Evolutionary biology must acknowledge Masatoshi Nei for three outstanding contributions: 1) an advancement in the scientific status of the discipline, which has been made by “molecular evolutionary biology” more quantitative through a set of statistical methods for studying genetic diversity, changes in DNA, neutral evolution, molecular phylogenies; 2) the application of Nei’s evolutionary Genetic Distance to the phylogenetic tree of human populations, supporting the Out of Africa model of global dispersal; 3) the overall recognition of the central role of mutations in evolution and the idea that the changes in DNA are not just “raw material” for the natural selection, but the main sources of innovation. Nei’s alternative theory of evolution, intended as a process driven by mutation, seems biased by a narrow focus on molecular determination and tends to underestimate the large corpus of interdisciplinary evidence supporting the causal role of selective processes in evolution.