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Estimating the central TMRCA using the ASD method
The formula above shows the Average Squared
Difference approach used in this application to calculate the
central TMRCA estimate for a given set of YDNA STR haplotypes. It draws its computational inspiration
from the statistical analysis section of the Behar et al. (2003) paper and its derivative Matlab/Octave program
Ytime, but with some differences/modifications:
Computing the unbiased estimate T (seen in square brackets above), by partitioning the ASD
over each locus using the specific mutation rate for that particular locus(m), and then finding
the mean across all the partitions, versus using a single mean mutation rate across all loci to
divide into an overall ASD that was computed across all markers. Note that these two methods
would have identical outcomes if all locus specific mutation rates were set to be equivalent
(for instance when using the Zhivotovsky rates).
of TMRCA estimates from 6 different sources of mutation rate
estimates. (see below for specifics).
The use of both Median and Modal repeats to represent the ancestral haplotype.
The ability to
explicitly specify any marker combination from the full marker set and the
automatic extraction, and computation with these specified markers on the given haplotype
The absence of confidence interval calculations.
Mutation Rate Sources
Theoretically, any published
mutation rate sets could be used in the application, but since it is
to maximize the number of markers available for analysis, a tradeoff has to be made between maximizing the
number of mutation rate sources and the total markers made available, since most mutation rate estimates come
for only a limited set of markers. Therefore, the application uses marker specific mutation rates* compiled
only from the following sources:
Stafford Bayesian Mutation Rates: Essentially a compilation of other mutation rates - Download
The effective mutation
rate estimate of Zhivotovsky: - Download *Note, Markers not found in the
were normalized using the pedigree relative rates, see procedure here .
Pre-defined Marker Lists
any marker combination drawn from the full marker list can be used with this application, listed below
are the Pre-defined marker lists included in the application, these lists come from different publications and
are a convenient way to conduct TMRCA estimates for comparison:
Full_marker_list.txt – The maximum number of markers that overlap with all mutation rate sets.
|Publication||Method||Substitution Rate (per site per generation)|
|Kuroki et al. (2006)||Chimp Comparison||4.50 X 10-8||2.30 X 10-8||6.30 X 10-8|
|Xue et al. (2009)||Deep-rooting Pedigree||3.00 X 10-8||8.90 X 10-9||7.00 X 10-8|
|Poznick et al. (2013)*||Founding Migrations||2.46 X 10-8||2.16 X 10-8||2.76 X 10-8|
|Francalacci et al. (2013)*||Founding Migrations||1.59 X 10-8||1.26 X 10-8||2.10 X 10-8|
|Mendez et al. (2013)**||Autosomal Adjustment||1.85 X 10-8||8.78 X 10-9||2.83 X 10-8|
|Scozzari et al. (2013)*||Autosomal Adjustment||1.92 X 10-8||1.41 X 10-8||2.46 X 10-8|
|Fu et al. (2014)*||Ancient DNA||2.40 X 10-8||2.10 X 10-8||2.70 X 10-8|