Biology subjects

Pedersen, M. W.

Publications and source records attributed to Pedersen, M. W..

13 recordsLinked to original sources

bioRxiv2026

Ancient environmental DNA reveals the distinct fingerprints of whaling and climate change on Antarctic marine biodiversity

The Southern Ocean is a disproportionately large contributor to Earth system processes, playing a crucial role in the global transport of carbon, oxygen and heat. It also hosts enormous seasonal biological productivity that supports diverse endemic marine biodiversity. Industrial whaling in the first half of the 20th century and recent human-driven climate change have both profoundly altered Antarctic ecosystems, but ecological surveys of these impacts are limited to well-known taxa in the short period since monitoring began. Here, we analysed five sediment records to reconstruct more than two centuries of ecosystem change across the Western Antarctic Peninsula, spanning periods before and during major human impacts. Environmental DNA metabarcoding of these records revealed substantial biodiversity shifts, with change accelerating in recent decades. We find a significant role for both climate change and whaling in restructuring communities, identifying unique variance in whole-community change explained by each driver. Moreover, we find a negative association between whaling and metazoan families which feed from the water column, suggesting that pre-whaling ecosystems had greater pelagic productivity. Overall, our results reveal baseline Antarctic biodiversity from long before observational records and identify a distinct fingerprint of human drivers in this fragile, rapidly changing ecosystem.

ecology↗

bioRxiv2025

Pleistocene reindeer dental calculus as a source for ancient oral and digestive flora

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.

evolutionary biology↗

bioRxiv2025

From bones to sediments: ancient human DNA from open-air archaeological sites

Ancient human bones degrade and sometimes disappear, especially in regions with acidic soils, making it difficult to obtain genetic information from past populations. To explore alternative sources, we analyzed ancient DNA from sediment samples collected from a burial site and a settlement site in Japan, both dating to around 1000 years ago. We found that ancient human mitochondrial DNA was obtained from sediments surrounding bones, particularly close to rib bones, while human DNA was rarely detected in the settlement site sediments. Furthermore, the mitochondrial haplogroups identified in the sediments were identical to those from human bones, confirming the reliability of this approach. Our findings suggest that genetic information about past human populations can be directly obtained from archaeological sediments in open-air sites. This method also provides a non-destructive alternative to bones and teeth, expanding possibilities for ancient DNA research in regions where skeletal remains are poorly preserved.

molecular biology↗

bioRxiv2025

Microbial sedimentary DNA from a cultural landscape disentangles the impacts of humans and nature over the past 13.5 thousand years

Bacteria and archaea are currently under-characterised in palaeoecological studies, despite their ubiquity, high diversity and tight integration with the biotic and abiotic environment and human activity. The complexity of their assemblages, and the difficulties in separating living- from paleo-prokaryotes renders analyses challenging. Here we present an ancient prokaryote metagenomic time-series from a sediment core of Lake Constance, a large and deep perialpine lake from temperate Europe, spanning the last 13,500 years of natural and anthropogenic impact. We mapped DNA to reference genomes and estimated the DNA damage of taxa, which displayed a monotonic relationship with time. By constructing co-abundance networks we recognize major microbial assemblages, containing both ancient and living microbes, that show specific dynamics. Short-term and often low-abundance assemblages are linked to the Pleistocene-Holocene transition, floods and human activities. Noticeably, certain lineages harbouring microbes common in human-impacted environments expanded during the Middle Ages and Modern time. Some abundant taxa that were linked to various freshwater and soil environments persisted through millennia. By extricating various sources and trajectories of change, we demonstrate the power of prokaryotic sedimentary DNA in revealing long-term eco-evolutionary outcomes caused by both nature- and humans.

ecology↗

bioRxiv2024

Ancient environmental DNA indicates limited human impact on marine biodiversity in pre-industrial Iceland

Human activities are affecting marine biodiversity globally by accelerating extinction rates, altering ecosystem conditions, and changing community structures. These changes can only be understood through establishing the ecosystem state prior to significant anthropogenic impact, and by disentangling the anthropogenic effect from natural climatic changes. Here, we reconstruct marine biodiversity in Iceland across three millennia (1315 BCE-1785 CE), encompassing periods of climatic fluctuation and human settlement, to explore the comparative effect of natural and anthropogenic forces on marine biodiversity. We performed 18S metabarcoding of ancient environmental DNA from two sediment cores collected from northern Icelandic shelf seas, integrating local climatic records, population estimates and zooarchaeological remains from published sources to estimate the influence of climatic and anthropogenic impacts. Against the backdrop of increasing human populations and marine exploitation, we observe no large-scale taxonomic shifts or anthropogenic biodiversity changes across the period. In contrast, we found a positive correlation between herring (Clupea harengus) detection rates and proxy-reconstructed sea surface temperature, suggesting a role for climate in shaping marine biodiversity. Overall, our data suggest that despite impacts on terrestrial ecosystems and the development of a substantial export fishery across the study period, Icelandic society may have had a limited effect on marine biodiversity.

