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Wednesday, January 18, 2017

Unusual Primate Mutations in Some Ketchum mtDNA Samples

“Shouldn’t we not throw the baby out with the bathwater?…Is there anything we can salvage from the Ketchum study?”     A Facebook Post

In my past work I have tried to treat each Ketchum et al. DNA sequence independently, and not to generalize without evidence.  Sometimes a tentative overall conclusion is suggested.  Here we look at some mtDNA sequences with common rare (human) mutations which are much more prevalent in other primates.  From everything I have learned, these several samples hold the most promise for actually originating from an unknown human-like primate.  This is a preliminary report, mostly just observations and suggestions for further study. Your comments are especially welcome here.
Comparisons between mtDNA extra mutations (i.e. those not found in the nearest haplogroup) revealed some unlikely coincidences.  Table 1 shows these.  Sample 26 has been shown to be a black bear [2a,b] from its nuclear DNA sequence taken from the original Ketchum paper [1], but the mtDNA results were much closer to human, though outside the normal range of number of extra mutations. [3]  Although the Ketchum et al. conclusion was that sasquatch is a hybrid of an unknown primate male and a modern human female, human mtDNA in this sample has been widely attributed to contamination. [4, 7]   ES-2 was discovered unlabeled below and to the right of other entries in the Ketchum Supplementary Data 2 and is not listed in the sample Table 1 there [1].  Sample 24 failed to produce human Amel X and Y STRs and had a very low 63% of 2.5 M human SNPs. Samples 29 and 138 are not included in any nDNA analyses in the Ketchum paper. Sample 28 appears in Table 5 of  ref. [1], where it shows human STRs in all but one locus (D3S1358) of sixteen total microsatellite loci.  It also matched nine of ten human SNP sites, with a heteroplasmic mutation at the tenth (478RHC) on the MC1R gene (Table 6, ref. [1]).  However, this sample failed to sequence at Amel X and at AmelY exons 1, 3, and 8, while showing human sequences at exons 2 and 4/5 (Table 4, ref. [1]).  Overall Sample 28 is the most human-like of those samples which were put through all of these nDNA tests.
Referring to Table 1, samples S1 and ES-2 have identical mtDNA sequences and the same two extra mutations.  C152T is common in humans, but G7332c is not found among the nearly 20,000 human mtDNA sequences in the Nucleotide database.  Further, it was not found in any other primates, though G7332A had a few examples.  Since we know nothing of the provenance of ES-2 and because it is identical to S1, it would be of great interest if Ketchum et al. would identify this sample.  However, the most significant similarity among the samples in Table 1 is the occurrence of 7852A, 9083C, and 13209T in samples S24, S26 (less 7852A), S28, S29, and S138.   These mutations are rare in both the NCBI Nucleotide database and the Phylotree of mtDNA mutations [6].  In fact, none of the nearly 20,000 complete human mtDNA genomes in the database have more than one of these mutations, i.e. none have two or three.  These five samples were collected by different teams in three widely separated locations, CA, NM, and BC.   Ketchum, et al.[1] maintain that all sample collectors and laboratory personnel were excluded from possible contamination based on their individual mtDNA profiles. 

Fig. 1 shows percentages of each primate group possessing each of these rare human mutations.  Percentages are based on all database entries (number in parentheses) for each group in GenBank(R) - Nucleotide database, without regard for species duplicates.    The groups collectively include all living primates: chimpanzees (two species), gorilla (several subspecies), orangutan (two species),
gibbons, tarsiers, Old World (OW) monkeys, New World (NW) monkeys, lemurs, Lorisiformes (loris’s and galagos), and Chiromyiformes (aye-ayes).  None of these extra mutations occurred in any Neanderthal (9 database examples), Heidelberg (1), or Denisovan (2) sequences, and are therefore not plotted in Fig. 1.  However, these small numbers of database examples may not be representative of these populations.   Full taxonomy of these families is found in ref. [5].that these three mutations, plus C9195T, are much more common in nonhuman primates, increasing generally with increasing taxonomic/genetic distance from human [5].  C6571T was only found in Old World monkeys.  C3626T was not found in other primates. 

Nothing definite can be concluded from these limited data, especially when considering the relatively low number of database entries for some of the primate families in Fig. 1.  Some intriguing questions might be explored further by collection of more DNA samples from the same geographical areas of CA, NM, and BC, along with photographic or video documentation:

1.  Could S26 (the black bear) be contaminated with sasquatch mtDNA?  In which case, it might be the result of a fight between bears over a sasquatch carcass. [7]

2.  Why doe
s S26 have so many (16) extra mutations? (so many that a haplogroup cannot be uniquely determined). [3] Phylotrees produced by two different methods did not agree. [4]
3.  Could S24, S28, S29, and S138 actually be sasquatch samples with a vestige of nonhuman primate mutations, either through parallel or reverse evolution?  The random occurrence of three rare mutations (7852A, 9083C, and 13209T) in all of these samples is a statistically improbable
coincidence. [See NOTE]  They must be related somehow.  Importantly, all four samples differ by only a few, mostly heteroplasmic, mutations.  A common human contamination is unlikely, given the rarity of these mutations in the human genome (Table 1, Fig. 1), especially in combination.  Even two human contaminants with these combined mutations seem unlikely (no GenBank(R) sequences had even two of these mutations).   Even more remarkable are the identical sequences of S29 and S138, which have in addition to these mutations three additional rare heteroplasmic mutations (C3626Y, C6571Y, and C9195Y) in common.  Sequencing errors would not likely be at the same three positions in two independent samples.  Both of these samples are from British Columbia and were collected by the same people (ref. 1,Table 1), whose mtDNA was found not to be in these samples [1].   These two samples may be from a single sasquatch or closely related individuals.

I openly encourage more field work and laboratory analysis of samples from these regions of OK, CA, NM, and BC. 

The occurrences of 7852A, 9083C, and 13209T are 27, 20, and 7 respectively in 19988 human
database entries.  The probability of all three occurring in the same individual is:

88)*(7/19988) = 4.73 x 10 exp -10.

The probability of these three mutations occurring in any four randomly selected individuals is:
(4.73 x 10 exp -10) exp 4 = 5.02 x 10 exp -38.


[1]  Ketchum, M. S. et al.,  Novel North American Hominins: Next Generation Sequencing of
Three Whole Genomes and Associated Studies. DeNovo, 2013, 1:1, Online only:
[2a]  Hart, H. V.,  Methodology and New Metrics for Distinguishing Related Species from
Incomplete nuDNA.,  Paper 1 at right (and related blogs)
[2b]  Hart, H. V., Not Finding Bigfoot in DNA.  Journal of Cryptozoology 4: 39-51.
[3]  Hart, H. V.,  “But the mtDNA Sequences are all Human…”  Really?,  Paper 2 at right:
[4]  Hart, H. V., More Inconsistencies and Evidence for Contamination in Ketchum et al.
Supplementary Figures, June 17, 2016, this blogsite.

[5]  National Center for Biotechnology,
[6]  van Oven,  M., Revision of the mtDNA Tree and Corresponding Haplogroup Nomenclature. Proc. Natl. Acad. Sci. USA, 2010, 107(11), E38-E39.
[7]  Hart, H. V., Ketchum Sample 26, The Smeja Kill: Independent Lab Reports, November
26, 2014, this blogsite.


FIG. 1

Numbers in parentheses for each group are the number of database entries in GenBank(R), which include duplicate entries for some species.