Regulatory Logic and Transposable Element Dynamics in Caenorhabditis Genomes

Area of Science:

• Evolutionary genetics
• Molecular evolution
• Population genetics

Background:

• Transposable elements (TEs) exhibit vast diversity in eukaryotes, yet the evolutionary forces shaping this are poorly understood.
• Theoretical models predict TE regulation via element interactions, but these conditions often conflict with observed TE abundance in natural populations.

Purpose of the Study:

• To investigate how TE regulatory logic interacts with population genetic factors, such as outcrossing and self-fertility, in regulating TE proliferation.
• To model the dynamics of autonomous and non-autonomous transposable elements under varying population structures and selection pressures.

Main Methods:

• Utilized stochastic simulations to implement three models of TE regulation.
• Analyzed the impact of population size, reproductive strategy (outcrossing vs. self-fertility), and TE fitness effects on TE dynamics.
• Annotated transposable elements (LINEs, SINEs, Mutator) in Caenorhabditis genomes to test model predictions.

Main Results:

• Large, outcrossing populations with negative epistatic interactions or asymmetric regulation between autonomous and non-autonomous TEs maintained TE stability.
• Small or self-fertile populations, or those with high TE insertion rates or moderate fitness costs, experienced TE proliferation leading to population extinction.
• Observed rapid mutational decay in TE sequences and varied autonomous-non-autonomous relationships in Caenorhabditis genomes.

Conclusions:

• TE regulation is influenced by a complex interplay of genetic interactions and population structure.
• Specific regulatory mechanisms and population conditions are crucial for stable TE coexistence, while others drive TE-induced extinction.
• Findings suggest that individual TE families may follow distinct evolutionary trajectories governed by unique regulatory rules, particularly during initial invasion phases.