After the last ice age, species migrated into a newly deglaciated Scandinavia. Brown bear recolonization is thought to have occurred from two directions—from the south and the northeast—resulting in a nonoverlapping distribution of two distinct mitochondrial clades. A contact zone in central Sweden separates populations with mitochondrial clade 1a in the south from those with clade 3a in the north. However, a paucity of brown bear subfossils in Scandinavia has limited testing of this prevailing model using ancient DNA. Here, we present a high-coverage brown bear mitogenome (231×) and nuclear genome-wide data (0.05×) extracted from lake sediment dated to 9.6 cal. ka BP from northern Sweden, representing the oldest known record of brown bear in the region. At this point in the Early Holocene, the Fennoscandian Ice Sheet was in its final stages of recession. Surprisingly, our analyses suggest that this environmental genome represents one male individual carrying clade 1a and with southern brown bear nuclear ancestry, despite being found far north of the contact zone. This suggests the individual was a migratory bear and had dispersed northward from its birthplace. Our finding adds to the scarce genomic record of Early Holocene brown bears and highlights the use of sedimentary ancient DNA as a powerful source of genomic information.

We identified a 3000-year-old specimen from the Traditional Territory of the Tr’ondëk Hwëch’in in central Yukon Territory, Canada as the first known mummified remains of an ancient North American porcupine (Erethizon dorsatum), known as “Ts’ey” in the Hän language, using genetic analysis and metagenomic validation. Our analysis of the sample yielded the first-ever complete ancient mitochondrial genome for (E. dorsatum) and only the second full mitogenome for the species. Its Holocene age is considerably younger than the Pleistocene megafauna typically recovered in the Yukon permafrost, demonstrating the potential for these deposits to preserve specimens from interglacial periods. Crucially, this finding confirms the presence of porcupines in the region 3000 years ago, in line with the hypothesis that this species only dispersed into Yukon and Alaska following the establishment of boreal forests after the Last Glacial Period.

Ancient environmental DNA is increasingly vital for reconstructing past ecosystems, particularly when paleontological and archaeological tissue remains are absent. Detecting ancient plant and animal DNA in environmental samples relies on using extensive eukaryotic reference genome databases for profiling metagenomics data. However, many eukaryotic genomes contain regions with high sequence similarity to microbial DNA, which can lead to the misclassification of bacterial and archaeal reads as eukaryotic. This issue is especially problematic in ancient eDNA datasets, where plant and animal DNA is typically present at very low abundance. In this study, we present a method for identifying bacterial- and archaeal-like sequences in eukaryotic genomes and apply it to nearly 3,000 reference genomes from NCBI RefSeq and GenBank (vertebrates, invertebrates, plants) as well as the 1,323 PhyloNorway plant genome assemblies from herbarium material from northern high-latitude regions. We find that microbial-like regions are widespread across eukaryotic genomes and provide a comprehensive resource of their genomic coordinates and taxonomic annotations. This resource enables the masking of microbial-like regions during profiling analyses, thereby improving the reliability of ancient environmental metagenomic datasets for downstream analyses.

During the last cold stage (115–11.7 cal kya BP), the non-glaciated part of Arctic Eurasia exhibited a distinctive plant composition consisting of steppe and xerophilous arctic plants. This vegetation formed the Pleistocene mammoth steppe, which provided a habitat for large herbivores like mammoths (Mammuthus primigenius) and steppe bison (Bison priscus). In this study, we analyzed the DNA sequences of well-preserved plant material from the intestinal tract of the frozen mummy of an extinct steppe bison discovered in the Kolyma Lowland, Northeastern Russia in 2009. Radiocarbon dating placed the specimen at >48 kyr. We leveraged genome-wide and skimmed genome accessions to maximize the retrieval of sequenced reads for identification. In line with macrofossil evidence, we identified alkali grass (Puccinellia), indicating high salinity, and Larch (Larix) in the DNA data of the steppe bison sample. The occurrence of larch north of the current tree line indicates warm temperatures during the growing season. Additionally, we confirmed the presence of plant genera typically associated with steppes and productive meadows under open and arid soil conditions such as Artemisia, Tanacetum, Koeleria, Festuca, Puccinellia, Taraxacum, Alopecurus, and Poa, while Phippsia suggests high soil water content, at least locally. We also attempted to infer the likely most closely related species for each genus. The most abundant authenticated genera, Artemisia and Puccinellia, align with their known prevalence in the mammoth steppe, reflecting broader environmental signals beyond the steppe bison's diet. Hence, the use of metagenomic approaches in combination with comprehensive reference databases offered insights into steppe bison diet, allowed us to obtain a more detailed view of the mammoth steppe vegetation, and provided extended interpretations of soil conditions.