Whole-genome sequencing reveals asymmetric introgression between two sister species of cold-resistant leaf beetles

A large number of genetic variation studies have identified cases of
mitochondrial genome introgression in animals, indicating that
reproductive barriers among closely related species are often permeable.
Because of its sheer size, the impact of hybridization on the evolution of
the nuclear genome is more difficult to apprehend. Only a few studies have
explored it recently thanks to recent progresses in DNA sequencing and
genome assembly. Here, we analysed whole-genome sequence variation among
multiple individuals of two sister species of leaf beetles inside their
hybrid zone, in which asymmetric mitochondrial genome introgression had
previously been established. We used a machine learning approach based on
computer simulations for training to identify regions of the nuclear
genome that were introgressed. We inferred asymmetric introgression of ≈2%
of the genome, in the same direction than was observed for the
mitochondrial genome. Because a previous study based on a
reduced-representation sequencing approach was not able to detect this
introgression, we conclude that whole-genome sequencing is necessary when
the fraction of the introgressed genome is small. We also analysed the
whole-genome sequence of a hybrid individual, demonstrating that hybrids
have the capacity to backcross with the species for which virtually no
introgression was observed. Our data suggest that one species has recently
invaded the range of the other and/or that positive selection has favoured
the mitochondrial genes of foreign origin for the invading species, along
with a series of nuclear genes, some of which possibly being co-adapted
with the mitochondrial genes.