A new, clade-specific, mutation rate for I-Y33765 based on a ten generation English pedigree

Two English men in the I-Y33765 clade whose Y-chromosomes are separated by ten generations have FTDNA Big Y-700 results.  They are 4^th cousins and their direct-line male patriarch, William Clement, was born in 1801 and baptised 12^th January 1802 at St Andrew, Chew Magna, Somerset, England.  These men have identical results when tested for 111 Short Tandem Repeat (STR) markers.  By comparing their Big Y-700 analyses, their most recent shared mutation downstream of I-Y33765 is I-FT314945 (equivalent level to I-BZ4354) for which the FTDNA Discover algorithm gives a mean formation date of 1700CE. 

According to their documented pedigree the ten generations that separate the two men represent a period of 328y which indicates an average generation time of 32.8y.  Interpretation of their vcf file, Y-chromosome sequence information, has identified five SNPs that form during the pedigree.  Of these mutations three are located within CombBED regions of the Y-chromosome and each of these are recorded with >2 reads and a read quality >90% (see Table1).  None of the SNPs are associated with nucleotide insertions or deletions (INDELS).  As a consequence of meeting these several criteria it is reasonable to use these three high-confidence SNPs to obtain an observed mutation rate.  In this way, during the period recorded in the pedigree we can predict one mutation every 109.3y (328y/3SNPs).   This directly observed mutation rate k can be used to calculate the base substitution rate constant µ as follows:                                          

In 2009 next generation sequencing (NGS) was used by Xue et al. to estimate the Y-chromosome mutation rate in a 13 generation Chinese pedigree belonging to Haplogroup O3a.  Their pedigree contained four SNP mutations and using these they calculated a mutation rate of 1.0*10^-9mutations per nucleotide per year.  The scale and character of our English pedigree, and of our estimated base substitution rate, appear to be similar totheir findings.  Mutation rates that have been published based on pedigrees tend to be slightly faster than evolutionary rates based on ancient DNA or other prehistoric samples (Balanovsky, 2017).  This seems to be the case with the estimated mutation rate for our English pedigree of Y33765.

There is very close agreement between the 109.3y rate obtained using this pedigree of two English men and that of 109.5y that I reported in 2021, which was obtained using a 19 generation pedigree of two Swedish men who were also derived (+) for I-Y33765.  Assuming that the MRCA of these two descendant genealogies lived circa 400CE then some 2600y separate the documented births of the named founders in England and Sweden.  The Swedish pedigree had a slightly longer average generation time of 34.6y.     

Table 1: Single Nucleotide Polymorphisms (SNPs) within the pedigree of two male descendants of William Clement (1801-1882). Based on the documented pedigree of these men their Y-chromosomes are separated by ten generations equivalent to 328y.  The position (within combBED region), reads (greater than 2), quality and absence of INDELS, of the three SNPs shown in red are criteria that together ensure these are suitable for use in the estimation of the pedigree specific SNP mutation rate.
 

References

Balanovsky, O (2017) Toward a consensus on SNP and STR mutation rates on the human Y-chromosome, Human Genetics, 136, 575-590

Xue, Y., Wang, Q., Long, Q., Ng, BL., Swerdlow, H., Burton, J., Skuce, C., Taylor, R., Abdellah, Z., Zhao, Y., Macarthur, DG., Quail, MA., Carter, NP., Yang, H. (2009) Human Y chromosome base-substitution mutation rate measured by direct sequencing in a Deep-rooting pedigree. Current Biology 19, 1453–1457

Latest draft chart for the I-Y33765 clade of I-Y4252. This incorporates the results of a FTDNA BigY700 test, completed 16 August 2023, for Clement IN128261.

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