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New insight on ancient and understudied cultures

Disease adaptation in the Amazon, dairy use in Tibet, and Indian ancestry in Thailand
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The takeaway: Recent discoveries that hinge on findings from sequencing ancient DNA shed light on ancient cultures and how they lived.

Genetic analyses of ancient DNA studies continue to reveal how long-lost cultures lived. These insights tell us how ancient and modern cultures lived, worked, and migrated, and even what they ate.

Early Amazonians: Living with disease and a rarely studied population

The Amazon covers a massive swath of South America, including the eastern part of Peru, which is home to 51 indigenous groups, the largest of which is the Ashaninka. Despite their relative size, few studies have delved into their genetic make-up. A new study, published in Current Biology, used array-based genotyping to find that the Ashaninka, genetically, had unexpectedly high levels of genetic variation. The genetic makeup of the group changed as migrations moved people away from the coast to the Amazonian interior, and as the Inca Empire flourished. They also found genetic links between the Ashaninka and populations known to be present in the Caribbean.

But how did those ancient groups manage to live in the Amazon, which, like many jungle regions around the world, has a climate favorable to the transmission of tropical diseases? For example, the Amazon is home to Chagas disease, an infectious disease caused by a parasite found in the feces of an insect. Chagas can be mild, but if left untreated can cause congestive heart failure.

Writing in Science Advances, a group of researchers analyzed genomic sequences from more than 100 indigenous Brazilians and found evidence of Chagas immune cell activation—which was not prevalent in populations that lived in the Andes to the west.

“The results based on genomic and functional analysis showed an intense signal of natural selection in a set of genes related to Trypanosoma cruzi infection, which is the pathogen responsible for Chagas disease, a neglected tropical parasitic disease native to the Americas that is currently spreading worldwide,” the authors wrote. "Our results provide insights into the population's adaptation to the Amazonian rainforest … the identification of a role for PPP3CA in T. cruzi infection contributes to the dissection of the molecular mechanisms of pathogen infection and, thus, potentially to the development of therapies for the disease."

Genetic studies of Tibet: An undiscovered human group and a dependence on dairy

Two ancient DNA research studies from 2023 looked at the genetic make-up of Tibetans and those who historically lived on the Tibetan plateau, and each arrived at interesting results.

The first, which was published in Science Advances, looked at the last 5,100 years of human genetic history on the Tibetan Plateau and found a specific ancestry that included northern East Asians and a diverging human group that has not been discovered yet.

The team of Chinese and American researchers used targeted enrichment sequencing to analyze SNPs in ancient remains recovered in archaeological sites in what is now Tibet and the adjacent Chinese province of Qinghai.

“Over the past ~700 years, substantial gene flow from lowland East Asia further shaped the genetic landscape of present-day plateau populations,” the authors wrote. “The high-altitude adaptive EPAS1 allele was found in plateau populations as early as in a 5100-year-old individual and showed a sharp increase over the past 2800 years.”

What did those early Tibetans do? Evidence from a separate 2023 study, also in Science Advances, used protein analysis to suggest that those early Tibetans eked out an existence on the high, cold plains by dairy farming.

Previous genetics-based research using ancient DNA found that occupants cultivated a frost-tolerant barley, which helped encourage permanent settlement about 3,600 years ago. Ancient texts note that cattle, yak, sheep, and goats were raised on the Tibetan Plateau at least 2,000 years ago.

“Our research suggests that dairy pastoralism was adopted on the interior plateau by at least 3500 years ago, with sustainable dairy resources from sheep, goat, and possibly cattle/yak supporting pastoralists as they expanded onto the extensive agriculturally poor steppes of the Tibetan Plateau,” the authors wrote.

Large scale genome sequencing study targets little-studied African populations

The more we know about our genetics the more knowledge we have to live longer and healthier lives. Our increasing genetics knowledge may someday allow us to tailor genetics-based health strategies to our benefit.

This idea was part of the impetus behind a recent large genome sequencing study of 12 indigenous African populations. The study, published in Cell, identified millions of unreported variants, identified their unique ancient common ancestry, and found signatures for local adaptation of skin color, immune response, height, and metabolism.

Looking at populations from Ethiopia, Tanzania, Cameroon, and Botswana, the study found variants that play a role in heart development among hunter-gatherers known to walk enormous distances, gene associated with bone growth in forest dwellers known for their short stature, and gene flow between geographically isolated cultures that share language similarities.

Indian genetic ancestry found in some Thai populations

During the first millennium, Indian culture spread around the Indian Ocean; a recent study in PLOS Genetics has confirmed that genetically. The study generated genome-wide SNP data on 10 ethnic groups from Thailand and found evidence of admixture with South Asian populations, perhaps Bengali. Those ethnic groups showing South Asian heritage include the Khmer and Mon, while other more isolated cultures, such as the Karen, showed no South Asian links.

“Our study revealed substantial South Asian admixture in various populations across Southeast Asia (~2–16% as inferred by qpAdm),” the authors wrote. “For four ethnolinguistic groups genotyped in our study (Khmer from Thailand, Kuy, Mon, and Nyahkur) and four groups from published data (Cambodian Khmer, Cham, Ede, and Giarai) South Asian admixture was not reported before in the literature … Thus, we for the first time demonstrate South Asian admixture in populations from Cambodia and Vietnam, extend earlier results detecting this ancestry component in Thailand, and confirm detection of this ancestry component in Myanmar and Singapore .”

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