Newly sequenced Neanderthal genomes shed light on family structure and population dynamics

An ancient family of Neanderthals once inhabited a cave in the Altai Mountains of Siberia over 49,000 years ago. From their vantage point, they could observe the nearby river valley where various animals like bison, red deer, and wild horses roamed. During their stay, a teenage girl lost a tooth, possibly from eating bison hunted by her father or other family members on the grasslands.

Recently, scientists have examined the genomes of this family, which consisted of a father, daughter, and 12 other relatives who occupied the same cave for under a century. This discovery has significantly increased the number of known Neanderthal genomes and provides a glimpse of the Neanderthal population in the eastern regions where they were on the brink of extinction.

Moreover, the genomes offer insights into the social structure of Neanderthal groups. According to Laurits Skov, a geneticist from the Max Planck Institute for Evolutionary Anthropology who presented the study virtually at the ninth International Symposium on Biomolecular Archaeology, the genetic evidence indicates that these male Neanderthals likely stayed with their family groups as adults, similar to men in various modern human societies.

According to Cosimo Posth, a paleogeneticist from Tübingen University, the ability to obtain genomes from seven males at one site is impressive. He further adds that the genetic evidence suggests that the group lived in small clusters consisting of closely related males.

Although scientists have sequenced the genomes of 19 Neanderthals in the past decade, the DNA mostly came from distantly related females who lived in various parts of Europe and Asia between 400,000 to 50,000 years ago.

A team led by computational biologist Benjamin Peter and paleogeneticist Svante Pääbo from Max Planck conducted the new study with the help of postdoc Skov. They extracted Neanderthal DNA from bone fragments, teeth, and a jawbone uncovered during ongoing excavations at Chagyrskaya and Okladnikov caves by archaeologists from the Russian Academy of Sciences in Novosibirsk. Optically stimulated luminescence dates of the surrounding sediments suggest that the Neanderthals lived between 49,000 to 59,000 years ago. Both caves are situated within 50 to 130 kilometers of the well-known Denisova Cave, which was intermittently inhabited by both Neanderthals and their close cousins, the Denisovans, between 270,000 to 50,000 years ago.

The team examined DNA from over 700,000 sites across the genomes of seven males and five females from Chagyrskaya, and a male and a female from Okladnikov. Their findings showed family relationships, including the nuclear DNA from a Chagyrskaya bone fragment that linked a father to his teenage daughter, who had lost a tooth. Additionally, several individuals shared two types of maternally inherited mitochondrial DNA, indicating they lived within the same century, as the genomes had not yet differentiated from one another.

The study provides insight into the social structure of Neanderthal society. Many Chagyrskaya males carried long sections of identical nuclear DNA inherited from a recent ancestor. Their Y chromosomes were similar and came from a modern human ancestor, similar to the only three other male Neanderthal genomes on record. The nuclear DNA also revealed that they were more closely related to later Neanderthals in Spain than earlier ones at the nearby Denisova Cave, indicating migration.

The similarities among the males suggest that they were part of a population of only a few hundred men who fathered children. This number is similar to the breeding males in today’s endangered mountain gorilla populations. As such, Skov suggests that if this Neanderthal population were equivalent to today’s populations, they would be considered an endangered group.

In contrast to the Y chromosome and nuclear DNA, the mtDNA of both males and females was relatively diverse, indicating that more female ancestors contributed to the population than males. This could be due to a founder effect or the fact that women moved more frequently between groups. Skov believes the latter is more likely based on modeling studies. He thinks these Neanderthals lived in very small groups of 30 to 110 breeding adults, and young females left their birth families to live with their mates’ families. This social structure is similar to most modern human cultures.

However, Posth cautions that 14 genomes cannot provide a complete understanding of Neanderthal social lives. The low diversity in males’ DNA raises concerns about their population’s viability. In just 5,000 to 10,000 years, our closest relatives would be extinct.

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