Y Chromosome Mutation Rate

[mwauthy]

Is there any data out there regarding how regularly the Y chromosome mutates? How many generations on average? There are some people who have taken Big Y and have been assigned a subclade about 2000 years old or 60 generations in the past. I think this is due to not enough people having had tested yet and not enough shared snps. On average how many more snp mutation markers should a person alive today have since that 2000 year old subclade?

Also, can the same location on the chromosome mutate multiple times in different generations? For example, if initially the ancestral allele was A and the derived was T, could it mutate back to A again some time in the future? Would that be detectable today?

 

[AntonVila]

1) As far as it concerns mutation rate: "Here we used whole-genome sequence data from 753 Icelandic males, grouped into 274 patrilines, to estimate the point mutation rate for 21.3 Mb of male-specific Y chromosome (MSY) sequence, on the basis of 1,365 meioses (47,123 years). The combined mutation rate for 15.2 Mb of X-degenerate (XDG), X-transposed (XTR) and ampliconic excluding palindromes (rAMP) sequence was 8.71 × 10⁻¹⁰ mutations per position per year (PPPY). " Nature Genetics 47, 453–457 (2015)

Xue et al. (2009) confirmed four snps in two men separated 13 generations.

2) Regarding your question about repetitive mutations in different generations the chances are really low. Moto Kimura proposed this 50 years ago, a neutral mutation is by definition not under selection; then the backwards mutations only following the rules of error mistakes in replication during the germ line production, logically is higher in the male germ line because fof fewer cell divisions in the female line but never higher than 8.71 × 10⁻¹⁰ mutations per position per year. To "repair" the snp at least one chance of mutation in the snp is needed, then a proxy of 8711 million years to one opportunity is OK. Taking in account that the mutation should be to the same nucleotide and considering equal chances of mutation per nucleotide that implies X4 less opportunities, that means you need four times the mutation rate: 34.840 million years. Older than the universe.

The problem arises when we realize that not all snps and mutations are equally neutral, even in Y DNA that we consider not under selection. Under evolutionary pressure and selection the same snp or DNA portion mutates at higher rate and not always following those rules. For instance, the Berber E-M81 haplogroup possibly appeared several times because was found in unrelated individuals of different clades that share the E-M81 but not the STRs markers meaning that they are not descendants of one unique event given rise to E-M81 but several. We call these snps "reiterative" and should be avoided, at least in forensic studies. For human population research are still in use but with a high degree of skepticism.

 

[mwauthy]

1) As far as it concerns mutation rate: "Here we used whole-genome sequence data from 753 Icelandic males, grouped into 274 patrilines, to estimate the point mutation rate for 21.3 Mb of male-specific Y chromosome (MSY) sequence, on the basis of 1,365 meioses (47,123 years). The combined mutation rate for 15.2 Mb of X-degenerate (XDG), X-transposed (XTR) and ampliconic excluding palindromes (rAMP) sequence was 8.71 × 10⁻¹⁰ mutations per position per year (PPPY). " Nature Genetics 47, 453–457 (2015)

Xue et al. (2009) confirmed four snps in two men separated 13 generations.

2) Regarding your question about repetitive mutations in different generations the chances are really low. Moto Kimura proposed this 50 years ago, a neutral mutation is by definition not under selection; then the backwards mutations only following the rules of error mistakes in replication during the germ line production, logically is higher in the male germ line because fof fewer cell divisions in the female line but never higher than 8.71 × 10⁻¹⁰ mutations per position per year. To "repair" the snp at least one chance of mutation in the snp is needed, then a proxy of 8711 million years to one opportunity is OK. Taking in account that the mutation should be to the same nucleotide and considering equal chances of mutation per nucleotide that implies X4 less opportunities, that means you need four times the mutation rate: 34.840 million years. Older than the universe.

The problem arises when we realize that not all snps and mutations are equally neutral, even in Y DNA that we consider not under selection. Under evolutionary pressure and selection the same snp or DNA portion mutates at higher rate and not always following those rules. For instance, the Berber E-M81 haplogroup possibly appeared several times because was found in unrelated individuals of different clades that share the E-M81 but not the STRs markers meaning that they are not descendants of one unique event given rise to E-M81 but several. We call these snps "reiterative" and should be avoided, at least in forensic studies. For human population research are still in use but with a high degree of skepticism.

Thanks for the reply. Complicated but fascinating!