Franziska Aron

A-Z of ancient DNA protocols for shotgun Illumina Next Generation Sequencing v2

James A. Fellows Yates Franziska Aron Gunnar U. Neumann Irina M. Velsko Eirini Skourtanioti

This collection contains established ancient DNA (aDNA) specific protocols for Illumina next generation sequencing. It covers sampling of skeletal remains for regions preserving higher amounts of aDNA, DNA extraction methods designed for retrieval of very short DNA fragments, and various library construction methods (including treatments for the 'removal' of typical aDNA damage). All protocols have been adapted after published protocols (see each for the corresponding original publication), and are used primarily in the Department of Archaeogenetics at the MPI-SHH (Jena, Germany). All protocols in this collection can be used together, and in some cases swapped out with others. All protocols prior indexing are mostly performed in a dedicated ancient DNA laboratory - please see the guidelines section of each protocol for more information. The order of protocols is as follows: 1. Sampling for aDNA Sampling of Pars petrosa (os temporale, ''petrous bones') for human aDNA extraction Sampling of teeth for human and microbial (e.g. pathogen) aDNA extraction Sampling of dental calculus for oral microbiome aDNA extraction 2. Retrieval of DNA Ancient DNA Extraction from Skeletal Material (based on the Dabney et al. 2013 Proc Natl Acad Sci U S A protocol) Ancient DNA extraction from dental calculus (based on the Dabney et al. 2013 Proc Natl Acad Sci U S A with extra washing steps from Ozga et al. 2016 Am J Phys Anthropol) 3. Library Preparation Library Adapter Preparation for Dual-Index Double Stranded DNA Illumina Sequencing (based on Meyer and Kircher 2010 Cold Spring Harb. Protoc. protocol) Non-UDG Treated double-stranded ancient DNA library preparation for Illumina sequencing (requires 3.1, based on Meyer and Kircher 2010 Cold Spring Harb. Protoc. protocol) Half-UDG Treated double-stranded ancient DNA library preparation for Illumina sequencing (Variant of 3.2, with partial damage removal treatment from Rohland et al. 2015 Philos Trans R Soc Lond B Biol Sci) Full-UDG Treated double-stranded ancient DNA library preparation for Illumina sequencing (Variant of 3.2, with complete damage removal treatment from Briggs et al. 2010 Nucleic Acids Res) Dual-Indexing of aDNA libraries for Illumina Sequencing (based on Meyer and Kircher 2010 Cold Spring Harb. Protoc. protocol) 4. Preparation for Sequencing Amplification and Pooling for dual-indexed Illumina library for sequencing

Ancient DNA

10.17504/protocols.io.bvt9n6r6

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Ancient DNA Extraction from Dental Calculus with Consolidant Removal v1

Franziska Aron Courtney A. Hofman Zandra Fagernäs Irina M. Velsko Guido Brandt

Silica-based total DNA extraction protocol optimised for the recovery of ultra-short DNA molecules from archaeological dental calculus, modified from Dabney et al. (2013) PNAS (doi: 10.1073/pnas.1314445110) and adapted for dental calculus by Mann et al. (2018) Scientific Reports (doi: https://doi.org/10.1038/s41598-018-28091-9). This protocol includes an optional acetone wash step to remove conservation consolidants (e.g. glue) from dental calculus that can sometimes be found on samples archived in museum collections.

10.17504/protocols.io.bqbmmsk6

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Citations (1)

Ancient DNA Extraction from Dental Calculus v1

Franziska Aron Courtney A. Hofman Zandra Fagernäs Irina M. Velsko Eirini Skourtanioti

Silica-based total DNA extraction protocol optimised for the recovery of ultra-short DNA molecules from archaeological dental calculus, modified from Dabney et al. (2013) PNAS (doi: 10.1073/pnas.1314445110) and adapted for dental calculus by Mann et al. (2018) Scientific Reports (doi: https://doi.org/10.1038/s41598-018-28091-9).

