Recent demography drives changes in linked selection across the maize genome.

Area of Science:

• Population Genetics
• Evolutionary Biology
• Genomics

Background:

• Genetic diversity arises from the interplay of genetic drift and selection.
• Population size, particularly effective population size (Ne), is a key factor influencing genetic drift.
• Shifts in population demographics can complicate the relationship between drift and selection.

Purpose of the Study:

• To investigate the impact of changing demography on selection patterns using whole-genome data.
• To understand linked selection during maize domestication and its demographic history.
• To analyze nucleotide diversity and selection efficiency in maize and teosinte.

Main Methods:

• Whole-genome sequencing of domesticated and wild maize (teosinte).
• Estimation of maize domestication demography, including population size changes.
• Analysis of nucleotide diversity patterns in and around genes.

Main Results:

• Maize experienced a severe population size bottleneck (approx. 5% of teosinte) followed by rapid expansion.
• Little evidence for selection on beneficial amino acid substitutions was found.
• The domestication bottleneck reduced purifying selection efficiency in maize, but young alleles show stronger selection in present-day larger populations.

Conclusions:

• Recent demographic changes in crops like maize have immediate and broad effects on genetic diversity.
• These effects can contradict predictions based solely on long-term effective population size.
• Understanding demographic history is crucial for interpreting genetic diversity patterns in domesticated species.