutations swept to fixation within ~1000 generations, which is over two million times faster than expected if this deletion was instead selectively neutral and thus evolving by genetic drift...
June 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28589220/binding-properties-of-split-trna-to-the-c-terminal-domain-of-methionyl-trna-synthetase-of-nanoarchaeum-equitans
#5
Hidemichi Suzuki, Akihiro Kaneko, Taro Yamamoto, Mahoko Nambo, Ito Hirasawa, Takuya Umehara, Hisashi Yoshida, Sam-Yong Park, Koji Tamura
The C-terminal domain of methionyl-tRNA synthetase (MetRS-C) from Nanoarchaeum equitans is homologous to a tRNA-binding protein consisting of 111 amino acids (Trbp111) from Aquifex aeolicus. The crystal structure of MetRS-C showed that it existed as a homodimer, and that each monomer possessed an oligonucleotide/oligosaccharide-binding fold (OB-fold). Analysis using a quartz crystal microbalance indicated that MetRS-C freshly isolated from N. equitans was bound to tRNA. However, binding of the split 3'-half tRNA species was stronger than that of the 5'-half species...
June 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28492967/a-test-for-gene-flow-among-sympatric-and-allopatric-hawaiian-picture-winged-drosophila
#6
Lin Kang, Harold R Garner, Donald K Price, Pawel Michalak
The Hawaiian Drosophila are one of the most species-rich endemic groups in Hawaii and a spectacular example of adaptive radiation. Drosophila silvestris and D. heteroneura are two closely related picture-winged Drosophila species that occur sympatrically on Hawaii Island and are known to hybridize in nature, yet exhibit highly divergent behavioral and morphological traits driven largely through sexual selection. Their closest-related allopatric species, D. planitibia from Maui, exhibits hybrid male sterility and reduced behavioral reproductive isolation when crossed experimentally with D...
June 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28492966/complex-genes-are-preferentially-retained-after-whole-genome-duplication-in-teleost-fish
#7
LETTER
Baocheng Guo
Gene duplication generates new genetic material which, if retained after duplication, may contribute to organismal evolution. A whole-genome duplication occurred in the ancestry of teleost fish and consequently there are many duplicated genes in teleost genomes. Indeed, it has been proposed that the evolutionary diversification of teleost fish may have been stimulated by the fish-specific genome duplication (FSGD). However, it is not clear which factors determine which genes are retained as duplicate copies and which return to a singleton state after duplication...
June 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28405712/emergence-of-new-srnas-in-enteric-bacteria-is-associated-with-low-expression-and-rapid-evolution
#8
Fenil R Kacharia, Jess A Millar, Rahul Raghavan
Non-coding small RNAs (sRNAs) are critical to post-transcriptional gene regulation in bacteria. However, unlike for protein-coding genes, the evolutionary forces that shape sRNAs are not understood. We investigated sRNAs in enteric bacteria and discovered that recently emerged sRNAs evolve at significantly faster rates than older sRNAs. Concomitantly, younger sRNAs are expressed at significantly lower levels than older sRNAs. This process could potentially facilitate the integration of newly emerged sRNAs into bacterial regulatory networks...
April 12, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28397003/plastome-wide-nucleotide-substitution-rates-reveal-accelerated-rates-in-papilionoideae-and-correlations-with-genome-features-across-legume-subfamilies
#9
Erika N Schwarz, Tracey A Ruhlman, Mao-Lun Weng, Mohammad A Khiyami, Jamal S M Sabir, Nahid H Hajarah, Njud S Alharbi, Samar O Rabah, Robert K Jansen
This study represents the most comprehensive plastome-wide comparison of nucleotide substitution rates across the three subfamilies of Fabaceae: Caesalpinioideae, Mimosoideae, and Papilionoideae. Caesalpinioid and mimosoid legumes have large, unrearranged plastomes compared with papilionoids, which exhibit varying levels of rearrangement including the loss of the inverted repeat (IR) in the IR-lacking clade (IRLC). Using 71 genes common to 39 legume taxa representing all the three subfamilies, we show that papilionoids consistently have higher nucleotide substitution rates than caesalpinioids and mimosoids, and rates in the IRLC papilionoids are generally higher than those in the IR-containing papilionoids...
