Biology subjects

Dalen, L.

Publications and source records attributed to Dalen, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Hic sunt dracones: ancient DNA from the extinct palaeofauna of the tiny Mediterranean archipelago of Columbretes and its implications for human visitation

The Columbretes archipelago in the Mediterranean is an example of deep isolation and sporadic human interaction during the Holocene. We recovered ancient DNA from 2,600-year-old microfauna and historical museum specimens to investigate the island's extinct fauna. Despite challenging preservation conditions, we successfully recovered mitogenomes from historical Vipera latastei specimens, and partial mitogenomes from snake, skink, and lizard subfossils. Phylogenetic analyses confirm the extinct Columbretes snake as Vipera latastei, sharing a haplotype with the historical specimen and clustering with modern populations from northeastern Iberia, validating its provenance and suggesting a single mitochondrial lineage since isolation. The extinct skink, Chalcides bedriagai, also shows affinities with eastern Iberia. These results point to a vicariant origin for the herpetofauna, likely isolated on the island following sea level rise after the Last Glacial Maximum. Conversely, a 2,600-year-old mouse incisor yielded a Mus musculus mitogenome, indicating Iron Age human-mediated introduction. Additionally, genomic analysis of a 11th-century CE human burial revealed an individual with genetic affinities to the Central Mediterranean and Balkans, highlighting medieval maritime mobility. This study resolves the long-debated Columbretes snake identity, traces biogeographic origins and illustrates the interplay of natural isolation and anthropogenic influence on the island biodiversity.

ecology↗

bioRxiv2026

G-ALN: a GPU-accelerated BWA-aln algorithm for palaeogenomics

Abstract Summary: The most commonly used method to achieve optimal mapping for short and damaged ancient DNA (aDNA) reads is the BWA-aln algorithm with seeding disabled. However, this CPU-based algorithm is computationally demanding, as the aligner must tolerate mismatches and indels across the entire read. To improve alignment speed, we present G-ALN: a GPU implementation of the BWA-aln and indexing algorithms. G-ALN first searches all reads on GPU cores, with reads that need a long search being shared dynamically between the GPU and any spare CPU cores. Every read is searched using the same algorithm as BWA, so the output is byte-identical, which we confirmed here using woolly mammoth and Neanderthal datasets with aDNA-specific parameters. In our benchmarking, G-ALN indexed a reference genome ~32 times faster than BWA, and read alignment speed increased ~6-fold. G-ALN was developed through AI-assisted coding (Claude Opus 5.5). It processes thousands of reads in parallel on each GPU and aligns more than twice as many aDNA reads per unit of energy. These results show that G-ALN offers a practical route to using GPU resources in established aDNA analysis workflows. Availability and Implementation: G-ALN is implemented in C++ and CUDA and is freely available under the GPLv3 license at https://github.com/bilalbioinfo/galn. It requires an NVIDIA GPU with compute capability 7.0 or higher and CUDA 11.8 or later.

bioinformatics↗

bioRxiv2026

The Muskox Way: Humans, plants and animals in northeast Greenland through the Holocene

The Muskox Way hypothesis suggests that the first humans entering northeast Greenland from Arctic Canada followed and hunted muskox. Yet whether muskox arrived before people remains debated, as only two bones predate the Independence culture (4500-3900 cal BP). More broadly, the arrival of plants and animals, and how the three periods of human settlement related to ecosystem changes, remain poorly understood. We analysed sedimentary ancient DNA from lakes in Wandel Dal (Late Sommersoe and Midsommersoe) and Zackenberg, identifying 121 native plants and nine animal taxa. In Wandel Dal, the plant assemblage indicates a warmer climate than today about 8200-3900 years ago, followed by an abrupt change in flora and sedimentation rate at 3900 cal BP, especially at Midsommersoe. Muskox DNA is present continuously at Midsommersoe from 7400 cal BP, about three millennia before humans arrived. The Zackenberg record dates to 12,200 cal BP, with arctic forbs, grasses, ferns and crowberry in the earliest layers, willow from 8200 cal BP and birch from 7200 cal BP, but muskox only in the last 2500 years, the latter period coinciding with Greenlandic Dorset culture. The arrival of the Thule culture in 1400 CE coincides with a slight increase in plant richness at Wandel Dal and an increase in mammal detections. Reindeer occurred only in samples older than 6000 years, consistent with their absence from archaeological bone records. Overall, humans arrived long after the first megafauna and appear to have had limited impact on their populations, although cultural periods coincided with environmental changes.

