Genomes of historical specimens reveal multiple invasions of LTR retrotransposons in Drosophila melanogaster populations during the 19^th century

Abstract

Transposable element invasions have a profound impact on the evolution of genomes and phenotype. It is thus an important open question on how often such TE invasions occur. Based on strains sampled at different times, previous work showed that four different TE families invaded D. melanogaster during the 20^th century. Here we utilize the genomes of historical specimens to extend this work by another 100 years. We found that the LTR retrotransposons Blood, Opus and 412 spread in D. melanogaster in the 19^th century. These invasions were found to constitute second waves, as degraded fragments were found for all three TEs. We show that two of the three invasions, Opus and 412, led to pronounced geographic heterogeneity, likely due to founder effects during the invasions. Finally, we identified species from the simulans complex as the likely origin of the TEs. In total, seven TE families invaded D. melanogaster during the last 200 years, increasing the genome size by 1.2 Mbp. Based on the analysis of strains and specimens sampled at different times, we provide a detailed timeline of TE invasions, making D. melanogaster the first organism where we could infer the invasion history of TEs during the last two centuries.