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Researchers Reconstruct 18th Century African Maternal Haploid Genome of Icelandic Man

NEW YORK (GenomeWeb) – An international team led by researchers at the University of Iceland has reconstructed the maternal genome of an 18th century Icelandic immigrant, finding that his mother came from a specific region in Africa.

In a study published today in Nature Genetics, the researchers reconstructed the genome of a person named Hans Jonatan (HJ), who was born in the Caribbean in 1784 to an enslaved African mother and European father, according to historical sources. Jonatan later lived in Copenhagen and emigrated to Iceland, fathering two children with an Icelandic woman.

"Apart from HJ, there is no evidence of African gene migration to Iceland before the twentieth century," the researchers noted.

The team genotyped 182 of 788 descendants using single-nucleotide polymorphism (SNP) chips, and whole-genome sequenced (WGS) 20 of those.

Using these data to construct 38 percent of HJ's maternal genome, the researchers inferred that his mother's origins could be traced to the African region spanned by Benin, Nigeria, and Cameroon.

The team identified 674 putative African chromosome fragments in the 182 genotyped descendants, ranging in length from 0.78 Mb to 82.98 Mb.

Among the 674 African fragments, the team excluded 64 samples because they were shared with one or more of more than 150,000 chip-typed Icelanders who are not descended from HJ. They then validated the rest of the fragments using HJ's genealogy.

First, the team expected that the parent of origin of any fragment would be consistent with the genealogical path to HJ. In cases where the path was through another genotyped descendant, a fragment from HJ should have fulfilled three criteria in the genotyped ancestor. The fragment needed to be present, identified as African, and have a parental origin consistent with the genealogical path leading to HJ.

Of the remaining chromosome fragments, only 282 passed all criteria in genotyped ancestors.  

The team then aimed to prove the claim that HJ's maternal and paternal haploid genomes were originally African and European.

The researchers used WGS data from a sixth-generation patrilineal descendant of HJ to find out that his Y chromosome belonged to haplogroup I2a2a3a2, which has a frequency of 0.15 percent in Iceland. Found mostly in Europe, this haplogroup is primarily absent from African populations.

A multidimensional scaling analysis plot based on pairwise identity-by-state (IBS) values and principal-component analysis placed HJ's maternal genome within West Africa. Therefore, the team decided that either HJ's mother, Emilia Regina, or her parents were likely to have been part of millions of Africans who were forcibly transported from the west coast of Africa to the Americas and the Caribbean between 1760 and 1790.

The researchers then used the same approach to narrow down HJ's reconstructed maternal genome origin within West Africa. They applied the pairwise wIBS measures, indicating HJ's mother was relatedly closely to populations from Benin, Cameroon and Nigeria. Using a series of permutation tests of wIBS values between HJ's moher and individuals from reference population pairs, the team determined she was significantly more related to the Yoruba from Benin than four of 16 other populations in West Africa.

According to the researchers, the study demonstrated "the first use of genotype data from contemporary individuals, along with information about their genealogical relationships, to reconstruct a sizeable portion of the genome from a single ancestor born more than 200 years ago."

The team saw that HJ's maternal genome was oddly tractable because chromosome fragments from recent African ancestors are very rare in the Icelandic gene pool. In future studies, however, a more definite assignment of maternal origin will require larger sample sizes and genotypic data from a wider range of populations in West Africa.  

As family-based genotype data increases for specific populations, the team believes that more explicit and systematic identical-by-descendant (IBD) studies to reconstruct genomes of ancestors will be feasible.

One application of IBD would involve studying and researching individuals of historical interest, such as HJ. In addition, the team also believes that IBD-based techniques could advance medical genetic research in situations where crucial phenotype data would be available for ancestors who cannot be sources for DNA and directly genotyped.  

While the technique sounds promising for future genetic research, the team admits that there are key constraints to the IBD-based efforts. Over multiple generations, the practical utility of using ancestor genomes diminishes and drops in accuracy. In addition, as researchers go back in time, the likelihood that an ancestor has provided any chromosome fragment to their descendants quickly reaches zero.

Despite the limitations, the team demonstrates that with extensive genealogical data, genotype data and divergent ancestry, genomic reconstruction involving an ancestor can be relatively simple.