September 20, 2005

BARCODE and the dating of sub-haplogroups

A new paper introduces BARCODE, a new software program that can be used to infer the age of different sub-haplogroups. The age is presented as a fraction of the time for the entire haplogroup, thus allowing for the comparative dating of the antiquity of lineages. Below is the dating of several sub-haplogroups within Y-haplogroups E, J, and I.

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Human Genetics (Online first)

Independent methods for evolutionary genetic dating provide insights into Y-chromosomal STR mutation rates confirming data from direct father–son transmissions

Francesca Luca et al.

Abstract Five datasets consisting of samples jointly typed for Y-chromosomal Unique Event Polymorphism (UEP) and simple tandem repeat (STR) markers were re-examined with independent methods for dating the different UEP-defined lineages. We report on the results obtained with an original program which performs comparative dating (BARCODE) in comparison with coalescent analyses performed with BATWING under various prior conditions. For the first time these are equalized across datasets. We also report on the results concerning STR mutability as obtained with both methods. The dating results for the entire series of sub-haplogroups are highly correlated. Within coalescent analyses, dating-estimates under a wide range of priors tend to converge. As to STR mutation rates the main findings are: (1) large variations among loci within the same dataset with both methods, also when the same prior was used for all loci; (2) figures in most cases above 1×10−3 and often above 2×10−3; (3) a few loci that mutate differently across studies. These results closely match those obtained from direct observation of father–son transmissions. Overall, this work supports the use of genetic dating procedures that take into account the complexity of the phenomenon, with a repertoire of priors tailored on the particular dataset.


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