ecology↗

bioRxiv2026

Paleogenomic time series reveal past population dynamics and their relevance for the conservation of the Alpine ibex

Endangered species often suffer from genetic threats such as inbreeding depression, the accumulation of mutation load and the general loss of genetic diversity, which may deprive them from future adaptation. Since the genetic make-up of a species is strongly affected by its evolutionary past, however, interspecific comparisons are difficult and absolute levels of genetic diversity may be a relatively poor predictor of extinction risk. To better interpret current levels of genetic diversity of actively managed species, the comparison of present-day genomic data to that of ancient material pre-dating recent anthropogenic population declines has been advocated, but remains rarely done at the evolutionary time scales necessary to understand past population dynamics. Here we demonstrate the usefulness of deep genomic time series through 40 high quality ancient genomes of the Alpine ibex, which faced near-extinction in the 19th century but has since been reintroduced across the Alps and recovered remarkably. The samples, which span the last 14,000 years, evidence strong and stable population structure at the continental scale, paired with frequent extinction and recolonization events at the local scale. These metapopulation dynamics resulted in small and largely isolated populations, with present-day, reintroduced populations only having 20% to 40% less neutral genetic diversity and 3% higher mutation load, likely due to efficient purging in the past. At the species level, however, the loss of genetic diversity was dramatic and reduced to the small fraction that segregated within the only surviving population in the Gran Paradiso area. Our analyses of ancient metapopulation dynamics in Alpine ibex underscore the importance of a healthy genetic pool for successful recolonization and long-term survival, as well as the real possibility of regional extinctions.

evolutionary biology↗

bioRxiv2026

MitoDate: a Nextflow pipeline for molecular clock dating and phylogenetic inference using ancient mitogenomes

SummaryAncient DNA studies are increasingly targeting samples that are beyond the limit of radiocarbon dating (>50 thousand years old) and are often difficult or impossible to date using other geochronological methods. In cases where complete mitochondrial genomes (mitogenomes) can be recovered from such samples, Bayesian molecular clock dating approaches are routinely used as an alternative method for estimating their age. However, molecular clock dating of ancient mitogenomes lacks a standardised, reproducible computational framework, and existing approaches rely heavily on graphical interfaces that limit automation and scalability. To address these gaps, we developed MitoDate, an automated Nextflow pipeline for reproducible molecular clock dating of ancient mitochondrial genomes. The workflow standardises Bayesian time-calibrated phylogenetic inference within a portable, containerised framework, reducing manual intervention and improving analytical consistency. Availability and implementationMitoDate is implemented in Nextflow and is freely available at https://github.com/CpgSthlm/MitoDate. The pipeline is distributed with containerised dependencies and detailed documentation, including example datasets and usage guidelines.

bioinformatics↗

bioRxiv2026

Evolutionary history and genomic vulnerability of the extinct giant deer Megaloceros giganteus