April 10, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28382496/molecular-evolutionary-constraints-that-determine-the-avirulence-state-of-clostridium-botulinum-c2-toxin
#10
A Prisilla, R Prathiviraj, P Chellapandi
Clostridium botulinum (group-III) is an anaerobic bacterium producing C2 toxin along with botulinum neurotoxins. C2 toxin is belonged to binary toxin A family in bacterial ADP-ribosylation superfamily. A structural and functional diversity of binary toxin A family was inferred from different evolutionary constraints to determine the avirulence state of C2 toxin. Evolutionary genetic analyses revealed evidence of C2 toxin cluster evolution through horizontal gene transfer from the phage or plasmid origins, site-specific insertion by gene divergence, and homologous recombination event...
April 5, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28378191/testing-for-the-occurrence-of-selective-episodes-during-the-divergence-of-otophysan-fishes-insights-from-mitogenomics
#11
Alejandro D'Anatro, Facundo Giorello, Matías Feijoo, Enrique P Lessa
How natural selection shapes biodiversity constitutes a topic of renewed interest during the last few decades. The division Otophysi comprises approximately two-thirds of freshwater fish diversity and probably underwent an extensive adaptive radiation derived from a single invasion of the supercontinent Pangaea, giving place to the evolution of the main five Otophysan lineages during a short period of time. Little is known about the factors involved in the processes that lead to lineage diversification among this group of fishes and identifying directional selection acting over protein-coding genes could offer clues about the processes acting on species diversification...
April 4, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28378190/autocatalytic-sets-and-rna-secondary-structure
#12
Wim Hordijk
The dominant paradigm in origin of life research is that of an RNA world. However, despite experimental progress towards the spontaneous formation of RNA, the RNA world hypothesis still has its problems. Here, we introduce a novel computational model of chemical reaction networks based on RNA secondary structure and analyze the existence of autocatalytic sub-networks in random instances of this model, by combining two well-established computational tools. Our main results are that (i) autocatalytic sets are highly likely to exist, even for very small reaction networks and short RNA sequences, and (ii) sequence diversity seems to be a more important factor in the formation of autocatalytic sets than sequence length...
April 4, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28409196/evolutionary-analysis-of-the-mammalian-tuftelin-sequence-reveals-features-of-functional-importance
#13
S Delgado, D Deutsch, J Y Sire
Tuftelin (TUFT1) is an acidic, phosphorylated glycoprotein, initially discovered in developing enamel matrix. TUFT1 is expressed in many mineralized and non-mineralized tissues. We performed an evolutionary analysis of 82 mammalian TUFT1 sequences to identify residues and motifs that were conserved during 220 million years (Ma) of evolution. We showed that 168 residues (out of the 390 residues composing the human TUFT1 sequence) are under purifying selection. Our analyses identified several, new, putatively functional domains and confirmed previously described functional domains, such as the TIP39 interaction domain, which correlates with nuclear localization of the TUFT1 protein, that was demonstrated in several tissues...
April 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28331938/involvement-of-clustered-genes-in-mammalian-functions-their-relation-in-a-rat-mutant-strain
#14
LETTER
Naoki Nanashima, Toshiyuki Yamada, Takeshi Shimizu, Shigeki Tsuchida
No abstract text is available yet for this article.
