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 middle 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.

Introductions and invasions provide opportunities for interaction and hybridization between colonists and closely related native species. We investigate this phenomenon using the mitochondrial DNA COI and 81,416 base-pairs of overlapping nuclear variation to examine the evolutionary histories and signatures of hybridization among introduced feral Rock Pigeon and Eurasian Collared-Dove and native White-winged and Mourning doves in southwestern North America. First, we report all four species to be highly divergent across loci (overall pair-wise species Φ_ST range = 0.17–0.70) and provide little evidence for gene flow at evolutionary timescales. Despite this, evidence from multiple population genetics analyses supports the presence of six putative contemporary late-stage hybrids among the 182 sampled individuals. These putative hybrids contain various ancestry combinations, but all involve the most populous species, the Mourning Dove. Next, we use a novel method to reconstruct demographic changes through time using partial genome sequence data. We identify recent, species-specific fluctuations in population size that are likely associated with changing environments since the Miocene and suggest that these fluctuations have influenced the genetic diversity of each dove species in ways that may impact their future persistence. Finally, we discuss the importance of using multiple marker types when attempting to infer complex evolutionary histories and propose important considerations when analyzing populations that were recently established or of domestic origins.

Anopheles stephensi invasion in the Horn of Africa (HoA) poses a substantial risk of increased malaria disease burden in the region. An understanding of the history of introduction(s), establishment(s) and potential A. stephensi sources in the HoA is needed to predict future expansions and establish where they may be effectively controlled. To this end, we take a landscape genomic approach to assess A. stephensi origins and spread throughout the HoA, information essential for vector control. Specifically, we assayed 2070 genome‐wide single nucleotide polymorphisms across 214 samples spanning 13 populations of A. stephensi from Ethiopia and Somaliland collected in 2018 and 2020, respectively. Principal component and genetic ancestry analyses revealed clustering that followed an isolation‐by‐distance pattern, with genetic divergence among the Ethiopian samples significantly correlating with geographical distance. Additionally, genetic relatedness was observed between the northeastern and east central Ethiopian A. stephensi populations and the Somaliland A. stephensi populations. These results reveal population differentiation and genetic connectivity within HoA A. stephensi populations. Furthermore, based on genetic network analysis, we uncovered that Dire Dawa, the site of a spring 2022 malaria outbreak, was one of the major hubs from which sequential founder events occurred in the rest of the eastern Ethiopian region. These findings can be useful for the selection of sites for heightened control to prevent future malaria outbreaks. Finally, we did not detect significant genotype–environmental associations, potentially due to the recency of their colonization and/or other anthropogenic factors leading to the initial spread and establishment of A. stephensi. Our study highlights how coupling genomic data at landscape levels can shed light into even ongoing invasions.