The extinct giant deer (Megaloceros giganteus) was one of the most striking megafaunal species of the Late Quaternary, distinguished by its enormous palmated antlers reaching up to 3.5 m across, the largest known among both living and extinct cervids. Despite its iconic status, little is known about its genomic history prior to extinction [~]8 thousand years ago (kya). We generated the first nuclear palaeogenomes for Megaloceros, represented by nine individuals from Germany ([~]40 kya) and Ireland ([~]11 kya), mapped to a new chromosome-level reference genome of the fallow deer (Dama dama). Phylogenomic analyses placed Megaloceros as sister to Dama (divergence [~]3.5 Ma) and revealed evidence of gene flow with ancestral Cervus lineages. Population analyses identified clear differentiation between German and Irish lineages, with higher genetic diversity in the German individuals. Two genes under strong positive selection, BNIPL and SLC10A7, are associated with apoptosis regulation and skeletal development/bone mineralisation, respectively, and may relate to the species large body and antler size. Demographic reconstructions indicate a long-term decline in effective population size, extremely low heterozygosity, little evidence of extensive runs of homozygosity, and an elevated burden of predicted deleterious alleles. Together, these results suggest that Megaloceros entered the terminal Pleistocene in a genomically fragile state, offering new insight into the biology and evolutionary legacy of one of the largest and most distinctive cervids that ever lived.

evolutionary biology↗

bioRxiv2026

DNAharvester: A Nextflow Pipeline for Analysing Highly Degraded DNA from Ancient and Historical Specimens

Ancient DNA (aDNA) research has advanced rapidly with the development of high-throughput sequencing, enabling genome-wide analyses of large collections of prehistoric specimens. However, analysing palaeontological and archaeological material with highly degraded DNA constitutes a major bioinformatic challenge. DNA from such samples is characterised by short fragment lengths, low endogenous content, post-mortem damage, and cross-species contamination, which can increase spurious mapping and reference bias, affecting downstream population genetic inferences. We present DNAharvester, a modular and reproducible pipeline designed specifically for processing highly degraded DNA from ancient and historical specimens. DNAharvester integrates metagenomic filtering, competitive mapping, adaptive aligner selection (incorporating BWA-aln, BWA-mem, and Bowtie2), and systematic evaluation of reference bias and spurious mapping. By incorporating flexible mapping and filtering strategies, the pipeline can be adapted to varying sample preservation, focusing on maximising authentic data recovery. DNAharvester features subworkflows for iterative assembly of mitogenomes, identification of genomic repeats and CpG sites, taxonomic classification, microbial/pathogen screening, genetic sex determination, and variant calling. To accommodate varying sequencing depths, the pipeline supports diploid variant calling, genotype likelihood estimation, and pseudo-haploid random allele calling. Implemented in Nextflow, DNAharvester provides a highly scalable, containerised framework that enhances reproducibility, portability, and robustness in aDNA analyses. We validated the pipeline using simulated and empirical datasets, demonstrating its ability to systematically mitigate complex background contamination while preserving authentic genomic signals. By streamlining complex bioinformatic tasks through simple configuration files, DNAharvester establishes a standardised approach for analysing aDNA datasets and makes genomic analyses of ancient remains accessible to the broader research community.

bioinformatics↗

bioRxiv2025

Ancient balanced polymorphism underlies long-standing adaptation for seasonal camouflage in the least weasel

Unraveling how adaptive traits originate and evolve is key to understanding the mechanisms shaping species diversity and their adaptive potential. Seasonal color molts, from summer-brown to winter-white, evolved in at least 21 mammals and birds to maintain camouflage in environments with seasonal snow, but the occurrence of winter-brown morphs reflects seemingly convergent local adaptation to distinct snow conditions. In the least weasel (Mustela nivalis), alternative winter morphs map to the pigmentation gene MC1R, but the evolutionary history and functional basis of this variation remain unknown. Using in vitro cellular assays, we show that winter-brown coats are caused by a derived protein-coding amino acid substitution that reduces MC1R affinity to its ligands, ASIP and -MSH. Using targeted enrichment and sequencing, we find that this mutation arose de novo within the species, around one million years ago, and was maintained across the geographically structured populations generated during its evolution in Europe. Using simulations, we show that genetic drift cannot explain the long-term maintenance of this variant, which is likely driven by spatially varying selection acting on the phenotypic polymorphism, anchoring local adaptive responses. Our results underscore how long-standing adaptive variation can fuel recurrent adaptation to heterogeneous environments through time.

