The extreme cold temperatures of Greenland have fostered an environment with a barren terrestrial ecosystem of low floral and faunal diversity. Despite these conditions, people have colonized the island in at least three distinct main migration waves1. The first migration into Greenland was formed by the Saqqaq people who settled along the coasts ~4,500 years ago2,3 but disappeared again some 1,700 years later, replaced by the Greenlandic Dorset culture (around 800 bc to ad 1)4 and, after a hiatus, the Late Dorset (around ad 800–1300). At approximately ad 985, the descendants of the Vikings, the Norse, arrived in South Greenland5. They established two settlements, the Eastern and Western Settlement and survived for ~500 years until the middle of the fifteenth century, after which they disappeared as well6. The last group of people to settle in Greenland was the Thule culture, who by current estimates arrived sometime in the thirteenth century ad7. With roots in eastern Siberia, the Thule people were already adapted to a life in the Arctic and they are the only people that have persisted in Greenland until the present day8. Still, the Thule culture came under increasing European influence from the late sixteenth century; first by whalers and then by Danish–Norwegian colonial rule beginning in ad 1721. These increasing interactions had profound impacts on the Inuit, especially in regard to settlement and subsistence patterns (for example, access to new technologies such as rifles, nets, iron hooks and harpoon heads)9,10.

Compared to what is known about the earlier Palaeo-Inuit cultures in the Arctic, the Thule culture stands out because of their sophisticated technology, such as the dogsled11, the kayak and the large skin boat3 or umiaq, which allowed them to travel long distances and hunt larger marine mammals. Accordingly, the Thule people were able to exploit the full range of subsistence animals available in Greenland, from small birds and fish to large whales. Although less archaeological material exists from the Palaeo-Inuit cultures, the apparent absence of an umiaq-sized vessel and the near absence of large harpoon heads suggests that the Palaeo-Inuit may have had a more limited range of subsistence animals. For example, walrus and large whales are rarely found in middens from the Palaeo-Inuit Saqqaq culture, although they are relatively abundant in archaeological sites from the Thule culture12. This apparent difference in subsistence strategies could help explain the disappearance of the Palaeo-Inuit and the success of the Thule culture.

A multitude of different factors have shaped the peopling of the Arctic. However, it is generally accepted that the survival of past arctic cultures was heavily dependent on their ability to adapt to changing environmental conditions with new subsistence strategies when required13. Testing that hypothesis, however, has proved difficult for some groups of species as the quantifiable data on past subsistence practices rely heavily on preserved faunal remains found in archaeological deposits2, which are subject to various taphonomic processes14. The importance of whaling, for example, is notoriously difficult to pinpoint on the basis of bone fragments excavated from middens, as the meat and blubber from a whale are often exploited without bringing bones back to the settlement15,16. In most midden layers, most large cetacean remains consist of artefacts or worked fragments of whalebone and (where preservation conditions are permitting) baleen. The fragmentary nature of large whale remains in middens further hampers species identification. Furthermore, although fish must be assumed to have contributed to the diet in Greenland, it is difficult to quantify as fish bones are generally small, cryptic, fragile and easily degrade under certain conditions17.

To illuminate aspects of the past Greenlandic resource exploitation that might be missed by traditional zoo-archaeological methods, we analysed faunal remains from across Greenland using a genetics approach. We applied bulk bone metabarcoding (BBM)18 on 2,500 small unidentifiable (usually fragmented) subfossil bones, excavated from 12 distinct archaeological sites, representing the Palaeo-Inuit (Saqqaq; n = 4), Norse (n = 2) and Neo-Inuit (Thule) culture (n = 6).