Reply to Chen and Schmera: Partitioning beta diversity into replacement and nestedness-resultant components is not controversial.

With reference to our recent paper addressing the global biogeography of human infectious diseases (1), Chen and Schmera (2) suggest that our method for evaluating beta diversity and its components is controversial. We used the method developed by Baselga (3) (hereafter, BAS framework) for partitioning compositional dissimilarity into replacement (turnover) and nestedness-resultant components. Chen and Schmera advance an alternative approach developed by Podani and Schmera (4) (hereafter, POD framework), which partitions beta diversity into replacement and richness-difference components. Chen and Schmera suggest that the BAS framework is inappropriate because (i) BAS nestedness (βnes) is not related to other nestedness measures, (ii) BAS replacement (βsim) overrepresents true replacement due to scaling differences, and (iii) interpretability of BAS components of beta diversity (βsor) is problematic. Although Chen and Schmera raise some interesting concerns, we reject their suggestion of a comparative analysis using the POD framework for the following reasons: