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Analysis of Ancient DNA Reveals Ancestry of Mysterious Individual in Southwest China

NEW YORK – Ancient DNA sequences from a Late Pleistocene female found in Southwest China suggest that the region was home to distinct, relatively diverse populations, including a lineage related to present-day populations in East Asia and elsewhere and to Indigenous populations that first settled the Americas.

In a paper appearing in Current Biology on Thursday, researchers from the Chinese Academy of Sciences, the Yunnan Institute of Cultural Relics and Archaeology, and other centers used in-solution DNA capture and shotgun sequencing to put together a mitochondrial genome and a low-coverage nuclear genome from remains found in a cave in China's Yunnan province.

The sample came from an ancient female known as MZR who lived during the Late Pleistocene period roughly 14,000 to 14,700 years ago, the authors explained. A series of previous anthropological analyses suggested that MZR had physical and morphological features resembling both anatomically modern humans (AMH) and archaic hominins, including Neanderthal-like skull features.

The new ancient genomic sequence data "confirm that [MZR] possesses diverse genetic components and represents an early diversified population, suggesting the scenarios of more diverse AMH lineages than previously thought during the Late Pleistocene in southern East Asia," senior and co-corresponding author Bing Su, a researcher with the Chinese Academy of Sciences' Kunming Institute of Zoology, and his colleagues explained, noting that the work "paves the way to explore genetic explanations of morphological complexities of early hominins."

After extracting ancient DNA from a cranium bone sample, the investigators relied on modified human whole-genome probes to nab human-like sequences for subsequent amplification and library preparation steps. With dozens of DNA libraries, they ultimately generated hundreds of millions of sequence reads, providing a low-coverage look at the nuclear genome and a mitochondrial genome covered at an average depth of roughly 125-fold.

Despite the archaic hominin-like features found in the ancient individual and the presence of archaic sequences introgressed from Denisovans and Neanderthals, the team's analyses indicated that MZR was part of an "early diversified" AMH lineage with genetic ties to existing populations.

When they considered the ancient genome in the context of sequences from ancient and contemporary individuals from global populations, the investigators found that MZR carried ancestry from southern portions of East Asia that is related to that reported in Native Americans, consistent with the notion that migrations across the Bering Strait involved individuals migrating to Siberia from the southern reaches of East Asia.

"Our results indicate that MZR is a modern human who represents an early diversified lineage in East Asia," the authors reported, noting that "MZR is linked deeply to the East Asian ancestry that contributed to First Americans."

On the mitochondrial DNA side, meanwhile, the researchers saw signs that MZR belonged to a maternal lineage that appeared to be basal to an M9 mitochondrial haplogroup with present-day offshoots believed to have moved south to north in mainland East Asia up to 28,000 years ago and into Southeast Asia, the Solomon Islands, and beyond.

"[T]he discovery of an extinct basal M9 lineage for the MZR [individual] suggests a rich matrilineal diversity of human populations in southern East Asia during the Late Pleistocene," the authors explained.

Together, the study's authors suggested, the new genomic insights support the notion that ancient populations from southern Asian sites were genetically nuanced, with more distinct genetic features than those found at more northerly sites in East or Southeast Asia. 

The team reportedly expects to sequence still more ancient individuals from southern China and other parts of East Asia, including individuals from populations appearing prior to those identified in the Maludong, or Red Deer, Cave where MZR's remains were discovered.

"Such data will not only help us paint a more complete picture of how our ancestors migrated but also contain important information about how humans change their physical appearance by adapting to local environments over time," Su said in a statement.