Ketchum Sample 26 (Justin Smeja’s) Matches Literature Black Bear Data Best

ABSTRACT

Black bear (Ursus americanus) genomic scaffolds from Cahill et al. were converted to a stand-alone PC BLAST™ database, which was queried with the Ketchum et al. Sample 26 (Smeja sample) nDNA sequence. Comparisons to polar bear (Ursus maritimus), giant panda (Ailuropoda melanoleuca), human, and other primates, showed conclusively that Sample 26 is a black bear. Human and other primates were much poorer matches than any of the bears. Sample 26 is a black bear, not a human-primate hybrid as claimed by Ketchum et al.


INTRODUCTION

Since the 2013 paper of Ketchum et al., “Novel North American Hominins…..” [1] was published we have attempted to verify the claim made therein:

“…the species (sasquatch) possesses a novel mosaic pattern of nuclear DNA comprising novel sequences that are related to primates interspersed with sequences that are closely homologous to humans.” 

The Ketchum paper included nDNA sequences for three samples, 26, 31, and 140. Our previous attempts [2] all resulted in the conclusion that Sample 26 (S26) was a bear, recently found to be a black bear. Here we compare the most comprehensive black bear data available to us so far [3] to S26, with the same conclusion.

Black bear nDNA data are relatively sparse in the NCBI databases, especially when compared to the whole genomes of the polar bear and the giant panda, both of which are endangered and of greater conservation interest. The only useful and significant black bear sequence lengths were found in the” Expressed sequence tags” and “RNA reference sequences” databases as previously reported.[4,5] Other useful black bear sequences, ultraconserved elements (UCE), were obtained from the literature [6].

This blog compares S26 to the black bear data of Cahill et al. in reference [3], which was the result of mapping black bear DNA to the 238 longest scaffolds (1Mb or greater in length) in the polar bear reference genome [7]. Coverage was 11.6 X. Their filtering reduced the error rate of each base to less than 1/1000 [3].

COMPUTATIONAL METHODS


S26 nDNA sequence was downloaded from the Sasquatch Genome Project website (see link at right). The black bear file [3], in FASTA format, was downloaded as a 600 Mb compressed gzip file, which was inflated to 2.1 Gb and converted to a stand-alone BLAST™ database for PC, using NCBI software (http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download). Each database entry was one of the 238 scaffolds mentioned above. The 2.7 Mb S26 nDNA sequence from [1] was queried against this database with PC BLAST™ software (above link). The hit table (converted from a text file to EXCEL®) was sorted by score, and the top 50 hits were examined and compared to the corresponding (in sequence range) best polar bear and giant panda matches to S26 from the NCBI “Reference genomic sequences database” (complete genomes). Additionally, the best human and other primate matches to S26 from the Reference genomic sequences database over the same sequence ranges were compared to the bear hits. All %IDs were computed based on mismatches only, excluding “N” designations, for unspecified bases, and gaps. This permitted the conservative base assignment approach of [3] to be compared consistently to the other matching sequences in our %ID comparisons.

RESULTS AND DISCUSSION

Table 1 shows partial results of our sequence comparisons. Within each grouping separated by a blank row, are, top to bottom, each in single row:

S26 match to black bear data in [3]

Best S26 match to polar bear

Best S26 match to giant panda

Best S26 match to human

Best S26 match to other primates (ex-human).

This table presents only the top 15 hits by score. When the top 50 hits were compared, 30 matched black bear best, eight matched polar bear best, 11 were tied between these two bears, and one was tied between polar bear and giant panda. Overall, black bear was the best species match to S26.

All the human and other primate hits were significantly poorer matches than any bear matches. For conserved genes with the highest scores, we found previously [2] that a few percentage points %ID can be the difference between phylogenetic orders (e.g. Carnivora (Ursidae family) vs. Primata), and such was the case here.


