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Journal of Molecular Evolution

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https://www.readbyqxmd.com/read/29429061/iterative-calibration-a-novel-approach-for-calibrating-the-molecular-clock-using-complex-geological-events
#1
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 10, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29379986/ancient-diversification-of-three-finger-toxins-in-micrurus-coral-snakes
#2
Daniel Dashevsky, Bryan G Fry
Coral snakes, most notably the genus Micrurus, are the only terrestrial elapid snakes in the Americas. Elapid venoms are generally known for their potent neurotoxicity which is usually caused by Three-Finger Toxin (3FTx) proteins. These toxins can have a wide array of functions that have been characterized from the venom of other elapids. We examined publicly available sequences from Micrurus 3FTx to show that they belong to 8 monophyletic clades that diverged as deep in the 3FTx phylogenetic tree as the other clades with characterized functions...
January 27, 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
#3
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...
January 22, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29349600/beneficial-mutations-from-evolution-experiments-increase-rates-of-growth-and-fermentation
#4
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...
January 18, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29349599/evolution-of-eukaryal-and-archaeal-pseudouridine-synthase-pus10
#5
Elisabeth Fitzek, Archi Joardar, Ramesh Gupta, Matt Geisler
In archaea, pseudouridine (Ψ) synthase Pus10 modifies uridine (U) to Ψ at positions 54 and 55 of tRNA. In contrast, Pus10 is not found in bacteria, where modifications at those two positions are carried out by TrmA (U54 to m5U54) and TruB (U55 to Ψ55). Many eukaryotes have an apparent redundancy; their genomes contain orthologs of archaeal Pus10 and bacterial TrmA and TruB. Although eukaryal Pus10 genes share a conserved catalytic domain with archaeal Pus10 genes, their biological roles are not clear for the two reasons...
January 18, 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
#6
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
https://www.readbyqxmd.com/read/29330556/evolution-of-the-phosphatidylcholine-biosynthesis-pathways-in-green-algae-combinatorial-diversity-of-methyltransferases
#7
Takashi Hirashima, Masakazu Toyoshima, Takashi Moriyama, Naoki Sato
Phosphatidylcholine (PC) is one of the most common phospholipids in eukaryotes, although some green algae such as Chlamydomonas reinhardtii are known to lack PC. Recently, we detected PC in four species in the genus Chlamydomonas: C. applanata NIES-2202, C. asymmetrica NIES-2207, C. debaryana NIES-2212, and C. sphaeroides NIES-2242. To reveal the PC biosynthesis pathways in green algae and the evolutionary scenario involved in their diversity, we analyzed the PC biosynthesis genes in these four algae using draft genome sequences...
January 12, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29260254/from-molecules-to-life-quantifying-the-complexity-of-chemical-and-biological-systems-in-the-universe
#8
Thomas Böttcher
Life is a complex phenomenon and much research has been devoted to both understanding its origins from prebiotic chemistry and discovering life beyond Earth. Yet, it has remained elusive how to quantify this complexity and how to compare chemical and biological units on one common scale. Here, a mathematical description of molecular complexity was applied allowing to quantitatively assess complexity of chemical structures. This in combination with the orthogonal measure of information complexity resulted in a two-dimensional complexity space ranging over the entire spectrum from molecules to organisms...
December 19, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29248946/elastic-multi-scale-mechanisms-computation-and-biological-evolution
#9
Juan G Diaz Ochoa
Explanations based on low-level interacting elements are valuable and powerful since they contribute to identify the key mechanisms of biological functions. However, many dynamic systems based on low-level interacting elements with unambiguous, finite, and complete information of initial states generate future states that cannot be predicted, implying an increase of complexity and open-ended evolution. Such systems are like Turing machines, that overlap with dynamical systems that cannot halt. We argue that organisms find halting conditions by distorting these mechanisms, creating conditions for a constant creativity that drives evolution...
