Traditionally, midden deposits have been investigated using zooarchaeological approaches, which typically require excavations of large volumes of sediment. Here we used a less intrusive DNA-based alternative that is independent of diagnostic bone fragments and is able to detect remains from a range of different organic sources such as skin, meat, fat, keratinaceous material and bone. Using a metagenomic approach, we characterized the faunal and floral diversity in four ancient midden deposits ranging as far back as ∼2000 BC.

Moreover, we were able to recover a diverse faunal profile at Fladstrand despite the high concentration of DNA from dog or wolf at this site. Apart from C. lupus, the faunal assemblage constituted hare, seals, caribou and narwhal, all of which are in agreement with the archaeological record11. The presence of the dog tapeworm T. multiceps suggests that dogs faeces were present in the sampled sediments. These results imply that the sampling site at Fladstrand might have been used as a tethering place for dogs as well as a waste dump. Unfortunately, the dominance of dog and the low concentration of other vertebrate DNA prevented a meaningful comparison of abundances in this layer with the biomass estimates from zooarchaeological analyses.

We found the midden samples from the Norse settlement of Sandnes to represent a short period in the fourteenth century out of the full settlement history at the site. This explains why the aDNA record exhibited no marked difference between the anthropogenic layers studied. However, the important status of Sandnes9,28 was evident in the faunal assemblage, which indicated that the subsistence on the farm was based primarily on domestic cattle, sheep and goat, supplemented with wild fauna such as seals, walrus and caribou. Although the species identified with sedaDNA were in agreement with the bone record9, the biomass estimated from the DNA data found livestock species to be ∼3 × higher than the values estimated from the bone record. This is supported by the higher number of uniquely assigned reads to T. hydatigena, indicative of a parasitic life cycle typical for domesticated ruminants, namely sheep, compared with less abundant T. multiceps and E. canadensis, indicative of life cycles in wild life hosts. Like the presence of dog at Fladstrand, this might reflect the presence of livestock species at Sandnes the year round, causing continuous accumulation of DNA in the midden deposits from urine and defecation29.

The ordination analysis clearly differentiates between the diet based on both domestic and marine animals for the Norse and the extreme reliance on marine ressources for the Inuit (Supplementary Fig. 1). This difference in subsistence practices is also reflected in stable isotope data from human bone remains from Saqqaq30, Dorset31, Thule32 and Norse32,33 cultural sites. Analysis of isotope composition in Inuit remains suggests a strong dependence on marine resources, while the Norse bone remains show evidence of subsistence based on both domestic and marine animals in comparable quantities.

The ordination analysis also distinguishes the three ancient Inuit cultures from each other, with layers from the same culture at different sites clustering together (Supplementary Fig. 1). In addition, the clear separation of the presumed Dorset layer at Qajaa in the ordination analysis confirms that this layer represents a distinct culture. This is in agreement with the identification of Dorset-like microblades, which further supports that this layer is of Dorset origin. Despite the low concentration of vertebrate DNA in this layer, we identify two novel species for the Dorset culture—bowhead whale and dog. Of the 29 canine reads identified in this layer, 7 could be assigned uniquely to dog (C. lupus familiaris), while two reads could be assigned unambiguously to wolf (C. lupus lupus). This represents the first identification of dog in the Dorset culture. However, the archaeological context from this layer remains unclear as these samples represent a profile outside of the main excavation area investigated originally by J. Meldgaard13.

Bowhead whale DNA was identified at both Saqqaq settlements (Fig. 2), in all sediment layers analysed. At Qeqertasussuk, bowhead whale was the most abundant species identified, constituting 49.2% of the DNA, while at Qajaa it ranked as the second or third most abundant species in each layer. These findings are in striking contrast to the bone record. At Qeqertasussuk, only 102 fragments of whale bone, teeth and baleen were found among a total of ∼100,000 excavated bones (0.04%) and, of these, only a single piece of baleen could be identified as either bowhead whale or North Atlantic right whale (Eubalaena glacialis)5. Similarly, at Qajaa, two narwhal bones were found along with a single bone from an unidentified cetacean out of ∼15,000 bones (0.02%)8. The underrepresentation of whale bones in archaeological sites is a well-known phenomenon, typically ascribed to difficulties in transporting large carcasses from shore to the settlement34,35 in combination with the higher value of blubber or meat compared with bones36. In the arctic, several studies have suggested that the fossil record may underestimate the importance of whales to ancient Arctic cultures4,5,9, however, the lack of suitable methods to detect remains of tissue like blubber and meat in sediment have prevented further investigations on this matter. As such, our findings represent the first tangible evidence that bone counts alone may underestimate large whales in Arctic midden remains.

Furthermore, sedaDNA results from Qajaa support that the fossil record underestimates other large mammals, such as caribou, walrus and narwhal, all of which have a higher representation in the sedaDNA faunal assemblage than observed in the fossil record. Likewise, at Qeqertasussuk, we found caribou to comprise 18.8% of total DNA reads, compared with an estimated 0.3% in the bone record.

