Molecular Approaches to Colonization and...

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

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

Mitochondrial lineages in the Americas

Haplogroup

Mitochondrial lineages in the Americas

Arctic-specific haplogroups

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

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.

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%

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

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

The Prehistory of the

North American Arctic

Use of aDNA data as

geographic and temporal

anchors in colonization

models

• 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

• 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

Sadlermiut

•Historic population

(1902)

•Sod, stone & skin

houses

•No umiaks or kayaks

•Considered foreign by

surrounding Inuit

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

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

North American Arctic colonization history

Adapted from Figure 1, Gilbert et al. 2008

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

We provide necessary sequences of early Thule in Alaska:

Figure 4,

Helgason et al.. 2006

Genetic Diversity and the Thule

GeANS project

DNA extracted from saliva samples

mtDNA HVSI (15993-16390) and II (16483-524) was amplified and directly sequenced.

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)

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

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

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)

.

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

Nuvuk at Pt. Barrow

Nuvuk

Nuvuk occupied from

>1000 BP –1936 AD; classic

Thule to modern Inupiat Eskimo

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)

Results

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

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.)

aDNA and Population Diversity

PCA of regional haplogroups freqs in ancient and modern samples

Raff et al. 2011

‘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

Laurentide Ice Sheet from

Flint(?) paradigm –

Dyke et al. 2002

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)

Probable ice margin at 27-30 14C yrs BC – Dyke et al. QSR 2002

Location of MIS 3 radiocarbon dates

Shrub tundra refugium – C. Beringia at LGM

Courtesy of Hoffecker 2013

Pre-LGM human

refugium?

Lake and ocean cores

from former Beringian

landmass confirms

areas of ‘mesic tundra’

suitable for continuous

habitation throughout

the LGM

Hoffecker et al. 2014

Upward Sun River – 11,500 bp

mtDNA

hg C1b

mtDNA

hg B2

Proxies and migration

Obligate human pathogens or

Parasites can serve as markers

of human migration and global

movement.

JC Virus

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.

“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)