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Journal of Molecular Evolution

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https://www.readbyqxmd.com/read/28004131/ancient-and-recent-duplications-support-functional-diversity-of-daphnia-opsins
#1
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...
December 21, 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27995274/emergence-of-life-on-earth-a-physicochemical-jigsaw-puzzle
#2
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...
December 19, 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27913840/finding-direction-in-the-search-for-selection
#3
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...
December 2, 2016: 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
#4
M J Madison-Villar, Cheng Sun, Nelson C Lau, Matthew L Settles, Rachel Lockridge Mueller
No abstract text is available yet for this article.
December 2, 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27889804/quest-for-ancestors-of-eukaryal-cells-based-on-phylogenetic-analyses-of-aminoacyl-trna-synthetases
#5
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...
November 26, 2016: 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
#6
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...
November 18, 2016: 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
#7
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...
November 3, 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27770175/measuring-accelerated-rates-of-insertions-and-deletions-independent-of-rates-of-nucleotide-substitution
#8
Omar Navarro Leija, Sanju Varghese, Mira V Han
Evolutionary constraint for insertions and deletions (indels) is not necessarily equal to constraint for nucleotide substitutions for any given region of a genome. Knowing the variation in indel-specific evolutionary rates across the sequence will aid our understanding of evolutionary constraints on indels, and help us infer how indels have contributed to the evolution of the sequence. However, unlike for nucleotide substitutions, there has been no phylogenetic method that can statistically infer significantly different rates of indels across the sequence space independent of substitution rates...
October 21, 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27921163/cells-molecules-and-evolution-historical-issues-in-molecular-evolution
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/27866234/the-rna-world-at-thirty-a-look-back-with-its-author
#16
REVIEW
Neeraja Sankaran
Thirty years ago, molecular biologist Walter Gilbert published his RNA world hypothesis, which posited that early in evolution living systems were composed entirely of RNA. Proposed in the immediate wake of the discovery that certain RNA molecules were capable of catalyzing biological reactions, the hypothesis ascribed both of life's essential functions, namely carrying information and catalysis-respectively, performed by DNA and proteins in most modern life systems-to RNA, which were labeled as ribozymes. In the years since its inception, the RNA world has been greeted with equal parts enthusiasm and opposition from the origins of life research community, of which Gilbert neither was, nor really became, a part...
December 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27766348/conservation-mutation-in-the-splice-sites-of-mitochondrial-solute-carrier-genes-of-vertebrates
#17
Rosa Calvello, Maria A Panaro, Rosaria Salvatore, Vincenzo Mitolo, Antonia Cianciulli
The "canonical" introns begin by the dinucleotide GT and end by the dinucleotide AG. GT, together with a few downstream nucleotides, and AG, with a few of the immediately preceding nucleotides, are thought to be the strongest splicing signals (5'ss and 3'ss, respectively). We examined the composition of the intronic initial and terminal hexanucleotides of the mitochondrial solute carrier genes (SLC25A's) of zebrafish, chicken, mouse, and human. These genes are orthologous and we selected the transcripts in which the arrangement of exons and introns was superimposable in the species considered...
October 20, 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27743002/an-autotrophic-origin-for-the-coded-amino-acids-is-concordant-with-the-coevolution-theory-of-the-genetic-code
#18
Massimo Di Giulio
The coevolution theory of the origin of the genetic code maintains that the biosynthetic relationships between amino acids co-evolved with the genetic code organization. In other words, the metabolism of amino acids co-evolved with the organization of the genetic code because the biosynthetic pathways of amino acids occurred on tRNA-like molecules. Thus, a heterotrophic origin of amino acids-also only of those involved in the early phase of the structuring of the genetic code-would seem to contradict the main postulate of the coevolution theory...
October 14, 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27743003/small-rnas-from-a-big-genome-the-pirna-pathway-and-transposable-elements-in-the-salamander-species-desmognathus-fuscus
#19
M J Madison-Villar, Cheng Sun, Nelson C Lau, Matthew L Settles, Rachel Lockridge Mueller
Most of the largest vertebrate genomes are found in salamanders, a clade of amphibians that includes 686 species. Salamander genomes range in size from 14 to 120 Gb, reflecting the accumulation of large numbers of transposable element (TE) sequences from all three TE classes. Although DNA loss rates are slow in salamanders relative to other vertebrates, high levels of TE insertion are also likely required to explain such high TE loads. Across the Tree of Life, novel TE insertions are suppressed by several pathways involving small RNA molecules...
October 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27677291/phylogenetic-analysis-of-molluscan-metallothioneins-evolutionary-insight-from-crassostrea-virginica
#20
Matthew J Jenny, Samantha L Payton, David A Baltzegar, Jeffrey D Lozier
Mechanisms by which organisms genetically adapt to environmental conditions are of fundamental importance to studies of evolutionary biology and environmental physiology. Natural selection acts on existing genetic variation leading to adaptation through selection of new mutations that confer beneficial advantages to populations. The American oyster, Crassostrea virginica, is an excellent model to investigate interactions between environmental and ecological factors as driving forces for natural selection. A great example of this is represented by the diversity of C...
October 2016: Journal of Molecular Evolution
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