PCA analysis of duck genotypes. The program smartpca from the Eigenstrat package was used to calculate multivariate eigenvectors of the duck genotypes. The first two eigenvectors for each individual are plotted and colour coded by locality or species. The percent variation explained by PCA axes 1 and 2 is given in brackets. a) only Anas platyrhynchos individuals, colour coded by locality (see additional file 4). b) other ducks, colour coded by species: An. acuta (Anas acuta, ANAC), An. crecca (Anas crecca, ANCR), An. penelope (Anas penelope, ANPE), An. strepera (Anas strepera, ANST), Ay. fuligula (Aythya fuligula, AYFU). c) A joint calculation of PCA axes including all ducks analysed in this study. Additionally, a hybrid between Anas acuta and Anas platyrhynchos was included (ANACPLA), which is placed between the Anas platyrhynchos and Anas acuta cluster as expected. Anas platyrhynchos clearly forms an own cluster and the genetic similarity to the other species clusters reflects phylogenetic placements (i.e., Anas platyrhynchos is more closely related to Anas acuta and Anas crecca than to Anas penelope or Anas strepera).