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Thursday, June 11, 2015

New Genetic Markers for Bears Show that Ketchum Sample 26 - the Smeja Sample - is a BLACK BEAR



ABSTRACT

New genetic markers for bears, UltraConserved Elements (UCE), are compared to Ketchum Sample 26 – The Smeja Sample. A phylotree of S26 and four bear species: giant panda, black bear, brown bear, brown bear – ABC Islands, and polar bear clearly showed that S26 matched a black bear best based on its phylotree location. Sample 26 is a BLACK BEAR. The Ketchum conclusion, a human-primate hybrid, IS WRONG.  

INTRODUCTION

Thus far in our nDNA study of Sample 26 (S26) from “Novel North American hominins…” [1] we have searched the NCBI (GenBank) databases, five in number, and consistently found that black and polar bears were always the best matches [2]. Here we investigate how new genetic markers, ultraconserved elements (UCE) of four bear species, match S26. The species are giant panda – Ailuropoda melanoleuca, black bear – Ursus americanus, brown bear – Ursus arctos, and polar bear – Ursus maritimus. A fifth genetic group, brown bear – ABC, includes brown bears from the Admiralty, Baranof, and Chichagof Islands off southeast Alaska, where significant past hybridization of brown and polar bears has occurred [3]
          


“UCE are highly conserved short DNA sequences that are shared by different organisms and are particularly useful for phylogeny estimation from genome sequence data.”[3] These sequences, <700 bp each, were concatenated into single long sequences for each species in the construction of a phylotree (Fig. 2 below). We used them here to compare to the 2,726,786 bp S26 nDNA sequence [1] as before with BLAST™ and found the resulting phylotree to be an excellent discriminator for comparing S26 to the various bear species.
 
COMPUTATIONAL METHODS

A UCE sequence alignments text file was downloaded from the link in [3] (http://jhered.oxfordjournals.org/lookup/suppl/doi:10.1093/jhered/est133/-/DC1). This file was edited by removal of extraneous information to form a FASTA file of five sequences, one each from giant panda (3,985,224 bp), black bear (996,347 bp), brown bear (996,346 bp), brown bear – ABC Islands (996,346 bp), and polar bear (996,348 bp). The sequences were compared to S26 in its entirety with BLAST™, using the “Align two or more sequences” option limited to 100 hits per sequence and word size = 64. Other search parameters were defaults.
 

An Excel® file of hits was downloaded, from which average %IDj for each species j was computed from Excel® columns C (%ID) and D (length) as:
   



 (1)

 


where %IDji is the %ID for the i-th hit of species j, and Lji is the length (bp) of the i-th hit of species j. The sums run over all hits for each species. 
  

The BLAST(TM) “Distance tree of results” option produced the phylotree in Fig. 1, with distances based on pairwise comparisons (mutations).
 
RESULTS AND DISCUSSION

Equation (1) was used to calculate average %ID for each species vs. S26. Hit ranges were between 104 and 682 bp long, and scores were between 171 and 1227. Average %IDs for each species were: giant panda = 98.17, black bear = 99.25, brown bear = 99.26, brown bear – ABC = 99.26, polar bear = 99.23. This shows a clear separation of the panda from the four Ursus bears, but not enough difference between these to make a species match to S26. This is because UCE sequences were used in [3].


Fig. 1 shows a phylotree of the search results. Now we see clearly a best match of S26 to the black bear, as shown by the relative position of S26 among the five bears. Compare Fig. 1 to Fig. 3 from the original paper [3], shown as Fig. 2 here. The relationships among the known bear species are the same in both figures. Keep in mind, however, that the distances were calculated differently, so lengths of branches are not exactly the same or in the same ratios. But the topologies are the same, and S26 is closer to black bear than any other bear. 



In order to test the Ketchum claim that S26 is a human hybrid, we next compared the five bear sequences to the human reference genomic sequence with BLAST™, and selected the distance tree of results for each species.  Distances from human to any bear were far greater in these phylotrees, 100's x farther, compared to distances from S26 to any bear in Fig. 1. Human is a poor match to these bears, whereas S26 is an excellent match. Therefore, S26 is a bear, and not human-like.

 
  

CONCLUSIONS

As determined by phylotree position among the bears giant panda, black bear, brown bear, brown bear – ABC, and polar bear, Ketchum Sample 26 is a BLACK BEAR. This agrees with our previous work [2] and the results of three independent laboratory analyses [4]. Also to be noted is that there is no direct proven connection between S26 and the Smeja Sample, since the sample was collected weeks later. Consequently, what Justin Smeja shot may not be represented by this sample. However, what Melba Ketchum claims – a human-primate hybrid - IS based on this sample, and IS WRONG.


REFERENCES

[1]  See link at right under Sasquatch Genome Project.

[2]  See Paper 1 link at right and previous “Ketchum DNA Study” blogs.

[3]  Cronin, M. A. et al., “Molecular Phylogeny and SNP Variation of Polar Bears (Ursus maritimus), Brown Bears (U. arctos), and Black Bears (U. americanus) Derived from Genome Sequences, Journal of Heredity 2014:105(3), pp. 312–323.
 
[4]  See The “Tyler Huggins Report” under Pages at right and on this blog, November 26, 2014, Ketchum Sample 26, The Smeja Kill: Independent Lab Reports.”


Fig. 1.  Phylotree: S26 vs. UCE for 5 Bears






Fig. 1.  Phylotree from BLAST(TM) comparison of S26 to UCE of five bears, names added in bold.  




Fig. 2.  Phylotree from [3]


 
 
 
Fig. 2.  Taken directly from [3] unchanged.