ecology↗

bioRxiv2024

Cleaning the Dead: Optimized decontamination enhances palaeoproteomic analyses of a Pleistocene hominin tooth from Khudji, Tajikistan

The study of ancient proteins preserved in a range of archaeological, cultural heritage, and palaeontological materials is increasingly contributing to our understanding of human evolution and archaeological research questions. Many of the specimens studied have been excavated and stored for a significant duration prior to their proteomic analysis. Human handling and storage environments therefore provide ample opportunities for protein contamination onto and into specimens of interest to palaeoproteomic studies. As such, modern protein contamination limits access to endogenous proteomes. Here, we compare five approaches of bone protein decontamination applied to a Pleistocene Equus sp. bone fragment contaminated with a modern dog salivary proteome. We find that all tested methods reduce the protein contamination, but with different efficiencies. We find that a brief bleach wash is the most effective approach in removing modern protein contamination, and that no additional damage is caused to the endogenous proteome by this treatment. Next, we apply this approach to a hominin tooth found at Khudji, a Late Pleistocene archaeological site in Tajikistan. We demonstrate that a brief bleach wash removes almost all human skin protein contamination while retaining the endogenous hominin dentine proteome. Subsequent phylogenetic analysis of the Khudji dentine proteome allowed determination that the specimen is likely not a Denisovan, but still leaves ambiguity between an assignment to either modern humans or Neanderthals.

evolutionary biology↗

bioRxiv2024

soibean: High-resolution Taxonomic Identification of Ancient Environmental DNA Using Mitochondrial Pangenome Graphs

Ancient environmental DNA (aeDNA) is becoming a powerful tool to gain insights about past ecosystems. However, several methodological challenges remain, particularly for classifying the DNA to species level and conducting phylogenetic placement. Current methods, primarily tailored for modern datasets, fail to capture several idiosyncrasies of aeDNA, including species mixtures from closely related species and ancestral divergence. We introduce soibean, a novel tool that utilises pangenomic graphs for identifying species from ancient environmental mitochondrial reads. It outperforms existing methods in accurately identifying species from multiple sources within a sample, enhancing phylogenetic analysis for aeDNA. soibean employs a damage-aware likelihood model for precise identification at low-coverage with high damage rate, demonstrating effectiveness through simulated data tests and empirical validation. Notably, our method uncovered new empirical results in published datasets, including using porpoise whales as food in a Mesolithic community in Sweden, demonstrating its potential to reveal previously unrecognised findings in aeDNA studies.

bioinformatics↗

bioRxiv2024

Digesting the data: Proper validation in ancient metagenomic studies is essential

In a recent publication in this journal, Reynoso-Garcia et al. [1] used shotgun sequencing to analyze human coprolites (paleofeces) from two pre-Columbian contexts in Puerto Rico to reconstruct the diet of the islands Indigenous population before the arrival of Europeans. Based on the results, the team claim to have identified various edible New World plant species, including maize (Zea mays), sweet potato (Ipomoea batatas), chili pepper (Capsicum annuum), peanut (Arachis spp.), papaya (Carica papaya), and tomato (Solanum lycopersicum), as well as other cultivars such as cotton (Gossypium barbadense) and tobacco (Nicotiana sylvestris) [1]. Reynoso-Garcia et al. [1] also claim to have identified edible fungi, including Ustilago spp., which according to the authors, further supports their findings and points to the consumption of huitlacoche or corn smut, a known delicacy in Mexico today that is believed to have originated in Aztec times [2]. Shotgun DNA sequencing of archaeological samples, such as dental calculus or coprolites, provides a powerful tool to reconstruct ancient microbial communities and to study the evolution of the human microbiome [e.g. 3,4-6]. In some instances, shotgun sequencing results can also provide insights into the diet and subsistence strategies of past communities [e.g. 7,8]. However, identifying DNA from dietary sources in complex shotgun metagenomic datasets is far from straightforward. As has been discussed previously [9,10], and as we demonstrate below, one of the main challenges is the risk of false positives. Any potential dietary signals should, therefore, be carefully assessed. Unfortunately, we feel that Reynoso-Garcia et al.s study [1] falls short in that regard and we conclude that while it is entirely possible (and even likely, based on other evidence [e.g. 11,12]) that the Indigenous inhabitants of Puerto Rico subsisted on a diet that included some, or even all of the edible plant taxa the team identified, the DNA results they present do not, in and of themselves, support that claim.

