Ancient Transposable Elements Sustain Global Ecological Adaptation Despite Chronically Low Nucleotide Diversity

Area of Science:

• Evolutionary biology
• Genomics
• Ecology

Background:

• Transposable elements (TEs) are key drivers of genomic variation.
• Their role in ecological adaptation, especially in low-diversity species, is poorly understood.
• Spirodela polyrhiza exhibits low nucleotide diversity, posing a puzzle for adaptive potential.

Purpose of the Study:

• To investigate the contribution of ancient transposable element (TE) polymorphisms to global ecological adaptation in Spirodela polyrhiza.
• To resolve how species with low nucleotide diversity achieve adaptive potential.

Main Methods:

• Analysis of ancient TE polymorphisms across continental populations of Spirodela polyrhiza.
• Identification of selective pressures, particularly cold-season temperature.
• Comparison of adaptive signals from TEs versus single nucleotide polymorphisms (SNPs).

Main Results:

• Ancient TE polymorphisms, predating population divergence, are linked to global ecological adaptation.
• Cold-season temperature is a major selective force, with adaptation primarily associated with TE polymorphisms, not SNPs.
• Adaptive TEs show signatures of selection on standing variation and are in regions with relaxed constraint, not recent hard sweeps.

Conclusions:

• Ancient TE variation is crucial for ecological adaptation in low-diversity species like Spirodela polyrhiza.
• This resolves the paradox of how adaptation occurs despite chronically depleted nucleotide diversity.
• TEs provide a significant source of adaptive variation over evolutionary timescales.