Sarah L. Fordyce

Once nearly eradicated from Europe, grey wolves ( Canis lupus ) have recently undergone a remarkable demographic recovery, but their long-term survival remains precarious. By analyzing 1,001 genomes, we uncover a mosaic of distinct evolutionary lineages, not a single recovering population. Northern populations exhibit Asian wolf ancestry, while southern populations preserve ancient Holocene lineages, with dog introgression varying by region. Isolated wolves from the Scandinavian, Italian, and Iberian peninsulas harbored particularly high levels of inbreeding and fixed deleterious mutations. Signatures of genome erosion were widespread across Europe, with many populations falling well short of the minimum size recommended for long-term survival. Our study reveals the complex tapestry of wolf ancestry and variation across Europe, which calls for nuanced, regional conservation plans founded in genetic monitoring.

The recovery of ancient DNA (aDNA) from non-mineralized archaeological materials remains a major methodological challenge, particularly in tropical and semi-arid contexts where high temperature and humidity accelerate molecular degradation. This study evaluates the feasibility of extracting, authenticating, and identifying aDNA from feathers and plant remains recovered at the Túcume Archaeological Complex, a major Lambayeque and later Inca administrative and ceremonial center on the northern coast of Peru. A total of 216 archaeological subsamples (135 feathers and 81 plant remains) were processed in a dedicated ancient DNA laboratory under strict contamination controls. DNA extraction followed protocols optimized for ancient DNA extraction, shallow shotgun sequencing data was generated, and metagenomic pipelines were used to assess authenticity and taxonomic assignment. DNA was successfully retrieved from both avian and plant materials, showing highly fragmented molecules and characteristic deamination patterns consistent with ancient DNA. Although endogenous DNA content was generally low but in many cases was sufficient for molecular classification. Avian sequences were assigned to multiple orders, including Passeriformes, Galliformes, Anseriformes, Strigiformes, and Columbiformes, while plant sequences corresponded primarily to high-level clades such as Mesangiospermae, Eudicotyledoneae, and Monocotyledoneae. The successful recovery of authentic DNA from such challenging substrates demonstrates the methodological viability of archaeogenomic analysis under tropical-arid conditions. This study emphasizes the need to expand genomic reference databases for South American fauna and flora to improve taxonomic resolution and supports the inclusion of unconventional biological materials in future archaeogenomic research in Peru and other tropical regions.

Welwitschia mirabilis , a unique gymnosperm native to Namibia and Angola, is a keystone plant species in the Namib Desert. It represents the only extremely long-lived non-clonal plant species occurring under hyperarid desert conditions, yet limited attempts have been made to accurately determine its age. Here, we present radiocarbon dates from a dead, sectioned Welwitschia of moderate size. We find the outer caudex tissue growth to progressively increase in age from the leaf base towards the ground level in this dwarf tree, while the inner cortex tissue becomes younger. Our sampling strategy revealed that the oldest tissue from this Welwitschia , found at the base of the caudex in the middle of the lobe, was dated to 531 ± 20 ¹⁴ C years, suggesting a vertical growth rate of approximately 0.47 to 0.67 mm/year. These findings can serve as a basis for future dating of larger, living individuals.

Background: Arctic and alpine insects experience extreme environmental stressors, yet the genomic basis of their adaptation is poorly understood. Diamesa midges (Diptera: Chironomidae) are cold-adapted insects inhabiting glacial and high-altitude freshwater ecosystems, but no chromosome-level genomes have been available to date. Findings: We present the first haplotype-resolved, chromosome-level genomes for four Diamesa species (Diamesa hyperborea, Diamesa lindrothi, Diamesa serratosioi, and Diamesa tonsa), assembled using PacBio HiFi sequencing and Hi-C scaffolding. The assemblies show high completeness and k-mer representation. Phylogenomic analyses place Diamesinae as sister to other Chironomidae except Podonominae, and comparisons suggest introgression between the distinct species D. hyperborea and D. tonsa. Comparative genomic analyses across 20 Diptera species identified significant gene family contractions in Diamesa related to oxygen transport and metabolism, consistent with adaptation to high-altitude, low-oxygen environments. Expansions were observed in histone-related and Toll-like receptor gene families, suggesting roles in chromatin remodeling and immune regulation under cold stress. A glucose dehydrogenase gene family was significantly expanded across all cold-adapted species studied, implicating it in cryoprotectant synthesis and oxidative stress mitigation. Diamesa exhibited the largest gene family contraction at any phylogenetic node, with limited overlap in expansions with other cold-adapted Diptera, indicating lineage-specific adaptation. Conclusions: Our findings support the hypothesis that genome size condensation and selective gene family changes underpin survival in cold environments. These new genome assemblies provide a valuable resource for studying adaptation, speciation, and conservation in cold-specialist insects. Future integration of gene expression and population genomics will further clarify the evolutionary resilience of Diamesa in a warming world.

Dental calculus offers an extraordinary window into the past, preserving a rich archive of genetic material that can unlock new insights into ancient ecosystems. By capturing traces of oral microbiomes, dietary components, and even gut microbes regurgitated by ruminants, dental calculus provides an extraordinary window into the past to reconstruct ecological interactions and past environmental conditions. Here, we harness the power of ancient metagenomics to explore the oral microbiome, digestive microbiomes and diet of Pleistocene reindeer ( Rangifer tarandus ) from archaeological sites in France, a region that once served as a glacial refugium before reindeer disappeared from the area. We used shotgun metagenomic sequencing to assemble microbial genomes (MAGs) and classify microbial and dietary reads from dental calculus of 19 ancient reindeer (ca. 12,000 - 23,000 years BP) and 27 modern and historical (1861 - 1958 CE) Scandinavian reindeer. Notably, six bacterial taxa associated with the rumen microbiome were consistently detected across both ancient and modern samples, offering a rare glimpse into the continuity of digestive adaptations over thousands of years. Our recovery of oral microbial and putative dietary plant DNA suggest adaptive capability. Our results suggest a spatio-temporal turnover in oral microbiome and putative dietary plant DNA, which might be explained by ecological differences between Pleistocene France and contemporary Scandinavia. As soft tissue preservation is rare in ancient remains, dental calculus emerges as an exciting and powerful tool for reconstructing the environmental and ecological histories of both past and extinct populations.

