scholarly journals Erratum: Corrigendum: Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Alexander S. Fokas ◽  
Daniel J. Cole ◽  
Sebastian E. Ahnert ◽  
Alex W. Chin
Keyword(s):  
Amino Acid ◽  
Evolutionary Rate ◽  
Rate Analysis

scholarly journals Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Alexander S. Fokas ◽  
Daniel J. Cole ◽  
Sebastian E. Ahnert ◽  
Alex W. Chin
Keyword(s):  
Amino Acid ◽  
Protein Function ◽  
Evolutionary Rate ◽  
Data Sets ◽  
Analysis Tool ◽  
Construction Technique ◽  
Strong Negative Correlation ◽  
Rate Analysis ◽  
Dynamics Simulations ◽  
Dynamical Function

Abstract Amino acid networks (AANs) abstract the protein structure by recording the amino acid contacts and can provide insight into protein function. Herein, we describe a novel AAN construction technique that employs the rigidity analysis tool, FIRST, to build the AAN, which we refer to as the residue geometry network (RGN). We show that this new construction can be combined with network theory methods to include the effects of allowed conformal motions and local chemical environments. Importantly, this is done without costly molecular dynamics simulations required by other AAN-related methods, which allows us to analyse large proteins and/or data sets. We have calculated the centrality of the residues belonging to 795 proteins. The results display a strong, negative correlation between residue centrality and the evolutionary rate. Furthermore, among residues with high closeness, those with low degree were particularly strongly conserved. Random walk simulations using the RGN were also successful in identifying allosteric residues in proteins involved in GPCR signalling. The dynamic function of these residues largely remain hidden in the traditional distance-cutoff construction technique. Despite being constructed from only the crystal structure, the results in this paper suggests that the RGN can identify residues that fulfil a dynamical function.

scholarly journals A New Basal Hadrosaurid (Dinosauria: Ornithischia) From the Latest Cretaceous Kita-ama Formation in Japan: the Rise of Hadrosaurs

2021 ◽  
Author(s):  
Yoshitsugu Kobayashi ◽  
Ryuji Takasaki ◽  
Katsuhiro Kubota ◽  
Anthony Fiorillo
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary Rate ◽  
First Record ◽  
Early Evolution ◽  
New Taxon ◽  
Geographical Distance ◽  
Rate Analysis ◽  
Occlusal Surfaces ◽  
Functional Tooth

Abstract Here we describe a partial hadrosaurid skeleton from the marine Maastrichtian Kita-ama Formation of the Izumi Group in Japan as a new taxon, Yamatosaurus izanagii gen. et sp. nov. Our phylogenetic analysis demonstrates it belongs to the Hadrosauridae, composed of Hadrosaurus foulkii + (Yamatosaurus izanagii + (Saurolophinae + Lambeosaurinae). Yamatosaurus izanagii is unique in having only one functional tooth/row in the middle of the dentary dental battery and complete absence of the branched ridges on the occlusal surfaces. The coracoid lacks a biceps tubercle as in non-hadrosaurid hadrosauroids, suggesting its presence is a key feature for the clade of Saurolophinae and Lambeosaurinae. The evolutionary rate analysis further supports that shoulder and forelimb features, which are likely to be involved in locomotion, are important for the early evolution of Hadrosauridae. Our biogeographic analyses show that the basal Hadrosauridae was widely distributed in Asia and Appalachia, and the clade of Saurolophinae and Lambeosaurinae originated in Asia. The contemporaneous occurrence of basal (Yamatosaurus izanagii) and derived (Kamuysaurus japonicus) hadrosaurids during the Maastrichtian in Japan is the first record in Asia. Because of a long geographical distance between these localities, they may not co-exist but show some level of provinciality.

scholarly journals Parallel Genomic Changes Drive Repeated Evolution of Placentas in Live-Bearing Fish

2021 ◽  
Author(s):  
Henri van Kruistum ◽  
Reindert Nijland ◽  
David N Reznick ◽  
Martien A M Groenen ◽  
Hendrik-Jan Megens ◽  
...  
Keyword(s):  
Complex Traits ◽  
Evolutionary Rate ◽  
Complex Trait ◽  
Regulatory Elements ◽  
Evolutionary Origin ◽  
Regulatory Change ◽  
Protein Coding ◽  
Genomic Changes ◽  
Rate Analysis ◽  
Repeated Evolution

Abstract The evolutionary origin of complex organs challenges empirical study because most organs evolved hundreds of millions of years ago. The placenta of live-bearing fish in the family Poeciliidae represents a unique opportunity to study the evolutionary origin of complex organs, because in this family a placenta evolved at least nine times independently. It is currently unknown whether this repeated evolution is accompanied by similar, repeated, genomic changes in placental species. Here, we compare whole genomes of 26 poeciliid species representing six out of nine independent origins of placentation. Evolutionary rate analysis revealed that the evolution of the placenta coincides with convergent shifts in the evolutionary rate of 78 protein-coding genes, mainly observed in transporter- and vesicle-located genes. Furthermore, differences in sequence conservation showed that placental evolution coincided with similar changes in 76 noncoding regulatory elements, occurring primarily around genes that regulate development. The unexpected high occurrence of GATA simple repeats in the regulatory elements suggests an important function for GATA repeats in developmental gene regulation. The distinction in molecular evolution observed, with protein-coding parallel changes more often found in metabolic and structural pathways, compared with regulatory change more frequently found in developmental pathways, offers a compelling model for complex trait evolution in general: changing the regulation of otherwise highly conserved developmental genes may allow for the evolution of complex traits.

scholarly journals Genetic characterization of G12P[6] and G12P[8] rotavirus strains collected in six African countries between 2010 and 2014

