Two types of ancient humans found to benefit the health of living people

Around 45,000 years ago, anatomically modern humans expanding into the Pacific region encountered archaic hominins on their journey. It wasn’t long before they started having sex with them. So much sex, that it continued for millennia.

What the humans didn’t know is they were picking up genes that would help them adapt to and survive island living. These genes continue to benefit people living in this region today, new research suggests.

The Pacific region is home to a deep history of early human evolution. However, genomic studies in the region are just emerging, says Etienne Patin, a human population geneticist with Institut Pasteur in France. Patin is the new study’s co-author.

“Today, 95 percent of genomic studies focus on European-descent individuals, while they represent only 16 percent of the human population,” Patin tells Inverse.

His research, published Thursday in the journal Nature, examines whether or not sex between modern humans and other species of humans facilitated the genetic adaption to island environments still observed in some Pacific Islanders today. This population has the highest levels of combined Neanderthal and Denisovan ancestry worldwide, the study suggests.

The background — The Pacific region is divided into Near Oceania (Papua New Guinea, the Bismarck Archipelago, and the Solomon Islands) and Remote Oceania (Micronesia, Santa Cruz, Vanuatu, New Caledonia, Fiji, and Polynesia).

Humans settled in Near Oceania around 45,000 years ago — about the same time the study indicates the first “introgression pulse” occurred, aka when modern humans mated with Denisovans (it’s also possible this occurred in Southeast Asia before migration to the Pacific islands). Remote Oceania was populated much later, around 3,200 years ago, with people migrating from what is now Taiwan.

What’s new — Scientists hypothesize nearly every person on the planet has Neanderthal genes to some degree — even people from Africa, which is a more recent discovery.

However, this study encountered something especially unique in the genomes of Pacific Islanders.

To dig into the human evolutionary history of the Pacific, the study team sampled genomes from the blood and saliva of 317 volunteers representing 20 populations in the region. The sampling was done between 1998 and 2018 in Taiwan, Vanuatu, Solomon Islands, and the Philippines

This analysis revealed new patterns in human migration. For example, the data suggests the gene pool of Near Oceanian individuals was small when they first came into the region, and subsequent populations diverged 20,000 to 40,000 years ago — the team describes the ancestors of Near Oceanin groups undergoing a “strong bottleneck” before entering the region.

Genetic analysis also revealed ancient peoples from East Asia, the Philippines and Near Oceania had sexual encounters with Denisovan-related groups of hominids at different periods over thousands of years as they expanded in the region. Study scientists detected at least four independent mixing events over the course of more than 20,000 years, with the last happening as recently as 21,000 years ago.

This suggests “mixing between modern humans and archaic hominins was a common phenomenon in the Asia-Pacific region,” the study team writes.

And overall, people living in this area today were found to harbor the genetic legacy of Denisovans and Neanderthals — a fact observed by other scientists before.

The big takeaway — The researchers also discovered present-day Pacific populations inherited Denisovan genetic mutations that control immune responses against pathogens. These mutations may have strengthened the original modern human’s immune systems, providing a reservoir of genes that helped them adapt to local pathogens.

“This suggests that modern humans have gained genetic resistance against infectious diseases from this admixture,” Patin says.

Ancient instances of natural selection, in turn, left genomic signatures that can be detected in present human populations.

“This suggests modern humans have gained genetic resistance against infectious diseases from this admixture.”

Neanderthal genes were associated with modern-day effects on the immune system, metabolism, neural development, and skin pigmentation. In some populations of Pacific Islanders, for example, the authors found evidence for genetic adaptation in genes associated with sharp vision and metabolism of food sources characteristic of Pacific islands.

For example, they pinpointed genomic signatures of natural selection favoring a low level of high-density lipoprotein cholesterol, or “good” cholesterol — possibly an adaptation that supports a fish-based diet. This finding could help scientists better understand how some populations of Pacific Islanders have responded to more recent changes in diet and why they suffer from high instances of metabolic diseases.

What’s next — Technological advances in genetics research, large sampling, and powerful statistical methods finally enabled this team to retrace "genetic history" in the Pacific region, says Patin.

“In my opinion, the most exciting aspect of this study is the wealth of information we can deduce from the genetic diversity of human populations,” he says.

Expanding the work to focus on other parts of the Pacific, such as Polynesia, could help scientists better understand links between past genetic adaptation and present-day disease risk in the region, the authors write. Future studies could combine this new work in genomics with archaeological and linguistic data to further hash out how humans migrated to new places, and how often isolated groups of archaic hominins met and mated with modern humans.

“All these apparently disconnected pieces of evidence, when analyzed jointly, will soon allow us to tackle major questions relating to human evolution,” says Patin.

Abstract: The Pacific region is of major importance for addressing questions regarding human dispersals, interactions with archaic hominins and natural selection processes¹. However, the demographic and adaptive history of Oceanian populations remains largely uncharacterized. Here we report high-coverage genomes of 317 individuals from 20 populations from the Pacific region. We find that the ancestors of Papuan-related (‘Near Oceanian’) groups underwent a strong bottleneck before the settlement of the region, and separated around 20,000–40,000 years ago. We infer that the East Asian ancestors of Pacific populations may have diverged from Taiwanese Indigenous peoples before the Neolithic expansion, which is thought to have started from Taiwan around 5,000 years ago. Additionally, this dispersal was not followed by an immediate, single admixture event with Near Oceanian populations, but involved recurrent episodes of genetic interactions. Our analyses reveal marked differences in the proportion and nature of Denisovan heritage among Pacific groups, suggesting that independent interbreeding with highly structured archaic populations occurred. Furthermore, whereas introgression of Neanderthal genetic information facilitated the adaptation of modern humans related to multiple phenotypes (for example, metabolism, pigmentation, and neuronal development), Denisovan introgression was primarily beneficial for immune-related functions. Finally, we report evidence of selective sweeps and polygenic adaptation associated with pathogen exposure and lipid metabolism in the Pacific region, increasing our understanding of the mechanisms of biological adaptation to island environments.