evolutionary biology↗

bioRxiv2025

On the ancestry and evolution of the extinct dire wolf

Dire wolves (Aenocyon dirus) are extinct predators of Pleistocene North America. Although phenotypically similar to living wolves (Canis lupus), dire wolves have yet to be placed confidently in the canid family tree. We generated 3.4x and 12.8x paleogenomes from two well-preserved dire wolves dating to > 13,000 and > 72,000 years ago, and estimated consensus species trees for these and 10 canid species. Our results revealed that [~]2/3 of dire wolf ancestry is derived from a lineage sister to the clade comprising the gray wolf, coyote, and dhole, and the remaining [~]1/3 from a lineage near the base of Canini diversity. We identified 80 genes evolving under diversifying selection in dire wolves. Our results underscore the power of paleogenomes to resolve long-standing taxonomic questions and contribute to growing evidence of the role of post-speciation gene flow as an evolutionary force.

evolutionary biology↗

bioRxiv2025

Multiplex-edited mice recapitulate woolly mammoth hair phenotypes

The woolly mammoth (Mammuthus primigenius) possessed a thick woolly coat and other cold-adaptive traits that enabled survival in harsh arctic environments. Current de-extinction efforts focus on genetically modifying the closely related Asian elephant to express woolly mammoth traits. In this study, we establish a multiplex-edited mouse model with modifications in genes associated with hair morphology and lipid metabolism, enabling insights into traits involved in developing woolly hair textures. Our optimized workflows achieved high editing efficiencies and produced genetically modified mice with simultaneous editing of up to seven different genes. Selected modifications include loss-of-function mutations in Fgf5, Tgm3, and Fam83g, among others. The resulting mice display exaggerated hair phenotypes including curly, textured coats, and golden-brown hair. This study advances methods of rapid establishment of complex genetic models. These approaches inform de-extinction efforts and research involving the genetic basis of mammalian hair development.

genetics↗

bioRxiv2023

Facilitated introgression from domestic goat into Alpine ibex at immune loci

Introgression is expected to be adaptive at loci under balancing selection, for instance at loci relevant for the immune response, but these loci generally also contain ancient polymorphisms. Ancient genomics is a promising tool to detect recent introgression and disentangle it from ancient polymorphisms. Alpine ibex (Capra ibex), a wild goat species native to the European Alps, faced near-extinction two centuries ago, but has recovered thanks to successful restoration programs. Previously, signals of introgression from the domestic goat (Capra aegagrus hircus) into the Alpine ibex genome were found at the major histocompatibility complex. This introgression was suggested to potentially be adaptive since it introduced new diversity at a gene locus important for immunity. But no genome-wide analyses of introgression have been performed to confirm the potential relevance of immune loci. Here we take advantage of two ancient whole genomes of Alpine ibex combined with 29 modern Alpine ibex genomes and 31 genomes representing six related Capra species to investigate genome-wide patterns of introgression. Our complementary analysis of putatively introgressed haplotypes and demographic modelling suggests 2.3% recent domestic goat ancestry among wild Alpine ibex. The introgression was estimated to have happened during the last 300 years coinciding with the time when the species had very small population size. Further analysis suggested an enrichment of immune-related genes, where the adaptive value of alternative alleles may give individuals with otherwise depleted genetic diversity a selective advantage.

