Impact of polymorphic transposable elements on linkage disequilibrium along chromosomes

Area of Science:

• Evolutionary genetics
• Population genetics
• Genomics

Background:

• Recombination and selection shape genetic variation and linkage disequilibrium (LD).
• The role of transposable elements (TEs) in recombinationally-inert regions and their impact on local recombination rates is not well understood.
• Investigating the interplay between TEs, recombination, and selection is crucial for understanding adaptive evolution.

Purpose of the Study:

• To investigate the fine-scale interaction between transposable elements (TEs) and recombination along chromosomes.
• To determine if polymorphic TEs can modify local recombination rates and support linked selection in natural populations.
• To explore the role of TEs in shaping adaptive genetic variation.

Main Methods:

• Whole-genome sequencing of 304 individuals from Arabis alpina populations.
• Analysis of the correlation between polymorphic TE density and local LD.
• Characterization of LD blocks to identify selective sweeps using site frequency spectrum and haplotype structure.

Main Results:

• Polymorphic TE density is specifically correlated with local LD along chromosomes.
• 28 LD blocks were identified, with evidence of selective sweeps and enrichment in ecologically relevant genes (e.g., cold stress, photoperiodism).
• The S-locus and cold-response/photoperiodism adaptive loci were found within LD blocks containing high levels of polymorphic TEs.

Conclusions:

• TEs modify recombination landscapes, interacting with selection to drive blocks of linked adaptive loci.
• TEs play a significant role in shaping adaptive genetic variation and facilitating adaptation in natural populations.
• The findings support the hypothesis that TEs are active participants in evolutionary processes by influencing recombination and selection.