Reconstructing an African haploid genome from the 18th century

This article is an example of what can be done by commercial DNA-sequencing cmpanies such as MyHeritage, Ancestry, Vitagene, LivingDNA, GPS Origins, 23andMe and dozens of other similar companies. The population of Iceland was founded by settlers from continental Scandinavia and the British Isles ~1100 years ago, and Iceland remained relatively isolated until recently. Post-settlement immigration to Iceland was rare, occurring mostly from Denmark and, to a lesser degree, from other neighboring countries. Records from 1930 to 1980 show that the number of individuals in Iceland from outside Europe ranged from 73 to 1,322 (0.07% to 0.6% of the entire population); in the early 1800s, it was most likely a much smaller percentage.

Because of his African ancestry, Hans Jonatan (HJ) –– born in the Caribbean in 1784 to an African mother and European father –– was an unusual immigrant when he arrived in Iceland in 1802. Consequently, the chromosomes transmitted by HJ to his two children would have been a mosaic of African-derived and European-derived fragments. Because his wife was Icelandic, their children would have inherited African fragments only from HJ. Owing to recombination and Mendelian segregation, authors [see attached article] expected to find fewer and smaller fragments from HJ in successive generations of descendants.

When chromosome fragments of one ancestor (e.g. HJ) can be distinguished from those of other ancestors among a group of descendants, his or her genome can be at least partially reconstructed. Thus, assuming that African chromosomal fragments can be reliably identified in genotyped descendants of HJ from Iceland, and that assuming these individuals have no other recent African ancestors, the reconstruction of HJ’s mother’s genome amounts to identifying and joining these fragments — similar to pieces in a jigsaw puzzle. To the knowledge of these authors, there is no evidence (apart from HJ) of African gene flow to Iceland before 1900. Therefore, authors expected African chromosomal fragments to be extremely rare in the Icelandic gene pool.

Anyone’s genome therefore represents a mosaic of chromosome fragments from ancestors who existed some arbitrary number of generations earlier. Authors decided to genotype 182 of HJ’s 788 descendants –– using single-nucleotide variant (SNV) chips, plus whole-genome sequencing (WGS) of 20 descendants. From their data, authors reconstructed 38% of HJ’s maternal genome and inferred that his mother had originated from the region encompassed by Benin, Nigeria and Cameroon.

Nature Genet Feb 2o18; 50: 199–205

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