evolutionary biology↗

bioRxiv2023

Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

Ancient DNA (aDNA) sequencing analysis typically involves alignment to a modern reference genome assembly from a related species. Since aDNA molecules are fragmentary, these alignments yield information about small-scale differences, but provide no information about larger features such as the chromosome structure of ancient species. We report the genome assembly of a female Late Pleistocene woolly mammoth (Mammuthus primigenius) with twenty-eight chromosome-length scaffolds, generated using mammoth skin preserved in permafrost for roughly 52,000 years. We began by creating a modified Hi-C protocol, dubbed PaleoHi-C, optimized for ancient samples, and using it to map chromatin contacts in a woolly mammoth. Next, we developed "reference-assisted 3D genome assembly," which begins with a reference genome assembly from a related species, and uses Hi-C and DNA-Seq data from a target species to split, order, orient, and correct sequences on the basis of their 3D proximity, yielding accurate chromosome-length scaffolds for the target species. By means of this reference-assisted 3D genome assembly, PaleoHi-C data reveals the 3D architecture of a woolly mammoth genome, including chromosome territories, compartments, domains, and loops. The active (A) and inactive (B) genome compartments in mammoth skin more closely resemble those observed in Asian elephant skin than the compartmentalization patterns seen in other Asian elephant tissues. Differences in compartmentalization between these skin samples reveal sequences whose transcription was potentially altered in mammoth. We observe a tetradic structure for the inactive X chromosome in mammoth, distinct from the bipartite architecture seen in human and mouse. Generating chromosome-length genome assemblies for two other elephantids (Asian and African elephant), we find that the overall karyotype, and this tetradic Xi structure, are conserved throughout the clade. These results illustrate that cell-type specific epigenetic information can be preserved in ancient samples, in the form of DNA geometry, and that it may be feasible to perform de novo genome assembly of some extinct species.

genomics↗

bioRxiv2023

Population genomics reveals extensive inbreeding and purging of mutational load in wild Amur tigers

The inbreeding is a big threat for the persistence of genetic diversity in small and isolated populations of endangered species. The homozygous genome could exacerbate inbreeding depression by introducing homozygous deleterious alleles in the population. However, purging of inbreeding loads as they become homozygotes in small populations could alleviate the depression. The Amur tiger (Panthera tigris altaica) is typically exists in small population living in forests in Northeast Asia and is among the most endangered animals on the planet with great symbolic significance of conservation. By comparing with captive individuals, we revealed substantially higher and more extensive inbreeding in the wild Amur tiger population (FROH=0.51) than in captive Amur tigers (FROH=0.26). We further found much less mutational loads in wild populations when compared with captive Amur tigers. However, the frequency of loss of function and deleterious nonsynonymous mutations inside ROH regions are much lower than that in non-ROH regions in both wild and captive Amur tigers, indicating the purging may had occurred in both populations but much effective in the wild population. In addition, we found the average frequency of deleterious alleles was much lower than that of neutral alleles in the wild population, indicating that the purifying selection contributed to the purging of mutational loads in the wild Amur tigers. These findings provide valuable genome-wide evidence to support the making of future conservation plans of wild Amur tigers.

genomics↗

bioRxiv2022

Contrasting genomic consequences of anthropogenic reintroduction and natural recolonisation in high-arctic wild reindeer

Anthropogenic reintroduction can supplement natural recolonisation in reestablishing a species distribution and abundance. However, both reintroductions and recolonisations can give rise to population bottlenecks that reduce genetic diversity and increase inbreeding, potentially causing accumulation of genetic load and reduced fitness. Most current populations of the endemic high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus) originate from recent reintroductions or recolonisations following regional extirpations due to past overharvesting. We investigated and compared the genomic consequences of these two paths to reestablishment using whole-genome shotgun sequencing of 100 Svalbard reindeer across their range. We found little admixture between reintroduced and natural populations. Two reintroduced populations, each founded by 12 individuals around four decades (i.e. 8 reindeer generations) ago, formed two distinct genetic clusters. Compared to the source population, these populations showed only small decreases in genome-wide heterozygosity and increases in inbreeding and lengths of runs of homozygosity. In contrast, the two naturally recolonised populations without admixture possessed much lower heterozygosity, higher inbreeding, and longer runs of homozygosity, possibly caused by serial population bottlenecks and/or fewer or more genetically related founders than in the reintroduction events. Naturally recolonised populations can thus be more vulnerable to the accumulation of genetic load than reintroduced populations. This suggests that in some organisms even small-scale reintroduction programs based on genetically diverse source populations can be more effective than natural recolonisation in establishing genetically diverse populations. These findings warrant particular attention in the conservation and management of populations and species threatened by habitat fragmentation and loss.

