Response to Comment on "Chromosomal Speciation and Molecular Divergence-Accelerated Evolution in Rearranged Chromosomes"

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Abstract
First, let us consider whether any differences in rates of protein evolution between rearranged and colinear chromosomes could be associated with the recent rearrangements that separated humans and chimpanzees. When computing KA/KS averages, we ignored genes with KS = 0 (2). In contrast, Lu et al. computed the KA/KS values of these genes by setting KS = 0.002. This biases toward much higher KA/KS ratios in smaller genes. Also, small changes in these KS values imply large changes in KA/KS ratios (e.g., using 0.001 would double some already large KA/KS values; most of the largest KA/KS values in the data set arise in this way). Introducing this arbitrary lower limit to KS has a greater impact on the KA/KS ratios of the human-chimpanzee comparison than on the human-outgroup comparison (because the latter has fewer KS = 0 values). Also, in the data used by Lu et al., KA/KS values are more affected in colinear than in rearranged chromosomes. If we ignore genes with KS = 0 in that data set, the KA/KS ratio for rearranged and colinear chromosomes (R/C) for the human-chimpanzee comparison is larger than the R/C ratio for human-outgroup comparison (1.65 versus 1.42). Furthermore, rearranged chromosomes tend to have a larger number of genes with KA/KS 1 than colinear chromosomes. However, this proportion is 2.04 for the human-chimpanzee comparison and only 1.37 when comparing humans with outgroups. Although these are not large differences, they hint at an acceleration of protein evolution in association with recent rearrangements.