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.

Ancient DNA has revolutionized the study of extinct and extant organisms that lived up to 2 million years ago, enabling the reconstruction of genomes from multiple extinct species, as well as the ecosystems where they once thrived. However, current DNA sequencing techniques alone cannot directly provide insights into tissue identity, gene expression dynamics, or transcriptional regulation, as these are encoded in the RNA fraction. Here, we report transcriptional profiles from 10 Late Pleistocene woolly mammoths. One of these, dated to be ∼39,000 years old, yielded sufficient detail to recover tissue-specific regulatory mechanisms and biological functions essential for skeletal muscle metabolism, representing the oldest ancient RNA sequences recorded to date. We showcase the potential to study ancient RNA molecules beyond preconceived limitations, providing an analytical framework for validating and decoding preserved transcriptomes through time. With our findings, we anticipate the emergence of integrative paleo-studies combining genomics, proteomics, and transcriptomics.

The collapse of the mammoth steppe ecosystem at the end of the Pleistocene fundamentally restructured northern communities across Beringia, yet the spatial variability of this transition remains poorly understood. We present a multi-proxy analysis of the Mint Gulch site in the Klondike region, Yukon Territory, spanning ca. 16,000 to 13,000 calibrated years before present (cal yr BP), integrating sedimentary ancient DNA (sedaDNA), macrofossils, pore-ice isotopes (δ¹⁸O), and radiocarbon chronology. Pore-ice isotope values increase from −33.9‰ at ca. 16,000 cal yr BP to −21.4‰ by ca. 13,180 cal yr BP, reflecting regional warming and changing hydroclimate. SedaDNA records document grazing megafauna (woolly mammoth, horse, steppe-bison) and grasses and forbs until ca. 13,910 cal yr BP, when shrub-dependent taxa and browsing herbivores (moose, willow ptarmigan) first appear, or appear in greater abundance. However, macrofossil evidence from an Arctic ground squirrel midden (ca. 13,680 cal yr BP) reveals continued presence of steppe-tundra indicator taxa, including Artemisia sp., Potentilla sp., and the weevil Connatichela artemisiae. Our results demonstrate that despite regional hydroclimate change beginning ca. 14,000 cal yr BP, steppe-tundra vegetation persisted in locations where topography and aspect favoured xeric taxa. The Mint Gulch site provides rare documentation of the transitional period between steppe-tundra and shrub-tundra ecosystems, capturing co-occurrence of both communities around 13,910 cal yr BP. This study highlights the spatially heterogeneous nature of late Pleistocene ecosystem transitions in eastern Beringia and the importance of multi-proxy approaches for understanding local-scale persistence of steppe-adapted taxa.

The Eurasian cave lion was abundant across the Northern Hemisphere before the Late Pleistocene megafaunal extinctions. However, the extent of the distinction between cave and modern lions and their adaptive differences have remained unclear. Using 12 cave lion genomes spanning more than 100,000 years, we show that modern and cave lions were distinct evolutionary lineages with separate demographic histories and unique non-synonymous variants. We also identify evidence of ancient gene flow between them, with the best modern lion proxy for this ancestry being an extinct Southwest Asian population. This admixture correlates with global ice extent, with 3.2%–4.4% modern lion ancestry detected in a ∼20,000-year-old cave lion from Central East Asia. These findings provide insight into the evolutionary history of the cave lion, once one of the Northern Hemisphere’s most ecologically impactful megafaunal species.

Biostratigraphy is a fundamental tool for age-calibrating marine sediments and enabling palaeoceanographic reconstructions. However, establishing age control in marine sediments of the Arctic Ocean is challenging, due to low micro- and nannofossil abundances, discontinuous occurrences across glacial and interglacial periods, as well as spatial and temporal variations in carbonate preservation. Gephyrocapsa huxleyi is a globally distributed coccolithophore whose first occurrence at ca 290 ka is widely used to date Quaternary marine sediments. Yet, its initial appearance and stratigraphic range in the Arctic Ocean are debated. Here, we present the first combined sedaDNA-nannofossil approach to trace the occurrence of G. huxleyi throughout three sediment cores from the Lomonosov Ridge recovered during the Arctic Ocean 2016 expedition on icebreaker Oden. SedaDNA was extracted from 87 samples spanning key lithological boundaries. Following shotgun sequencing, the presence of G. huxleyi was assessed using three independent bioinformatic tools Kraken2, BWA and BLAST. These results were integrated with lithological data and Gephyrocapsa nannofossil assemblages to evaluate the potential of palaeogenomics as a biostratigraphic tool in the Arctic that could potentially overcome the limitations of conventional nannofossil-based approaches. Although we found broadly overlapping sedaDNA and nannofossil results, key discrepancies and methodological limitations do not allow us to confidently identify the first occurrence of G. huxleyi in the studied sequences. We discuss both the potential and the challenges of sedaDNA as a complementary biostratigraphic tool to improve age control of Arctic marine sediments.

