**Difference in assortativity among eukaryote PINs**. **(***A*) <*K*_{nn}(*k*)>, the mean of the degrees among the neighbors of *k*-degree nodes, in the PINs of yeast (black square), worm (magenta plus), fly (blue triangle), human (green cross), and malaria parasite (red diamond). For yeast and human PINs, <*K*_{nn}(*k*)> for MIPS and Rual et al. datasets, respectively, are shown, and the results for the other yeast and human datasets are provided in Additional file : Figure S2. Dashed lines in black, magenta, blue, green, and red represent *k*^{-0.47}, *k*^{-0.29}, *k*^{-0.35}, *k*^{-0.26}, and *k*^{-0.02}, respectively. **(***B*) Duplication of a node changes the value of *ν *in <*K*_{nn}(*k*)> ~ *k*^{-ν}. A diagram below each network indicates the distribution of <*K*_{nn}(*k*)> and the value of *ν*. **(***C*) The distribution of <*K*_{nn}(*k*)> in the networks generated by the DDD model with the asymmetric divergence (DDD+A; left) and the symmetric divergence (DDD+S; right). Blue diamonds, green crosses, and red diamonds indicate the results with *σ *= -0.05 (-0.05), -0.03 (-0.03), and 0 (0), respectively, for DDD+A (DDD+S). These results were obtained by taking the mean among 100 networks generated by simulations. Black squares indicate <*K*_{nn}(*k*)> in the yeast PIN for MIPS. Dashed lines in black, blue, green, and red represent *k*^{-0.47 }(*k*^{-0.47}), *k*^{-0.51 }(*k*^{-0.48}), *k*^{-0.37 }(*k*^{-0.38}), and *k*^{-0.18 }(*k*^{-0.26}), respectively, for DDD+A (DDD+S).

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