The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata

Abstract

Background: Transposable Elements (TEs) make up the majority of plant genomes, and thus understanding TE evolutionary dynamics is key to understanding plant genome evolution. Plant reproductive systems are diverse and mating type variation is one factor among many hypothesized to influence TE evolutionary dynamics. Here, we collected a large TE-display data set in self-fertilizing Arabidopsis thaliana, and compared it to data gathered in outcrossing Arabidopsis lyrata. We analyzed seven TE families in four natural populations of each species to tease apart the effects of mating system, demography, transposition, and selection in determining patterns of TE diversity.

Results: Measures of TE band differentiation were largely consistent across TE families. However, patterns of diversity in A. thaliana Ac elements differed significantly from that other TEs, perhaps signaling a lack of recent transposition. Across TE families, we estimated higher allele frequencies and lower selection coefficients on A. thaliana TE insertions relative to A. lyrata TE insertions.

Conclusions: The differences in TE distributions between the two Arabidopsis species represents a synthesis of evolutionary forces that include the transposition dynamics of individual TE families and the demographic histories of populations. There are also species-specific differences that could be attributed to the effects of mating system, including higher overall allele frequencies in the selfing lineage and a greater proportion of among population TE diversity in the outcrossing lineage.

Figure 1

AMOVA Φ_PT per TE family in each population pairwise comparison in both species. A. lyrata data from [5]. A. thaliana populations: UK, Ascot, United Kingdom; Ger, Anholt, Germany; IN, Knox, Indiana, USA; NY, Long Island, New York, USA. A. lyrata populations: Ger, Plech, Germany; N.Am, North America; Rus, Russia; Swe, Sweden. "N"s indicate comparisons that show no significant population differentiation (Φ_PT = 0, p > 0.05).

Figure 2

Ac AMOVA Φ_PT compared to bootstrap replicates subsampled from all TE family TE display bands.

Figure 3

AMOVA percent molecular variation within and among populations ("pops").

Figure 4

Site Frequency Spectra of all pooled TEs ("Pooled"), and each TE family in species-wide samples of A. thaliana (black bordered bars) and A. lyrata (grey bars with grey borders).

Figure 5

Maximum Likelihood N_es estimates for in species-wide samples of A. thaliana and A. lyrata in pooled TEs ("Pooled") and each TE family. Horizontal bars are the 95% Confidence Interval and the diamond represents the ML N_es point estimate. The vertical line is N_es = 0.