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Journal of Molecular Evolution

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https://www.readbyqxmd.com/read/28331938/involvement-of-clustered-genes-in-mammalian-functions-their-relation-in-a-rat-mutant-strain
#1
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
#2
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 11, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28243688/the-origin-of-life-models-and-data
#3
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...
February 27, 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
#4
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...
February 27, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28233029/experimental-evolution-of-escherichia-coli-harboring-an-ancient-translation-protein
#5
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...
February 23, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28224181/photosystem-ii-is-a-chimera-of-reaction-centers
#6
LETTER
Tanai Cardona
No abstract text is available yet for this article.
February 21, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28220195/molecular-convergent-evolution-of-the-mybpc2-gene-among-three-high-elevation-amphibian-species
#7
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...
February 20, 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
#8
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...
February 16, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28168328/patterns-of-evolutionary-trajectories-and-domestication-history-within-the-genus-hordeum-assessed-by-remap-markers
#9
Georgi Bonchev, Roman Dusinský, Pavol Hauptvogel, Miroslav Švec
The patterns of genetic diversity related to the taxonomy and domestication history of 85 accessions representing the main four species of the genus Hordeum were examined by retrotransposon-microsatellite amplified polymorphism (REMAP) markers based on the retrotransposon BARE-1. A substantial level of genetic polymorphisms at among- and within-species level was observed showing that this retrotransposon family and its adjacent genomic regions has been a target for genome dynamics during the evolution and domestication of barley...
February 6, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28116472/the-role-of-microsatellites-in-streptophyta-gene-evolution
#10
LETTER
Abdulqader Jighly, Ayed M Al-Abdallat, Loai M Alnemer
Microsatellites form hotspot regions for recombination. In this research, we investigated whether genic microsatellites can be responsible for generating new genes by enhancing crossover between gene containing microsatellites and other genomic regions. We tested our hypothesis on 33,531 UniGene entries containing microsatellites. Each sequence was divided into microsatellites upstream and downstream fragments, and each pair of sequences was compared to study the microsatellites effect. The candidate pairs of genes are supposed to share a high similar fragment in one side of the microsatellites, while the other fragments should be completely different...
January 23, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28004131/ancient-and-recent-duplications-support-functional-diversity-of-daphnia-opsins
#11
Christopher S Brandon, Matthew J Greenwold, Jeffry L Dudycha
Daphnia pulex has the largest known family of opsins, genes critical for photoreception and vision in animals. This diversity may be functionally redundant, arising from recent processes, or ancient duplications may have been preserved due to distinct functions and independent contributions to fitness. We analyzed opsins in D. pulex and its distant congener Daphnia magna. We identified 48 opsins in the D. pulex genome and 32 in D. magna. We inferred the complement of opsins in the last common ancestor of all Daphnia and evaluated the history of opsin duplication and loss...
January 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27995274/emergence-of-life-on-earth-a-physicochemical-jigsaw-puzzle
#12
REVIEW
Jan Spitzer
We review physicochemical factors and processes that describe how cellular life can emerge from prebiotic chemical matter; they are: (1) prebiotic Earth is a multicomponent and multiphase reservoir of chemical compounds, to which (2) Earth-Moon rotations deliver two kinds of regular cycling energies: diurnal electromagnetic radiation and seawater tides. (3) Emerging colloidal phases cyclically nucleate and agglomerate in seawater and consolidate as geochemical sediments in tidal zones, creating a matrix of microspaces...
January 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27913840/finding-direction-in-the-search-for-selection
#13
Grant Thiltgen, Mario Dos Reis, Richard A Goldstein
Tests for positive selection have mostly been developed to look for diversifying selection where change away from the current amino acid is often favorable. However, in many cases we are interested in directional selection where there is a shift toward specific amino acids, resulting in increased fitness in the species. Recently, a few methods have been developed to detect and characterize directional selection on a molecular level. Using the results of evolutionary simulations as well as HIV drug resistance data as models of directional selection, we compare two such methods with each other, as well as against a standard method for detecting diversifying selection...
