Upward Sun River site

Human remains

The first excavation at Upward Sun River in 2010 yielded the cremated remains of a 3-year-old individual. The individual had been cremated inside a hearth, which was then filled in, with an abandonment of the site quickly afterwards. This individual was given the name Xaasaa Cheege Ts'eniin (Upward Sun River Mouth Child) by the local Healy Lake Tribe and is referred to by archaeologists as USR3. Researchers were unable to recover DNA from this individual.

Infant burials

In a 2013 excavation of the site, researchers discovered the remains of two female infants in a layer directly underneath the cremated individual. The two individuals were covered in red ochre and buried together in a pit burial with grave goods, including four decorated antler rods, two lithic dart points and bifaces. The antler rods and dart points were likely part of a weapon system. The two individuals were given the names Xach'itee'aanenh t'eede gaay (Sunrise child-girl) and Yełkaanenh t'eede gaay (Dawn twilight child-girl) by the local people and are referred to by archaeologists as USR1 and USR2, respectively.

One of the individuals (USR2) was a prenatal, possibly stillborn 30-week-old fetus, while the other (USR1) was a 6- to 12-week-old infant. The prenatal individual is the only prenate and youngest Late Pleistocene individual to be recovered in the Americas. All three died during the summer. Their teeth show features most similar to those found in Native Americans and Northeast Asians.

Archaeogenetics

In 2015, researchers were able to extract the entire mitochondrial genome from both individuals. In 2018, researchers successfully sequenced the nuclear DNA from the petrous bone of both individuals, yielding around 17-fold coverage from USR1 and low coverage from USR2. Based on osteological analysis, the two infants were thought to be female; this assessment is corroborated by evidence from DNA analysis.

Comparisons with other populations

When compared with ancient populations, USR1 and USR2 show closest genetic affinity to Shuká Káa from On Your Knees Cave. USR1 shows extra genetic affinity for Siberians and East Asians in a way that is not found in later ancient individuals from the Americas such as Anzick-1, Kennewick Man, or the woman from the Lucy Islands dated to around 6,000 years ago. USR1 belongs to a population that predates the hypothesized splitting of ancient Native American populations into the Northern Native American and Southern Native American branches and does not cluster genetically with either later population. USR1 forms a distinct clade with the individual from Cave 2 of the Trail Creek Caves on the Seward Peninsula.

When compared with modern populations, USR1 shows closest genetic affinity to modern Native Americans, then Siberians and East Asians. USR1 does not cluster genetically with any modern Native American population. The genetic distance from USR1 to Mal'ta boy is the same as that from modern Native American populations to Mal'ta boy. USR1 shows additional genetic affinity for Denisovans that is not matched by modern Native Americans; this additional Denisovan affinity is likely due to sampling variation from an ancient population with higher levels of heterogenous Denisovan admixture.

Kinship

Nuclear DNA analysis suggests that USR1 and USR2 are closely related, probably somewhere roughly in the range from half-siblings to first cousins. However, mtDNA analysis shows that the two infants are not maternally related. The two infants carry mtDNA lineages that are only found in the Americas. USR1, the 6- to 12-week-old infant, comes from C1b. The prenatal infant, USR2, carries a basal lineage of Haplogroup B2 that is also matched by the individual from Trial Creek Cave; this specific mtDNA lineage is different from the derived B2 lineage generally found in the Americas.

Both individuals represent the northernmost discovery of these mtDNA lineages and show that the mtDNA diversity in the ancient population is higher than in the modern, lending credence to the Beringia Standstill Hypothesis.

Ancient Beringian

USR1 is thought to be representative of a hypothesized ancient population referred to as Ancient Beringian. Ancient Beringian is now considered to be composed of three individuals: USR1, USR2 and the 9,000 year-old individual from Trail Creek Cave. This genetic clustering is matched by the archaeological evidence, as the Upward Sun River Site and Trail Creek Cave, despite being located over 750 km (466 mi) away from each other, both share similarities in artefact technology. Based on DNA analysis of USR1, the Ancient Beringians are hypothesized to have split off from East Asians around 36,000 years ago, with continuous gene flow occurring until around 25,000 years ago. The Ancient Beringians are also hypothesized to have diverged from the ancestors of Native Americans around 22,000 to 18,100 years ago.

Phenotypic analysis

Phenotypic analysis shows that USR1 does not carry the derived EDAR allele commonly found in modern East Asians and Native Americans. However, USR1 does carry the derived rs174570 FADS2 allele that was targeted by a selective sweep.

Salmon

Around 300 bone fragments from salmonids were recovered at Upward Sun River, representing the earliest surviving evidence of salmon eating in North America. DNA analysis types the salmon remains as coming from Oncorhynchus keta (chum salmon). Isotopic analysis shows that the salmon were anadromous.

Other material remains

An obsidian flake discovered as part of the grave goods found in the infant burial was chemically identified as coming from the Hoodoo Mountain primary source site in Kluane National Park, Yukon, Canada, a location 600 km (370 mi) away from the Upward Sun River site.