Reconstruction of Ancestral Human Genomes from Genome-Wide DNA Matches.
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 ancestor’s 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 couple’s 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.
Blaine Bettinger has a longer post, The Science Fiction Future of Genetic Genealogy, inspired by the abstract.
While the potential for this sort of thing has been apparent for years, it's good to see concrete steps being taken in this direction. A related (perhaps slightly over-optimistic) 2010 post by Tamura Jones:
[. . .] The eventual future is that all vital sources will be online, and that’s vitally different.
Genealogical databases will not only contain DNA information for those whose DNA was sampled, but even DNA for earlier ancestors inferred from the DNA of their descendants. [. . .]
All sources will be online and have been used in the construction of genealogies. New events will be added as they occur. The eventual future is that all genealogies will have been done, verified against records, and amended through DNA research.
For a while researchers will try to fill in gaps and extend genealogies by locating information in unlikely sources not consulted before. Some genetic genealogy detectives will use DNA to try and solve challenging cases caused by a lack of reliable records, but their research will be replaced by automated techniques that calculate the probabilities for various possibilities.
Similar techniques will be used to extend existing genealogies a few more generations back into the past, using DNA to infer relations for which there are no records. Eventually, all genealogical research that can be done will have been done.
Genealogy is doomed, long live genealogy. Genealogy will not become obsolete, but pervasive. Our descendants will have well-documented ancestries even before they are born.
That does not imply that the thrill of discovery will be gone. With the vital but bare genealogical facts laid out, the discovery will not be about who your ancestors are, but about exploring who they were.