Shotgun metagenomics data from non-frozen archaeological and lake sediments from Alaska

Sedimentary ancient DNA (sedaDNA) has huge potential to expand our knowledge of past human resource use and exploitation from open and near-surface archaeological sites. However, sediment from such sites is often not water-logged or frozen, and so the vertical movement of free water through the sediment, coupled with root penetration of overlaying vegetation, has the potential to blur and mix sedaDNA signals from different stratigraphic horizons. Here, we generated shotgun metagenomics data from archaeological sites and a nearby lake from interior Alaska. By using the lake record as a positive control for expected plant taxa and levels of ancient DNA damage in sediments of concurrent age, we show evidence for a temporally mixed plant sedaDNA signal in the archaeological sediments. This suggests that root penetration may be the dominant driver of cross-stratigraphic sedaDNA mixing in non-frozen sediments and that such taphonomic factors should be accounted for when assembling plant taxonomic inventories from these settings.