Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations

The interactions between transposable elements (TEs) and their hosts
constitute one of the most profound co-evolutionary processes found in
nature. The population dynamics of TEs depends on factors specific to each
TE families, such as the rate of transposition and insertional preference,
the demographic history of the host and the genomic landscape. How these
factors interact has yet to be investigated holistically. Here we are
addressing this question in the green anole ( Anolis carolinensis ) whose
genome contains an extraordinary diversity of TEs (including non-LTR
retrotransposons, SINEs, LTR-retrotransposons and DNA transposons). We
observe a positive correlation between recombination rate and TEs
frequencies and densities for LINEs, SINEs and DNA transposons. For these
elements, there was a clear impact of demography on TE frequency and
abundance, with a loss of polymorphic elements and skewed frequency
spectra in recently expanded populations. On the other hand, some
LTR-retrotransposons displayed patterns consistent with a very recent
phase of intense amplification. To determine how demography, genomic
features and intrinsic properties of TEs interact we ran simulations using
SLiM3. We determined that i) short TE insertions are not strongly
counter-selected, but long ones are, ii) neutral demographic processes,
linked selection and preferential insertion may explain positive
correlations between average TE frequency and recombination, iii) TE
insertions are unlikely to have been massively recruited in recent
adaptation. We demonstrate that deterministic and stochastic processes
have different effects on categories of TEs and that a combination of
empirical analyses and simulations can disentangle these mechanisms.