molecular approaches to colonization and...
TRANSCRIPT
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Molecular Approaches to Colonization and
Population History in the North American Arctic
and
Jennifer Raff, Margarita Rzhetskaya, Justin Tackney, and Geoffrey Hayes
Dennis H. O’Rourke
University of Utah
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Mitochondrial DNA
http://io9.com/5605549/we-may-have-been-looking-at-the-wrong-dna-for-the-secrets-of-longevity
http://lslab.lscore.ucla.edu/Mitochondria/HVSI.htm
Fast-evolving
Maternally inherited
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Mitochondrial lineages in the Americas
Haplogroup
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Mitochondrial lineages in the Americas
Arctic-specific haplogroups
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Aleutian Islands
• 1000BP: Morphological transition (Hrdlička)
• Paleo-Aleuts Neo-Aleuts: Population replacement?
--but--
• Near archaeological continuity
• First archaeological evidence of human occupation 9-8,000 YBP
• Colonized east west
Chaluka
X X Kagamil
Shiprock x
X Port Moller
X Brooks River
Mink Island X
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Results
All samples date to well before Russian contact
(n=80).
The oldest sample in our data set is from
Chaluka midden with a date of cal. 3434 BP and a
two sigma range of cal. 3301-3594 BP.
All samples older than cal. 1000 BP are Paleo-
Aleuts from Chaluka midden.
Shortly after cal. 1000 BP Neo-Aleuts appear at
Chaluka midden and elsewhere.
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Haplogroup Distributions
Sites N Hap. A Hap. D No data
Kagamil 32 25% 75% 12
Ship Rock 12 17% 83% 0
Chaluka 36 48% 52% 7
Total 80 34% 66% 19
Groups
Paleo-Aleut 42 53% 47% 12
Neo-Aleut 38 19% 81% 7
Total 80 36% 64% 19
Time
Pre-1000 AD 11 73% 27% 4
Post-1000 AD 52 23% 77% 12
Total 63 32% 68% 16
Living Aleuts 198 28% 72%
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Which population is a
likely source for migrants
southeast to the Aleutian
chain?
Implications for Aleutian prehistory
Mink Island
Brooks River Area
X
Hot Springs Site
17% A
83% D
63% A
12% D
3% B
33% A
67% D
Pre-1000 BP
73% A
27% D
Post-1000 BP
23% A
77% D
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Haplogroup B in the Arctic?
Identified by HVSI sequencing, confirmed by 9bp deletion
Common among populations further south in the Americas and coastal
populations of southwest British Columbia (e.g., Bella Coola and Nuu-Chal-Nuth;
Ward et al. 1991)
The two individuals from Brooks river are the first Hg-B2 reported in pre-
contact northern North American populations
Merriwether et al. (1995) reported three modern Hg-B2 individuals from Old
Harbor on Kodiak Island, just across Shelikof Strait from Brooks River
area.
Our results reveal more genetic diversity in the upper peninsula than has
been seen previously in ancient Aleuts
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The Prehistory of the
North American Arctic
Use of aDNA data as
geographic and temporal
anchors in colonization
models
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• Generalized tool kit
• Seals, walrus, musk ox, caribou
• Lack dog sleds, snow houses, and bows and arrows
• Low population density
Paleo-Eskimo
(Dorset)
Pre-transition
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• kayaks, umiaks, and large whaling harpoons
• Whales, whales, whales!
• Supplemented with other marine and terrestrial mammals, fish
• Higher Population density
Neo-Eskimo
(Thule)
Post-transition
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Sadlermiut
•Historic population
(1902)
•Sod, stone & skin
houses
•No umiaks or kayaks
•Considered foreign by
surrounding Inuit
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Eastern Arctic
Dorset
• n = 2/3
• 100 % D
• 2260 ±50 BP 1216
±35BP
Thule
• n = 17/20
• 100 % A
• 1130 ±50BP 628 ±37BP
Sadlermiut
• n = 18/19
• 56 % A, 44% D
• 977 ±54 BP 682 ±42 BP
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Conclusions - Eastern Arctic
Thule = Inuit
Dorset ≠ Thule
• Genetic evidence for a population
‘replacement’ of Dorset by Thule
• Coincident with the observed archaeological
transition
Sadlermiut = Dorset + Thule • Remnant Dorset; subsequent admixture with Thule
• Evidence of contact between Thule and Dorset
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North American Arctic colonization history
Adapted from Figure 1, Gilbert et al. 2008
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Genetics of Arctic Populations
Near monomorphism for Haplogroup A2
• Reduced genetic variability
Geographic cline in Haplo-A2 subtypes
• A2a higher in west (nearly fixed in Aleuts)
• A2b higher in east
Inupiat populations characterized by Haplo-D4b, Aleuts by D2
Hypothesized population replacements in both Eastern and Western arctic
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We provide necessary sequences of early Thule in Alaska:
Figure 4,
Helgason et al.. 2006
Genetic Diversity and the Thule
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GeANS project
DNA extracted from saliva samples
mtDNA HVSI (15993-16390) and II (16483-524) was amplified and directly sequenced.
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A2 A2a A2b D2 D3 C Other
Haplogroups
Aleut
Chukchi
Siberian Eskimos
Kitikmeot Region
North Greenland
West Greenland
East Greenland
South Greenland
A2a=A2b
D4b
A2b>A2a
D4b
A2a>A2b
D2,D3
A2a
D2
??