The Arctic Ocean is changing rapidly due to global warming, but how this will impact marine Arctic ecosystems remains uncertain. Several Pleistocene interglacials, like Marine Isotope Stages (MIS) 5e, 9 and 11 form potential analogues to a future warmer Arctic and can give important insights on how Arctic ecosystems may respond to climate warming. However, micro- and nannofossils are scarce in many Pleistocene marine sediment cores, and are often not in agreement with biomarker data. Sedimentary ancient DNA (sedaDNA) is an emerging method that does not require the preservation of fossils and can therefore be used to detect taxa without any hard body parts, like most protist groups and zooplankton. Thanks to this method, it is now possible to detect organisms from all trophic layers of marine ecosystems. SedaDNA provides us with new opportunities to reconstruct past sea ice conditions, changes to ocean currents, and borealisation of the Arctic Ocean. Developments in bioinformatics software and new techniques like shotgun metagenomics and hybridisation capture, now enable the study of ancient DNA from Middle and even Early Pleistocene sediments. Moreover, the marine sedaDNA field is working towards detecting within-species genetic variation, which can provide information on population bottlenecks, recolonisation histories, and may lead to important insights for marine conservation. Combined with traditional proxies, sedaDNA is a powerful tool for Arctic Ocean palaeo-environmental reconstructions and can help provide critical proxy data to facilitate climate model calibrations and ultimately improve climate and environmental predictions for the Arctic.

Large-scale DNA screening of palaeontological and archaeological collections remains a limiting and costly factor for ancient DNA studies. Several DNA extraction protocols are routinely used in ancient DNA laboratories and have even been automated on robotic platforms. Robots offer a solution for high-throughput screening but the costs, as well as necessity for trained technicians and engineers, can be prohibitive for some laboratories. Here, we present a high-throughput alternative to robot-based ancient DNA extraction using a 96-column plate. When compared to routine single MinElute columns, we retrieved highly similar endogenous DNA contents, an important metric in ancient DNA screening. Mitogenomes with a coverage depth greater than 0.1× could be generated and allowed for taxonomic assignment. However, average fragment lengths, DNA damage and library complexities significantly differed between methods but these differences became nonsignificant after modification of our library purification protocol. Our high-throughput extraction method allows generation of 96 extracts within approximately 4 hours of laboratory work while bringing the cost down by ~39% compared to using single columns. Additionally, we formally demonstrate that the addition of Tween-20 during the elution step results in higher complexity libraries, thereby enabling higher genome coverage for the same sequencing effort.

The genomic study of specimens dating to the Early and Middle Pleistocene (EP and MP), a period spanning from 2.6 million years ago (Ma) to 126 thousand years ago (ka), has the potential to elucidate the evolutionary processes that shaped present-day biodiversity. Obtaining genomic data from this period is challenging, but mitochondrial DNA, given its higher abundance compared to nuclear DNA, could play an important role to understand evolutionary processes at this time scale. In this study, we report 34 new mitogenomes, including two EP and nine MP mammoth (Mammuthus spp.) specimens from Siberia and North America and analyze them jointly with >200 publicly available mitogenomes to reconstruct a transect of mammoth mitogenome diversity throughout the last million years. We find that our EP mitogenomes fall outside the diversity of all Late Pleistocene (LP) mammoths, while those derived from MP mammoths are basal to LP mammoth Clades 2 and 3, supporting an ancient Siberian origin of these lineages. In contrast, the geographical origin of Clade 1 remains unresolved. With these new deep-Time mitogenomes, we observe diversification events across all clades that appear consistent with previously hypothesized MP and LP demographic changes. Furthermore, we improve upon an existing methodology for molecular clock dating of specimens >50 ka, demonstrating that specimens need to be individually dated to avoid biases in their age estimates. Both the molecular and analytical improvements presented here highlight the importance of deep-Time genomic data to discover long-lost genetic diversity, enabling better assessments of evolutionary histories.

Monitoring species’ occurrences is essential for understanding ecosystem dynamics, tracking biodiversity changes, and guiding conservation efforts. Traditional monitoring methods, such as visual surveys, are challenging, particularly for elusive and endangered species. This proof-of-concept study explores the potential of environmental DNA (eDNA) collected from peck marks as a non-invasive tool for detecting and identifying woodpecker species. We collected nine samples from fresh peck marks on birch and spruce trees in the forests of Swedish Lapland. In two samples, we successfully amplified an 81 base-pair fragment of the woodpecker mitochondrial 16S rRNA gene. Taxonomic assignment identified the Eurasian three-toed woodpecker (Picoides tridactylus), a species classified as “Near Threatened” in Sweden. We collected an additional 15 samples from 4-19 years old peck marks preserved inside the trunks of birch and pine trees in the same area. No woodpecker DNA was detected in these samples, likely due to DNA degradation. Our findings demonstrate the potential of using eDNA from peck marks as a non-invasive approach for monitoring elusive woodpecker species.

Climate changes profoundly impact species distributions and can drastically alter dynamics between formerly isolated taxa. The evolution of mammoths within North America was characterized by repeated cycles of dispersal and putative gene flow between woolly and Columbian mammoths. However, as genome-wide studies on mammoths have predominantly focused on Siberia, the consequences of these North American range shifts remain unclear. Here, we generated genome-wide and morphological data for two Late Pleistocene mammoth molars from British Columbia, Canada (BC), and jointly analysed these with previously published data. Our genome-wide analysis (n = 16) revealed gene flow between woolly and Columbian mammoths that would have gone undiscovered based on morphological (n = 48) and mitochondrial analysis (n = 124) alone. Consistent with their hybrid nature, our analyses suggest that these two BC mammoths had elevated genomic diversity. Our results highlight the importance of combining data types to reconstruct past evolutionary events. These findings demonstrate how the geographical range expansion of woolly mammoths resulted in long-term hybridization with local Columbian mammoths and enhance our understanding of the genomic and morphological consequences of climate-mediated dispersal.