CONCLUSION


S26 is a black bear, consistent with our previous conclusions. Human and all primates don’t even come close to matching S26. The Ketchum et al. conclusion above IS WRONG. There are no good human or primate matches to S26 among the 50 highest scores.

Incomplete genomes can be useful in forensic investigations if the scaffolds are sufficiently long and well selected, coverage is good, and base assignment is conservative, as was the case here [3]. The sequence matches here were approximately twice as long as our previous best black bear matches

Beginning with this blog, S26 will no longer be referred to here as “The Smeja Kill” as it does not fit the description of what Justin Smeja (an experienced bear hunter) said he killed. Also, since this sample was collected five weeks later as a hand-sized patch of fur and flesh found under two feet of snow, it therefore has no verifiable connection to the actual “Smeja Kill.” Three other independent laboratory analyses found S26 to be a black bear [8]. Our computational analysis of the original Ketchum nDNA sequence is in agreement with these independent laboratory analyses and our own previous interpretations of the Ketchum et al. sequence [2].

ACKNOWLEDGEMENT

We are grateful to James Cahill and Prof. Beth Shapiro of the Department of Ecology and Evolutionary Biology, UC-Santa Cruz, for making the black bear data from [3] available for this study and also to the Sasquatch Genome Project for making the S26 nDNA sequence available on their website.


CONFLICT OF INTEREST

The author declares no conflict of interest.


REFERENCES

[1] See Sasquatch Genome Project link at right.

[2] See Paper 1 links at right and blogs under “Ketchum DNA Study” tab above.

[3] Cahill J A, et al., Genomic Evidence for Island Population Conversion Resolves Conflicting Theories of Polar Bear Evolution, PLOS Genetics, March 14, 2013, DOI: 10.1371/journal.pgen.1003345. 

[4] See on this blog, May 22, 2015, “New Black Bear Data Show Ketchum Sample 26 (the Smeja Kill) is a Bear.”

[5] See on this blog, June 4, 2015, “RNA Data Show Ketchum Sample 26 - the Smeja Kill - is a Black Bear.” 

[6] See on this blog, June 11, 2015, “New Genetic Markers for Bears Show that Ketchum Sample 26 - the Smeja Sample - is a BLACK BEAR” 

[7] Li B, Zhang G, Willerslev E, Wang J, Wang J (2011) Genomic data from the Polar Bear (Ursus maritimus). Available from: http://dx.doi.org/10.5524/100008. GigaScience.

[8] 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.”

  

Table 1. Top 15 Black Bear Hits and

Comparisons

Accession	%ID	Length	Start	End	Species
scaffold152	99.58	1681	1655920	1657569	black bear
NW_007907230.1	99.88	1679	1655920	1657569	polar bear
NW_003217478.1	99.59	1688	1655920	1657569	giant panda
NM_001039618.2	95.69	1695	1655921	1657569	human
XM_003254601.2	95.68	1690	1655921	1657569	northern white-
					cheecked gibbon
scaffold156	99.92	1279*	189026	190304	black bear
NW_007929448.1	100.00	2139	189028	191141	polar bear
NW_003218202.1	100.00	2141	189026	191141	giant panda
BC038508.1	94.68	2142	189026	191141	human
XM_003951836.1	94.54	2142	189026	191141	chimpanzee
scaffold46	99.34	1359	759948	761288	black bear
NW_007907078.1	99.93	1359	759948	761288	polar bear
NW_003217489.1	99.49	1364	759948	761288	giant panda
NM_001278163.1	97.42	1354	759948	761288	human
XM_003254384.2	97.49	1353	759948	761288	northern white-
					cheecked gibbon
scaffold46	100.00	1237	690618	691854	black bear
NW_007907078.1	99.92	1237	690618	691854	polar bear
NW_003217489.1	99.35	1237	690618	691854	giant panda
Z83001.1	98.79	1239	690618	691855	human
NC_006478.3|	98.87	1239	690618	691855	chimpanzee
scaffold180	99.84	1243	326857	328097	black bear
NW_007907318.1	99.69	1299	326857	328153	polar bear
NW_003217713.1	99.00	1300	326857	328153	giant panda
NG_012881.1	95.18	1308	326857	328153	human
NC_018435.1	95.03	1308	326857	328153	gorilla

