the peopling of eurasia and the delayed expansion...
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The peopling of Eurasia and the
delayed expansion hypothesis
Chad Huff
The peopling of Eurasia
Disotell TR 1999
The delayed-expansion hypothesis
~70-140 thousand years ago
~30-60 thousand years ago
Archaic admixture
One 100 kb region on Chr12 (ENr123) sequenced in 814 individuals from 12 populations.
Datasets 250,000 SNPs genotyped in 850 individuals from 40 populations
Xing et al., 2010. Genome Biology. “Sequence data”
Xing et al., 2010. Genome Research. “Microarray data”
Evidence for Eurasian bottleneck(s): Mitochondrial Mismatch Distributions
Evidence for Eurasian bottleneck(s): Site frequency spectra
Evidence for Eurasian bottleneck(s): Site frequency spectra from sequence data
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0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
Num
ber o
f pol
ymor
phic
site
s
Allele frequency
Africa
Expected
Observed
0 50
100 150 200 250 300 350
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
Num
ber o
f pol
ymor
phic
site
s
Allele frequency
India
Expected
Observed
0 50
100 150 200 250 300 350 400
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
Num
ber o
f pol
ymor
phic
site
s
Allele frequency
Europe
Expected
Observed
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300
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
Num
ber o
f pol
ymor
phic
site
s
Allele frequency
East Asia
Expected
Observed
How large was the Eurasian bottleneck?
Microarray data • Average heterozygosity within Africa: 0.91 • Average heterozygosity immediately outside of Africa: 0.82
With a one generation bottleneck:
H1= ( 1 - 1/2N ) H0
H1=0.82, H0=0.91
Solving for N:
N = 5
This suggests a VERY small population founded Eurasia
With a delayed expansion, the founding population size of Eurasia could have
been much larger
Africa
East Asia
Europe
India
To test the delayed expansion hypothesis, we estimated the timing of out of Africa and the timing of the Eurasian separation. Is the out of Africa event significantly older than the Eurasian separation?
Timing of out of Africa
Timing of Eurasian separation
Inferring demographic history with dadi
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500
600
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 Num
ber
of p
olym
orph
ic s
ites
Allele frequency
Africa
Expected
Observed
0
50
100
150
200
250
300
350
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 Num
ber
of p
olym
orph
ic s
ites
Allele frequency
India
Expected
Observed
0 50
100 150 200 250 300 350 400
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 Num
ber
of p
olym
orph
ic s
ites
Allele frequency
Europe
Expected
Observed
0
50
100
150
200
250
300
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 Num
ber
of p
olym
orph
ic s
ites
Allele frequency
East Asia
Expected
Observed
Site frequency spectra (sequence data) Model of demographic history dadi inputs
dadi output
maximum likelihood estimates for all parameters specified in the model
The timing of the peopling of Eurasia
The timing of the peopling of Eurasia
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40
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160
Out of Africa Eurasian Separation
(kya)
EastAsia Europe India EastAsia India Europe
How large was the
bottleneck?
0
20
40
60
80
100
120
140
160
Out of Africa Eurasian Separation
(kya)
EastAsia Europe India EastAsia India Europe
N=12000
t = 60,000 years
or
t = 2400 generations
How large was the Eurasian bottleneck?
Microarray data • Average heterozygosity within Africa: 0.91 • Average heterozygosity immediately outside of Africa: 0.82
With a 2400 generation bottleneck and with
N=12000:
H1= ( 1 - 1/2N )2400 H0
H0=0.91, N=12000
Solving for H1:
H1 = 0.82, which equals our observed H1
The delayed-expansion hypothesis
~100 thousand years ago
~40 thousand years ago
Archaic admixture
N~12,000
Evidence for a single Eurasian bottleneck:
Shared history of genetic drift
Neighbor joining tree with microarray data