Introduction
Material and Methods
Recruitment and Genotyping of Jewish Populations
DNA Preparation for SNP Array Analysis
Genotyping
Reference Populations
HGDP Data Set
PopRes Data Set
Fst, Observed Heterozygosity, and Phylogenetic Analysis
Principal Component and STRUCTURE Analysis
Differences between Subgroups Pairwise Fst, IBS, and ANOVA
CNV Analysis
IBD Discovery
Inference of Population History
Statistical Analyses of Interpopulation Differences and Neighbor Joining Trees
GERMLINE Analysis
Genotype Extension
Filtering Regions for Informative SNPs
Sharing Densities
Sharing Graphs
Sharing Statistics
where Wij is the total sharing between individuals i and j from populations I and J, respectively, and n and m are the number of individuals in populations I and J. The average lengths of the shared segments across populations were computed through the arithmetic mean of the shared segments for each pair of populations. To compute the distribution of longest segments (Table 1, Figure 3), the longest shared segments for all possible pairs was considered. The observed probability of a pair sharing a longest segment of a specified length was computed normalizing the observed counts by the number of possible pairs within or between the considered populations. The counts for all the histograms were obtained through floor rounding of the values.
Populations | n | Ho | IRN | IRQ | SYR | ASH | ITJ | GRK | TUR | N. Italian | Sardinian | French | Basque | Adygei | Russian | Palestinian | Druze | Bedouin |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
IRN | 28 | 0.291 | 0.015 | 0.015 | 0.017 | 0.018 | 0.015 | 0.014 | 0.018 | 0.027 | 0.022 | 0.030 | 0.018 | 0.028 | 0.017 | 0.017 | 0.021 | |
IRQ | 37 | 0.293 | 4.906 | 0.008 | 0.013 | 0.012 | 0.009 | 0.008 | 0.012 | 0.019 | 0.016 | 0.024 | 0.013 | 0.023 | 0.010 | 0.012 | 0.015 | |
SYR | 25 | 0.296 | 0.999 | 3.145 | 0.008 | 0.008 | 0.004 | 0.003 | 0.007 | 0.014 | 0.010 | 0.018 | 0.010 | 0.018 | 0.007 | 0.009 | 0.012 | |
ASH | 34 | 0.294 | 0.746 | 0.827 | 1.926 | 0.009 | 0.006 | 0.005 | 0.008 | 0.014 | 0.009 | 0.017 | 0.012 | 0.016 | 0.011 | 0.012 | 0.016 | |
ITJ | 37 | 0.294 | 0.609 | 0.857 | 1.566 | 3.093 | 0.005 | 0.005 | 0.008 | 0.014 | 0.011 | 0.018 | 0.012 | 0.018 | 0.010 | 0.011 | 0.015 | |
GRK | 42 | 0.296 | 0.564 | 0.773 | 1.570 | 2.153 | 2.476 | 0.001 | 0.004 | 0.010 | 0.007 | 0.014 | 0.009 | 0.015 | 0.006 | 0.008 | 0.011 | |
TUR | 34 | 0.297 | 0.747 | 1.043 | 2.049 | 2.954 | 2.411 | 2.556 | 0.004 | 0.010 | 0.007 | 0.014 | 0.008 | 0.014 | 0.005 | 0.007 | 0.010 | |
N_Italian | 21 | 0.295 | 0.675 | 0.740 | 0.865 | 1.015 | 0.978 | 0.906 | 0.899 | 0.007 | 0.002 | 0.008 | 0.008 | 0.009 | 0.010 | 0.011 | 0.016 | |
Sardinian | 28 | 0.289 | 0.675 | 0.683 | 0.970 | 1.098 | 0.852 | 0.955 | 0.946 | 1.386 | 0.009 | 0.013 | 0.019 | 0.020 | 0.017 | 0.017 | 0.022 | |
French | 28 | 0.296 | 0.498 | 0.623 | 0.999 | 1.012 | 0.948 | 0.889 | 0.937 | 1.361 | 1.353 | 0.007 | 0.009 | 0.005 | 0.014 | 0.014 | 0.020 | |
Basque | 24 | 0.291 | 0.584 | 0.662 | 0.854 | 1.153 | 0.862 | 0.935 | 0.905 | 1.427 | 1.472 | 2.078 | 0.018 | 0.015 | 0.021 | 0.021 | 0.027 | |
Adygei | 17 | 0.298 | 0.604 | 0.504 | 0.655 | 0.738 | 0.748 | 0.805 | 0.699 | 0.840 | 0.647 | 0.831 | 1.073 | 0.012 | 0.012 | 0.012 | 0.019 | |
Russian | 25 | 0.295 | 0.470 | 0.524 | 0.623 | 0.913 | 0.822 | 0.642 | 0.811 | 1.236 | 0.933 | 1.460 | 1.205 | 0.905 | 0.021 | 0.021 | 0.028 | |
Palestinian | 39 | 0.303 | 0.530 | 0.642 | 0.597 | 0.580 | 0.659 | 0.609 | 0.708 | 0.514 | 0.670 | 0.549 | 0.590 | 0.562 | 0.480 | 0.009 | 0.009 | |
Druze | 36 | 0.296 | 0.656 | 0.638 | 0.754 | 0.778 | 0.671 | 0.738 | 0.752 | 0.658 | 0.713 | 0.595 | 0.675 | 0.797 | 0.568 | 0.623 | 0.013 | |
Bedouin | 40 | 0.301 | 0.572 | 0.606 | 0.564 | 0.576 | 0.567 | 0.541 | 0.590 | 0.606 | 0.545 | 0.529 | 0.542 | 0.386 | 0.371 | 1.013 | 0.649 | |
Total Sharing | 41.947 | 33.360 | 17.261 | 11.620 | 28.446 | 6.005 | 4.458 | 2.366 | 10.839 | 1.629 | 15.966 | 6.285 | 5.799 | 25.504 | 49.590 | 25.361 |
Sharing between Remote Relatives
Selecting Loci with Significantly Excessive Sharing
Results
Jewish Populations Form Distinctive Clusters with Genetic Proximity to European and Middle Eastern Groups
Jewish Communities Show High Levels of IBD
Frequent IBD between Different Jewish Populations Reflects Their Genetic Proximity
Specific Regions of the Genome Are Frequently Shared between Jewish Populations
Timing of the Middle Eastern-European Jewish Divergence
Discussion
Acknowledgments
Supplemental Data
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Document S1. Ten Figures and Six Tables
Web Resources
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Jewish Hapmap Project, http://pediatrics.med.nyu.edu/genetics/research/jewish-hapmap-project
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