2021 ◽  
Author(s):  
Kebareng G. Rakau ◽  
Martin M. Nyaga ◽  
Maemu P. Gededzha ◽  
Jason M. Mwenda ◽  
M. Jeffrey Mphahlele ◽  
...  
Keyword(s):  
Amino Acid ◽  
Evolutionary Rate ◽  
Time Frame ◽  
Amino Acid Sequences ◽  
Sub Saharan Africa ◽  
Evolutionary Analysis ◽  
African Countries ◽  
Similar Time ◽  
Vaccine Introduction ◽  
Rotavirus Vaccination

Abstract Background: G12 rotaviruses were first observed in sub-Saharan Africa in 2004 and since then have continued to emerge and spread across the continent and are reported as a significant human rotavirus genotype in several African countries, both prior to and after rotavirus vaccine introduction. This study investigated the genetic variability of 15 G12 rotavirus strains associated with either P[6] or P[8] identified between 2010 and 2014 from Ethiopia, Kenya, Rwanda, Tanzania, Togo and Zambia.Methods: The investigation was carried out by comparing partial VP7 and partial VP4 sequences of the African G12P[6] and G12P[8] strains with the available GenBank sequences and exploring the recognized neutralization epitopes of these strains. Additionally, Bayesian evolutionary analysis was carried out using Markov Chain Monte Carlo (MCMC) implemented in BEAST to estimate the time to the most recent ancestor and evolutionary rate for these G12 rotavirus strains.Results: The findings suggested that the VP7 and VP4 nucleotide and amino acid sequences of the G12 strains circulating in African countries are closely related, irrespective of country of origin and year of detection, with the exception of the Ethiopian strains that clustered distinctly. Neutralization epitope analysis revealed that rotavirus VP4 P[8] genes associated with G12 had amino acid sequences similar to those reported globally including the vaccine strains in RotaTeq and Rotarix. The estimated evolutionary rate of the G12 strains was 1.016 x10−3 substitutions/site/year and was comparable to what has been previously reported. Three sub-clusters formed within the current circulating lineage III shows the diversification of G12 from three independent ancestries within a similar time frame in the late 1990s.Conclusions: At present it appears to be unlikely that widespread vaccine use has driven the molecular evolution and sustainability of G12 strains in Africa. Continuous monitoring of rotavirus genotypes is recommended to assess the long-term impact of rotavirus vaccination on the dynamic nature of rotavirus evolution on the continent.

scholarly journals Comparative genomics reveal shared genomic changes in syngnathid fishes and signatures of genetic convergence with placental mammals

2020 ◽  
Vol 7 (6) ◽  
pp. 964-977 ◽  
Author(s):  
Yan-Hong Zhang ◽  
Vydianathan Ravi ◽  
Geng Qin ◽  
He Dai ◽  
Hui-Xian Zhang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Comparative Genomics ◽  
Embryonic Development ◽  
Evolutionary Rate ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Amino Acid Substitutions ◽  
Genomic Changes ◽  
Genome Wide

Abstract Syngnathids (seahorses, pipefishes and seadragons) exhibit an array of morphological innovations including loss of pelvic fins, a toothless tubular mouth and male pregnancy. They comprise two subfamilies: Syngnathinae and Nerophinae. Genomes of three Syngnathinae members have been analyzed previously. In this study, we have sequenced the genome of a Nerophinae member, the Manado pipefish (Microphis manadensis), which has a semi-enclosed brood pouch. Comparative genomic analysis revealed that the molecular evolutionary rate of the four syngnathids is higher than that of other teleosts. The loss of all but one P/Q-rich SCPP gene in the syngnathids suggests a role for the lost genes in dentin and enameloid formation in teleosts. Genome-wide comparison identified a set of 118 genes with parallel identical amino acid substitutions in syngnathids and placental mammals. Association of some of these genes with placental and embryonic development in mammals suggests a role for them in syngnathid pregnancy.

scholarly journals The pattern of mammalian evolution and the relative rate of molecular evolution.

Genetics ◽  
1990 ◽  
Vol 124 (1) ◽  
pp. 165-173
Author(s):  
S Easteal
Keyword(s):  
Amino Acid ◽  
Nucleotide Substitution ◽  
Evolutionary Rate ◽  
Relative Rate ◽  
Neutral Theory ◽  
Divergence Time ◽  
Rate Variation ◽  
Mammalian Evolution ◽  
Branching Order ◽  
Rate Of Molecular Evolution

Abstract The rates of nucleotide substitution at four genes in four orders of eutherian mammals are compared in relative rate tests using marsupial orthologs for reference. There is no evidence of systematic variation in evolutionary rate among the orders. The sequences are used to reconstruct the phylogeny of the orders using maximum likelihood, parsimony and compatibility methods. A branching order of rodent then ungulate then primate and lagomorph is overwhelmingly indicated. The nodes of the nucleotide based cladograms are widely separated in relation to the total lengths of the branches. The assumption of a star phylogeny that underlies Kimura's test for molecular evolutionary rate variation is shown to be invalid for eutherian mammals. Excess variance in nucleotide or amino acid differences between mammalian orders, above that predicted by neutral theory is explained better by variation in divergence time than by variation in evolutionary rate.

scholarly journals Transcriptomics and molecular evolutionary rate analysis of the bladderwort (Utricularia), a carnivorous plant with a minimal genome

2011 ◽  
Vol 11 (1) ◽  
pp. 101 ◽  
Author(s):  
Enrique Ibarra-Laclette ◽  
Victor A Albert ◽  
Claudia A Pérez-Torres ◽  
Flor Zamudio-Hernández ◽  
María de J Ortega-Estrada ◽  
...  
Keyword(s):  
Evolutionary Rate ◽  
Carnivorous Plant ◽  
Minimal Genome ◽  
Rate Analysis ◽  
Molecular Evolutionary Rate
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