This is a very important paper that showed that 4 base substitutions occurred a length of 10 million base pairs (or about 1/6th) of the Y chromosome in two individuals separated by 13 generations. What this means is:
- Even when we are able to routinely sequence entire Y chromosomes, we will still not generally be able to tell apart fathers and sons as sons (via their Y chromosome) only sometimes have different Y chromosomes than their fathers. In a large number of cases there will be no mutations.
- On the positive side, relationships in the entire human Y-chromosome phylogeny will be resolved with an accuracy of a few generations. We will no longer have to rely on poor resolution Y-STR "genetic distance" methods to determine relatedness of individuals. The chunky huge haplogroups dominating modern Y-chromosome pools will be resolved into a hierarchy of more exclusive families and really precise patterns of migration and admixture may be inferred.
UPDATE: It occurred to me that the new mutation rate could also be used to directly infer the age of Y-chromosome Adam -and other haplogroups-, using the SNP counting method of Karafet et al. One simply needs to find out how many bases were sequenced in that study to infer the expected number of mutations/generation.
Current Biology doi:0.1016/j.cub.2009.07.032
Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree
Yali Xue et al.
Understanding the key process of human mutation is important for many aspects of medical genetics and human evolution. In the past, estimates of mutation rates have generally been inferred from phenotypic observations or comparisons of homologous sequences among closely related species [1,2,3]. Here, we apply new sequencing technology to measure directly one mutation rate, that of base substitutions on the human Y chromosome. The Y chromosomes of two individuals separated by 13 generations were flow sorted and sequenced by Illumina (Solexa) paired-end sequencing to an average depth of 11 or 20, respectively . Candidate mutations were further examined by capillary sequencing in cell-line and blood DNA from the donors and additional family members. Twelve mutations were confirmed in 10.15 Mb; eight of these had occurred invitro and four invivo. The latter could be placed in different positions on the pedigree and led to a mutation-rate measurement of 3.0 108 mutations/nucleotide/generation (95% CI: 8.9 1097.0 108), consistent with estimates of 2.3 1086.3 108 mutations/nucleotide/generation for the same Y-chromosomal region from published human-chimpanzee comparisons  depending on the generation and split times assumed.