
Mikkel Winther PedersenUniversity of Copenhagen · Faculty of Health and Medical Sciences
Mikkel Winther Pedersen
PhD
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65
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Introduction
Originally I am physical geographer of education with interests in climatic and environmental change, however I have since 2008 directed my interests towards the applicability of ancient DNA in the environmental science. Graduating my masters on ancient DNA, which also was the focus of my PhD, the past few years I have gained a huge interest in the applicability of ancient DNA, environmentally and in an archaeological perspective.
Additional affiliations
November 2015 - November 2017
Publications
Publications (65)
Understanding the environmental and microbial processes involved in DNA degradation from archaeological remains is a fundamental part of managing bone specimens. We investigated the state of DNA preservation in 33 archaeozoological caribou (Rangifer tarandus) ribs excavated from the same excavation trench at a former Inuit hunting camp in West Gree...
Ancient environmental DNA (aeDNA) is becoming a powerful tool to gain insights about past ecosystems, overcoming the limitations of conventional fossil records. However, several methodological challenges remain, particularly for classifying the DNA to species level and conducting phylogenetic analysis. Current methods, primarily tailored for modern...
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 c...
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....
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...
In a recent publication in this journal, Reynoso-García 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 island’s Indigenous population before the arrival of Europeans. Based on the results, the team claim to have identified various edible New W...
How does nature change through time and across space? How might it change in the future? While time travel has long been the domain of science fiction, scientists have approached these questions using techniques that examine the traces of the past remaining in today’s environment. The use of ancient environmental DNA (ancient eDNA) is the latest me...
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...
Ancient environmental DNA (aeDNA) is a crucial source of information for past environmental reconstruction. However, the computational analysis of aeDNA involves the inherited challenges of ancient DNA (aDNA) and the typical difficulties of eDNA samples, such as taxonomic identification and abundance estimation of identified taxonomic groups. Curre...
Using ancient environmental DNA (eDNA) we reconstructed microbial and viral communities from the Kap København Formation in North Greenland. We find pioneer microbial communities, along with likely dormant methanogens from the permafrost's seed bank. Our findings reveal that at the time of the formation, the terrestrial input of the Kap København s...
Environmental archives, such as lake sediments, harbour DNA of past and present ecosystems. However, our understanding of the provenance, deposition and distribution of sedimentary DNA in lake systems is largely unknown, limiting the breadth of derived spatiotemporal inferences. By mapping the distribution of aquatic and terrestrial taxa in a large...
Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age in...
1. Ancient environmental DNA (eDNA) is a crucial source of information for past environmental reconstruction. However, the computational 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 estimation of identified...
Traditional zooarchaeological and archaeobotanical methods based on morphological identification of the excavated faunal and floral remains have been broadly used in reconstructing ancient subsistence economies. However, the accuracy and reliability of these methods rely heavily on the preservation state of the remains. By sequencing the ancient DN...
Motivation: 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 pron...
Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago¹ had climates resembling those forecasted under future warming². Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11–19 °C above contemporary values3,4. The biological communities inhabiting the Arctic during this time remain poorly known...
Recent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous...
Environmental archives, such as lake sediments, harbor DNA evidence from past and present ecosystems. However, our understanding of the provenance, taphonomy and distribution of sedimentary DNA in lake systems is largely unknown, limiting the breadth of spatiotemporal inferences drawn from it. To address this gap, we studied surface sediments acros...
Metagenomic data generated from environmental samples is increasingly common in the analysis of modern and ancient biological communities. To obtain taxonomic profiles from this type of data, DNA sequences are aligned against large genomic reference databases and the lowest common ancestor (LCA) needs to be inferred for each sequence with multiple...
Multi-proxy palaeoecological analyses of lake cores from two sites on northern Vancouver Island reveal previously undocumented non-arboreal environments in the region during the late Pleistocene. Radiocarbon, pollen, sedimentary ancient DNA (sedaDNA), diatom, and grain size analyses indicate that Topknot Lake on the west coast of northern Vancouver...
Many metagenomic and environmental DNA studies require the taxonomic assignment of individual reads or sequences by aligning reads to a reference database, known as taxonomic binning. When a read aligns to more than one reference sequence, it is often classified based on sequence similarity. This step can assign reads to incorrect taxa, at a rate w...
Over the past few decades there has been a growing demand for genome analysis of ancient human remains. Destructive sampling is increasingly difficult to obtain for ethical reasons, and standard methods of breaking the skull to access the petrous bone or sampling remaining teeth are often forbidden for curatorial reasons. However, most ancient huma...
This paper is a reply to Chatters et al. (2021. “Evaluating Claims of Early Human Occupation at Chiquihuite Cave, Mexico.” PaleoAmerica 8, doi:10.1080/20555563.2021.1940441), in which they raise a large number of doubts about the legitimacy of our claims of earlier-than-expected human presence at Chiquihuite Cave, in northern Zacatecas, Mexico, mai...
During the last glacial–interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1–8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across t...
