The genome-wide signature of short-term temporal selection

The genome-wide signature of short-term temporal selection

July 3, 2024 | Michael Lynch, Wen Wei, Zhiqiang Ye, and Michael Pfrender
The study by Lynch et al. investigates the temporal dynamics of allele-frequency changes in a natural population of the microcrustacean *Daphnia pulex* over a 10-year period. The analysis of nearly 1,000 genetic isolates reveals that short-term variation in selection intensity significantly influences nucleotide polymorphism and divergence. Key findings include: 1. **Quasi-Neutrality**: Most nucleotide sites experience fluctuating selection with mean selection coefficients near zero, indicating a near steady state of selection. 2. **Weak Positive Selection**: Minor alleles are under weak positive selection, likely due to linkage disequilibrium with selected sites. 3. **Genomic Distribution**: Selection is distributed across numerous genomic islands of linked sites, suggesting that the effects of selection are not isolated but are influenced by nearby genetic variants. 4. **Temporal Covariance**: There is some temporal covariance in selection intensities, but it is generally small and not consistent across intervals, indicating that selection pressures change over time. 5. **Genome-Wide Covariance**: The study identifies 241 islands of significant selection (ISSs), which are regions with strong collective selective effects. These ISSs are more prevalent in centromeric regions and contain young gene duplicates and genes with higher levels of divergence from related species. 6. **Implications for Diversity**: Fluctuating selection can lead to underestimation of nucleotide diversity and overestimation of neutrality, challenging the conventional interpretation of nucleotide diversity and divergence as measures of random genetic drift and selection intensities. The results highlight the importance of considering fluctuating selection in the interpretation of population-genetic data and suggest that longer-term studies are necessary to fully understand the dynamics of genetic variation in natural populations.The study by Lynch et al. investigates the temporal dynamics of allele-frequency changes in a natural population of the microcrustacean *Daphnia pulex* over a 10-year period. The analysis of nearly 1,000 genetic isolates reveals that short-term variation in selection intensity significantly influences nucleotide polymorphism and divergence. Key findings include: 1. **Quasi-Neutrality**: Most nucleotide sites experience fluctuating selection with mean selection coefficients near zero, indicating a near steady state of selection. 2. **Weak Positive Selection**: Minor alleles are under weak positive selection, likely due to linkage disequilibrium with selected sites. 3. **Genomic Distribution**: Selection is distributed across numerous genomic islands of linked sites, suggesting that the effects of selection are not isolated but are influenced by nearby genetic variants. 4. **Temporal Covariance**: There is some temporal covariance in selection intensities, but it is generally small and not consistent across intervals, indicating that selection pressures change over time. 5. **Genome-Wide Covariance**: The study identifies 241 islands of significant selection (ISSs), which are regions with strong collective selective effects. These ISSs are more prevalent in centromeric regions and contain young gene duplicates and genes with higher levels of divergence from related species. 6. **Implications for Diversity**: Fluctuating selection can lead to underestimation of nucleotide diversity and overestimation of neutrality, challenging the conventional interpretation of nucleotide diversity and divergence as measures of random genetic drift and selection intensities. The results highlight the importance of considering fluctuating selection in the interpretation of population-genetic data and suggest that longer-term studies are necessary to fully understand the dynamics of genetic variation in natural populations.
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