Reconstruction of Ancestral Human Genomes from Genome-Wide DNA Matches. J. M. Granka1, R. E. Curtis2, J. K. Byrnes1, M. J. Barber1, N. M. Myres2, K. Noto1, Y. Wang1, C. A. Ball1, K. G. Chahine2 1) AncestryDNA, San Francisco, CA; 2) AncestryDNA, Provo, UT.
Individuals who lived long ago may still have much or all of their genome present in modern populations. The genomes of these individuals exist in small segments broken down by recombination and inherited in part by his or her descendants. If such an individual had many children, leading to a large number of descendants today, much of the ancestral genome will be present in modern populations. For the pairs of descendants with the target ancestor as their most recent common ancestor (MRCA), any region of their genomes shared identical-by-descent (IBD) most likely represents the corresponding region of the ancestors genome. Given a set of pairs of individuals linked to the same MRCA, we develop a novel computational approach to reconstruct the haplotypes of the MRCA from the IBD segments and haplotypes of the descendants. With simulated data we assess the performance of our method, affected by factors such as quality of genealogical trees used to infer the MRCA, reliability of inferred IBD, coverage of IBD segments, number of descendants of the MRCA, and number of sampled descendants. To demonstrate the utility of our method, we examine over 125,000 individuals in the AncestryDNA database with phased genome-wide single nucleotide polymorphism data and detailed genealogical information. After first identifying regions of the genome shared IBD between all individuals, we selected one group of several hundred individuals with an 18th century couple as a known MRCA. Using our method to tile together these individuals IBD segments, we are able to reliably construct the ancestral couples four haplotypes in large genomic regions with high coverage of IBD segments. In regions of the genome with lower IBD coverage, we are unable to identify and construct all haplotypes with certainty. Our study demonstrates the possibility of reconstructing the genomes of human ancestors, with large family sizes and a large number of living descendants, who lived one to even 12 generations ago. The ability to reconstruct the genomes of human ancestors using genetic and genealogical data has exciting implications in the fields of population genetics, medical genetics, and genealogy research.
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