Evidence for positive selection on recent human transposable element insertions.

Area of Science:

• Genomics
• Evolutionary Biology
• Population Genetics

Background:

• Transposable elements (TEs) significantly contribute to human genome structure and variation.
• Active TE families like Alu, L1, and SVA generate polymorphisms, but their evolutionary impact is understudied.
• Understanding natural selection's role in shaping TE-driven genetic variation is crucial.

Purpose of the Study:

• To investigate the effects of natural selection on human genetic variation driven by recent transposable element activity.
• To systematically evaluate the impact of TE insertions on host fitness and population-level polymorphisms.
• To identify specific TE insertions that have been positively selected in human populations.

Main Methods:

• Developed a genome-wide scan to detect selection on human TE polymorphisms.
• Analyzed a dataset of 14,384 TE insertions across 1511 individuals from 15 populations.
• Utilized time-forward simulations to model neutral evolution and control for demographic history.

Main Results:

• Identified seven polymorphic TE insertions showing evidence of positive selection in specific human populations.
• Five selected TE insertions are located in tissue-specific enhancers.
• Two selected TE insertions are associated with expression quantitative trait loci (eQTLs) and gene regulation.

Conclusions:

• This study provides the first evidence of recent local adaptation acting on polymorphic transposable elements in humans.
• Putatively selected TE insertions may play roles in human adaptation by influencing gene regulation.
• Population genomic analyses of TE polymorphisms offer insights into ongoing human evolution.