Radiocarbon-dated fossils indicate woolly mammoths were extirpated from mainland Beringia around 13 000 years ago. However, environmental DNA in permafrost suggests small “cryptic“ populations survived into the Holocene. Resolving this discrepancy is crucial to understanding the drivers of mammoth extinction. The Adopt-a-Mammoth project, launched in 2022, is increasing the number of radiocarbon-dated mammoth fossils to locate the chronologically youngest specimens. Here, we report results from two “mammoth“ vertebral epiphyseal plates from interior Alaska that produced the youngest radiocarbon ages associated with mammoth specimens (~1900–2700 cal a BP). However, isotopic data indicated that these individuals consumed marine resources, and subsequent ancient DNA analysis revealed the specimens were in fact from a North Pacific Right whale and a Minke whale. Solving the mystery of recent “mammoth” fossils raised new questions. How did the remains of ancient whales become emplaced in sediment so far from the coastline? We briefly consider four scenarios to account for this.

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.

Using temporarily spaced high-coverage ancient genomes, we can assess population decline prior to extinction. However, finding suitable ancient remains for recovering this type of data is challenging. Here, we sequenced a high-coverage genome from muscle tissue of a 14,400-year-old woolly rhinoceros (Coelodonta antiquitatis)—a cold-adapted herbivore that went extinct ∼14,000-years ago—found inside a permafrost-preserved wolf's stomach. We compared genome-wide diversity, inbreeding, genetic load, and population size changes in this sample with two other Late Pleistocene Siberian woolly rhinoceros. We found no evidence of population size decline, nor any genomic erosion, shortly prior to the species' demise. Given the few long homozygous segments, typically indicative of recent inbreeding, we infer a stable population size only a few centuries before extinction. Thus, the woolly rhinoceros' extinction likely happened rapidly, during the Bølling–Allerød interstadial. This study demonstrates the ability to recover high-quality DNA from unlikely sources to elucidate species' extinction dynamics.

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.

After the last ice age, the brown bear (Ursus arctos) recolonized Scandinavia, likely from two different source populations, resulting in two subpopulations with distinct mitochondrial haplogroups. In the early 1900s, human persecution led to a severe bottleneck that reduced the overall population size from around 5000 to approximately 130 individuals. After protective measures were taken, the population recovered and today it comprises roughly 3000 individuals. Such bottlenecks can lead to loss of genetic variation, which can have long-lasting effects on population viability and population recovery. In this study, we generated whole-genome data of seven historical and 21 contemporary Scandinavian brown bears to estimate heterozygosity, inbreeding and mutational load, as well as population structure in the pre- and post-bottleneck subpopulations. Surprisingly, no significant decrease in heterozygosity and no significant increase in inbreeding and mutational load were found when comparing the historical and modern subpopulations. However, analyses of population structure and admixture suggest that the southern subpopulation has lost most of its genetic uniqueness, except in the mitochondrial genome. Our results indicate that the bottleneck led to an increase in male-driven gene flow from the north to the south, which maintained the subpopulation’s genome-wide diversity and may have contributed to its successful recovery.

Background: The field vole, an abundant and widespread microtine rodent, is a complex comprised of three cryptic species: the short-tailed field vole (Microtus agrestis) which is present over much of Eurasia, the Mediterranean field vole (Microtus lavernedii) in southern Europe, and the Portuguese field vole (Microtus rozianus) in western Spain and Portugal. Previous research has shown high genomic differentiation of these three lineages. However, the details of the process underlying their divergence remain unknown.

Results: We analyse 70 mitogenomes and 16 nuclear genomes of modern specimens, and 83 mitogenomes and 12 nuclear genomes of ancient specimens spanning the last 75 thousand years (ka). We estimate the divergence of Portuguese from short-tailed and Mediterranean field voles to be ca. 220 ka ago and of the latter two species to be ca. 110 ka ago, earlier than previous estimates involving only modern sequences. The divergence times we obtain match those between major mitochondrial lineages of cold-adapted and steppe rodents in Europe. We find signatures of gene flow within and between field vole lineages, with some analyses suggesting a hybrid origin of the Mediterranean lineage. Ancient specimens from the Italian Peninsula reveal a previously unrecognised lineage that show evidence of genetic exchange with other populations.

Conclusions: The pattern of genetic variation in the field vole species complex demonstrates the impact of stadial-interstadial cycles in generating recurrent episodes of allopatry and connectivity of populations, a situation which could only be revealed by our dense genomic sampling over time.

BACKGROUND: The Norwegian lemming (Lemmus lemmus) is a small rodent endemic to the Fennoscandian alpine and arctic tundra. The species is known for cyclic population outbreaks and mass movements during peak years. Previous research based on microsatellites revealed high genetic variation but a weak population structure in the Norwegian lemming. RESULTS: In this study, we revisit the population structure of the species using genome-wide data. To do this, we generated a high-quality de novo reference genome for Lemmus lemmus, and resequenced genomes to 2.5-5 × coverage, from 86 lemmings sampled across the species' entire geographic distribution. Our results reveal that the population is geographically structured into distinct subpopulations, with an overall pattern characterised by isolation-by-distance among subpopulations. Furthermore, our results are consistent with earlier work suggesting that the species survived the last ice age within a northern refugium. CONCLUSIONS: Together, these findings provide a genome-wide perspective on today's population structure of the Norwegian lemming. In addition, we provide a de novo reference genome, which we believe will be a valuable resource to the research community.

During the last glacial period (~118 to 11.7 ka), the Arctic has been characterized by a major redistribution of flora and fauna as a consequence of extreme climatic fluctuations, with associated glacial advances and retreats, sea-level changes, and shifting sea ice extent. In the high-latitude regions of Northern Europe that are currently subject to rapid climate warming, we lack a comprehensive understanding of faunal biodiversity in the last glacial period due to the extreme rarity of preserved organic remains. Here, we present a stratified sediment deposit with a diverse faunal composition preserved in a bone-bearing layer in Arne Qvamgrotta, part of the Storsteinhola cave system (68.10° N 16.38° E) in Northern Norway. Chronological analyses of sediments and bones including radiocarbon, optically stimulated luminescence, uranium–thorium, and phylogenetic dating place the faunal assemblage in Marine Isotope Stage 5a (MIS 5a, Odderade interstadial, ~85 to 71 ka). Combining comparative osteology and bulk-bone metabarcoding, we identify 46 taxa, including mammals, birds, and fish, with several species not previously found in Fennoscandia. The fauna implies a nonanalogous cold-adapted coastal community, with close proximity to sea ice and nearby freshwater bodies. Mitogenome analyses of a subset of taxa identify extinct lineages which attest to a lack of habitat tracking and the absence of a local refugium during the subsequent fully glaciated periods. This faunal record demonstrates long-term faunal dynamics and coastal environmental conditions during MIS 5a in the European 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.