Population genomics infer different modes of divergence and speciation with gene flow in the green-winged teal duck complex

The processes of divergence and speciation differ broadly among taxa, but might also differ among closely related taxa with different life histories. We examine these processes in a small clade of ducks with historically uncertain relationships and species limits. The green-winged teal (Anas crecca) complex is a Holarctic species of dabbling duck currently categorized as three subspecies (Anas crecca crecca, A. c. nimia, and A. c. carolinensis) with a close relative, the South American yellow-billed teal (Anas flavirostris). We examined divergence and speciation in this group, determining their phylogenetic relationships and the presence and levels of gene flow among lineages using both mitochondrial and nuclear DNA (ultraconserved elements, UCEs, 1,393 loci). Phylogenetic relationships using nuclear DNA among these taxa showed A. c. crecca, A. c. nimia, and A. c. carolinensis clustering together to form one polytomous clade, with A. flavirostris sister to this clade. However, whole mitogenomes show a different phylogeny: A. c. crecca sister to A. c. nimia, and A. c. carolinensis sister to A. flavirostris. The best demographic model for key pairwise comparisons showed divergence with migration (gene flow) in all pairwise comparisons Given prior work, gene flow was expected among the Holarctic taxa, but gene flow between North American carolinensis and South American flavirostris (m was approximately 0.1 - 0.4 individuals per generation), albeit low, was not. Ultraconserved elements are a powerful tool for simultaneously studying systematics and population genomics in systems like this.