Zoé Pochon
About me
Welcome to my page!
I am a PhD student in ancient metagenomics, particularly interested in ancient pathogens. I'm from the Department of Archaeology and Classical Studies and work at the Centre for Palaeogenetics. Trained in biology and history, I am mostly driven by a curiosity about human history and how we can use ancient DNA to bring new clues to its study.
The main goal of my PhD is to detect the presence of pathogens in ancient human remains and authenticate them as truly present and truly ancient. The first chapter of my thesis focuses on a pipeline we developed with NBIS bioinformaticians called aMeta. The second chapter provides a general overview of infectious diseases that circulated in the Medieval community of Las Gobas in northern Spain. The three remaining chapters will explore the infectious diseases circulating in two sites in present-day Sweden from the Iron Age and the Viking Age, as well as those found onboard warships from the early modern period.
As for my background, I hold a Bachelor of Science in Biology with a minor in History (Antiquity and Modern Times) and a Master of Science in Evolutionary and Population Genetics with a minor in History (specialisation in Antiquity). Both my Bachelor’s and Master’s theses were conducted in the Wegmann Lab at the University of Fribourg, focusing on ancient DNA from the Bronze Age Battlefield (now recognised as a massacre) of the Tollense Valley in northeastern Germany. In particular, we estimated a strong selection coefficient for the lactase persistence allele from the Bronze Age onwards.
I am passionate about the field of archaeogenetics because I believe it provides new insights into historical and archaeological questions. I moved to Sweden from Switzerland to pursue the opportunity to work in this field.
I am also an active member of the SPAAM community (Standards, Precautions, and Advances in Ancient Metagenomics) and had the opportunity to co-organise SPAAM5 in Tartu in 2023.
Publications
A selection from Stockholm University publication database
-
aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow
2023. Zoé Pochon (et al.). Genome Biology 24 (1)
ArticleRead more about aMetaAnalysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.
-
Historical RNA expression profiles from the extinct Tasmanian tiger
2023. Emilio Mármol-Sánchez (et al.). Genome Research 33 (8), 1299-1316
ArticleRead more about Historical RNA expression profiles from the extinct Tasmanian tigerPaleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a ∼130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.
-
Unveiling Hunnic legacy: Decoding elite presence in Poland through a unique child’s burial with modified cranium
2024. Jakub M. Niebylski (et al.). Journal of Archaeological Science 56
ArticleRead more about Unveiling Hunnic legacyThis article presents a double burial from Czulice indicating elements of the Hunnic culture. Individual I, aged 7–9, and Individual II, aged 8–9 with a skull deformation, were both genetically identified as boys. Individual II, who exhibited genetic affinity to present day Asian populations, was equipped with gold and silver items. In contrast, Individual I displayed European ancestry. The application of strontium isotope analysis shed light on the origins of the individuals. Individual I was non-local, while Individual II was identified as a local, but also falling within the range commonly associated with the Pannonian Plain. Stable isotope analysis suggested a diet consisting of inland resources. Through radiocarbon dating, this burial was determined to date back to the years 395–418 CE, making it the earliest grave of its kind discovered in Poland. The analyses have provided new insights into the nature of the relationship between the Huns and the local inhabitants.