genomics↗

bioRxiv2023

Early Pastoralism in Central European Forests: Insights from Ancient Environmental Genomics

Central European forests have been shaped by complex human interactions throughout the Holocene, with significant changes following the introduction of domesticated animals in the Neolithic ([~]7.5 - 6.0 kyr BP). However, understanding early pastoral practices and their impact on forests is limited by methods for detecting animal movement across past landscapes. Here we examine ancient sedimentary DNA (sedaDNA) preserved at the Velky Mamu[t]ak rock shelter, in northern Bohemia (Czech Republic), which has been a forested enclave since the early Holocene. We find that domesticated animals, their associated microbiomes, and plants potentially gathered for fodder, have clear representation by the Late Neolithic, around 6.0 kyr BP, and persist throughout the Bronze Age into recent times. We identify a change in dominant grazing species from sheep to pigs in the Bronze Age ([~]4.1 - 3.0 kyr BP) and interpret the impact this had in the mid-Holocene retrogressions that still define the structure of Central European forests today. This study highlights the ability of ancient metagenomics to bridge archaeological and paleoecological methods and provide an enhanced perspective on the roots of the Anthropocene.

genomics↗

bioRxiv2023

A 2-million-year-old microbial and viral communities from the Kap Kobenhavn Formation in North Greenland

Environmental DNA (eDNA) from the 2-million-year-old Kap Kobenhavn Formation of northern Greenland has revealed an ecosystem of plants and animals with no contemporary analogue1. Here, we reconstruct the microbial (bacterial, archaeal, and viral) communities that thrived at the site during this time. By leveraging a novel analytical framework that integrates taxonomic profiling, DNA damage estimates, and functional reconstructions, we identify and distinguish pioneer microbial communities from later permafrost microbial assemblages. We show that at the time of sediment deposition, the terrestrial input at the Kap Kobenhavn site originated from a palustrine wetland, suggesting warmer, non-permafrost conditions. During this period, the detection of methanogenic archaea and signals of their carbon metabolism is consistent with Kap Kobenhavn and similar northern ecosystems contributing moderate methane emissions. Intriguingly, we discover a remarkable nucleotide sequence similarity--exceeding 98%--between pioneer methanogens and present-day analogues in thawing permafrost. This aligns with the concept of "time-traveling" microbes2 surviving across geological time and waiting for conditions to turn favourable rather than evolving to adapt to changing conditions. Importantly, in contrast to the plant and animal communities of the Kap Kobenhavn, a striking similarity in microbial composition to that of a contemporary thawing Arctic suggests that microbial communities may serve as the first indication of broader climate-driven ecosystem disruptions.

microbiology↗

bioRxiv2023

euka: Robust detection of eukaryotic taxa from modern and ancient environmental DNA using pangenomic reference graphs.

1. Ancient environmental DNA (eDNA) is a crucial source of in-formation for past environmental reconstruction. However, the com-putational analysis of ancient eDNA involves not only the inherited challenges of ancient DNA (aDNA) but also the typical difficulties of eDNA samples, such as taxonomic identification and abundance esti-mation of identified taxonomic groups. Current methods for ancient eDNA fall into those that only perform mapping followed by taxo-nomic identification and those that purport to do abundance estima-tion. The former leaves abundance estimates to users, while methods for the latter are not designed for large metagenomic datasets and are often imprecise and challenging to use. 2. Here, we introduce euka, a tool designed for rapid and accurate characterisation of ancient eDNA samples. We use a taxonomy-based pangenome graph of reference genomes for robustly assigning DNA sequences and use a maximum-likelihood framework for abundance estimation. At the present time, our database is restricted to mito-chondrial genomes of tetrapods and arthropods but can be expanded in future versions. 3. We find euka to outperform current taxonomic profiling tools as well as their abundance estimates. Crucially, we show that regardless of the filtering threshold set by existing methods, euka demonstrates higher accuracy. Furthermore, our approach is robust to sparse data, which is idiosyncratic of ancient eDNA, detecting a taxon with an average of fifty reads aligning. We also show that euka is consistent with competing tools on empirical samples and about ten times faster than current quantification tools. 4. eukas features are fine-tuned to deal with the challenges of ancient eDNA, making it a simple-to-use, all-in-one tool. It is available on GitHub: https://github.com/grenaud/vgan. euka enables re-searchers to quickly assess and characterise their sample, thus allowing it to be used as a routine screening tool for ancient eDNA.

