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Journal of Molecular Evolution

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https://www.readbyqxmd.com/read/29855654/transposable-elements-activity-is-positively-related-to-rate-of-speciation-in-mammals
#1
Ricci Marco, Peona Valentina, Guichard Etienne, Taccioli Cristian, Boattini Alessio
Transposable elements (TEs) play an essential role in shaping eukaryotic genomes and generating variability. Speciation and TE activity bursts could be strongly related in mammals, in which simple gradualistic models of differentiation do not account for the currently observed species variability. In order to test this hypothesis, we designed two parameters: the Density of insertion (DI) and the Relative rate of speciation (RRS). DI is the ratio between the number of TE insertions in a genome and its size, whereas the RRS is a conditional parameter designed to identify potential speciation bursts...
May 31, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29748740/exploration-of-rna-sequence-space-in-the-absence-of-a-replicase
#2
Madhan R Tirumalai, Quyen Tran, Maxim Paci, Dimple Chavan, Anuradha Marathe, George E Fox
It is generally considered that if an RNA World ever existed that it would be driven by an RNA capable of RNA replication. Whether such a catalytic RNA could emerge in an RNA World or not, there would need to be prior routes to increasing complexity in order to produce it. It is hypothesized here that increasing sequence variety, if not complexity, can in fact readily emerge in response to a dynamic equilibrium between synthesis and degradation. A model system in which T4 RNA ligase catalyzes synthesis and Benzonase catalyzes degradation was constructed...
May 11, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29725703/chiral-monomers-ensure-orientational-specificity-of-monomer-binding-during-polymer-self-replication
#3
Hemachander Subramanian, Robert A Gatenby
Biomolecular homochirality is universally observed in living systems but the molecular and evolutionary dynamics that led to its emergence are unknown. In fact, there are significant disadvantages in using chiral monomers for polymerization, which include enantiomeric cross-inhibition in racemic medium and under-utilization of available resources for self-replication in the primordial environment. Nevertheless, most investigations of homochirality in living systems assume that the individual primordial monomers were chiral prior to the formation of self-replicating polymer and therefore focus on identifying a symmetry-breaking mechanism that might choose one enantiomer over the other in a racemic medium...
May 3, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29721580/domain-specific-proteogenomic-analysis-of-collagens-to-evaluate-de-novo-sequencing-results-and-database-information
#4
Anne J Kleinnijenhuis, Frédérique L van Holthoon
Collagen is an important structural protein and the most abundant protein in mammals. In several research fields, structural analysis of collagens is performed. Fibrillar collagens almost entirely consist of continuous repeats of GXY, where G is glycine, X is often proline or alanine and Y is often hydroxyproline or alanine. In the present study, the collagen structure was investigated in detail at the nucleotide, codon group, amino acid and target peptide level using sequence analyses. One of the most important findings was that a selection of codon groups is predominantly involved in amino acid changes between closely related collagens and that other change routes come up when collagens are less related...
May 2, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29691606/phylogenetic-reconstruction-shows-independent-evolutionary-origins-of-mitochondrial-transcription-factors-from-an-ancient-family-of-rna-methyltransferase-proteins
#5
LETTER
Aj Harris, Aaron David Goldman
Here, we generate a robust phylogenetic framework for the rRNA adenine N(6)-methyltransferase (RAMTase) protein family that shows a more ancient and complex evolutionary history within the family than previously reported. RAMTases occur universally by descent across the three domains of life, and typical orthologs within the family perform methylation of the small subunits of ribosomal RNA (rRNA). However, within the RAMTase family, two different groups of mitochondrial transcription factors, mtTFB1 and mtTFB2, have evolved in eukaryotes through neofunctionalization...
April 25, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29679096/protein-evolution-is-potentially-governed-by-protein-stability-directed-evolution-of-an-esterase-from-the-hyperthermophilic-archaeon-sulfolobus-tokodaii
#6
Ryo Kurahashi, Satoshi Sano, Kazufumi Takano
The study of evolution is important to understand biological phenomena. During evolutionary processes, genetic changes confer amino acid substitutions in proteins, resulting in new or improved functions. Unfortunately, most mutations destabilize proteins. Thus, protein stability is a significant factor in evolution; however, its role remains unclear. Here, we simply and directly explored the association between protein activity and stability in random mutant libraries to elucidate the role of protein stability in evolutionary processes...
April 20, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29623351/primitive-dark-phase-cycle-of-photosynthesis-at-the-origin-of-life
#7
LETTER
Michel Koenig
Simple phosphorylation, isomerization, and aldolisation reactions starting from glyceraldehyde have the potential to lead to the synthesis of pre-ribonucleotide polymers through a primitive form of the Calvin cycle (dark phase of photosynthesis) involving the unusual formation of phospho-nonulose phosphate and phospho-deculose phosphate, as key intermediates. These reactions involve activated phosphates which are generated from schreibersite minerals, geochemically available in Hadean times.
