GENETIC ANALYSIS OF THE TOMMY
AND MINE CANYON SITES IN
CONTEXT OF SOUTHWEST
POPULATIONS
Meradeth Snow, Kathy Durand, David Glenn Smith
mtDNA
Briefly…
• 5 Native American haplogroups:
– A, B, C, D, and X
• Defined by mutations identified by:
– RFLP analysis
– Direct sequencing
Previous aDNA Research in
the Southwest
• Shearin et al. 1989
• Horai et al. 1991
– hap B
• O’Rourke et al. 1996—11 samples
– 3 hap B, 1 hap A, 1 hap C
– 2 other, and 4 N or D
• Carlyle, 2000 & 2003—27 samples
– 26 hap B, 3 hap A, 5 hap C, and no D
– 4 other
Previous aDNA Research in
the Southwest
• Regional continuity of the general
Southwest mtDNA pattern:
– high haplogroup B
– low to moderate levels of A and C
– no haplogroup D
• Maintained in modern Pueblo groups
such as the Zuni and Jemez.
(Lorenz and Smith 1996; Kaestle and Smith 2001)
Methods
• Extractions carried out in the aDNA
Molecular Anthropology Lab at UC Davis.
– Bones and teeth both yielded DNA
• RFLP analysis to determine haplogroup.
• Sequencing results obtained.
RFLP Results
Haplogroup
Haplogroup
Haplogroup
Haplogroup Total
A
B
C
D
Tommy
Site
1 (5%)
14 (66%)
3 (14%)
3 (14%)
21
Mine
Canyon
7 (58%)
4 (33%)
1 (8%)
0
12
Total
8 (22%) 18 (49%)
4 (11%)
3 (8%)
37
• Sites were distinct at the 0. 00005 level.
RFLP Results
TS
MC
Anasazi
Apache
Jemez
MC
0.0000
Anasazi
0.0137
Apache
0.0000 0.1412
0.0000
Jemez
0.0017
0.0000
0.0004
0.0000
Navajo
0.0000 0.2545
0.0000
0.0000 0.0000
Navajo Zuni
0.0000
Zuni
0.0776
0.0011
0.8249
0.0000 0.0057
0.0000
Fremont
0.1941
0.0000
0.0114
0.0000 0.0619
0.0000 0.0315
RFLP Results
0.05
MC
Fremont
Anasazi
0.00
Zuni
Apache
Jemez
-0.05
c[,2]
TS
Navajo
-0.3
-0.2
-0.1
0.0
c[,1]
0.1
0.2
0.3
Preliminary Sequencing
Results
• Mine Canyon Haplogroup A samples
• Possible Athapaskan connection?
– mutations at specific sites:
• nsp 16331
• nsp 16192
• All Mine Canyon hap A samples do
not have these mutations
Preliminary Sequencing
Results
• Did have three other mutations:
– nps 16257 (C→T)
– nps 16263 (T→A)
– nps 16360 (C→T)
• 4 Zuni hap A samples have these
same unique mutations.
(Kemp, 2006)
Discussion
• Not all sites maintain the general
Southwest mtDNA pattern.
Discussion
• Regional variability may be due to:
– Sampling error…
• Mine Canyon—7 out of 12
• Carlyle’s data—3 out of 38
– Drift (chance)
• Founder’s effect or
• Reduction in population size
Discussion
• Haplogroup D
– Often absent in the Southwest.
– Was present at the Tommy Site, and
possibly other sites.
– Low frequency may have influenced
previous identification.
Discussion
• Haplogroup A
– RFLP frequency similarities between
the Mine Canyon site and the
Athapascans.
• High frequency of hap A
– Sequences demonstrate cultural
continuity.
• Zuni hap A’s
Future Reseach
• Further analysis of the sequence
data for the remainder of the
samples.
• HVII sequence analysis, particularly
of the hap A samples.
• Sex identification of unidentifiable
samples.
• Correlation with the remainder of the
analyses presented here.
Acknowledgments
• Many thanks to the other students,
previous students, and employees at
the UC Davis MAL: Wendy Garnica,
Debbie George, Sree Kathaswamy,
Brian Kemp, Jessica Satkoski, Kari
Schroeder, Monalyn Umali, and
Venkat. Thanks!