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

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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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Acknowledgements

We gratefully acknowledge two anonymous reviewers for their helpful comments on a first version of this paper. We thank Drs. F. Cruciani and O. Semino for providing listings of the original data. Work supported by PRIN-MIUR 2003.

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Authors and Affiliations

  1. Department of Cell Biology, University of Calabria, via P. Bucci, 87030, Rende, Italy

    Francesca Luca & A. Novelletto

  2. Department of Electronics, Informatics and Systems, University of Calabria, Rende, Italy

    M. Basile

  3. Department of Biology, University “Tor Vergata”, Rome, Italy

    F. Di Giacomo

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  1. Francesca Luca
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  2. M. Basile
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  3. F. Di Giacomo
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  4. A. Novelletto
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Correspondence to Francesca Luca.

Appendices

Appendix 1

Table 5 Mean and variance of repeat size at STR loci in the different sub-haplogoups
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Appendix 2

Table 6 Confidence intervals for the central values reported in Table 1
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Luca, F., Basile, M., Giacomo, F.D. et al. Independent methods for evolutionary genetic dating provide insights into Y-chromosomal STR mutation rates confirming data from direct father–son transmissions. Hum Genet 118, 153–165 (2005). https://doi.org/10.1007/s00439-005-0028-6

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