April 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29623350/group-selection-may-explain-cancer-predisposition-and-other-human-traits-evolution
#8
EDITORIAL
Konstantinos Voskarides
Group selection is a matter of acute controversy among evolutionary biologists. The most well-publicized debate in this regard is that between Edward O. Wilson and Richard Dawkins. As is widely known, Edward O. Wilson is very excited about the idea of social selection and eusociality; by contrast Richard Dawkins favors the idea of gene selection. As is often the case, the truth is somewhere in the middle. Evolution is most likely a multilevel procedure, where selection forces act on genes, individuals, and groups...
April 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29594426/mineral-grains-dimples-and-hot-volcanic-organic-streams-dynamic-geological-backstage-of-macromolecular-evolution
#9
Nikolai E Skoblikow, Andrei A Zimin
The hypothesis of hot volcanic organic stream as the most probable and geologically plausible environment for abiogenic polycondensation is proposed. The primary synthesis of organic compounds is considered as result of an explosive volcanic (perhaps, meteorite-induced) eruption. The eruption was accompanied by a shock wave propagating in the primeval atmosphere and resulting in the formation of hot cloud of simple organic compounds-aldehydes, alcohols, amines, amino alcohols, nitriles, and amino acids-products, which are usually obtained under the artificial conditions in the spark-discharge experiments...
April 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29574604/evolution-of-melanoma-antigen-a11-magea11-during-primate-phylogeny
#10
Christopher S Willett, Elizabeth M Wilson
Melanoma antigen-A11 (MAGE-A11) is an X-linked and primate-specific steroid hormone receptor transcriptional coregulator and proto-oncogenic protein whose increased expression promotes the growth of prostate cancer. The MAGEA11 gene is expressed at low levels in normal human testis, ovary, and endometrium, and at highest levels in castration-resistant prostate cancer. Annotated genome predictions throughout the surviving primate lineage show that MAGEA11 acquired three 5' coding exons unique within the MAGEA subfamily during the evolution of New World monkeys (NWM), Old World monkeys (OWM), and apes...
April 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29564489/first-report-of-a-mitochondrial-pseudogene-in-agnathan-vertebrates-cyclostomata-petromyzontidae
#11
LETTER
Rex Meade Strange, Kimberly J Delaney
We report herein the characterization of a nuclear paralog of a fragment of the mitochondrial genome (a numt) in two closely related species of lampreys (Ichthyomyzon spp.). Although numts have been characterized in several vertebrate taxa, numts have yet to be reported for fishes in general. Given the phylogenetic position of lampreys relative to other vertebrates, the presence of numts within the lamprey genome is either evidence of an ancestral trait lost in other fishes but uniquely retained in agnathans and amniotes, or (more intriguingly) a product of the genome rearrangements these animals undergo during development...
April 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29556741/application-of-chloroplast-phylogenomics-to-resolve-species-relationships-within-the-plant-genus-amaranthus
#12
Erika Viljoen, Damaris A Odeny, Martin P A Coetzee, Dave K Berger, David J G Rees
Amaranthus species are an emerging and promising nutritious traditional vegetable food source. Morphological plasticity and poorly resolved dendrograms have led to the need for well resolved species phylogenies. We hypothesized that whole chloroplast phylogenomics would result in more reliable differentiation between closely related amaranth species. The aims of the study were therefore: to construct a fully assembled, annotated chloroplast genome sequence of Amaranthus tricolor; to characterize Amaranthus accessions phylogenetically by comparing barcoding genes (matK, rbcL, ITS) with whole chloroplast sequencing; and to use whole chloroplast phylogenomics to resolve deeper phylogenetic relationships...
April 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29556740/horizontal-gene-transfer-building-prokaryote-genomes-genes-related-to-exchange-between-cell-and-environment-are-frequently-transferred
#13
Apuã C M Paquola, Huma Asif, Carlos Alberto de Bragança Pereira, Bruno César Feltes, Diego Bonatto, Wanessa Cristina Lima, Carlos Frederico Martins Menck
Horizontal gene transfer (HGT) has a major impact on the evolution of prokaryotic genomes, as it allows genes evolved in different contexts to be combined in a single genome, greatly enhancing the ways evolving organisms can explore the gene content space and adapt to the environment. A systematic analysis of HGT in a large number of genomes is of key importance in understanding the impact of HGT in the evolution of prokaryotes. We developed a method for the detection of genes that potentially originated by HGT based on the comparison of BLAST scores between homologous genes to 16S rRNA-based phylogenetic distances between the involved organisms...
