Data from: Idenitfying hybrids & the genomics of hybridization: mallards & American black ducks of Eastern North America

Resolving evolutionary relationships and establishing population structure
depends on molecular diagnosability that is often limited for closely
related taxa. Here, we use 3,200 ddRAD-seq loci across 290 mallards,
American black ducks, and putative hybrids to establish population
structure and estimate hybridization rates. We test between traditional
assignment probability and accumulated recombination events based analyses
to assign hybrids to generational classes. For hybrid identification, we
report the distribution of recombination events complements ADMIXTURE
simulation by extending resolution past F4 hybrid status; however, caution
against hybrid assignment based on accumulated recombination events due to
an inability to resolve F1 hybrids. Nevertheless, both analyses suggest
that there are relatively few backcrossed stages before a lineage’s hybrid
ancestry is lost and the offspring are effectively parental again. We
conclude that despite high rates of observed interspecific hybridization
between mallards and black ducks in the mid part of the 20th century, our
results do not support the predicted hybrid swarm. Conversely, we report
that mallard samples genetically assigned to western and non-western
clusters. We indicate that these non-western mallards likely originated
from game-farm stock, suggesting landscape level gene flow between
domestic and wild conspecifics.