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From: Gary Felix <>
Subject: Re: [DNA] R1b Origins (was OurEuropeangeographicalblock. . .)
Date: Sun, 12 Jul 2009 18:40:49 -0700 (PDT)


Hello Andrew,
in response to your message:
Although there might be exceptions sometimes, most attempts to "calibrate"
in this way are circular. First you estimate a time, and then you look for
an event to "calibrate" against.

My response:
Mtdna has been calibrated to population events as seen in this recent paper:
"Correcting for Purifying Selection:
An Improved Human Mitochondrial Molecular Clock" by Soares
I can't think of a reason Y dna couldn't stand the same scrutiny.

As this Zhivotovsky paper has done they use the Bantu, Maori and Gypsy expansions to calibrate their mutation estimates. This is a valid means of checking mutation rates. The fact that they came up with different mutation rates reflects the complexity of the task.

"A mutation rate of 2×10-3 per generation has been estimated for Y chromosome microsatellites by direct count in deep-rooted pedigrees (Heyer et al.1997)"

This appears to be the one used in TMRCA calculation (1999) and clearly this new calculation is an attempt to take in as much of these more recently discovered complexities as possible.

They cite the following inconsistencies to this rate as follows:

"A similar average mutation rate value of 3×10-3 per locus per generation was estimated by studying Y chromosome STRs (Y-STRs) in father/son pairs of confirmed paternity, although locus-specific values varied from 0 to 8×10-3 (Kayser et al.2000)

Not much difference so far.

"By counting the number of mutations in the branches of a haplotype network from samples of Native American populations, Forster et al. (2000) found a striking difference between their “evolutionary” estimate (2.6 × 10−4 per 20 years) and the “pedigree” estimate described above."

"...haplotype history might not represent the population history. In addition, such a network assumes single-repeat–unit mutational changes. Multistep Y-STR mutations, which have been observed recently (Forster et al 1998 Kayser et al.2000 Nebel et al.2001), can contribute significantly to the effective mutation rate (w, the product of the mutation rate and the variance of mutational changes in repeat scores), which determines the rate of microsatellite evolution (Slatkin 1995) Zhivotovsky and Feldman (1995). Furthermore, Forster et al.(2000 ) used for calibration an estimate of the time of population expansion in North America of 20,000 before the present (BP)—an estimate upon which there is no general agreement."

"Comparison of the Maoris and Cook Islanders gave an average value (over the seven loci; see...) for (δμ)2/2 of 0.00998, which suggests an average effective mutation rate of 0.000312 per 25 years (25×0.00998/800)."

Significantly slower than the rate used in 1999 (TMRCA).

"Pairwise comparisons of the 11 Bulgarian Gypsy populations (without the Darakchii sample, in which only one M82 individual was found) gave (δμ)2/2 of 0.01272 (averaged across population pairs and loci) or 0.000454 for the average effective mutation rate.


A more significant mutation rate than 1999 (TMRCA)

"However, these are most probably underestimates, because the (δμ)2 distance assumes constant size for each SNP lineage over time, and it also assumes the same within-lineage variation in an ancestral population prior to its split as at the present generation. It is more likely that each of those populations was founded by a small number of haplotypes and, thus, had lower STR variation prior to divergence; this can lead to an underestimate of the rate of divergence (Zhivotovsky 2001). Therefore, we apply the second estimator, the average squared difference, to the Maori and the Gypsy populations."

"Our estimate of the average effective mutation rate at Y chromosome STR loci (6.9×10-4 per 25 years) is close to those at autosomal microsatellites with tri- and tetranucleotide repeats, 8.5×10-4 and 9.3×10-4 (Zhivotovsky et al.2000) and 7.1×10-4 and 7.0×10-4 (Zhivotovsky et al.2003), which probably reflect the same slippage machinery that underlies STR mutations. It should be kept in mind that our estimate of effective mutation rate was based on STRs with three- and four-nucleotide motifs; inclusion of loci with dinucleotide repeats may increase this value, because they generally have a higher (effective) mutation rate (Chakraborty et al. 1997); Zhivotovsky et al. 2000)."

Here there is compensation for high allele length slippage for all loci, which is not the same as within loci increased mutations at higher alleles and stability at lower allele values as proposed by Dupuy et al in 2005.

 
"Comparison with Data Obtained by Forster and Colleagues
Forster et al. (2000) estimated a mutation rate of 2.6×10-4 per 20 years (3.3×10-4 per 25 years), which is about half our estimate."

Still much slower than the original estimate of 1999 (TMRCA)

"Furthermore, we cannot exclude the possibility that mutation rates at the same STR locus vary among haplogroups because of differences in allele repeat scores, repetitive structures, or other factors (Nebel et al.2001)

This is critial in my opinion in light of the numerous papers I have posted to this list supporting Dupuy et all 2005 and could be the major factor confounding different mutation rates among haplogroups.

This paper is a good indication of the complexities of estimating mutation rates and is the reason we should be wary of estimates that are too far from actual events for whatever lineage being discussed.

Finally in 1998 Dr. Hammer used a Y chromosome haplotype common to great apes and Sub Saharan Africans to age genetic Adam at 147K ya. Source: Genes Culture and Human Evolution by Stone. Gives you an idea how slow things move on the Y.  His estimate came out only a few months before Pritchards estimate of 59K ya (guess who got all the press).

Best Regards,
Gary
Mexico DNA Project Admin.







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