Gülfirde Akgül

University of Zurich

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Research Field

Ancient Bacterial Genomes Reveal a High Diversity of Treponema pallidum Strains in Early Modern Europe

Current Biology (2020)

Kerttu Majander Saskia Pfrengle Arthur Kocher Judith Neukamm Louis du Plessis

Syphilis is a globally re-emerging disease, which has marked European history with a devastating epidemic at the end of the 15th century. Together with non-venereal treponemal diseases, like bejel and yaws, which are found today in subtropical and tropical regions, it currently poses a substantial health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis' potential introduction into Europe from the Americas. Here, we present the first genetic data from archaeological human remains reflecting a high diversity of Treponema pallidum in early modern Europe. Our study demonstrates that a variety of strains related to both venereal syphilis and yaws-causing T. pallidum subspecies were already present in Northern Europe in the early modern period. We also discovered a previously unknown T. pallidum lineage recovered as a sister group to yaws- and bejel-causing lineages. These findings imply a more complex pattern of geographical distribution and etiology of early treponemal epidemics than previously understood.

Subspecies

Old World

Lineage (genetic)

10.1016/j.cub.2020.07.058

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Citations (64)

Ongoing tissue changes in an experimentally mummified human leg

The Anatomical Record (2019)

Ирина Морозова Lena Öhrström Patrick Eppenberger Beata Bode‐Lesniewska Dominic Gascho

Artificial mummification has been used since antiquity and is best known from ancient Egypt. Despite ancient Egyptian mummies being studied for several decades, the mummification techniques of that time are not well understood. Modern mummification experiments involving animal and human tissues have contributed additional insights relevant to a broad field of research. In the current study, we present follow-up results of an experiment on artificial mummification, which began in 2009. A human leg was artificially mummified and monitored for almost a year with histological, molecular, and radiological techniques. Since then, it has remained in a dry, natron salt blend for 9 years. The current analyses show further progression of dehydration and tissue alterations, as well as DNA degradation, suggesting an ongoing process. Our results add new insights into the mechanisms of tissue mummification. Taking into account that the process is still ongoing, further research is required, including a re-evaluation of the human leg in the future.

Ancient DNA

10.1002/ar.24333

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Citations (3)

Insights into Treponema pallidum genomics from modern and ancient genomes using a novel mapping strategy

BMC Biology (2025)

Marta Pla-Díaz Gülfirde Akgül Martyna Molak Louis du Plessis Hanna Panagiotopoulou

Treponemal diseases are a significant global health risk, presenting challenges to public health and severe consequences to individuals if left untreated. Despite numerous genomic studies on Treponema pallidum and the known possible biases introduced by the choice of the reference genome used for mapping, few investigations have addressed how these biases affect phylogenetic and evolutionary analysis of these bacteria. In this study, we ascertain the importance of selecting an appropriate genomic reference on phylogenetic and evolutionary analyses of T. pallidum. We designed a multiple-reference-based (MRB) mapping strategy using four different reference genomes and compared it to traditional single-reference mapping. To conduct this comparison, we created a genomic dataset comprising 77 modern and ancient genomes from the three subspecies of T. pallidum, including a newly sequenced seventeenth century genome (35X mean coverage) of a syphilis-causing strain (designated as W86). Our findings show that recombination detection was consistent across different references, but the choice of reference significantly affected ancient genome reconstruction and phylogenetic inferences. The high-coverage W86 genome introduced in this study also provided a new calibration point for Bayesian molecular clock dating, improving the reconstruction of the evolutionary history of treponemal diseases. Additionally, we identified novel recombination events, positive selection targets, and refined dating estimates for key events in the species' history. This study highlights the importance of considering methodological implications and reference genome bias in high-throughput sequencing-based whole-genome analysis of T. pallidum, especially of ancient or low-coverage samples, contributing to a deeper understanding of the treponemal pathogen and its subspecies.

Comparative Genomics

10.1186/s12915-024-02108-4

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Citations (0)

Using historic fixed soft tissues for retrospective genomic analyses: a methodological evaluation

The 86th Annual Meeting of the American Association of Physical Anthropologists, New Orleans (2017)

Giada Ferrari Heidi E. L. Lischer Gülfirde Akgül Frank Rühli Abigail Bouwman

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Historical CCR5Δ32 Frequencies in Central Europe

Abigail Bouwman Christina Warinner N Shved Gülfirde Akgül Frank Rühli

10.5167/uzh-94048

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Ancient DNA Analysis Reveals High Frequency of European Lactase Persistence Allele (T-13910) in Medieval Central Europe

PLoS ONE (2014)

Annina Krüttli Abigail Bouwman Gülfirde Akgül Philippe Della Casa Frank Rühli

Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71–80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary history of the European lactase persistence trait and its global cultural implications.