Sedimentary ancient DNA (sedaDNA) has been proposed as a key methodology for reconstructing paleoclimates and biodiversity over time. To a lesser extent, it has been explored as a complementary tool for reconstructing human-driven local environmental changes over time, such as those explored in open air archaeological sites. Our study employs a sedaDNA metagenomic approach to investigate land use and environmental change at the archaeological site of Torgårdsletta in central Norway, spanning from the Bronze Age through the Medieval period. Stratigraphic sediment samples reveal temporal shifts in plant, animal and microbial communities, reflecting evolving human practices and climatic conditions. Progression through the layers indicate signs or land clearance, cultivation and animal husbandry in the region. Notably, a significant reduction in microbial and plant diversity during periods of climatic upheaval—such as the AD 536–540 volcanic event—correlates with landscape and societal adjustments. The findings demonstrate that sedaDNA complements traditional proxies, providing high-resolution insights into past land use, environmental interactions, and societal organization. The successful extraction of ancient genetic material underscores sedaDNA’s potential to reconstruct dynamic prehistoric landscapes and anthropogenic impacts, offering further potential for understanding long-term human-environment relationships in Scandinavia.

SUMMARY: Essential E3 ubiquitin ligase HUWE1 (HECT, UBA and WWE domain containing 1) regulates key factors, as p53. Mutations in HUWE1 have been associated with neurodevelopmental X-linked intellectual disabilities (XLIDs), however the pathomechanism at the onset of heterogenous XLIDs remains unknown. In this work, we identify p53 signaling as the process hyperactivated in lymphoblastoid cells from patients with HUWE1-promoted XLIDs. The hiPSCs-based modeling of the severe HUWE1-promoted XLID, the Juberg Marsidi syndrome (JMS), reviled majorly impaired neural differentiation, accompanied by increased p53 signaling. The impaired differentiation results in loss of cortical patterning and overall undergrowth of XLID JMS patient-specific cerebral organoids, thus closely recapitulating key symptoms, as microcephaly. Importantly, the neurodevelopmental potential of JMS hiPSCs is successfully rescued by restoring p53 signaling, upon reduction of p53 levels. In summary, our findings indicate that increased p53 signaling leads to impaired neural differentiation and is the common cause of neurodevelopmental HUWE1-promoted XLIDs.

Base excision repair (BER) initiated by alkyladenine DNA glycosylase (AAG) is essential for removal of aberrantly methylated DNA bases. Genome instability and accumulation of aberrant bases accompany multiple diseases, including cancer and neurological disorders. While BER is well studied on naked DNA, it remains unclear how BER efficiently operates on chromatin. Here, we show that AAG binds to chromatin and forms complex with RNA polymerase (pol) II. This occurs through direct interaction with Elongator and results in transcriptional co-regulation. Importantly, at co-regulated genes, aberrantly methylated bases accumulate towards the 3′end in regions enriched for BER enzymes AAG and APE1, Elongator and active RNA pol II. Active transcription and functional Elongator are further crucial to ensure efficient BER, by promoting AAG and APE1 chromatin recruitment. Our findings provide insights into genome stability maintenance in actively transcribing chromatin and reveal roles of aberrantly methylated bases in regulation of gene expression.

New Guinea is a topographically and biogeographically complex region that supports unique endemic fauna. Studies describing the population connectivity of species through this region are scarce. We present a population and landscape genetic study on the endemic malaria‐transmitting mosquito, Anopheles koliensis (Owen). Using mitochondrial and nuclear sequence data, as well as microsatellites, we show the evidence of geographically discrete population structure within Papua New Guinea (PNG). We also confirm the existence of three rDNA ITS2 genotypes within this mosquito and assess reproductive isolation between individuals carrying different genotypes. Microsatellites reveal the clearest population structure and show four clear population units. Microsatellite markers also reveal probable reproductive isolation between sympatric populations in northern PNG with different ITS2 genotypes, suggesting that these populations may represent distinct cryptic species. Excluding individuals belonging to the newly identified putative cryptic species (ITS2 genotype 3), we modeled the genetic differences between A. koliensis populations through PNG as a function of terrain and find that dispersal is most likely along routes with low topographic relief. Overall, these results show that A. koliensis is made up of geographically and genetically discrete populations in Papua New Guinea with landscape topography being important in restricting dispersal.

Base excision repair (BER) initiated by alkyladenine DNA glycosylase (AAG; aka MPG) is essential for removal of aberrantly methylated DNA bases. Genome instability and accumulation of aberrant bases accompany multiple diseases including cancer and neurological disorders. While BER is well studied on naked DNA, it remains unclear how BER efficiently operates on chromatin. Here we show that AAG binds to chromatin and forms complex with active RNA polymerase (pol) II. This occurs through direct interaction with Elongator and results in transcriptional co-regulation. Importantly, at co-regulated genes aberrantly methylated bases accumulate towards 3’end, in regions enriched for BER enzymes AAG and APE1, Elongator and active RNA pol II. Active transcription and functional Elongator are further crucial to ensure efficient BER, by promoting AAG and APE1 chromatin recruitment. Our findings provide novel insights to maintaining genome stability in actively transcribing chromatin, and reveal roles of aberrantly methylated bases in regulation of gene expression.