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Journal of Molecular Evolution

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https://www.readbyqxmd.com/read/28233029/experimental-evolution-of-escherichia-coli-harboring-an-ancient-translation-protein
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
https://www.readbyqxmd.com/read/27913841/membranes-and-the-origin-of-life-a-century-of-conjecture
#17
REVIEW
David Deamer
Cells are the units of all life today, and are defined by their membranous boundaries. The membranes have multiple functions; the most obvious being that, in the absence of a boundary, the systems of functional macromolecular components of the cytosol would spill into the environment and disperse. Membranes also contain the pigments essential for photosynthesis, electron transport enzymes that pump and maintain proton gradients, the ATP synthase that uses proton gradients to produce energy for the cell, and enzymes that use ATP to maintain ion gradients essential for life...
December 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27900404/erasing-borders-a-brief-chronicle-of-early-synthetic-biology
#18
REVIEW
Juli Peretó
Synthetic Biology is currently presented as an emergent field involving the application of engineering principles to living matter. However, the scientific pursuit of making life in a laboratory is not new and has been the ultimate, if somewhat distant, aim of the origin-of-life research program for many years. Actually, over a century ago, the idea that the synthesis of life was indispensable to fully understand its nature already appealed to material scientists and evolutionists alike. Jacques Loeb proposed a research program from an engineering standpoint, following a synthetic method (experimental abiogenesis) and based on his mechanist vision of living beings, which he considered true chemical machines...
December 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27896387/alexandr-i-oparin-and-the-origin-of-life-a-historical-reassessment-of-the-heterotrophic-theory
#19
Antonio Lazcano
The heterotrophic origin of life proposed by A. I. Oparin in the 1920s was part of a Darwinian framework that assumed that living organisms were the historical outcome of a gradual transformation of lifeless matter. Eighty years ago, he presented a much more detailed scheme of the processes that may have led to life. As argued here, the development of the heterotrophic theory has been shaped by an entangled scenario in which a number of technical and scientific developments concur, as well as non-scientific issues including the Stalinist period and the tensions of the Cold War atmosphere...
December 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27872952/molecular-phylogenetics-and-the-perennial-problem-of-homology
#20
REVIEW
S Andrew Inkpen, W Ford Doolittle
The concept of homology has a long history, during much of which the issue has been how to reconcile similarity and common descent when these are not coextensive. Although thinking molecular phylogeneticists have learned not to say "percent homology," the problems are deeper than that and unresolved.
December 2016: Journal of Molecular Evolution
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