Ancient DNA

10.17504/protocols.io.bidyka7w

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Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague

Proceedings of the National Academy of Sciences (2022)

Aida Andrades Valtueña Gunnar U. Neumann Maria A. Spyrou Lyazzat Musralina Franziska Aron

Significance The bacterium Yersinia pestis has caused numerous historically documented outbreaks of plague and research using ancient DNA could demonstrate that it already affected human populations during the Neolithic. However, the pathogen’s genetic diversity, geographic spread, and transmission dynamics during this early period of Y. pestis evolution are largely unexplored. Here, we describe a set of ancient plague genomes up to 5,000 y old from across Eurasia. Our data demonstrate that two genetically distinct forms of Y. pestis evolved in parallel and were both distributed across vast geographic distances, potentially occupying different ecological niches. Interpreted within the archeological context, our results suggest that the spread of plague during this period was linked to increased human mobility and intensification of animal husbandry.

Yersinia pestis

plague

Ancient DNA

10.1073/pnas.2116722119

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Citations (54)

Extensive pedigrees reveal the social organization of a Neolithic community

Nature (2023)

Maïté Rivollat Adam B. Rohrlach Harald Ringbauer Ainash Childebayeva Fanny Mendisco

Abstract Social anthropology and ethnographic studies have described kinship systems and networks of contact and exchange in extant populations 1–4 . However, for prehistoric societies, these systems can be studied only indirectly from biological and cultural remains. Stable isotope data, sex and age at death can provide insights into the demographic structure of a burial community and identify local versus non-local childhood signatures, archaeogenetic data can reconstruct the biological relationships between individuals, which enables the reconstruction of pedigrees, and combined evidence informs on kinship practices and residence patterns in prehistoric societies. Here we report ancient DNA, strontium isotope and contextual data from more than 100 individuals from the site Gurgy ‘les Noisats’ (France), dated to the western European Neolithic around 4850–4500 bc . We find that this burial community was genetically connected by two main pedigrees, spanning seven generations, that were patrilocal and patrilineal, with evidence for female exogamy and exchange with genetically close neighbouring groups. The microdemographic structure of individuals linked and unlinked to the pedigrees reveals additional information about the social structure, living conditions and site occupation. The absence of half-siblings and the high number of adult full siblings suggest that there were stable health conditions and a supportive social network, facilitating high fertility and low mortality 5 . Age-structure differences and strontium isotope results by generation indicate that the site was used for just a few decades, providing new insights into shifting sedentary farming practices during the European Neolithic.

Exogamy

Pedigree chart

Lineage (genetic)

10.1038/s41586-023-06350-8

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Citations (45)

The evolution and changing ecology of the African hominid oral microbiome

Proceedings of the National Academy of Sciences (2021)

James A. Fellows Yates Irina M. Velsko Franziska Aron Cosimo Posth Courtney A. Hofman

Significance The microbiome plays key roles in human health, but little is known about its evolution. We investigate the evolutionary history of the African hominid oral microbiome by analyzing dental biofilms of humans and Neanderthals spanning the past 100,000 years and comparing them with those of chimpanzees, gorillas, and howler monkeys. We identify 10 core bacterial genera that have been maintained within the human lineage and play key biofilm structural roles. However, many remain understudied and unnamed. We find major taxonomic and functional differences between the oral microbiomes of Homo and chimpanzees but a high degree of similarity between Neanderthals and modern humans, including an apparent Homo -specific acquisition of starch digestion capability in oral streptococci, suggesting microbial coadaptation with host diet.

Oral Microbiome

Hominidae

10.1073/pnas.2021655118

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Citations (130)

Dynamic changes in genomic and social structures in third millennium BCE central Europe

Science Advances (2021)

Luka Papac Michal Ernée Miroslav Dobeš Michaela Langová Adam B. Rohrlach

Archaeogenetic time transect in Europe unravels genetic and social changes before and after the arrival of “steppe” ancestry.

