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You searched for: Journal Genome Biology and Evolution Remove constraint Journal: Genome Biology and Evolution Publication Year 2015 Remove constraint Publication Year: 2015 Subject genes Remove constraint Subject: genes Subject natural selection Remove constraint Subject: natural selection
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1. A Neutrality Test for Detecting Selection on DNA Methylation Using Single Methylation Polymorphism Frequency Spectrum

Author:
Wang, Jun; Fan, Chuanzhu
Source:
Genome Biology and Evolution 2015 v.7 no.1 pp. 154-171
Subject:
Arabidopsis; DNA; DNA methylation; computer simulation; epigenetics; genes; humans; loci; mutation; natural selection; phenotypic variation
Abstract:
... Inheritable epigenetic mutations (epimutations) can contribute to transmittable phenotypic variation. Thus, epimutations can be subject to natural selection and impact the fitness and evolution of organisms. Based on the framework of the modified Tajima’s D test for DNA mutations, we developed a neutrality test with the statistic “ D ᵐ” to detect selection forces on DNA methylation mutations using ...
DOI:
10.1093/gbe/evu271
PubMed:
25539727
PubMed Central:
PMC4316624

2. A Simple Method for Estimating the Strength of Natural Selection on Overlapping Genes

Author:
Wei, Xinzhu; Zhang, Jianzhi
Source:
Genome Biology and Evolution 2015 v.7 no.1 pp. 381-390
Subject:
DNA; computer simulation; genes; humans; natural selection; nucleotide sequences; proteins; viruses
Abstract:
... Overlapping genes, where one DNA sequence codes for two proteins with different reading frames, are not uncommon in viruses and cellular organisms. Estimating the direction and strength of natural selection acting on overlapping genes is important for understanding their functionality, origin, evolution, maintenance, and potential interaction. However, the standard methods for estimating synonymou ...
DOI:
10.1093/gbe/evu294
PubMed:
25552532
PubMed Central:
PMC4316641

3. Environmental Selection Pressures Related to Iron Utilization Are Involved in the Loss of the Flavodoxin Gene from the Plant Genome

Author:
Pierella Karlusich, Juan J.; Ceccoli, Romina D.; Graña, Martín; Romero, Héctor; Carrillo, Néstor
Source:
Genome Biology and Evolution 2015 v.7 no.3 pp. 750-767
Subject:
Archaea; algae; autotrophs; bacteria; bioavailability; electron transfer; freshwater; genes; habitats; horizontal gene transfer; iron; metagenomics; natural selection; oceans; oxidative stress; photosynthesis; phylogeny; starvation; transgenic plants
Abstract:
... Oxidative stress and iron limitation represent the grim side of life in an oxygen-rich atmosphere. The versatile electron transfer shuttle ferredoxin, an iron-sulfur protein, is particularly sensitive to these hardships, and its downregulation under adverse conditions severely compromises survival of phototrophs. Replacement of ferredoxin by a stress-resistant isofunctional carrier, flavin-contain ...
DOI:
10.1093/gbe/evv031
PubMed:
25688107
PubMed Central:
PMC5322553

4. Genome-Wide Analysis Reveals Diverged Patterns of Codon Bias, Gene Expression, and Rates of Sequence Evolution in Picea Gene Families

Author:
De La Torre, Amanda R.; Lin, Yao-Cheng; Van de Peer, Yves; Ingvarsson, Pär K.
Source:
Genome Biology and Evolution 2015 v.7 no.4 pp. 1002-1015
Subject:
Picea abies; Picea glauca; abiotic stress; gene duplication; gene expression; gene expression regulation; genes; natural selection; translation (genetics)
Abstract:
... The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies and Picea glauca). We use genome-wide estimates of gene expression (>50,000 expressed genes) to study ...
DOI:
10.1093/gbe/evv044
PubMed:
25747252
PubMed Central:
PMC4419791

5. Genome-Wide Patterns of Genetic Polymorphism and Signatures of Selection in Plasmodium vivax

Author:
Cornejo, Omar E.; Fisher, David; Escalante, Ananias A.
Source:
Genome Biology and Evolution 2015 v.7 no.1 pp. 106-119
Subject:
Plasmodium cynomolgi; Plasmodium falciparum; Plasmodium knowlesi; Plasmodium vivax; genes; genetic polymorphism; genetic variation; immune system; loci; malaria; natural selection; parasites; Africa
Abstract:
... Plasmodium vivax is the most prevalent human malaria parasite outside of Africa. Yet, studies aimed to identify genes with signatures consistent with natural selection are rare. Here, we present a comparative analysis of the pattern of genetic variation of five sequenced isolates of P. vivax and its divergence with two closely related species, Plasmodium cynomolgi and Plasmodium knowlesi , using a ...
DOI:
10.1093/gbe/evu267
PubMed:
25523904
PubMed Central:
PMC4316620

6. Recent Coselection in Human Populations Revealed by Protein–Protein Interaction Network

Author:
Qian, Wei; Zhou, Hang; Tang, Kun
Source:
Genome Biology and Evolution 2015 v.7 no.1 pp. 136-153
Subject:
Africans; Asians; Europeans; genes; human population; humans; loci; natural selection; neurogenesis; protein-protein interactions; signal transduction
Abstract:
... Genome-wide scans for signals of natural selection in human populations have identified a large number of candidate loci that underlie local adaptations. This is surprising given the relatively short evolutionary time since the divergence of the human population. One hypothesis that has not been formally examined is whether and how the recent human evolution may have been shaped by coselection in ...
DOI:
10.1093/gbe/evu270
PubMed:
25532814
PubMed Central:
PMC4316623