Interrogating a High-Density SNP Map for Signatures of Natural Selection

Interrogating a High-Density SNP Map for Signatures of Natural Selection

2002 | Joshua M. Akey, Ge Zhang, Kun Zhang, Li Jin, and Mark D. Shriver
This study presents an analysis of 26,530 single nucleotide polymorphisms (SNPs) from three populations—African-American, East Asian, and European-American—to identify genomic regions influenced by natural selection. The researchers calculated genetic differentiation (FST) for each SNP and compared it to the genome-wide distribution of FST values. They found statistically significant evidence supporting the hypothesis that natural selection has shaped human genetic variation. The study identified 174 candidate genes with genetic variation patterns indicative of selection. The results suggest that natural selection has played a key role in shaping the human genome, and the findings provide a foundation for constructing a high-resolution natural selection map of the human genome. Natural selection is the process by which genetic variants that confer a survival or reproductive advantage become more common in a population. Despite extensive research, only a small number of genes have been directly linked to selection in the human genome. Understanding how and where natural selection has shaped genetic variation can provide insights into evolutionary mechanisms, guide population genetic studies, and help elucidate genotype-phenotype correlations in complex diseases. Detecting natural selection is challenging because its effects on genetic variation can be mimicked by population demographic history. However, the recent availability of large SNP datasets offers an opportunity to identify genome-wide signatures of selection. The study used FST to detect these signatures, as it measures genetic differentiation between populations. Under neutral conditions, FST is influenced by genetic drift, but natural selection can cause systematic deviations in FST values for selected genes and nearby markers. The study found that the empirical distribution of FST values differed significantly from simulated neutral distributions, suggesting the influence of natural selection. The results indicate that natural selection has affected human genetic variation, with some genes showing unusually high or low FST values. The study also found that FST values tend to cluster across chromosomes, suggesting that selection may have influenced genetic variation in specific genomic regions. The study identified 174 candidate genes that may have been subject to natural selection, including genes associated with diseases such as cystic fibrosis and type 2 diabetes. The study also found that genes involved in immune function were more likely to have low FST values, consistent with balancing selection. The results suggest that natural selection has played a significant role in shaping human genetic variation, and the findings provide a foundation for further research into the mechanisms of evolutionary change.This study presents an analysis of 26,530 single nucleotide polymorphisms (SNPs) from three populations—African-American, East Asian, and European-American—to identify genomic regions influenced by natural selection. The researchers calculated genetic differentiation (FST) for each SNP and compared it to the genome-wide distribution of FST values. They found statistically significant evidence supporting the hypothesis that natural selection has shaped human genetic variation. The study identified 174 candidate genes with genetic variation patterns indicative of selection. The results suggest that natural selection has played a key role in shaping the human genome, and the findings provide a foundation for constructing a high-resolution natural selection map of the human genome. Natural selection is the process by which genetic variants that confer a survival or reproductive advantage become more common in a population. Despite extensive research, only a small number of genes have been directly linked to selection in the human genome. Understanding how and where natural selection has shaped genetic variation can provide insights into evolutionary mechanisms, guide population genetic studies, and help elucidate genotype-phenotype correlations in complex diseases. Detecting natural selection is challenging because its effects on genetic variation can be mimicked by population demographic history. However, the recent availability of large SNP datasets offers an opportunity to identify genome-wide signatures of selection. The study used FST to detect these signatures, as it measures genetic differentiation between populations. Under neutral conditions, FST is influenced by genetic drift, but natural selection can cause systematic deviations in FST values for selected genes and nearby markers. The study found that the empirical distribution of FST values differed significantly from simulated neutral distributions, suggesting the influence of natural selection. The results indicate that natural selection has affected human genetic variation, with some genes showing unusually high or low FST values. The study also found that FST values tend to cluster across chromosomes, suggesting that selection may have influenced genetic variation in specific genomic regions. The study identified 174 candidate genes that may have been subject to natural selection, including genes associated with diseases such as cystic fibrosis and type 2 diabetes. The study also found that genes involved in immune function were more likely to have low FST values, consistent with balancing selection. The results suggest that natural selection has played a significant role in shaping human genetic variation, and the findings provide a foundation for further research into the mechanisms of evolutionary change.
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