genomics↗

bioRxiv2022

aMeta: an accurate and memory-efficient ancient Metagenomic profiling workflow

Analysis of microbial data from archaeological samples is a rapidly growing field with a great potential for understanding ancient environments, lifestyles and disease spread in the past. However, high error rates have been a long-standing challenge in ancient metagenomics analysis. This is also complicated by a limited choice of ancient microbiome specific computational frameworks that meet the growing computational demands of the field. Here, we propose aMeta, an accurate ancient Metagenomic profiling workflow designed primarily to minimize the amount of false discoveries and computer memory requirements. Using simulated ancient metagenomic samples, we benchmark aMeta against a current state-of-the-art workflow, and demonstrate its superior sensitivity and specificity in both microbial detection and authentication, as well as substantially lower usage of computer memory. aMeta is implemented as a Snakemake workflow to facilitate use and reproducibility.

bioinformatics↗

bioRxiv2022

Convergent evolution of skim feeding in baleen whales

The origin of pygmy right whales (Caperea marginata), the smallest and most enigmatic of the living baleen whales, remains contentious. Morphological analyses largely continue to ally Caperea with right whales (balaenids) based on shared cranial features like a tall braincase and a narrow, highly arched rostrum. By contrast, molecular data and some anatomical evidence suggest a closer relationship with rorquals (balaenopterids), but fail to explain "the substantial issue of convergence posed by the many balaenid features of Caperea" (Berta & Demere, 2017). To resolve this question, we sequenced the nuclear genome of C. marginata (812,269,251 paired reads; 47X average depth of coverage, with 89.33% of the genome covered at [≥]10X) and subjected it to a multispecies coalescent analysis including representatives of all baleen whale families. Our results confirm Caperea as sister to rorquals and, thus, the convergent origin of its right whale-like anatomy. Considering this overwhelming molecular evidence, we propose that the traditional taxonomic grouping of Caperea with right whales be abandoned.

evolutionary biology↗

bioRxiv2022

When blue turns to grey - Paleogenomic insights into the evolutionary history and extinction of the blue antelope (Hippotragus leucophaeus)

The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (H. equinus) or sable (H. niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are unfavourable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4x mean coverage from a historical specimen (~200 years old) and one at 2.1x mean coverage from a fossil specimen dating to 9,800-9,300 cal BP, making it currently the oldest palaeogenome from Africa. Phylogenomics show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelopes, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene-Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely a decisive factor in the blue antelopes extinction.

evolutionary biology↗

bioRxiv2022

GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

BackgroundMany wild species have suffered drastic population size declines over the past centuries, which have led to genomic erosion processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling population sizes and conservation status of threatened species. One way to directly quantify the genomic consequences of population declines is to compare genome-wide data from pre-decline museum samples and modern samples. However, doing so requires computational data processing and analysis tools specifically adapted to comparative analyses of degraded, ancient or historical, DNA data with modern DNA data as well as personnel trained to perform such analyses. ResultsHere, we present a highly flexible, scalable, and modular pipeline to compare patterns of genomic erosion using samples from disparate time periods. The GenErode pipeline uses state-of-the-art bioinformatics tools to simultaneously process whole-genome re-sequencing data from ancient/historical and modern samples, and to produce comparable estimates of several genomic erosion indices. No programming knowledge is required to run the pipeline and all bioinformatic steps are well-documented, making the pipeline accessible to users with different backgrounds. GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub (https://github.com/NBISweden/GenErode). ConclusionsGenErode is a user-friendly and reproducible pipeline that enables the standardization of genomic erosion indices from temporally sampled whole genome re-sequencing data.

bioinformatics↗