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The Time and Place of European Gene Flow into Ashkenazi Jews

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1 The Time and Place of European Gene Flow into Ashkenazi Jews
Shai Carmi The Hebrew University of Jerusalem 2016 Joint work with Itsik Pe’er, James Xue (Columbia University)

2 Ashkenazi History: Known
Ca. 1000: Small communities in Northern France, Rhineland Migration east Expansion Migration to US and Israel

3 Ashkenazi History: Genetics
Origin? Middle-Eastern/European Relation to other Jews? Close to Sephardi Jews Founder event? Effective size: hundreds Time: ≈25-35 generations ago European gene flow: How much? ≈50-60% When? Where?

4 The Geographic Origin of Polish Jews
“Most of these theories … are myths or speculation … based on some vague or misunderstood references. … It will probably be impossible to say definitely where the ... Jews in Poland … came from.” B. Weinryb, The Jews of Poland, 1972

5 The Geographic Origin of Polish Jews
“Most of these theories … are myths or speculation … based on some vague or misunderstood references. … It will probably be impossible to say definitely where the ... Jews in Poland … came from.” B. Weinryb, The Jews of Poland, 1972

6 Simple Approach: Problem
ME EU An Ashkenazi genome ME x x x x x x x x EU x x x x x o o o PC2 x x o o o x x x x x x x x x x x x AJ PC1 Kopelman et al., BMC Genet, 2009 Atzmon et al., AJHG, 2010 Behar et al., Nature, 2010 Bray et al., PNAS, 2010 Guha et al., Genome Biol, 2012 Behar et al., Hum Biol, 2014 Carmi et al., Nat Commun, 2014 O’connor et al., Mol Biol Evol, 2015 Turkic origin hypothesis

7 Our Approach: Local Ancestry Inference
ME EU An Ashkenazi genome ME x x x x x x x x EU x x x x x o o o ME EU PC2 x x o o o x x x x x x x x x x x x AJ EU PC1 x x x x ME x x x x x x x x x x x o o x x x x x x o o o o x x x x x o o o o o x PC2 x x o PC2 x x x x x x x x x x x x x x x x x x x x x x x x x Use RFMix (Maples et al., AJHG, 2013) Per-SNP accuracy ≈70-80% PC1 PC1 Johnson et al., PLoS Genet, 2011 Moreno-Estrada et al., PLoS Genet, 2013

8 Localization of AJ admixture Sources
Used Naïve Bayes approach Likelihood of source X: Product of allele frequencies of all SNPs in EU/ME segments Most likely source is Southern-EU (mostly Italy) Simulations suggest that Southern-EU is ≈34% of AJ ancestry or ≈2/3 of EU ancestry Minor sources? Real data

9 Localization of the Minor Source
IBD sharing between AJ and other populations Sharing with Eastern-EU is highest

10 Comments on Localization
We ran other methods to find localization Alder, f4 stats, TreeMix were not robust in simulations Globetrotter (Hellenthal et al., Science, 2014) worked better Also identified Southern-EU as the predominant source Middle-Eastern most likely source was the Levant

11 Time of Admixture Multiple methods:
The mean EU segment lengths The distribution of total EU ancestry The decay of admixture LD (Alder, Globetrotter) Inferred admixture time: ≈25-40 generations ago What if there were multiple events?

12 Admixture vs Bottleneck
EU EU ME ME 25-35 gen ago EU Time Ancestry of IBD segments ≈ Ancestry at the bottleneck IBD Genome

13 Admixture vs Bottleneck
EU ME EU Replacing ≈20% Higher Eastern-EU ancestry ME EU IBD 42% Genome 53%

14 A Very Speculative Historical Model
Time (generations ago) Ancestral Middle-Eastern population Southern EU admixture Replacing ≈35-60% ≈25-50 Eastern EU admixture Bottleneck Replacing ≈15-25% ≈25-35 ≈10-20 Population size

15 Thank you for your attention!
Acknowledgements Columbia University: Itsik Pe’er James Xue Harvard) AJ genotypes: Todd Lencz (LIJMC) Ariel Darvasi (HUJI) Discussion: Ashkenazi Genome Consortium members Manuscript available on Thank you for your attention!

16 Local Ancestry Inference
LAMP-LD on simulate admixed individuals (Baran et al., 2012) Admixture FST Accuracy (6 generations) CEU:YRI 7.2% 99% CHB:TSI 5.4% 94.7% FIN:TSI 0.6% Same as random CEU:TSI 0.15% For EU/ME, FST≈1-2% RFMix (Maples et al., 2013) Simulated EU/ME admixed genomes, 30 generations Accuracy was 70-80%

17 Geographic Inference Advertised PCA method does not work
Used “Naïve Bayes” to classify the source of each chr Likelihood of source X: product of allele freq of all SNPs in EU/ME segments Does it work even for low LAI accuracy?

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