March 22, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28285392/a-consensus-method-for-ancestral-recombination-graphs
#15
Mary K Kuhner, Jon Yamato
We propose a consensus method for ancestral recombination graphs (ARGs) that generates a single ARG representing commonalities among a cloud of ARGs defined for the same genomic region and set of taxa. Our method, which we call "threshold consensus," treats a genomic location as a potential recombination breakpoint only if the number of ARGs in the cloud possessing a breakpoint at that location exceeds a chosen threshold. The estimate is further refined by ignoring recombinations that do not change the local tree topologies, as well as collapsing breakpoint locations separated only by invariant sites...
March 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28243688/the-origin-of-life-models-and-data
#16
Kathryn A Lanier, Loren Dean Williams
A general framework for conventional models of the origin of life (OOL) is the specification of a 'privileged function.' A privileged function is an extant biological function that is excised from its biological context, elevated in importance over other functions, and transported back in time to a primitive chemical or geological environment. In RNA or Clay Worlds, the privileged function is replication. In Metabolism-First Worlds, the privileged function is metabolism. In Thermal Vent Worlds, the privileged function is energy harvesting from chemical gradients...
March 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28243687/the-isochores-as-a-fundamental-level-of-genome-structure-and-organization-a-general-overview
#17
REVIEW
Maria Costantini, Héctor Musto
The recent availability of a number of fully sequenced genomes (including marine organisms) allowed to map very precisely the isochores, based on DNA sequences, confirming the results obtained before genome sequencing by the ultracentrifugation in CsCl. In fact, the analytical profile of human DNA showed that the vertebrate genome is a mosaic of isochores, typically megabase-size DNA segments that belong to a small number of families characterized by different GC levels. In this review, we will concentrate on some general genome features regarding the compositional organization from different organisms and their evolution, ranging from vertebrates to invertebrates until unicellular organisms...
March 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28233029/experimental-evolution-of-escherichia-coli-harboring-an-ancient-translation-protein
#18
Betül Kacar, Xueliang Ge, Suparna Sanyal, Eric A Gaucher
The ability to design synthetic genes and engineer biological systems at the genome scale opens new means by which to characterize phenotypic states and the responses of biological systems to perturbations. One emerging method involves inserting artificial genes into bacterial genomes and examining how the genome and its new genes adapt to each other. Here we report the development and implementation of a modified approach to this method, in which phylogenetically inferred genes are inserted into a microbial genome, and laboratory evolution is then used to examine the adaptive potential of the resulting hybrid genome...
March 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28220195/molecular-convergent-evolution-of-the-mybpc2-gene-among-three-high-elevation-amphibian-species
#19
LETTER
Weizhao Yang, Bin Lu, Jinzhong Fu
We report a strong pattern of molecular-level convergent/parallel evolution of the MYBPC2 gene. Three high-elevation amphibian species, Bufo gargarizans minshanicus, Nanorana pleskei, Rana kukunoris, revealed remarkable numbers of convergent and parallel amino acid substitutions. On the MYBPC2 gene tree of eleven anurans, the three distantly related species formed a strongly supported clade that was away from their respective relatives. Furthermore, we generated both model-based and empirical data-based null distributions for neutral convergent evolution...
March 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28210761/the-evolutionary-loss-of-rnai-key-determinants-in-kinetoplastids-as-a-multiple-sporadic-phenomenon
#20
Andrey V Matveyev, João M P Alves, Myrna G Serrano, Vladimir Lee, Ana M Lara, William A Barton, André G Costa-Martins, Stephen M Beverley, Erney P Camargo, Marta M G Teixeira, Gregory A Buck
We screened the genomes of a broad panel of kinetoplastid protists for genes encoding proteins associated with the RNA interference (RNAi) system using probes from the Argonaute (AGO1), Dicer1 (DCL1), and Dicer2 (DCL2) genes of Leishmania brasiliensis and Crithidia fasciculata. We identified homologs for all the three of these genes in the genomes of a subset of these organisms. However, several of these organisms lacked evidence for any of these genes, while others lacked only DCL2. The open reading frames encoding these putative proteins were structurally analyzed in silico...
March 2017: Journal of Molecular Evolution
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