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Published by Aleksandr Shtrunov

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Published by: Aleksandr Shtrunov on Mar 07, 2010
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Michael F. Hammer
Doron M. Behar
Tatiana M. Karafet
Fernando L. Mendez
Brian Hallmark
Tamar Erez
Lev A. Zhivotovsky
Saharon Rosset
Karl Skorecki
Springer-Verlag 2009
We thank Dr. Klyosov for his Comment. The speed of response is unusually impressive, and it covers a widescope. However, we are concerned that this haste may notbe in the best interest of the sound scientific process, asevidenced by the heavy reliance on non-refereed publica-tions, unpublished work and work not accessible to thescientific reading audience through usual scientificchannels (categories that cover all five citations toDr. Klyosov’s previous work). Reference to non-peerreviewed and poorly accessible data and formulationsrenders the constructive critique process problematic.Furthermore, the use of unconventional and ‘private’terms without definition or reference renders responseproblematic. This includes terms such as
genealogichaplotype series’’. Moreover, a statement such as ‘‘Sincethe logarithmic and linear methods give the same datingthe common ancestor, it means that there was indeed justone common ancestor for the whole series of 98 of 22marker haplotypes’’, lacks scientific rigor and robustness.Nevertheless, we wish to provide some responses to thebest of our ability, given some of the limitations andconstraints noted above.Before dealing with some of the specifics of the Com-ment, we would like to address the issue of Y-STR muta-tion rates and age estimates in general. Estimating times of divergence and expansion requires knowledge regardingthe rate at which newly arisen genetic variation occurs andis maintained in populations. Are these the usual mutationrates that occur during meiosis or evolutionarily significantsubstitution rates for randomly surviving mutations withinevolving haplogroups? Forster et al. (2000) and Heyer et al.(2001) discovered up to a sevenfold difference between‘familial’and ‘evolutionary’mutation rates (i.e., esti-mated from pedigrees and phylogenetic trees, respectively)for Y-chromosomal STRs and mtDNA. As discussed byZhivotovsky et al. (2004), there are several factors that mayunderly this discrepancy. By examining Y-STR variationwithin Y chromosome haplogroups (i.e., defined by uniqueevent polymorphisms) in populations with documented
histories, they inferred an evolutionarily effec-tive mutation rate of 0.00069 per 25 years on average,which was threefold lower than previous estimates of thefamilial mutation rate (Zhivotovsky et al.2004). Togetherwith other methods, we used this approach in our paperbecause it involved estimating the divergence time of Ychromosome lineages with putative ages that were within asimilar time frame as those in the original Zhivotovskyet al. (2004) study (i.e., the effective rate was calibrated for
M. F. Hammer
T. M. Karafet
B. Hallmark 
T. ErezARL Division of Biotechnology, University of Arizona,Tucson, AZ 85721, USAM. F. Hammer
F. L. MendezDepartment of EEB, University of Arizona, Tucson,AZ 85721, USAD. M. Behar
K. SkoreckiMolecular Medicine Laboratory, Rambam Health Care Campus,31096 Haifa, IsraelL. A. ZhivotovskyInstitute of General Genetics, Russian Academy of Sciences,119991 Moscow, RussiaS. RossetDepartment of Statistics and Operations Research,School of Mathematical Sciences, Tel Aviv University,69978 Tel Aviv, IsraelK. Skorecki (
)Rappaport Faculty of Medicine and Research Institute,Technion, Israel Institute of Technology, 31096 Haifa, Israele-mail: skorecki@tx.technion.ac.il
Hum GenetDOI 10.1007/s00439-009-0747-1

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