During the last glacial–interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1–8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe–tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe–tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.

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The middle Tanana Valley of central Alaska contains a well‐preserved record of human occupation and paleoenvironmental change since the Late Glacial period (c. 16,000 cal yr BP) and is a critical region for understanding human dispersal into the Americas. Micromorphology analysis of soils and sediments from six archaeological sites yields valuable information about soil formation processes and landscape evolution during the Late Glacial and into the Holocene. At the macroscale, site stratigraphies are very similar, and thin organic‐rich layers (locally known as “stringers”) are commonly interpreted as buried soils. However, at the microscale, these layers exhibit significant differences in the degree of bioturbation, organic matter humification, and boundary abruptness, indicating that pedogenesis was not the sole process at every site. In this way, our microscale analysis addresses issues of equifinality related to site formation interpretations, a persistent problem with subarctic and high‐latitude stratigraphy. Additionally, this study reveals a certain level of landform and landscape instability within a broader trend of regional increases in pedogenesis and vegetation coverage, adding to the existing model of heterogeneity across this subarctic landscape. Here we demonstrate the utility of micromorphology to test field interpretations and improve models of Late Glacial landscape evolution in high‐latitude contexts.

The Dog Creek archaeological site (NcVi-3), located in the northern Yukon, provides evidence of complex site transformational processes related to microclimatic conditions occurring since the mid-Holocene. Geoarchaeological research at Dog Creek sought to interpret site formation processes in order to understand the relationship between surficial artifacts, buried artifacts, and stratified sediments. It also attempted to reconstruct the periglacial processes that were active in transforming the site and their relationships to microclimatic conditions. Sedimentology and fabric analysis show that artifacts were buried by solifluction and disturbed by frost heave and cryoturbation. Radiocarbon dating and pollen analysis demonstrated that solifluction took place approximately 5200-2000 years ago when a spruce forest existed at the site. This evidence suggests an onset of cooling conditions that continues to the present. After the mid-Holocene, the spruce treeline began to move south toward its present position.