scaffold180	99.84	1244	349476	350698	black bear
NW_007907318.1	99.92	1244	349476	350698	polar bear
NW_003217713.1	99.36	1243	349476	350698	giant panda
NC_000011.9	94.28	1241	349476	350700	human
NW_002885339.1	94.18	1237	349476	350697	orangutan
scaffold31	99.82	1112	2257274	2258385	black bear
NW_007907111.1	99.73	1112	2257274	2258385	polar bear
NW_003218653.1	99.28	1112	2257274	2258385	giant panda
NC_000011.9	94.96	1112	2257274	2258385	human
NC_013906.1	95.23	1112	2257274	2258385	white-tufted-
					ear marmoset
scaffold24	99.66	1174	1835440	1836608	black bear
NW_007907090.1	99.66	1174	1835440	1836608	polar bear
NW_003218271.1	99.06	1174	1835440	1836608	giant panda
NW_004078072.1	94.47	1175	1835440	1836608	human
XM_004052006.1	94.38	1175	1835440	1836608	gorilla
scaffold46	100.00	1115	673215	674328	black bear
NW_007907078.1	100.00	1115	673215	674328	polar bear
NW_003217489.1	99.55	1114	673215	674328	giant panda
AC093262.2	98.30	1117	673215	674328	human
NC_022285.1	98.66	1118	673215	674327	crab-eating
					macaque
scaffold31	100.00	1140	2258573	2259712	black bear
NW_003218653.1	99.57	1173	2258573	2259743	polar bear
NW_007907111.1	99.65	1157	2258573	2259729	giant panda
NG_027813.1	96.37	1156	2258575	2259729	human
DQ977225.1	96.45	1156	2258575	2259729	pygmy
					chimpanzee
scaffold137	99.92	1260	1624428	1625637	black bear
NW_007907229.1	99.44	1260	1624428	1625637	polar bear
NW_003218719.1	99.13	1260	1624428	1625637	giant panda
XM_005273811.1	95.71	1374	1624428	1625746	human
NW_010810287.1	95.39	1259	1624428	1625637	golden snub-
					nosed monkey
scaffold93	99.83	1151	1508093	1509231	black bear
NW_007907285.1	100.00	1151	1508093	1509231	polar bear
NW_003217421.1	99.04	1151	1508093	1509231	giant panda
AP000609.5	94.59	1147	1508092	1509231	human
XM_003808137.1	94.77	1147	1508090	1509231	chimpanzee
scaffold46	99.91	1141	710570	711698	black bear
NW_007907078.1|	99.91	1141	710570	711698	polar bear
NW_003217489.1	98.16	1140	710570	711698	giant panda
AC_000143.1	95.90	1146	710568	711698	human
NW_002885202.1	96.06	1142	710570	711698	orangutan
scaffold46	99.91	1080	630428	631502	black bear
NW_007907078.1	99.07	1079	630428	631501	polar bear
NW_003218059.1	98.24	1082	630426	631502	giant panda
AC_000143.1	94.38	1085	630427	631501	human
NC_019830.1	94.37	1083	630428	631501	northern white-
					cheecked gibbon
scaffold180	100.00	1083	321092	322174	black bear
NW_007907318.1	99.82	1083	321092	322174	polar bear
NW_003217713.1	99.35	1083	321092	322174	giant panda
NG_012881.1	95.87	1090	321092	322174	human
NC_018435.1	96.24	1091	321092	322174	gorilla

Top 15 hits only – top 50 were compared in text. 

%ID is based on mismatches only.  Length is in bp.  Start and End sequence positions refer to S26 sequence.

*   Note shorter sequence length.