January 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27909757/erratum-to-small-rnas-from-a-big-genome-the-pirna-pathway-and-transposable-elements-in-the-salamander-species-desmognathus-fuscus
#14
M J Madison-Villar, Cheng Sun, Nelson C Lau, Matthew L Settles, Rachel Lockridge Mueller
No abstract text is available yet for this article.
January 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27889804/quest-for-ancestors-of-eukaryal-cells-based-on-phylogenetic-analyses-of-aminoacyl-trna-synthetases
#15
Ryutaro Furukawa, Mizuho Nakagawa, Takuya Kuroyanagi, Shin-Ichi Yokobori, Akihiko Yamagishi
The three-domain phylogenetic system of life has been challenged, particularly with regard to the position of Eukarya. The recent increase of known genome sequences has allowed phylogenetic analyses of all extant organisms using concatenated sequence alignment of universally conserved genes; these data supported the two-domain hypothesis, which place eukaryal species as ingroups of the Domain Archaea. However, the origin of Eukarya is complicated: the closest archaeal species to Eukarya differs in single-gene phylogenetic analyses depending on the genes...
January 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27864608/viper-venom-botox-the-molecular-origin-and-evolution-of-the-waglerin-peptides-used-in-anti-wrinkle-skin-cream
#16
LETTER
Jordan Debono, Bing Xie, Aude Violette, Rudy Fourmy, Marc Jaeger, Bryan G Fry
The molecular origin of waglerin peptides has remained enigmatic despite their industrial application in skin cream products to paralyse facial muscles and thus reduce the incidence of wrinkles. Here we show that these neurotoxic peptides are the result of de novo evolution within the prepro region of the C-type natriuretic peptide gene in Tropidolaemus venoms, at a site distinct from the domain encoding for the natriuretic peptide. It is the same region that yielded the azemiopsin peptides from Azemiops feae, indicative of a close relationship of this toxin gene between these two genera...
January 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27812751/a-method-for-the-annotation-of-functional-similarities-of-coding-dna-sequences-the-case-of-a-populated-cluster-of-transmembrane-proteins
#17
Miguel Angel Fuertes, José Ramón Rodrigo, Carlos Alonso
The analysis of a large number of human and mouse genes codifying for a populated cluster of transmembrane proteins revealed that some of the genes significantly vary in their primary nucleotide sequence inter-species and also intra-species. In spite of that divergence and of the fact that all these genes share a common parental function we asked the question of whether at DNA level they have some kind of common compositional structure, not evident from the analysis of their primary nucleotide sequence. To reveal the existence of gene clusters not based on primary sequence relationships we have analyzed 13574 human and 14047 mouse genes by the composon-clustering methodology...
January 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27921163/cells-molecules-and-evolution-historical-issues-in-molecular-evolution
#18
EDITORIAL
Antonio Lazcano
No abstract text is available yet for this article.
December 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27913843/molecular-evolution-in-historical-perspective
#19
Edna Suárez-Díaz
In the 1960s, advances in protein chemistry and molecular genetics provided new means for the study of biological evolution. Amino acid sequencing, nucleic acid hybridization, zone gel electrophoresis, and immunochemistry were some of the experimental techniques that brought about new perspectives to the study of the patterns and mechanisms of evolution. New concepts, such as the molecular evolutionary clock, and the discovery of unexpected molecular phenomena, like the presence of repetitive sequences in eukaryotic genomes, eventually led to the realization that evolution might occur at a different pace at the organismic and the molecular levels, and according to different mechanisms...
December 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27913842/alfonso-luis-herrera-and-the-beginnings-of-evolutionism-and-studies-in-the-origin-of-life-in-mexico
#20
Ismael Ledesma-Mateos, H James Cleaves
Alfonso Luis Herrera (1868-1942) was a Mexican biologist, and significant as the principal promoter of Darwinian thought in that country. However, Herrera's thinking went beyond the evolution of living beings, and extended to the question of the origin of life itself and the place of living phenomena in the larger context of the cosmos. Perhaps more significantly, though now largely forgotten, Herrera was among the first to embark on an experimental program to understand the origin of life, one which may be seen as foundational for later workers, most notably Sidney Fox and Alexander Oparin, and which has been resuscitated recently...
December 2016: Journal of Molecular Evolution
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