VCF files for D. serrata transposable elements

Transposable elements are an important element of the complex genomic
ecosystem. Transposable element insertion also appears to be bursty –
either due to invasion of new transposable elements that are not yet
repressed, de-repression due to instability of organismal defense systems,
stress, or genetic variation in hosts. Here, we characterize the
transposable element landscape in an important model Drosophila, D.
serrata, and investigate variation in transposable element copy number
between genotypes and in the population at large.  We find that a
subset of transposable elements are clearly related to elements annotated
in D. melanogaster and D. simulans, suggesting they spread between species
more recently than other transposable elements. We also find that some
transposable elements proliferate in particular genotypes compared to
population levels. In natural populations an active transposable element
and a potentially permissive background would not be held in association
as in inbred lines, thus this could be a product of inbreeding. Yet many
of the inbred lines have actively proliferating transposable elements
suggesting that active transposable elements are not uncommon and that
genotypes vary in their permissiveness in populations.