Fig. 6

Reconstruction of ancestral states and mapping of mitogenomic duplications onto the Palaeognathae trees. Two methods, maximum parsimony (a, c) and maximum likelihood (b, d) were applied for two tree topologies: t1 based on sequences of mitochondrial genes (a, b) and t2 supported by nuclear markers in coalescent-based approaches (c, d). The area of colors at nodes in b and d corresponds to the probability of the given state, single or duplicated region. The probability value for a more likely state was also given at these nodes. Mk1 model was applied for ML approach