scholarly journals Signals of recent positive selection in a worldwide sample of human populations

2009 ◽  
Vol 19 (5) ◽  
pp. 826-837 ◽  
Author(s):  
J. K. Pickrell ◽  
G. Coop ◽  
J. Novembre ◽  
S. Kudaravalli ◽  
J. Z. Li ◽  
...  
Keyword(s):  
Positive Selection ◽  
Human Populations ◽  
Recent Positive Selection

scholarly journals Soft sweeps are the dominant mode of adaptation in the human genome

2016 ◽  
Author(s):  
Daniel R. Schrider ◽  
Andrew D. Kern
Keyword(s):  
Positive Selection ◽  
Human Evolution ◽  
System Development ◽  
Dominant Mode ◽  
Nervous System Development ◽  
Human Populations ◽  
Beneficial Mutation ◽  
Recent Positive Selection ◽  
Machine Learning Approach

ABSTRACTThe degree to which adaptation in recent human evolution shapes genetic variation remains controversial. This is in part due to the limited evidence in humans for classic “hard selective sweeps,” wherein a novel beneficial mutation rapidly sweeps through a population to fixation. However, positive selection may often proceed via “soft sweeps” acting on mutations already present within a population. Here we examine recent positive selection across six human populations using a powerful machine learning approach that is sensitive to both hard and soft sweeps. We found evidence that soft sweeps are widespread and account for the vast majority of recent human adaptation. Surprisingly, our results also suggest that linked positive selection affects patterns of variation across much of the genome, and may increase the frequencies of deleterious mutations. Our results also reveal insights into the role of sexual selection, cancer risk, and central nervous system development in recent human evolution.

scholarly journals Interrogating 11 Fast-Evolving Genes for Signatures of Recent Positive Selection in Worldwide Human Populations

2009 ◽  
Vol 26 (10) ◽  
pp. 2285-2297 ◽  
Author(s):  
A. Moreno-Estrada ◽  
K. Tang ◽  
M. Sikora ◽  
T. Marques-Bonet ◽  
F. Casals ◽  
...  
Keyword(s):  
Positive Selection ◽  
Human Populations ◽  
Recent Positive Selection

scholarly journals Chromosome X-wide analysis of positive selection in human populations: from common and private signals to selection impact on inactivated genes and enhancers-like signatures

2021 ◽  
Author(s):  
Pablo Villegas Mirón ◽  
Sandra Acosta ◽  
Jessica Nye ◽  
Jaume Bertranpetit ◽  
Hafid Laayouni
Keyword(s):  
Positive Selection ◽  
X Chromosome ◽  
Target Genes ◽  
Regulatory Elements ◽  
Human Populations ◽  
Third Phase ◽  
Recent Positive Selection ◽  
Genome Wide ◽  
Private Signals ◽  
Sub Saharan

The ability of detecting adaptive (positive) selection in the genome has opened the possibility of understanding the genetic bases of population-specific adaptations genome-wide. Here we present the analysis of recent selective sweeps specifically in the X chromosome in different human populations from the third phase of the 1000 Genomes Project using three different haplotype-based statistics. We describe numerous instances of genes under recent positive selection that fit the regimes of hard and soft sweeps, showing a higher amount of detectable sweeps in sub-Saharan Africans than in non-Africans (Europe and East Asia). A global enrichment is seen in neural-related processes while numerous genes related to fertility appear among the top candidates, reflecting the importance of reproduction in human evolution. Commonalities with previously reported genes under positive selection are found, while particularly strong new signals are reported in specific populations or shared across different continental groups. We report an enrichment of signals in genes that escape X chromosome inactivation, which may contribute to the differentiation between sexes. We also provide evidence of a widespread presence of soft-sweep-like signatures across the chromosome and a global enrichment of highly scoring regions that overlap potential regulatory elements. Among these, enhancers-like signatures seem to present putative signals of positive selection that might be in concordance with selection in their target genes. Also, particularly strong signals appear in regulatory regions that show differential activities, which might point to population-specific regulatory adaptations.

scholarly journals Patterns of shared signatures of recent positive selection across human populations

2017 ◽  
Author(s):  
Kelsey Elizabeth Johnson ◽  
Benjamin F. Voight
Keyword(s):  
Positive Selection ◽  
Selective Pressure ◽  
Human Populations ◽  
Biological Mechanisms ◽  
Molecular Phenotype ◽  
Fundamental Interest ◽  
Adaptive Introgression ◽  
Recent Positive Selection ◽  
Single Positive ◽  
Selection Event

ABSTRACTScans for positive selection in human populations have identified hundreds of sites across the genome with evidence of recent adaptation. These signatures often overlap across populations, but the question of how often these overlaps represent a single ancestral event remains unresolved. If a single positive selection event spread across many populations, the same sweeping haplotype should appear in each population and the selective pressure could be common across diverse populations and environments. Identifying such shared selective events would be of fundamental interest, pointing to genomic loci and human traits important in recent history across the globe. Additionally, genomic annotations that recently became available could help attach these signatures to a potential gene and molecular phenotype that may have been selected across multiple populations. We performed a scan for positive selection using the integrated haplotype score on 20 populations, and compared sweeping haplotypes using the haplotype-clustering capability of fastPHASE to create a catalog of shared and unshared overlapping selective sweeps in these populations. Using additional genomic annotations, we connect these multi-population sweep overlaps with potential biological mechanisms at several loci, including potential new sites of adaptive introgression, the glycophorin locus associated with malarial resistance, and the alcohol dehydrogenase cluster associated with alcohol dependency.

scholarly journals dbPSHP: a database of recent positive selection across human populations

2013 ◽  
Vol 42 (D1) ◽  
pp. D910-D916 ◽  
Author(s):  
Mulin Jun Li ◽  
Lily Yan Wang ◽  
Zhengyuan Xia ◽  
Maria P. Wong ◽  
Pak Chung Sham ◽  
...  
Keyword(s):  
Positive Selection ◽  
Human Populations ◽  
Recent Positive Selection

scholarly journals Genetic Variation and Recent Positive Selection in Worldwide Human Populations: Evidence from Nearly 1 Million SNPs

PLoS ONE ◽  
2009 ◽  
Vol 4 (11) ◽  
pp. e7888 ◽  
Author(s):  
David López Herráez ◽  
Marc Bauchet ◽  
Kun Tang ◽  
Christoph Theunert ◽  
Irina Pugach ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Positive Selection ◽  
Human Populations ◽  
Recent Positive Selection
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