Kilin-Klyosov TMRCA Calculator for Time Spans up to Millions of Years

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DOI: 10.4236/aa.2016.63007    1,193 Downloads   1,682 Views  


A TMRCA (Time to the Most Recent Common Ancestor) calculator has been developed, with a capacity to handle up to 10,000 haplotypes simultaneously, for haplotypes being in any format within the 111 markers in the FTDNA (Family Tree DNA, a leading company in systematics of the haplotypes) nomenclature, for haplotypes being in any combination with respect to number of their markers, and for the TMRCA values from a few hundred years to millions of years. The calculator shows the TMRCA data calculated separately and simultaneously in the 6-, 12-, 25-, 37, 67, and 111-marker formats by the linear method, and for haplotypes of any format, such as 7-, 8-, 9-, 10-, 17-, 19-, 23- and any other format by the quadratic method. The calculator also shows a number of mutations (in the whole given dataset of haplotypes), so the TMRCA values can be verified manually, if desired so. The calculator automatically makes corrections for back mutations (in the linear method; there is no need for corrections in the quadratic method), and considers multi-marker mutations and zero alleles, counting them correctly as one mutation. The calculator can be navigated to exclude markers which show an excessive dispersion, which likely is an indication of “admixtures”, which do not belong to the given set of haplotypes. The paper provides a number of examples of TMRCA calculations for datasets of different haplogroups, and shows that the mutation rate constants are the same in different haplogroups. The papers provides a comparison of mutation rate tables by Chandler (2006), Ballantyne et al. (2010), Heinila (2012) and an anonymous investigator (2014) with the mutation rate constants determined and examined in this study. It is shown that the above authors noticeably and significantly overestimated their mutation rates, which often lead to unrealistic TMRCAs.

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Klyosov, A. and Kilin, V. (2016) Kilin-Klyosov TMRCA Calculator for Time Spans up to Millions of Years. Advances in Anthropology, 6, 51-71. doi: 10.4236/aa.2016.63007.


[1] Anonymous (2014). Mutation Rates.
[2] Ballantyne, K. N., Goedbloed, M., Fang, R., Schaap, O., Lao, O., Wollstein, A. et al. (2010). Mutability of Y-Chromosomal Microsatellites: Rates, Characteristic, Molecular Bases, and Forensic Implications. American Journal of Human Genetics, 7, 341-353.
[3] Burgarella, С., & Navascues, М. (2011). Mutation Rate Estimates for 110 Y-Chromosome STRs Combining Population and Father-Son Pair Data. European Journal of Human Genetics, 19, 70-75.
[4] Chandler, J. F. (2006). Estimating Per-Locus Mutation Rates. Journal of Genetic Genealogy, 2, 27-33.
[5] Elhaik, E., Tatarinova, T. V., Klyosov, A. A., & Graur, D. (2014). The “Extremelyancient” Chromosome That Isn’t: A Forensic Bioinformatic Investigation of Albert Perry’s X-Degenerate Portion of the Y-Chromosome. European Journal of Human Genetics, 22, 1111-1116.
[6] Felsenstein, J. (2004). PHYLIP (Phylogeny Inference Package). Version 3.6., Seattle: Department of Genome Sciences, University of Washington.
[7] Goldstein, D. B., Linares, A. R., Cavalli-Sforza, L. L., & Feldman, M. W. (1995). Genetic Absolute Dating Based on Microsatellites and the Origin of Modernhumans. Proceedings of the National Academy of Sciences of the United States of America, 92, 6723-6727.
[8] Heinila, M. (2012).
[9] Klyosov, A. A. (2009a). DNA Genealogy, Mutation Rates, and Some Historical Evidences Written in Y-Chromosome. I. Basic Principles and the Method. Journal of Genetic Genealogy, 5, 186-216.
[10] Klyosov, A. A. (2009b). DNA Genealogy, Mutation Rates, and Some Historical Evidences Written in Y-Chromosome. II. Walking the Map. Journal of Genetic Genealogy, 5, 217-256.
[11] Klyosov, A. A. (2009c). A Comment on the Paper: Extended Y Chromosome Haplotypes Resolve Multiple and Unique Lineages of the Jewish Priesthood. Human Genetics, 126, 719-724.
[12] Klyosov, A. A. (2012). Ancient History of the Arbins, Bearers of Haplogroup R1b, from Central Asia to Europe, 16,000 to 1500 Years before Present. Advances in Anthropology, 2, 87-105.
[13] Klyosov, A. A., & Rozhanskii, I. L. (2012a). Haplogroup R1a as the Proto Indo-Europeans and the Legendary Aryans as Witnessed by the DNA of Their Current Descendants. Advances in Anthropology, 2, 1-13.
[14] Klyosov, A. A., & Rozhanskii, I. L. (2012b). Re-Examining the “Out of Africa” Theory and the Origin of Europeoids (Caucasoids) in Light of DNA Genealogy. Advances in Anthropology, 2, 80-86.
[15] Klyosov, A. A., Rozhanskii, I. L., & Ryanbchenko, L. E. (2012). Re-Examining the Out-of-Africa Theory and the Origin of Europeoids (Caucasoids). Part 2. SNPs, Haplogroups and Haplotypes in the Y Charomosome of Chimpanzee and Humans. Advances in Anthropology, 2, 198-213.
[16] Mendez, F. L., Krahn, T., Schrack, B., Krahn, A.-M., Veeramah, K. R., Woerner, A. E. et al. (2013). An Аfrican Аmerican Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree. American Journal of Human Genetics, 92, 454-459.
[17] Poznik, G. D., Xue, Y., Mendez, F. L., Willems, T. F., Massaia, A., Wilson Sayres, M. A. et al. (2016). Punctuated Bursts in Human Male Demography Inferred from 1,244 Worldwide Y-Chromosome Sequences. Nature Genetics, 48, 593-599.
[18] Rozhanskii, I. L., & Klyosov, A. A. (2011). Mutation Rate Constants in DNA Genealogy (Y Chromosome). Advances in Anthropology, 1, 26-34.
[19] Zhivotovsky, L. A., Underhill, P. A., Cinnioglu, C., Kayser, M., Morar, B., Kivisild, T. et al. (2004). The Effective Mutation Rateat Y Chromosome Short Tandem Repeats, with Application Tohuman Population-Divergence Time. American Journal of Human Genetics, 74, 50-61.

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