December 16, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29192334/putative-independent-evolutionary-reversals-from-genotypic-to-temperature-dependent-sex-determination-are-associated-with-accelerated-evolution-of-sex-determining-genes-in-turtles
#10
Robert Literman, Alexandria Burrett, Basanta Bista, Nicole Valenzuela
The evolutionary lability of sex-determining mechanisms across the tree of life is well recognized, yet the extent of molecular changes that accompany these repeated transitions remain obscure. Most turtles retain the ancestral temperature-dependent sex determination (TSD) from which multiple transitions to genotypic sex determination (GSD) occurred independently, and two contrasting hypotheses posit the existence or absence of reversals back to TSD. Here we examined the molecular evolution of the coding regions of a set of gene regulators involved in gonadal development in turtles and several other vertebrates...
December 1, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29189888/on-the-early-evolution-of-catabolic-pathways-a-comparative-genomics-approach-i-the-cases-of-glucose-ribose-and-the-nucleobases-catabolic-routes
#11
Mario Rivas, Arturo Becerra, Antonio Lazcano
Compared with the large corpus of published work devoted to the study of the origin and early development of anabolism, little attention has been given to the discussion of the early evolution of catabolism in spite of its significance. In the present study, we have used comparative genomics to explore the evolution and phylogenetic distribution of the enzymes that catalyze the extant catabolic pathways of the monosaccharides glucose and ribose, as well as those of the nucleobases adenine, guanine, cytosine, uracil, and thymine...
November 30, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29177973/phylogenetic-profiling-of-mitochondrial-proteins-and-integration-analysis-of-bacterial-transcription-units-suggest-evolution-of-f1fo-atp-synthase-from-multiple-modules
#12
Yulong Niu, Shayan Moghimyfiroozabad, Sepehr Safaie, Yi Yang, Elizabeth A Jonas, Kambiz N Alavian
ATP synthase is a complex universal enzyme responsible for ATP synthesis across all kingdoms of life. The F-type ATP synthase has been suggested to have evolved from two functionally independent, catalytic (F1) and membrane bound (Fo), ancestral modules. While the modular evolution of the synthase is supported by studies indicating independent assembly of the two subunits, the presence of intermediate assembly products suggests a more complex evolutionary process. We analyzed the phylogenetic profiles of the human mitochondrial proteins and bacterial transcription units to gain additional insight into the evolution of the F-type ATP synthase complex...
November 24, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29177972/conservation-of-the-enzyme-coenzyme-interfaces-in-fad-and-nadp-binding-adrenodoxin-reductase-a-ubiquitous-enzyme
#13
Israel Hanukoglu
FAD and NAD(P) together represent an ideal pair for coupled redox reactions in their capacity to accept two electrons and their redox potentials. Enzymes that bind both NAD(P) and FAD represent large superfamilies that fulfill essential roles in numerous metabolic pathways. Adrenodoxin reductase (AdxR) shares Rossmann fold features with some of these superfamilies but remains in a group of its own in the absence of sequence homology. This article documents the phylogenetic distribution of AdxR by examining whole genome databases for Metazoa, Plantae, Fungi, and Protista, and determines the conserved structural features of AdxR...
November 24, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29143083/the-polyphyletic-origins-of-primase-helicase-bifunctional-proteins
#14
Ankita Gupta, Supriya Patil, Ramya Vijayakumar, Kiran Kondabagil
We studied the evolutionary relationships of different primase-helicase bifunctional proteins, found mostly in viruses, virophages, plasmids, and organellar genomes, by phylogeny and correlation analysis. Our study suggests independent origins of primase-helicase bifunctional proteins resulting from multiple fusion events between genes encoding primase and helicase domains of different families. The correlation analysis further indicated strong functional dependencies of domains in the bifunctional proteins that are part of smaller genomes and plasmids...
November 15, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29127445/negative-epistasis-in-experimental-rna-fitness-landscapes
#15
REVIEW
Devin P Bendixsen, Bjørn Østman, Eric J Hayden
Mutations and their effects on fitness are a fundamental component of evolution. The effects of some mutations change in the presence of other mutations, and this is referred to as epistasis. Epistasis can occur between mutations in different genes or within the same gene. A systematic study of epistasis requires the analysis of numerous mutations and their combinations, which has recently become feasible with advancements in DNA synthesis and sequencing. Here we review the mutational effects and epistatic interactions within RNA molecules revealed by several recent high-throughput mutational studies involving two ribozymes studied in vitro, as well as a tRNA and a snoRNA studied in yeast...
