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Secondary contact and hybridization between recently diverged taxa have been increasing due to anthropogenic changes to the environment. Determining whether secondary contact leads to gene flow between species is important for understanding both the evolutionary consequences of such events (i.e. genetic swamping, speciation reversal, hybrid speciation) and for establishing proper conservation measures. Mallards (Anas platyrhynchos), which natively have a Holarctic distribution, have been introduced nearly worldwide due to game-farm and domestic pet releases. Their expanding range has resulted in secondary contact and increased incidences of hybridization with many closely related Mallard-like ducks that comprise the Mallard complex. Here, we assay molecular diversity for 19 nuclear introns and the mitochondrial DNA for wild Mallards (n = 50) across their Holarctic range and Yellow-billed Ducks (n = 30–75; Anas undulata) from southern Africa to determine population genetic structure and test for evidence of Mallard introgression into Yellow-billed Ducks. While we found limited support for contemporary gene flow across nuclear markers, we provide evidence from mitochondrial DNA that best supports ancient gene flow between Yellow-billed Ducks and Mallards. Yellow-billed Ducks best fit a single population at nuclear markers but show some location-specific mtDNA structure that suggests recent founder or bottleneck events. Although we find that introgression from Mallards into Yellow-billed Duck is limited, Yellow-billed Duck populations should be monitored to determine if expanding feral Mallard populations in southern Africa are increasing introgression.

Strong population structure and limited gene flow between Yellow-billed Ducks and Mallards in southern Africa