Pervasive gene flow despite strong and varied reproductive barriers in swordtails

The evolution of reproductive barriers leads to the formation of new
species. However, recent research has demonstrated that hybridization has
been pervasive across the tree of life even in the presence of strong
barriers. Using swordtail fishes (genus Xiphophorus), an emerging model
system, we document overlapping mechanisms that act as barriers to gene
flow between X. birchmanni and X. cortezi by combining genomic sequencing
from natural hybrid populations, experimental laboratory crosses,
behavioral assays, sperm performance, and developmental studies. We show
that assortative mating plays a role in maintaining subpopulations with
distinct ancestry within natural hybrid populations. Using F2 hybrids we
identify several genomic regions that strongly impact hybrid viability.
Strikingly, two of these regions underlie genetic incompatibilities in
hybrids between X. birchmanni and its sister species X. malinche. Our
results demonstrate that ancient hybridization has played a role in the
origin of this shared genetic incompatibility. Moreover, ancestry mismatch
at these incompatible regions has remarkably similar consequences for
phenotypes and hybrid survival in X. cortezi  × X.
birchmanni hybrids as in X. malinche × X. birchmanni hybrids. Our
findings identify varied reproductive barriers that shape genetic exchange
between naturally hybridizing species and highlight the complex
evolutionary outcomes of hybridization.