Since the seminal paper in 1998 (Coolen and Overmann), sedimentary ancient DNA (sedaDNA) has become a powerful tool in paleoecology to reconstruct past changes in terrestrial and aquatic biodiversity. Still, sedaDNA is an emerging tool and there is a need for calibrations and validations to ensure the reliability of sedaDNA as a proxy to reconstruc...
Analysis of ancient environmentalDNA(eDNA) has revolutionized our ability to describe biological communities in space and time, by allowing for parallel sequencing of DNA from all trophic levels. However, because
environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species, the field...
A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03328-2.
The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building...
Community assembly processes are important in structuring aquatic microbial communities; however, the influence of these processes on the dynamics of bacterial communities in glacial streams and lakes remains largely unstudied. To investigate the assembly processes underlying the temporal variation of the bacterial community, we collected 50 water...
The maritime expansion of Scandinavian populations during the Viking Age (about ad 750–1050) was a far-flung transformation in world history1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking pe...
The initial colonization of the Americas remains a highly debated topic1, and the exact timing of the first arrivals is unknown. The earliest archaeological record of Mexico—which holds a key geographical position in the Americas—is poorly known and understudied. Historically, the region has remained on the periphery of research focused on the firs...
The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed pl...
The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed pl...
The rise of ancient genomics has revolutionised our understanding of human prehistory but this work depends on the availability of suitable samples. Here we present a complete ancient human genome and oral microbiome sequenced from a 5700 year-old piece of chewed birch pitch from Denmark. We sequence the human genome to an average depth of 2.3× and...
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...
The lake sediments of Hässeldala Port in south-east Sweden provide an archive of local and regional environmental conditions ~14.5–9.5 ka BP (thousand years before present) and allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun sequencing with plant micro- and macrofossil analyses to investigate sedi...
with In this Article, Angela M. Taravella and Melissa A. Wilson Sayres have been added to the author list (associated with: School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University, Tempe, AZ, USA). The author list and Author Information section have been corrected online.
Over the last decade, studies of ancient biomolecules—particularly ancient DNA, proteins, and lipids—have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, the field now stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signa...
For thousands of years the Eurasian steppes have been a centre of human migrations and cultural change. Here we sequence the genomes of 137 ancient humans (about 1× average coverage), covering a period of 4,000 years, to understand the population history of the Eurasian steppes after the Bronze Age migrations. We find that the genetics of the Scyth...
The Lateglacial/early Holocene sediments from the ancient lake at H€ asseldala Port, southern Sweden provide an important archive for the environmental and climatic shifts at the end of the last ice age and the transition into the present Interglacial. The existing multi-proxy data set highlights the complex interplay of physical and ecological cha...
Deep-sea sediments constitute a unique archive of ocean change, fueled by a permanent rain of mineral and organic remains from the surface ocean. Until now, paleo-ecological analyses of this archive have been mostly based on information from taxa leaving fossils. In theory, environmental DNA (eDNA) in the sediment has the potential to provide infor...
The final stages of the Last Glacial in the Northern Hemisphere, between 19 and 11.7 thousand years before present, were punctuated by distinct and alternating warmer and colder climate states before Interglacial temperatures were attained, which in turn strongly influenced past vegetation. One of the best studied Lateglacial lake sedimentary recor...
Contents I. II. III. IV. V. VI. VII. VIII. IX. X. XI. References SUMMARY: Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules,...
The demographic history of Greenland is characterized by recurrent migrations and extinctions since the first humans arrived 4,500 years ago. Our current understanding of these extinct cultures relies primarily on preserved fossils found in their archaeological deposits, which hold valuable information on past subsistence practices. However, some e...
Deep-sea sediments constitute a unique archive of ocean change, fueled by a permanent rain of mineral and organic remains from the surface ocean. Until now, paleo-ecological analyses of this archive have been mostly based on information from taxa leaving fossils. In theory, environmental DNA (eDNA) in the sediment has the potential to provide infor...
Population genetics is essential for understanding and managing marine ecosystems, but sampling remains challenging. We demonstrate that high-throughput sequencing of seawater environmental DNA can provide useful estimates of genetic diversity in a whale shark (Rhincodon typus) aggregation. We recover similar mitochondrial haplotype frequencies in...
During the Last Glacial Maximum, continental ice sheets isolated Beringia (northeast Siberia and northwest North America) from unglaciated North America. By around 15 to 14 thousand calibrated radiocarbon years before present (cal. kyr bp), glacial retreat opened an approximately 1,500-km-long corridor between the ice sheets. It remains unclear whe...
Ancient DNA (aDNA) in lake sediments opens novel approaches to a better understanding of past environmental changes in aquatic and terrestrial ecosystems. The lake sediment sequences of Hässeldala and Atteköpsmosse in southern Sweden form two excellent records to investigate the wide spectrum of aquatic and terrestrial floral, faunal and microbial...
DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for...
Reconstructing past vegetation and species diversity from arctic lake sediments can be challenging because of low pollen and plant macrofossil concentrations. Information may be enhanced by metabarcoding of sedimentary ancient DNA (sedaDNA). We developed a Holocene record from Lake Skartjørna, Svalbard, using sedaDNA, plant macrofossils and sedimen...
DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for...