scholarly journals Evolutionary Rate Heterogeneity of Primary and Secondary Metabolic Pathway Genes inArabidopsis thaliana

2015 ◽  
Vol 8 (1) ◽  
pp. 17-28 ◽  
Author(s):  
Dola Mukherjee ◽  
Ashutosh Mukherjee ◽  
Tapash Chandra Ghosh
Keyword(s):  
Metabolic Pathway ◽  
Evolutionary Rate ◽  
Rate Heterogeneity ◽  
Secondary Metabolic Pathway

scholarly journals Evolutionary rate heterogeneity of Alu repeats upstream of the APOA5 gene: do they regulate APOA5 expression?

2008 ◽  
Vol 53 (3) ◽  
pp. 247-253 ◽  
Author(s):  
Edward A. Ruiz-Narváez ◽  
Hannia Campos
Keyword(s):  
Evolutionary Rate ◽  
Rate Heterogeneity ◽  
Alu Repeats ◽  
Apoa5 Gene

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.

scholarly journals LSX: automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Carlos J. Rivera-Rivera ◽  
Juan I. Montoya-Burgos
Keyword(s):  
Evolutionary Rate ◽  
Rate Heterogeneity ◽  
Gene Phylogeny

scholarly journals Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)

2020 ◽  
Author(s):  
Tamara Spasojevic ◽  
Gavin R Broad ◽  
Ilari E Sääksjärvi ◽  
Martin Schwarz ◽  
Masato Ito ◽  
...  
Keyword(s):  
Evolutionary Rate ◽  
Total Evidence ◽  
Morphological Data ◽  
Phylogenetic Study ◽  
Phylogenetic Distance ◽  
Rate Heterogeneity ◽  
The Family ◽  
The Impact ◽  
Age Estimates

Abstract Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We analyze a data set comprising 201 extant and 79 fossil taxa, including the oldest fossils of the family from the Early Cretaceous and the first unequivocal representatives of extant subfamilies from the mid Paleogene. Based on newly compiled molecular data from ten nuclear genes and a morphological matrix that includes 222 characters, we show that age estimates become both older and less precise with the inclusion of more distant and more poorly sampled outgroups. These outgroups not only lack morphological and temporal information, but also sit on long terminal branches and considerably increase the evolutionary rate heterogeneity. In addition, we discover an artefact that might be detrimental for total-evidence dating: “bare-branch attraction”, namely high attachment probabilities of certain fossils to terminal branches for which morphological data are missing. Using computer simulations, we confirm the generality of this phenomenon and show that a large phylogenetic distance to any of the extant taxa, rather than just older age, increases the risk of a fossil being misplaced due to bare-branch attraction. After restricting outgroup sampling and adding morphological data for the previously attracting, bare branches, we recover a Jurassic origin for Pimpliformes and Ichneumonidae. This first age estimate for the group not only suggests an older origin than previously thought, but also that diversification of the crown group happened well before the Cretaceous-Paleogene boundary. Our case study demonstrates that in order to obtain robust age estimates, total-evidence dating studies need to be based on a thorough and balanced sampling of both extant and fossil taxa, with the aim of minimizing evolutionary rate heterogeneity and missing morphological information.

Detecting evolutionary rate heterogeneity among mangroves and their close terrestrial relatives

2002 ◽  
Vol 5 (3) ◽  
pp. 427-432 ◽  
Author(s):  
Yang Zhong ◽  
Qiong Zhao ◽  
Suhua Shi ◽  
Yelin Huang ◽  
Masami Hasegawa
Keyword(s):  
Evolutionary Rate ◽  
Rate Heterogeneity

Evolutionary Rate Heterogeneity in Proteins with Long Disordered Regions

2002 ◽  
Vol 55 (1) ◽  
pp. 104-110 ◽  
Author(s):  
Celeste J. Brown ◽  
Sachiko Takayama ◽  
Andrew M. Campen ◽  
Pam Vise ◽  
Thomas W. Marshall ◽  
...  
Keyword(s):  
Evolutionary Rate ◽  
Rate Heterogeneity ◽  
Disordered Regions

scholarly journals Macroevolutionary analysis of discrete traits with rate heterogeneity

2020 ◽  
Author(s):  
Michael C. Grundler ◽  
Daniel L. Rabosky
Keyword(s):  
New World ◽  
Evolutionary Rate ◽  
Simulated Data ◽  
Data Sets ◽  
Rate Heterogeneity ◽  
Trait Evolution ◽  
Discrete Traits ◽  
Simulated Data Sets ◽  
Dramatic Variation ◽  
Ancestral Character States

AbstractOrganismal traits show dramatic variation in phylogenetic patterns of origin and loss across the Tree of Life. Understanding the causes and consequences of this variation depends critically on accounting for heterogeneity in rates of trait evolution among lineages. Here, we describe a method for modeling among-lineage evolutionary rate heterogeneity in a trait with two discrete states. The method assumes that the present-day distribution of a binary trait is shaped by a mixture of stochastic processes in which the rate of evolution varies among lineages in a phylogeny. The number and location of rate changes, which we refer to as rate-shift events, are inferred automatically from the data. Simulations reveal that the method accurately reconstructs rates of trait evolution and ancestral character states even when simulated data violate model assumptions. We apply the method to an empirical dataset of mimetic coloration in snakes and find elevated rates of trait evolution in two clades of harmless snakes that are broadly sympatric with dangerously venomous New World coral snakes, recapitulating an earlier analysis of the same dataset. Although the method performed well on many simulated data sets, we caution that overall power for inferring heterogeneous dynamics of single binary traits is low.

In silico study of binding motifs in squalene synthase enzyme of secondary metabolic pathway solanaceae family

2014 ◽  
Vol 41 (11) ◽  
pp. 7201-7208 ◽  
Author(s):  
Sanchita ◽  
Garima Singh ◽  
Ashok Sharma
Keyword(s):  
Metabolic Pathway ◽  
In Silico ◽  
Squalene Synthase ◽  
Binding Motifs ◽  
Secondary Metabolic Pathway ◽  
In Silico Study ◽  
Solanaceae Family

scholarly journals Evolution of a secondary metabolic pathway from primary metabolism: shikimate and quinate biosynthesis in plants

2018 ◽  
Vol 95 (5) ◽  
pp. 823-833 ◽  
Author(s):  
Yuriko Carrington ◽  
Jia Guo ◽  
Cuong H. Le ◽  
Alexander Fillo ◽  
Junsu Kwon ◽  
...  
Keyword(s):  
Metabolic Pathway ◽  
Primary Metabolism ◽  
Secondary Metabolic Pathway
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