Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata

Abstract

Transposable elements (TEs) are the major component of most plant genomes, and characterizing their population dynamics is key to understanding plant genome complexity. Yet there have been few studies of TE population genetics in plant systems. To study the roles of selection, transposition, and demography in shaping TE population diversity, we generated a polymorphism dataset for six TE families in four populations of the flowering plant Arabidopsis lyrata. The TE data indicated significant differentiation among populations, and maximum likelihood procedures suggested weak selection. For strongly bottlenecked populations, the observed TE band-frequency spectra fit data simulated under neutral demographic models constructed from nucleotide polymorphism data. Overall, we propose that TEs are subjected to weak selection, the efficacy of which varies as a function of demographic factors. Thus, demographic effects could be a major factor driving distributions of TEs among plant lineages.

Fig. 1.

A. lyrata Ac-like diversity data. (A) A plot of TE-display data. A colored cell represents the presence of a TE; a white cell is a lack of TE detection. Each column represents a TE band, and each row represents an individual. Colors show population of origin. (B) TE BFS for observed data (circles) and simulated data (bars and vertical black lines). The bars represent the 95% credible intervals, the white horizontal lines in the bars are the medians, and the vertical black lines show the full ranges of the simulations.

Fig. 2.

Hypothetical genealogy to illustrate the simulation of TE distributions under a neutral bottleneck model. Black circles represent transposition events.

Fig. 3.

Relative probabilities of the observed data for different values of θ in Germany, scaled to the original demographic model (24).

Fig. 4.

Mann–Whitney U statistics of pooled TE-band frequency spectra. Histograms depict the distribution of 1,000 mean U statistics for data simulated under the neutral demographic model for each population, and arrows point to the mean U value obtained by comparing observed data with the model. The observed value in Germany is P = 0.05.