Lactase

Ancient DNA

Lactose Intolerance

10.1371/journal.pone.0086251

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Citations (53)

Non-destructive extraction of DNA from preserved tissues in medical collections

bioRxiv (Cold Spring Harbor Laboratory) (2021)

Enrique Rayo Giada Ferrari Judith Neukamm Gülfirde Akgül Abagail Breidenstein

Abstract Museum and medically fixed material are valuable samples for the study of historical soft tissues and represent a pathogen-specific source for retrospective molecular investigations. However, current methods for the molecular analysis are inherently destructive, posing a dilemma between performing a study with the available technology thus damaging the sample - or conserving the material for future investigations. Here we present an unprecedented non-destructive alternative that facilitates the genetic analysis of fixed wet tissues while avoiding tissue damage. We extracted DNA from the fixed tissues as well as their embedding fixative solution, to quantify the DNA that was transferred to the liquid component. Our results prove that human ancient DNA can be retrieved from the fixative material of stored medical specimens and provide new options for the sampling of valuable curated collections. Method summary We compared the metagenomic content of historical tissues and their embedding liquid to retrieve DNA from the host and specified pathogens based on the diagnosis of the sample. We applied ancient DNA research techniques, including in-solution hybridization capture with DNA baits for human mitochondrial DNA, Mycobacterium tuberculosis, Mycobacterium leprae , and Treponema pallidum .

Fixative

Ancient DNA

genomic DNA

10.1101/2021.02.17.431618

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Citations (0)

First case of cd39 β-thalassemia found in a Sardinian man from 2000 years ago

The 86th Annual Meeting of the American Association of Physical Anthropologists, New Orleans (2017)

Claudia Viganò Gülfirde Akgül Frank Rühli Abigail Bouwman

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Ancient bacterial genomes reveal a formerly unknown diversity ofTreponema pallidumstrains in early modern Europe

bioRxiv (Cold Spring Harbor Laboratory) (2020)

Kerttu Majander Saskia Pfrengle Judith Neukamm Arthur Kocher Louis du Plessis

Summary Sexually transmitted (venereal) syphilis marked European history with a devastating epidemic at the end of the 15 th century, and is currently re-emerging globally. Together with non-venereal treponemal diseases, like bejel and yaws, found in subtropical and tropical regions, it poses a prevailing health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis’ potential introduction into Europe from the Americas. Here, we present the first genetic data from archaeological human remains reflecting a previously unknown diversity of Treponema pallidum in historical Europe. Our study demonstrates that a variety of strains related to both venereal syphilis and yaws were already present in Northern Europe in the early modern period. We also discovered a previously unknown T. pallidum lineage recovered as a sister group to yaws and bejel. These findings imply a more complex pattern of geographical prevalence and etiology of early treponemal epidemics than previously understood.

Lineage (genetic)

Old World

Etiology

10.1101/2020.06.09.142547

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Citations (4)

Inferring patterns of recombination and divergence with ancient and modern treponemal genomes

bioRxiv (Cold Spring Harbor Laboratory) (2023)

Gülfirde Akgül Marta Pla-Díaz Martyna Molak Louis du Plessis Hanna Panagiotopoulou

Background: Treponemal diseases pose significant global health risks, presenting severe challenges to public health due to their serious health impacts if left untreated. Despite numerous genomic studies on Treponema pallidum and the known possible biases introduced by the choice of the reference genome used for mapping, few investigations have addressed how these biases affect phylogenetic and evolutionary analysis of these bacteria. In this study, we assessed the impact of selecting an appropriate genomic reference on phylogenetic and evolutionary analyses of T. pallidum. Results: We designed a multiple-reference-based (MRB) mapping strategy using four different reference genomes and compared it to traditional single-reference mapping. To conduct this comparison, we created a genomic dataset comprising 77 modern and ancient genomes from the three subspecies of T. pallidum, including a newly sequenced 17th-century genome (35X coverage) of a syphilis-causing strain (designated as W86). Our findings show that recombination detection was consistent across different references, but the choice of reference significantly affected ancient genome reconstruction and phylogenetic inferences. The high-coverage W86 genome obtained here also provided a new calibration point for Bayesian molecular clock dating, improving the reconstruction of the evolutionary history of treponemal diseases. Additionally, we identified novel recombination events, positive selection targets, and refined dating estimates for key events in the species' history. Conclusions: This study highlights the importance of considering methodological implications and reference genome bias in High-Throughput Sequencing-based whole-genome analysis of T. pallidum, especially of ancient or low-coverage samples, contributing to a deeper understanding of this pathogen and its subspecies.

Subspecies

10.1101/2023.02.08.526988

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Citations (1)