In summary, our results demonstrate that large mammals such as caribou, walrus, narwhal and bowhead whale are underrepresented in the osteological record while domestic species such as cow, sheep, goat and dog are overrepresented in the DNA profile. Hence, to confidently reconstruct subsistence practices from midden remains, it is strongly encouraged to apply a combination of sedaDNA and morphological analyses, as both of these approaches may be misinterpreted when standing alone (discussed further in Supplementary Note 3).

The identification of bowhead DNA in 4,000-year-old Saqqaq deposits raises questions about the history of whale hunting and whale scavenging centred in the North Pacific and Bering Strait. The origins of active whaling has been tied to the development of toggling harpoons that appear about 4000 BC among North Pacific and Bering Sea peoples for hunting small sea mammals like seals in ice-infested waters37. Intermediate-sized toggling harpoons suitable for hunting walrus appear in Alaskan Old Whaling culture ca. 1000 BC (refs 38, 39), and large whaling harpoons and floats in Old Bering Sea and Norton cultures between 500 and 800 AD (ref. 40). Systematic whaling with large umiak boat crews became a central economic feature of the Thule culture that migrated into the Eastern Arctic and Greenland around 1200–1400 AD, replacing Dorset Paleo-Inuit culture whose main quarry were seals, walrus and caribou41,42. So far, a single Saqqaq harpoon measuring 16.6 cm remains the only example of large toggling harpoons suitable for hunting large whales in the Paleo-Inuit record4.

As opposed to whale hunting, scavenging of stranded cetacean carcases was common in pre-historic times and has been described across multiple sites in Europe43, North America44 and Africa34. Hence, the relative abundance of bowhead whale DNA in the Saqqaq sediment layers could be explained by scavenging whale carcasses. Whales were probably abundant along the nutrient-rich West Greenland waters that were so attractive to European whalers, and dead (drift) whales could have been driven ashore by wind and tides making them available to Saqqaq beach-comers. The warmer Saqqaq climate may also have influenced the frequency of whale strandings; today killer whales appearing in the less ice-congested Arctic waters often cause whales and other sea mammals to seek shelter in shallow bays and inlets, causing them to strand. Dependent on the rate of decomposition, the meat and blubber from drift whales might have been used for human food, oil lamps or feeding of dogs.

On the other hand, large whale hunting is not contingent on Thule style technology. In the Paamiut area in Southern Greenland, humpback whales were traditionally hunted using simple lances and toggling harpoons. By approaching the docile animals noiselessly, the hunters could kill the whales by spearing them behind the flipper45. Similarly, single kayak-equipped eighteenth-century Unangan (Aleut) hunters of the Bering region used barbed non-toggling harpoons coated with aconite poison to immobilize the whales by spearing them near the flipper46. After a few days the whale could no longer remain upright and would drown and be towed to shore. While it is unlikely that aconite poison was part of the Saqqaq hunting strategy, a similar effect might have been achieved from harpoons infested with rotten meat or blubber, as even small flesh wounds can cause inflammation and, within days, immobilization of the flipper or death of such large whales47. Hence, using the Paamiut or the Aleut method, Saqqaq hunters armed only with penetrating lances and small harpoons may have been able to kill large, slow-swimming bowheads without Thule-style technology and large umiak boat crews.

The presented evidence of Saqqaq whale exploitation requires re-evaluating maritime history. Western history has always considered European whaling as the originator and pinnacle of marine exploitation, beginning with Basque whaling in the Bay of Biscay in the 1400s AD (refs 48, 49). However, 1,500 years earlier, Inuit people of the Bering Strait region had developed technology sufficient for large whale hunting. The utilization of whale products thousands of years before the technology and communal organization of Thule whaling pushes back the first evidence of whale product usage in the Arctic and can be seen as a logical development of the powers of indigenous observation and ingenuity in the efficient use of a plentiful northern marine energy resource. We should not be surprised if Ocean Bay Kodiak Islanders, Early Jomon of Japan, and others around the Greater North Pacific Rim also found ways to use whale products long before purposeful whaling became a routine indigenous economic and social enterprise or a European Arctic industry.

Taken together, the high level of agreement between this DNA-based approach and previous morphological analyses along with the identification of previously unidentified species demonstrates that DNA deposited simultaneously with the fossils represents an equally important and complementary fraction of the faunal assemblage. We found that the subsistence contribution of some previously identified species such as caribou (Qajaa and Qeqertasussuk) and narwhal (Qajaa) had probably been underestimated by faunal analyses. Furthermore, the genomic approach allowed us to identify several species for the first time, including the bowhead whale (Qajaa and Qeqertasussuk), walrus (Qajaa) and hooded seal (Qajaa). These findings expand our current knowledge of the Paleo-Inuit and illustrates that the Saqqaq people had a wider diet-breadth than was previously thought and were able to exploit most of the mammals available to them.