Factors affecting the rate and pattern of the mutational process are being identified for human
autosomes, but the same relationships for the male specific portion of the Y chromosome
(MSY) are not established. We considered 3,390 mutations occurring in 19 sequence bins
identified by sequencing 1.5 Mb of the MSY from each of 104 present-day chromosomes.
The occurrence of mutations was not proportional to the amount of sequenced bases in each
bin, with a 2-fold variation. The regression of the number of mutations per unit sequence
against a number of indicators of the genomic features of each bin, revealed the same fundamental
patterns as in the autosomes. By considering the sequences of the same region from
two precisely dated ancient specimens, we obtained a calibrated region-specific substitution
rate of 0.716 × 10-9/site/year. Despite its lack of recombination and other peculiar features,
the MSY then resembles the autosomes in displaying a marked regional heterogeneity of the
mutation rate. An immediate implication is that a given figure for the substitution rate only
makes sense if bound to a specific DNA region. By strictly applying this principle we obtained
an unbiased estimate of the antiquity of lineages relevant to the genetic history of the human
Y chromosome. In particular, the two deepest nodes of the tree highlight the survival, in Central-Western
Africa, of lineages whose coalescence (291 ky, 95% C.I. 253–343) predates the
emergence of anatomically modern features in the fossil record.