Alaskan North Slope
Note: The size of each pie chart reflects sample size from the region.
A2a>A2b
D2,D4b
Saqqaq (Paleo-Eskimo)
Dorset (Paleo-Eskimo)
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Coalescence dates from North Slope
Haplogroup Date of Siberian
vs. Inuit
divergence
D4b1a2a1a1a 4,554 YBP (+/-
4554)
D2a 6,666 YBP (2699-
10629)
(4,554-6,666 YBP)
Inuit Siberian
Courtesy of J. Raff, 2013
TMRCA
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Genetic substructure: Is the North Slope a “population”?
Fst test : Significant (though small) Fst between Anaktuvuk Pass and Barrow.
A global test of differentiation failed to reject the null hypothesis
of non-differentiation within the sample (p=0.058)ktuvuk Pass
may be skewing results due to a) small sample size, b) different genetic composition.
Results – modern populations
Fst: 0.22
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Many maternal lineages are shared
between villages
Anaktuvuk Pass Point Hope
Point Lay
Kaktovik
Barrow
Nuiqsut
Wainwright
Interior Alaska
Kotzebue
--All but three of the shared lineages are found in Barrow.
--Anaktuvuk Pass only shares two lineages (with Point Hope and
Barrow)
.
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Paternal history
Male history can be traced through the Y-chromosome.
Male and female population histories for the North Slope
were very different. Most male lineages in the North
Slope are European in origin, while nearly all female
lineages are Inuit.
Inuit
Non-Inuit
Y-chromosome lineages
Inuit
Non-Inuit
mtDNA lineages
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Nuvuk at Pt. Barrow
Nuvuk
Nuvuk occupied from
>1000 BP –1936 AD; classic
Thule to modern Inupiat Eskimo
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2 Major Archaeological Components:
• Extensive Thule Cemetery – most dates
between 980-1300 AD
• From contact until 1940s, an historic village
Implies a nearly 1200 year occupation
Classic Thule to modern Inupiat Eskimo
The Nuvuk Site
Rapidly eroding coast-
line (~15-30m/yr)
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Results
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Results – cont.
139 modern samples
~45 ancient samples
The ancient samples from Barrow, AK had the genetic variants (haplotypes)
expected for a Neo-Eskimo (Thule) source population
Some haplotypes that had only been observed in the E. arctic have now been
found in Alaska; These results demonstrate a further shared ancestry
between all circumpolar populations
There are some haplotype differences between the ancient
Barrow samples and the modern North Slope populations;
showing that population change has occurred over the last
millennium
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Summary of North Slope DNA results (courtesy of J. Raff)
Nuvuk Modern
N 39 137
A2a 25.6% 56%
A2b 66.7% 36%
A2 root 2.6% 0.7%
D2a 0 2.2%
D4b 5.1% 0.7%
C 0 0.7%
So far: ancient haplotypes match
modern lineages of the region.
Presence of A2 root lineage
reinforces North Slope as
geographic origin of Thule.
(Nuvuk results – J. Tackney, unpubl.
Modern results – Hayes and Raff, unpubl.)
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aDNA and Population Diversity
PCA of regional haplogroups freqs in ancient and modern samples
Raff et al. 2011
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‘Goldilocks’ and
the Three Glacial Models
Flint paradigm - < late 1960s - Laurentide ice uniformly
reached edge of continental shelf in Eastern Canadian Arctic
Minimalist paradigm - < late 1980s – large coastal
stretches remained ice-free – based on undisturbed coastal
deposits
New paradigm - >1990s – S. Baffin
glaciated but N. uplands of Cumberland sound
ice free - Fiord glaciers reached
continental shelf, upland lakes frozen
Miller et al. QSR 2001
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Laurentide Ice Sheet from
Flint(?) paradigm –
Dyke et al. 2002
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Faunal Evidence for LGM Refugia
Grayling – Stamford & Taylor 2004
Mountain Sheep - Loehr, et al. 2006
Rock Ptarmigan – Holder, et al. 1999
Collard lemming – Federov & Stenseth 2002
Implication: NA LGM glaciers less
continuous and monolithic than
generally assumed
(Berendregt & Duk-Rodkin 2004; Catto, et al. 1996)
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Probable ice margin at 27-30 14C yrs BC – Dyke et al. QSR 2002
Location of MIS 3 radiocarbon dates
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Shrub tundra refugium – C. Beringia at LGM
Courtesy of Hoffecker 2013
Pre-LGM human
refugium?
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Lake and ocean cores
from former Beringian
landmass confirms
areas of ‘mesic tundra’
suitable for continuous
habitation throughout
the LGM
Hoffecker et al. 2014
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Upward Sun River – 11,500 bp
mtDNA
hg C1b
mtDNA
hg B2
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Proxies and migration
Obligate human pathogens or
Parasites can serve as markers
of human migration and global
movement.
JC Virus
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Proxies and migration
Distribution of human pathogens in the Americas only
consistent with ≥2 colonizations.
Genetic diversity in H. pylori indicates colonization
>12,000 years ago, and with
no population bottleneck.
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“Often [anthropologists] practice
selective vision, neglecting or rejecting
evidence to pursue preconceived
definitions: Names assume a magical
quality.”
With apologies to Owen K. Mason (2000)