November 10, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29110026/pirnas-and-evolutionary-trajectories-in-genome-size-and-content
#16
LETTER
Rachel Lockridge Mueller
No abstract text is available yet for this article.
November 6, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29094190/evolution-of-single-domain-globins-in-hydrothermal-vent-scale-worms
#17
J Projecto-Garcia, A-S Le Port, T Govindji, D Jollivet, S W Schaeffer, S Hourdez
Hypoxia at deep-sea hydrothermal vents represents one of the most basic challenges for metazoans, which then requires specific adaptations to acquire oxygen to meet their metabolic needs. Hydrothermal vent scale-worms (Polychaeta; Polynoidae) express large amounts of extracellular single- and multi-domain hemoglobins, in contrast with their shallow-water relatives that only possess intracellular globins in their nervous system (neuroglobins). We sequenced the gene encoding the single-domain (SD) globin from nine species of polynoids found in various vent and deep-sea reduced microhabitats (and associated constraints) to determine if the Polynoidae SD globins have been the targets of diversifying selection...
November 1, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29075833/transcriptome-profiling-of-neurosensory-perception-genes-in-wing-tissue-of-two-evolutionary-distant-insect-orders-diptera-drosophila-melanogaster-and-hemiptera-acyrthosiphon-pisum
#18
Sandra Agnel, Martine da Rocha, Alain Robichon
The neurogenesis and neuronal functions in insect wing have been understudied mainly due to technical hindrances that have prevented electrophysiology studies for decades. The reason is that the nano-architecture of the wing chemosensory bristles hampers the receptors accessibility of odorants/tastants to receptors in fixed setup, whereas in nature, the wing flapping mixes these molecules in bristle lymph. In this report, we analyzed the transcriptome of the wing tissue of two species phylogenetically strongly divergent: Drosophila melanogaster a generic model for diptera order (complete metamorphosis) and the aphid acyrthosiphon pisum, representative of hemiptera order (incomplete metamorphosis) for which a conditional winged/wingless polyphenism is under control of population density and resources...
October 26, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29103173/a-role-for-the-mutagenic-dna-self-catalyzed-depurination-mechanism-in-the-evolution-of-7sl-derived-rnas
#19
Maxwell P Gold, Jacques R Fresco
The Alu element, the most prevalent SINE (short interspersed element) in the human genome, is one of the many RNA-encoding genes that evolved from the 7SL RNA gene. During analysis of the evolution of 7SL-derived RNAs, two distinct evolutionary intermediates capable of self-catalyzed DNA depurination (SDP) were identified. These SDP sequences spontaneously create apurinic sites that can result in increased mutagenesis due to their error-prone repair. This DNA self-depurination mechanism has been shown both in vitro and in vivo to lead to substitution and short frameshift mutations at a frequency that far exceeds their occurrence due to random errors in DNA replication...
October 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29085968/evolution-of-the-aux-iaa-gene-family-in-hexaploid-wheat
#20
Linyi Qiao, Li Zhang, Xiaojun Zhang, Lei Zhang, Xin Li, Jianzhong Chang, Haixian Zhan, Huijuan Guo, Jun Zheng, Zhijian Chang
The Aux/IAA (IAA) gene family, involved in the auxin signalling pathway, acts as an important regulator in plant growth and development. In this study, we explored the evolutionary trajectory of the IAA family in common wheat. The results showed ten pairs of paralogs among 34 TaIAA family members. Seven of the pairs might have undergone segmental duplication, and the other three pairs appear to have experienced tandem duplication. Except for TaIAA15-16, these duplication events occurred in the ancestral genomes before the divergence of Triticeae...
October 2017: Journal of Molecular Evolution
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