Supplementary Tables are currently available at: https://github.com/signor-molevol/serrata_transposable Transposable elements are an important component of the complex genomic ecosystem. Understanding the tempo and mode of transposable element proliferation, i.e. whether it is in maintained in transposition selection balance, or is induced periodically by environmental stress or other factors, is important for understanding the evolution of organismal genomes through time. While TEs have been characterized in individuals or limited samples, a true understanding of the population genetics of transposable elements, and therefore the tempo and mode of transposition, is still lacking. Here, we characterize the transposable element landscape in an important model Drosophila, D. serrata using the D. serrata reference panel which is comprised of 102 sequenced inbred genotypes. We annotate the families of transposable elements in the D. serrata genome and investigate variation in transposable element copy number between genotypes. We find that many TEs have low copy number in the population, but this varies by family, and includes a single TE making up to 50% of the genome content of TEs. We find that some transposable elements proliferate in particular genotypes compared to population levels. In addition, we characterize variation in each TE family allowing copy number to vary in each genotype and find that some TEs have diversified very little between individuals suggesting recent spread. TEs are important sources of spontaneous mutations in Drosophila, making up a large fraction of the total number of mutations in particular genotypes. Understanding the dynamics of TEs within populations will be an important step towards characterizing the origin of variation within and between species.
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