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Based on Haplotype Sharing, Researchers Present Atlas of Human Admixture Events

NEW YORK (GenomeWeb News) – Researchers at Oxford University and elsewhere have developed a sort of atlas that maps out admixture events between various human populations, they reported in Science today.

This method, dubbed Globetrotter, analyzes haplotype chunks, which are often shared by populations with common ancestors, to determine whether there was admixture between particular populations and gauges the time since that mixture occurred.

Many of the admixture events uncovered using this approach correspond to known historical movements, the researchers said.

For instance, using Globetrotter, the researchers found that Cambodians have genetic contributions from sources related to modern-day Central, South, and East Asians, admixture that occurred between 1194 and 1502, which includes the tail end of the powerful Khmer empire in Southeast Asia, and that populations like the Hazara, Uygur, and Mongola have admixture events that trace back to the expansion of Genghis Khan's Mongol empire.

"DNA really has the power to tell stories and uncover details of humanity's past," co-senior author Simon Myers from Oxford University and the Wellcome Trust Centre for Human Genetics said in a statement. "Because our approach uses only genetic data, it provides information independent from other sources. Many of our genetic observations match historical events, and we also see evidence of previously unrecorded genetic mixing."

Admixture, Myers and his colleagues noted, appears to have influenced all global populations.

To determine whether human populations had admixture events, Myers and his colleagues examined the portion of haplotypes those groups shared with others. Using Chromopainter, they, in essence, painted haplotypes based on their origins to disentangle the groups' ancestry, leading to a somewhat colorful and messy view of that ancestry. However, through model fitting, they developed cleaner haplotype paintings that narrowed down the donor populations.

"Each population has a particular genetic 'palette,'" Daniel Falush, a co-senior author from the Max Planck Institute for Evolutionary Anthropology in Leipzig, said. "If you were to paint the genomes of people in modern-day Maya, for example, you would use a mixed palette with colors from Spanish-like, West African, and Native American DNA. … Though we can't directly sample DNA from the groups that mixed in the past, we can capture much of the DNA of these original groups as persisting, within a mixed palette of modern-day groups."

Using co-ancestry curves for each donor population pair, the researchers gauged the evidence for an admixture event as well as estimated how long ago such an event took place based on the decay of the curves. Additionally, eigenvectors, similar to how they are used in principal components analysis calculations, allowed the researchers to estimate the percentage that each donor group contributed.

Myers and his colleagues tested this approach, which they named Globetrotter, in a number of simulated situations. From those simulations, they estimated that their power to detect admixture was 94 percent and that 95 percent of their bootstrapped confidence intervals included the actual admixture date.

While they said that their approach was robust, the researchers noted that certain situations — such as the sampling of very closely related populations or distinguishing pulses of admixture versus continuous mixing, among others — could be challenging to sort out.

The researchers used Globetrotter to analyze 1,490 people from 95 groups worldwide, including 17 recently genotyped groups, 53 groups from the Human
Genome Diversity Panel, and 25 from other sources, for a total of 474,491 autosomal SNPs. They phased the individuals using IMPUTE2 and used fineSTRUCTURE to make sure the populations were homogenous.

Eighty of those human populations showed evidence of admixture, Myers and his colleagues reported. Globetrotter, they added, appears to be more powerful than other approaches. For instance, it found evidence of admixture in 43 of the 53 groups from the HGDP, while the original analysis uncovered 34 admixture events.

While many instances of admixture the researchers uncovered corresponded with known historical events like the spread of the Mongol empire or the Bantu expansion in southern Africa, others traced back to times from which there is little historical evidence.

For example, the Kalash, living in north Pakistan, showed a strong signal of an admixture event occurring between 990 BC and 210 BC with a population related to modern-day Western Eurasians, though the researchers could not tease out the precise origin. While this timeframe corresponds with the reign of Alexander the Great (between 356 BC and 323 BC) and local tradition says that the Kalash descended from his army, the researchers said confident interpretation of that data cannot be made as the timing precedes written history in the area.

Other populations show complex admixture signals. Eastern Europeans, for instance, couldn't be distinguished at first using fineSTRUCTURE — the researchers had to repaint the group without using populations from that region as donors.

After that, they found that eastern Russians and the Chuvash had admixture signals from both Northeast Asians and Europeans that preceded the Mongol Empire, as did a few other eastern European populations. The researchers suggested that this may be genetic evidence of invasions during the first millennium of people from the Asian steppes.

The researchers also presented an atlas of this human world ancestry online where users can click on different populations to see what admixture the researchers have uncovered in them. For instance, clicking on Maya shows an admixture event dating back to about 1670 between Spanish-like, Pima-like, and West African populations, while clicking on Melanesian shows an admixture event from about 1138 between Papuan-like and Myanmar-like populations. Other groups, like Adygei, Ethiopians, and the Spanish, show evidence of admixture events at multiple points in time.

While approaches like Globetrotter allow researchers a glimpse into human history and movements, knowing how similar and different human populations are can also help public health efforts, the researchers argued.

"Some populations are more at risk of certain diseases than others, and drug efficacy is also known to vary significantly. Rare genetic mutations are particularly likely to show strong differences between populations, and understanding their role in our health is an area of intense current research efforts," Myers said. "We hope in the future to include even more detailed sequencing, to spot these rare mutations and better understand their global spread."