Beschreibung:
<jats:title>Abstract</jats:title><jats:p>Active transposable elements (<jats:styled-content style="fixed-case">TE</jats:styled-content>s) may result in divergent genomic insertion and abundance patterns among conspecific populations. Upon secondary contact, such divergent genetic backgrounds can theoretically give rise to classical Dobzhansky–Muller incompatibilities (<jats:styled-content style="fixed-case">DMI</jats:styled-content>), thus contributing to the evolution of endogenous genetic barriers and eventually causing population divergence. We investigated differential <jats:styled-content style="fixed-case">TE</jats:styled-content> abundance among conspecific populations of the nonbiting midge <jats:italic>Chironomus riparius</jats:italic> and evaluated their potential role in causing endogenous genetic incompatibilities between these populations. We focussed on a <jats:italic>Chironomus</jats:italic>‐specific <jats:styled-content style="fixed-case">TE</jats:styled-content>, the minisatellite‐like <jats:italic>Cla‐element</jats:italic>, whose activity is associated with speciation in the genus. Using a newly generated and annotated draft genome for a genomic study with five natural <jats:italic>C. riparius</jats:italic> populations, we found highly population‐specific <jats:styled-content style="fixed-case">TE</jats:styled-content> insertion patterns with many private insertions. A significant correlation of the pairwise <jats:italic>F</jats:italic><jats:sub>ST</jats:sub> estimated from genomewide single‐nucleotide polymorphisms (<jats:styled-content style="fixed-case">SNP</jats:styled-content>s) and the <jats:italic>F</jats:italic><jats:sub>ST</jats:sub> estimated from <jats:styled-content style="fixed-case">TE</jats:styled-content>s is consistent with drift as the major force driving <jats:styled-content style="fixed-case">TE</jats:styled-content> population differentiation. However, the significantly higher <jats:italic>Cla‐element F</jats:italic><jats:sub>ST</jats:sub> level due to a high proportion of differentially fixed <jats:italic>Cla‐element</jats:italic> insertions also indicates selection against segregating (i.e. heterozygous) insertions. With reciprocal crossing experiments and fluorescent in situ hybridization of <jats:italic>Cla‐elements</jats:italic> to polytene chromosomes, we documented phenotypic effects on female fertility and chromosomal mispairings. We propose that the inferred negative selection on heterozygous <jats:italic>Cla‐element</jats:italic> insertions may cause endogenous genetic barriers and therefore acts as <jats:styled-content style="fixed-case">DMI</jats:styled-content> among <jats:italic>C. riparius</jats:italic> populations. The intrinsic genomic turnover exerted by <jats:styled-content style="fixed-case">TE</jats:styled-content>s may thus have a direct impact on population divergence that is operationally different from drift and local adaptation.</jats:p>