Data from: Subsistence practices, past biodiversity, and anthropogenic impacts revealed by New Zealand-wide ancient DNA survey

New Zealand’s geographic isolation, lack of native terrestrial mammals, and Gondwanan origins make it an ideal location to study evolutionary processes. However, since the archipelago was first settled by humans (c. 1280 AD), its unique biodiversity has been under pressure, and today an estimated 49% of the terrestrial avifauna is extinct. Current efforts to conserve the remaining fauna rely on a better understanding of the composition of past ecosystems, as well as the causes and timing of past extinctions. The exact temporal and spatial dynamics of New Zealand’s extinct fauna, however, can be difficult to interpret, as only a small proportion of animals are preserved as morphologically identifiable fossils. Here, we conduct the first large-scale genetic survey of sub-fossil bone assemblages to elucidate the impact of humans on the environment in New Zealand. By genetically identifying over 5000 non-diagnostic bone fragments from archaeological and palaeontological sites, we reconstruct a rich faunal record of 111 species of birds, fish, reptiles, amphibians, and marine mammals. We report evidence of five whale species rarely reported from New Zealand archaeological middens, and characterise new extinct lineages of leiopelmatid frog (Leiopelma sp.) and kākāpō (Strigops habroptilus) haplotypes lost from the gene pool. Taken together, this molecular audit of New Zealand’s sub-fossil record not only contributes to our understanding of past biodiversity and pre-contact Māori subsistence practices, but also provides a more nuanced snapshot of anthropogenic impacts on native fauna following first human arrival.

Usage Notes

Seersholm2018_NZ_BBMObitools style filtered OTUs, assigned to the lowest possible taxonomic node based Blast hits. Reads with a best hit below 95% similarity to the database have not been assigned to a node (taxon_name=NA).