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Wednesday, November 26, 2014

Ketchum Sample 35: The Arizona Toenail

The brief report below “The First Mitochondrial DNA Evidence for the Existence of a New Hominid” was recently brought to my attention.  The subject of the report is a toenail sample that was part of the Ketchum study (Sample 35).   Unfortunately, the alleged author, Richard Stubstad has passed away.  I would certainly have tried to resolve the issues with him directly.  Efforts to get clarification through members of the AZCRO (Arizona Cryptozoological Research Organization), http://www.azcro.net/, which submitted Sample 35, have not produced a response, so I went ahead with my interpretation.

1.  Checking the patent (EP1373558A1) for the specific cytochrome b primers used (MCB 398/MCB 869) and verifying by alignments of forward and reverse primer with the entire human mtDNA sequence, the amplicon should be 446 bp long, NOT 360 bp long as implied in the figure, which says “(out of 360)”.  This indicates mispriming, due to contamination or degradation.  The data in the figure are therefore not positively tied to cyt b or, in fact, even to hominids.

2.  If the basis of the report is the Ketchum Sample 35 mtDNA sequence from this toenail (expressed as mutations from rCRS in her Supp. Data 2), then the following results, notwithstanding 1.  above, are incorrect:

            a.  The statement in the report “The 2 mtDNA pairs that the nail owner consistently differs from humans….”(mutations)  is an incorrect result.  Sample 35 aligns 100%ID (no mutations) with 13,185 GenBank human sequences over the range of the specified cyt b primers, rCRS positions 15,169-15,614 on the human mtDNA molecule.  It aligns with one mutation over an addition 6,797 database sequences.    Thus, the sample aligns better than 2 mutations with 19, 982 humans in the database.  It is human.

            b.  Neanderthal aligns with eight mutations (“consistently differing pairs”) from Sample 35 over the 446 bp cyt b region, NOT the “4” claimed in the report.  Were it not for 1. and 2.a., however, this would strengthen the report’s conclusion that the sample is not Neanderthal; rather, it is another incorrect result.

            c.   A random selection of 18 database entries with “2” mutations from S35 showed no consistent pattern of mutations, although we do not know if this set was representative.

3.  If the basis of the report is a separate cytochrome b (only) sequencing, then :

a.  the results conflict with the full mtDNA sequence in Supp. Data 2 of the Ketchum paper and the results in  2. above.

b.  The amplicon length, 360 bp, still does not match the stated primers, which give a 446 bp amplicon.

Primarily because of 2.a. but also buttressed by 1.,  2.b., and 2.c. above, it cannot be concluded that this toenail is from a ”new hominid” as claimed in the report “The First Mitochondrial DNA Evidence for the Existence of a New Hominid”.   The toenail is human.  The analysis in the report is incorrect based on the NCBI database contents as of 11-16-14.  The reported amplicon length (360 bp) does not correspond to the specified primer alignments, which produce a 446 bp human amplicon.

Finally, due to the paucity of Neanderthal mtDNA sequences (only 9), any statistical argument is always of questionable validity if extrapolated to the whole Neanderthal population.

BLAST™ search parameters and output results will be provided on request.

Anyone with additional information on the subject report, please contact me on Facebook.