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Mitochondrial Genome Analysis Points to Early Asian Migrations to the Americas, Japan

NEW YORK – A research team led by investigators in China has found that the ancestors of Native Americans hailed not only from Siberia but also from northern China.

For a study published in Cell Reports on Tuesday, the investigators retraced the spread of mitochondrial DNA lineages originating on China's northern coast, including a radiation that gave rise to a haplogroup known as D4h3a that is found in maternal ancestors of some Native Americans.

"Our study … uncovered an additional ancestral source for the ancestors of [Native Americans] beyond Siberia from the matrilineal perspective," the study's authors wrote, noting that the findings "also shed important light on the dispersal route of early [Native Americans] into the Americas."

Using mitochondrial genome sequence data for 216 modern-day individuals within the broader D4h mitogenome group, along with more than three dozen D4h mitochondrial genome sequences from ancient individuals, the researchers tracked down two key migration events starting on the northern coast of China and reaching sites in the Americas and Japanese archipelago.

"[B]y investigating a female lineage (D4h), we identified two population radiation events in northern coastal China," co-first author Yu-Chun Li, a researcher with the Chinese Academy of Sciences, the KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, and the Kunming Key Laboratory of Healthy Aging Study, noted in an email.

In the first of these migration events, which took place during the Last Glacial Maximum (LGM), Li explained, the D4h lineage diversified into the D4h1 and D4h2 sub-lineages, along with a D4h3 sub-lineage found in Native Americans. In a second key migration event in a deglaciation period roughly 11,500 to 19,000 years ago, meanwhile, individuals from the D4h lineage radiated from the region during a period of rapid population growth.

"The coastal distributions of the [Native American] (D4h3a) and Japanese lineages (D4h1a and D4h2), in combination with the Paleolithic archaeological similarities among Northern China, the Americas, and Japan, lend support to the coastal dispersal scenario of early [Native Americans]," the authors wrote.

Since the Native American-linked D4h3 mitochondrial lineage and ancestral D4h group are relatively rare across present-day populations, the investigators surveyed more than 40,300 complete and nearly 61,000 partial mitochondrial genome sequences to find 110 confirmed D4h haplogroup representatives. They also tracked down 112 suspected D4h mitogenomes, using targeted sequencing to link 106 more mitogenomes to D4h.

Together with 39 ancient D4h mitogenomes found by sifting through some 15,460 ancient mitochondrial genome sequences, the present-day D4h samples made it possible to get a more detailed look at Dh4 and D4h3 phylogeny and historical patterns.

The team's analyses linked many contemporary D4h mitogenomes to North-Central China, Japan, Southeast Asia, and the Americas, while ancient representatives from this haplogroup turned up primarily in samples from northern China.

"Taken together, these results indicate that the phylogenetic differentiation of D4h occurred somewhere in Central or North China, most likely in a region geographically close to the northern coast of China," the authors reported, suggesting that "the northern coast of China might have played a critical role in the divergence and spread of D4h and its sub-haplogroups."

Along with radiocarbon dating clues and coalescent age estimates used to retrace radiation events out of the northern coastal region of China, the researchers detected sub-haplogroup differentiation and spread coinciding with these events, including the advent of sub-haplogroups later found in Native American populations and populations in the Japanese archipelago.

"According to our results, the majority of the D4h lineages further dispersed from northern China into different regions, among which a small number of groups further dispersed into Japan and even outside of East Asia into as far away as the Americas," Li wrote, noting that it remains to be determined how and why migrants reached such distant sites.

"One possibility is the sea level drop of Bohai, Huanghai, and the East China Seas until the end of the deglaciation period, which … probably allowed these expansions to occur," Li explained. "Another possibility is that these travelers would have migrated via the Pacific coast, which is different from the other ancestors who probably migrated into the Americas through the ice-free corridor."