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Thursday, June 18, 2015

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.