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Ancient Genome Analysis Indicates Three Ancestral Populations Contributed to Modern-day Europeans

NEW YORK (GenomeWeb) – By peering into the genomes from various ancient Europeans, researchers have found that at least three ancestral populations have contributed to the genetic makeup of most modern-day Europeans.

An international team of researchers led by Harvard Medical School's David Reich sequenced ancient genomes belonging to a 7,000-year-old farmer from Germany, an 8,000 year-old hunter-gatherer from Luxembourg, and seven hunter-gatherers from Sweden who lived some 8,000 years ago. They compared the sequences they generated to other ancient human genomes as well as to 2,345 genomes from contemporary humans.

Their analysis, presented in Nature today, indicated that most present-day Europeans are derived from three populations, namely, western European hunter-gatherers, ancient north Eurasians, and early European farmers who themselves were of mostly Near Eastern origin, but who were also related to western European hunter-gatherers.

"What we find is unambiguous evidence that people in Europe today have all three of these ancestries: early European farmers who brought agriculture to Europe, the indigenous hunter-gatherers who were in Europe prior to 8,000 years ago, and these ancient north Eurasians," Reich said in a statement.

By sequencing these ancient Europeans and comparing their genomes to those from modern humans, Reich and his team sought to understand the genetic contributions of ancient populations to modern Europeans.

They sequenced the Stuttgart farmer to 19-fold coverage, the Loschbour hunter-gatherer to 22-fold coverage, and the Swedish hunter-gatherers to between 0.01-fold and 2.4-fold coverage for using the Illumina Genome Analyzer or MiSeq platforms. Deeper UDG sequencing of the samples were performed on the HiSeq 2000 machine.

The researchers noted that the sequences they generated resembled other ancient genomes in that they had deamination-derived mismatches at the ends of the molecules. They further estimated the nuclear contamination rate for the Stuttgart and Loschbour samples to be 0.3 percent and 0.4 percent, respectively.

Additionally, Reich and his colleagues reported that the ancient individuals belonged to expected mtDNA haplotypes and, for the male samples, Y chromosome haplotypes. For instance, the Stuttgart sample belongs to the mtDNA haplotype T2, which is typical of Neolithic farmers, while the Loschbour and Swedish Motala samples belong to the U2 haplogroup or the U5 haplogroup, which are typical of hunter-gatherers.

By examining the ancient genomes, the researchers got a glimpse of what these ancient Europeans may have looked like. The Loschbour and Stuttgart individuals likely had dark hair, though Loschbour and Motala12 — the Swedish sample with the highest coverage — probably had light-colored eyes. Loschbour did not have the skin-lightening SLC24A5 allele that is nearly fixed in modern Europeans and that was homozygous in the Stuttgart sample and heterozygous in the Motala12 sample.

To put together a picture of modern Europeans' ancestry, Reich and his team compared the genomes of these ancient Europeans to 2,345 present-day humans from 203 populations that were genotyped at more than half a million SNPs using the HumanOrigins array.

Through a combination of ADMIXTURE and principal component analysis, they identified ancient European population clusters: namely, an ancient north Eurasian population, a west European hunter-gatherer population (including the Loschbour samples), a Scandinavian hunter-gatherer population (including the Motala samples), and an early European farmer cluster (including the Stuttgart sample).

Using f-statistics and various population models, the researchers calculated the possible ancestry of modern-day Europeans by drawing on these populations.

Their results indicated that modern-day Europeans are mostly a mix of three source populations: an ancient north Eurasian population, the early European farmer population, and the west European hunter-gatherer population.

Intriguingly, the researchers' analysis indicated that the early European farmer population, represented by the Stuttgart sample, was partially derived from a lineage that split before eastern non-Africans separated from the common ancestor of west European hunter-gatherers and ancient north Eurasians.

"This deep lineage of non-African ancestry branched off before all the other non-Africans branched off from one another," Reich said. "Before Australian Aborigines and New Guineans and South Indians and Native Americans and other indigenous hunter-gatherers split, they split from Basal Eurasians. This reconciled some contradictory pieces of information for us."

While modern Europeans, they noted, are a three-way mixture of these ancient populations, the percentage that each ancient population has contributed to modern ones varies. For instance, the early European farmer ancestry ranges from about 30 percent in the Baltics to some 90 percent in the Mediterranean, the researchers said.

Additionally, Reich and his colleagues noted that ancient north Eurasian ancestry is present in nearly all modern Europeans, though it was not found in farmers and hunter-gatherers living in central and western Europe during the Neolithic transition. It was, though, present in the 8,000-year-old Scandinavian hunter-gatherers.

"We have this amazing observation that only two ancestries are represented among the first farmers, from about 7,000 to 5,000 years ago. And then suddenly everybody today has ancient north Eurasian ancestry," Reich said. "So there must have been a later movement of this ancestry into Europe."

Reich and his colleagues noted that some European populations don't fit their model. Sicilians, Maltese, and Ashkenazi Jews have a higher estimate of ancestry from early European farmers, suggesting great Near Eastern ancestry, while Finns, Mordovians, and northwestern Russian have greater gene flow from East Eurasian sources.