April 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29536136/genomic-insights-into-evolution-of-adpa-family-master-regulators-of-morphological-differentiation-and-secondary-metabolism-in-streptomyces
#14
Mariia Rabyk, Oleksandr Yushchuk, Ihor Rokytskyy, Maria Anisimova, Bohdan Ostash
The AdpA protein from a streptomycin producer Streptomyces griseus is a founding member of the AdpA family of pleiotropic regulators, known to be ubiquitously present in streptomycetes. Functional genomic approaches revealed a huge number of AdpA targets, leading to the claim that the AdpA regulon is the largest one in bacteria. The expression of adpA is limited at the level of translation of the rare leucyl UUA codon. All known properties of AdpA regulators were discovered on a few streptomycete strains. There are open questions about the true abundance and diversity of AdpA across actinobacterial taxa (and beyond) and about the possible evolutionary forces that shape the AdpA orthologous group in Streptomyces...
April 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29460038/the-performance-of-two-supertree-schemes-compared-using-synthetic-and-real-data-quartet-input
#15
Eliran Avni, Zahi Yona, Reuven Cohen, Sagi Snir
Despite impressive advancements in technological and theoretical tools, construction of phylogenetic (evolutionary) trees is still a challenging task. The availability of enormous quantities of molecular data has made large-scale phylogenetic reconstruction involving thousands of species, a more viable goal. For this goal, separate trees over different, overlapping subsets of species, representing histories of various markers of these species, are collected. These trees, typically with conflicting signals, are subsequently combined into a single tree over the full set, an operation denoted as supertree construction...
February 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29455279/divergent-selection-of-pattern-recognition-receptors-in-mammals-with-different-ecological-characteristics
#16
Ran Tian, Meixiu Chen, Simin Chai, Xinghua Rong, Bingyao Chen, Wenhua Ren, Shixia Xu, Guang Yang
Pattern recognition receptors (PRRs) are specialized receptors that represent a key component of the host innate immune system. Whether molecular evolutionary history of different PRR classes have involved different genetic mechanisms underlying diverse pathogen environment in mammals, and whether distinct ecology of mammals may have imposed divergent selective pressures on the evolution of the PRRs, remained unknown. To test these hypotheses, we investigated the characterization of 20 genes belonging to four PRR classes in mammals...
February 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29429061/iterative-calibration-a-novel-approach-for-calibrating-the-molecular-clock-using-complex-geological-events
#17
Tzitziki Loeza-Quintana, Sarah J Adamowicz
During the past 50 years, the molecular clock has become one of the main tools for providing a time scale for the history of life. In the era of robust molecular evolutionary analysis, clock calibration is still one of the most basic steps needing attention. When fossil records are limited, well-dated geological events are the main resource for calibration. However, biogeographic calibrations have often been used in a simplistic manner, for example assuming simultaneous vicariant divergence of multiple sister lineages...
February 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29356848/artificial-gene-amplification-in-escherichia-coli-reveals-numerous-determinants-for-resistance-to-metal-toxicity
#18
Kenric J Hoegler, Michael H Hecht
When organisms are subjected to environmental challenges, including growth inhibitors and toxins, evolution often selects for the duplication of endogenous genes, whose overexpression can provide a selective advantage. Such events occur both in natural environments and in clinical settings. Microbial cells-with their large populations and short generation times-frequently evolve resistance to a range of antimicrobials. While microbial resistance to antibiotic drugs is well documented, less attention has been given to the genetic elements responsible for resistance to metal toxicity...
February 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29349600/beneficial-mutations-from-evolution-experiments-increase-rates-of-growth-and-fermentation
#19
Aysha L Sezmis, Martino E Malerba, Dustin J Marshall, Michael J McDonald
A major goal of evolutionary biology is to understand how beneficial mutations translate into increased fitness. Here, we study beneficial mutations that arise in experimental populations of yeast evolved in glucose-rich media. We find that fitness increases are caused by enhanced maximum growth rate (R) that come at the cost of reduced yield (K). We show that for some of these mutants, high R coincides with higher rates of ethanol secretion, suggesting that higher growth rates are due to an increased preference to utilize glucose through the fermentation pathway, instead of respiration...
February 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29344693/triplet-based-codon-organization-optimizes-the-impact-of-synonymous-mutation-on-nucleic-acid-molecular-dynamics
#20
Gregory A Babbitt, Erin E Coppola, Jamie S Mortensen, Patrick X Ekeren, Cosmo Viola, Dallan Goldblatt, André O Hudson
Since the elucidation of the genetic code almost 50 years ago, many nonrandom aspects of its codon organization remain only partly resolved. Here, we investigate the recent hypothesis of 'dual-use' codons which proposes that in addition to allowing adjustment of codon optimization to tRNA abundance, the degeneracy in the triplet-based genetic code also multiplexes information regarding DNA's helical shape and protein-binding dynamics while avoiding interference with other protein-level characteristics determined by amino acid properties...
January 17, 2018: Journal of Molecular Evolution
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