bioinformatics↗

bioRxiv2022

metaDMG - A Fast and Accurate Ancient DNA Damage Toolkit for Metagenomic Data

O_LIMotivation Under favourable conditions DNA molecules can persist for hundreds of thousands of years. Such genetic remains make up invaluable resources to study past assemblages, populations, and even the evolution of species. However, DNA is subject to degradation, and hence over time decrease to ultra low concentrations which makes it highly prone to contamination by modern sources. Strict precautions are therefore necessary to ensure that DNA from modern sources does not appear in the final data is authenticated as ancient. The most generally accepted and widely applied authenticity for ancient DNA studies is to test for elevated deaminated cytosine residues towards the termini of the molecules: DNA damage. To date, this has primarily been used for single organisms and recently for read assemblies, however, these methods are not applicable for estimating DNA damage for ancient metagenomes with tens and even hundreds of thousands of species. C_LIO_LIMethods We present metaDMG, a novel framework and toolkit that allows for the estimation, quantification and visualization of postmortem damage for single reads, single genomes and even metagenomic environmental DNA by utilizing the taxonomic branching structure. It bypasses any need for initial classification, splitting reads by individual organisms, and realignment. We have implemented a Bayesian approach that combines a modified geometric damage profile with a beta-binomial model to fit the entire model to the individual misincorporations at all taxonomic levels. C_LIO_LIResults We evaluated the performance using both simulated and published environmental DNA datasets and compared to existing methods when relevant. We find metaDMG to be an order of magnitude faster than previous methods and more accurate - even for complex metagenomes. Our simulations show that metaDMG can estimate DNA damage at taxonomic levels down to 100 reads, that the estimated uncertainties decrease with increased number of reads and that the estimates are more significant with increased number of C to T misincorporations. C_LIO_LIConclusion metaDMG is a state-of-the-art program for aDNA damage estimation and allows for the computation of nucleotide misincorporation, GC-content, and DNA fragmentation for both simple and complex ancient genomic datasets, making it a complete package for ancient DNA damage authentication. C_LI

bioinformatics↗

bioRxiv2019

Population genomics of the Viking world

The Viking maritime expansion from Scandinavia (Denmark, Norway, and Sweden) marks one of the swiftest and most far-flung cultural transformations in global history. During this time (c. 750 to 1050 CE), the Vikings reached most of western Eurasia, Greenland, and North America, and left a cultural legacy that persists till today. To understand the genetic structure and influence of the Viking expansion, we sequenced the genomes of 442 ancient humans from across Europe and Greenland ranging from the Bronze Age (c. 2400 BC) to the early Modern period (c. 1600 CE), with particular emphasis on the Viking Age. We find that the period preceding the Viking Age was accompanied by foreign gene flow into Scandinavia from the south and east: spreading from Denmark and eastern Sweden to the rest of Scandinavia. Despite the close linguistic similarities of modern Scandinavian languages, we observe genetic structure within Scandinavia, suggesting that regional population differences were already present 1,000 years ago. We find evidence for a majority of Danish Viking presence in England, Swedish Viking presence in the Baltic, and Norwegian Viking presence in Ireland, Iceland, and Greenland. Additionally, we see substantial foreign European ancestry entering Scandinavia during the Viking Age. We also find that several of the members of the only archaeologically well-attested Viking expedition were close family members. By comparing Viking Scandinavian genomes with present-day Scandinavian genomes, we find that pigmentation-associated loci have undergone strong population differentiation during the last millennia. Finally, we are able to trace the allele frequency dynamics of positively selected loci with unprecedented detail, including the lactase persistence allele and various alleles associated with the immune response. We conclude that the Viking diaspora was characterized by substantial foreign engagement: distinct Viking populations influenced the genomic makeup of different regions of Europe, while Scandinavia also experienced increased contact with the rest of the continent.

genetics↗