Rapid radiation and hybridization contribute to weak differentiation and hinder phylogenetic inferences in the New World Mallard complex (Anas spp.)

Of the 13 taxa composing the Mallard complex, 4 occur in North America: the sexually monochromatic American Black Duck (A. rubripes), Mexican Duck (A. [platyrhynchos] diazi), and Mottled Duck (A. fulvigula), and the dichromatic Mallard (Anas platyrhynchos). Although morphologically distinct, inferring the evolutionary relationships of this group is confounded by extensive genic sharing due to incomplete lineage sorting and ongoing hybridization. The objective of this study was to examine the underlying cause (i.e. incomplete lineage sorting vs. contemporary gene flow) of phylogenetic uncertainty. Whereas most taxa were fairly structured at mitochondrial DNA, a starburst pattern of divergence consistent with a rapid radiation was recovered with 17 nuclear introns. Furthermore, nuclear-based divergence estimates and tests of population structure recovered Florida and West Gulf Coast Mottled Ducks as well-differentiated and genetically diagnosable from each other and the remaining taxa, whereas Mallards, American Black Ducks, and Mexican Ducks were indistinguishable. In general, neither population structure analyses nor coalescent-based gene flow estimates conclusively identified the presence of hybrids or significant gene flow, suggesting that genetic similarity within the group is largely influenced by incomplete lineage sorting. However, we also cannot reject potentially high levels of gene flow. Moreover, inconsistent relationships among species trees indicated that phylogenetic results were sensitive to which individuals were included. Taxa within the New World group are phenotypically distinguishable, yet genetically similar and seemingly lack the apparent reproductive isolation that is consistent with early stages of (incomplete) speciation. Future work should focus on genomic regions under selection to better understand the stage of speciation among the various incipient forms.