Faculty Opinions recommendation of Evolutionary rate variation in anthocyanin pathway genes.

2004 ◽  
Author(s):  
Michael Purugganan
Keyword(s):  
Evolutionary Rate ◽  
Rate Variation ◽  
Anthocyanin Pathway

Chromosomal location and evolutionary rate variation in enterobacterial genes

Science ◽  
1989 ◽  
Vol 246 (4931) ◽  
pp. 808-810 ◽  
Author(s):  
P. Sharp ◽  
D. Shields ◽  
K. Wolfe ◽  
W. Li
Keyword(s):  
Evolutionary Rate ◽  
Chromosomal Location ◽  
Rate Variation

scholarly journals Identification and Visualization of Functionally Important Domains and Residues in Herpes Simplex Virus Glycoprotein K(gK) Using a Combination of Phylogenetics and Protein Modeling

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Paul J. F. Rider ◽  
Lyndon M. Coghill ◽  
Misagh Naderi ◽  
Jeremy M. Brown ◽  
Michal Brylinski ◽  
...  
Keyword(s):  
Herpes Simplex ◽  
Evolutionary Rate ◽  
Quantitative Measure ◽  
Rate Variation ◽  
Human Pathogens ◽  
Herpes Simplex Viruses ◽  
Varicella Zoster ◽  
Conserved Sequence ◽  
Glycoprotein K ◽  
Herpes Simplex Virus Glycoprotein

Abstract Alphaherpesviruses are a subfamily of herpesviruses that include the significant human pathogens herpes simplex viruses (HSV) and varicella zoster virus (VZV). Glycoprotein K (gK), conserved in all alphaherpesviruses, is a multi-membrane spanning virion glycoprotein essential for virus entry into neuronal axons, virion assembly, and pathogenesis. Despite these critical functions, little is known about which gK domains and residues are most important for maintaining these functions across all alphaherpesviruses. Herein, we employed phylogenetic and structural analyses including the use of a novel model for evolutionary rate variation across residues to predict conserved gK functional domains. We found marked heterogeneity in the evolutionary rate at the level of both individual residues and domains, presumably as a result of varying selective constraints. To clarify the potential role of conserved sequence features, we predicted the structures of several gK orthologs. Congruent with our phylogenetic analysis, slowly evolving residues were identified at potentially structurally significant positions across domains. We found that using a quantitative measure of amino acid rate variation combined with molecular modeling we were able to identify amino acids predicted to be critical for gK protein structure/function. This analysis yields targets for the design of anti-herpesvirus therapeutic strategies across all alphaherpesvirus species that would be absent from more traditional analyses of conservation.

scholarly journals Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin

2013 ◽  
Vol 368 (1614) ◽  
pp. 20120334 ◽  
Author(s):  
Austin G. Meyer ◽  
Eric T. Dawson ◽  
Claus O. Wilke
Keyword(s):  
Protein Structure ◽  
Sialic Acid ◽  
Avian Influenza ◽  
Evolutionary Rate ◽  
Solvent Accessibility ◽  
Rate Variation ◽  
Structural Constraints ◽  
Binding Region ◽  
Site Specific ◽  
Sialic Acid Binding

We investigate the causes of site-specific evolutionary-rate variation in influenza haemagglutinin (HA) between human and avian influenza, for subtypes H1, H3, and H5. By calculating the evolutionary-rate ratio, ω = d N /d S as a function of a residue's solvent accessibility in the three-dimensional protein structure, we show that solvent accessibility has a significant but relatively modest effect on site-specific rate variation. By comparing rates within HA subtypes among host species, we derive an upper limit to the amount of variation that can be explained by structural constraints of any kind. Protein structure explains only 20–40% of the variation in ω . Finally, by comparing ω at sites near the sialic-acid-binding region to ω at other sites, we show that ω near the sialic-acid-binding region is significantly elevated in both human and avian influenza, with the exception of avian H5. We conclude that protein structure, HA subtype, and host biology all impose distinct selection pressures on sites in influenza HA.

Evolutionary rate variation among vertebrate β globin genes: Implications for dating gene family duplication events

Gene ◽  
2006 ◽  
Vol 380 (1) ◽  
pp. 21-29 ◽  
Author(s):  
Gabriela Aguileta ◽  
Joseph P. Bielawski ◽  
Ziheng Yang
Keyword(s):  
Gene Family ◽  
Evolutionary Rate ◽  
Rate Variation ◽  
Globin Genes ◽  
Duplication Events

scholarly journals Large Evolutionary Rate Heterogeneity among and within HIV-1 Subtypes and CRFs

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1689
Author(s):  
Arshan Nasir ◽  
Mira Dimitrijevic ◽  
Ethan Romero-Severson ◽  
Thomas Leitner
Keyword(s):  
Evolutionary Rate ◽  
Virus Genome ◽  
Rate Variation ◽  
Human Populations ◽  
Host Immune System ◽  
Virus Spread ◽  
Rate Heterogeneity ◽  
Hiv 1 ◽  
Subtype 3 ◽  
Diverse Virus

HIV-1 is a fast-evolving, genetically diverse virus presently classified into several groups and subtypes. The virus evolves rapidly because of an error-prone polymerase, high rates of recombination, and selection in response to the host immune system and clinical management of the infection. The rate of evolution is also influenced by the rate of virus spread in a population and nature of the outbreak, among other factors. HIV-1 evolution is thus driven by a range of complex genetic, social, and epidemiological factors that complicates disease management and prevention. Here, we quantify the evolutionary (substitution) rate heterogeneity among major HIV-1 subtypes and recombinants by analyzing the largest collection of HIV-1 genetic data spanning the widest possible geographical (100 countries) and temporal (1981–2019) spread. We show that HIV-1 substitution rates vary substantially, sometimes by several folds, both across the virus genome and between major subtypes and recombinants, but also within a subtype. Across subtypes, rates ranged 3.5-fold from 1.34 × 10−3 to 4.72 × 10−3 in env and 2.3-fold from 0.95 × 10−3 to 2.18 × 10−3 substitutions site−1 year−1 in pol. Within the subtype, 3-fold rate variation was observed in env in different human populations. It is possible that HIV-1 lineages in different parts of the world are operating under different selection pressures leading to substantial rate heterogeneity within and between subtypes. We further highlight how such rate heterogeneity can complicate HIV-1 phylodynamic studies, specifically, inferences on epidemiological linkage of transmission clusters based on genetic distance or phylogenetic data, and can mislead estimates about the timing of HIV-1 lineages.

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