Steppe

10.1126/sciadv.abi6941

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Citations (74)

Genomic transformation and social organization during the Copper Age–Bronze Age transition in southern Iberia

Science Advances (2021)

Vanessa Villalba‐Mouco Camila Oliart Caravatti Cristina Rihuete Herrada Ainash Childebayeva Adam B. Rohrlach

The emerging Bronze Age (BA) of southeastern Iberia saw marked social changes. Late Copper Age (CA) settlements were abandoned in favor of hilltop sites, and collective graves were largely replaced by single or double burials with often distinctive grave goods indirectly reflecting a hierarchical social organization, as exemplified by the BA El Argar group. We explored this transition from a genomic viewpoint by tripling the amount of data available for this period. Concomitant with the rise of El Argar starting ~2200 cal BCE, we observe a complete turnover of Y-chromosome lineages along with the arrival of steppe-related ancestry. This pattern is consistent with a founder effect in male lineages, supported by our finding that males shared more relatives at sites than females. However, simple two-source models do not find support in some El Argar groups, suggesting additional genetic contributions from the Mediterranean that could predate the BA.

Grave goods

Social Organization

Steppe

Chalcolithic

10.1126/sciadv.abi7038

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Citations (56)

Exploring the impact of primer length on efficient gene detection via high-throughput sequencing

Nature Communications (2024)

Julia Micheel Aram Safrastyan Franziska Aron Damian Wollny

Abstract Reverse transcription (RT) is a crucial step in most RNA analysis methods. Optimizing protocols for this initial stage is critical for effective target detection, particularly when working with limited input RNA. Several factors, such as the input material quality and reaction conditions, influence RT efficiency. However, the effect of RT primer length on gene detection efficiency remains largely unknown. Thus, we investigate its impact by generating RNA-seq libraries with random RT primers of 6, 12, 18, or 24 nucleotides. To our surprise, the 18mer primer shows superior efficiency in overall transcript detection compared to the commonly used 6mer primer, especially in detecting longer RNA transcripts in complex human tissue samples. This study highlights the critical role of primer length in RT efficiency, which has significant potential to benefit various transcriptomic assays, from basic research to clinical diagnostics, given the central role of RT in RNA-related analyses.

Primer (cosmetics)

10.1038/s41467-024-49685-0

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A-Z of ancient DNA protocols for shotgun Illumina Next Generation Sequencing v1

James A. Fellows Yates Franziska Aron Gunnar U. Neumann Irina M. Velsko Eirini Skourtanioti

This collection contains established ancient DNA (aDNA) specific protocols for Illumina next generation sequencing. It covers sampling of skeletal remains for regions preserving higher amounts of aDNA, DNA extraction methods designed for retrieval of very short DNA fragments, and various library construction methods (including treatments for the 'removal' of typical aDNA damage). All protocols have been adapted after published protocols (see each for the corresponding original publication), and are used primarily in the Department of Archaeogenetics at the MPI-SHH (Jena, Germany). All protocols in this collection can be used together, and in some cases swapped out with others. All protocols prior indexing are mostly performed in a dedicated ancient DNA laboratory - please see the guidelines section of each protocol for more information. The order of protocols is as follows: 1. Sampling for aDNA Sampling of Pars petrosa (os temporale, ''petrous bones') for human aDNA extraction Sampling of teeth for human and microbial (e.g. pathogen) aDNA extraction Sampling of dental calculus for oral microbiome aDNA extraction 2. Retrieval of DNA Ancient DNA Extraction from Skeletal Material (based on the Dabney et al. 2013 Proc Natl Acad Sci U S A protocol) Ancient DNA extraction from dental calculus (based on the Dabney et al. 2013 Proc Natl Acad Sci U S A with extra washing steps from Ozga et al. 2016 Am J Phys Anthropol) 3. Library Preparation Library Adapter Preparation for Dual-Index Double Stranded DNA Illumina Sequencing (based on Meyer and Kircher 2010 Cold Spring Harb. Protoc. protocol) Non-UDG Treated double-stranded ancient DNA library preparation for Illumina sequencing (requires 3.1, based on Meyer and Kircher 2010 Cold Spring Harb. Protoc. protocol) Half-UDG Treated double-stranded ancient DNA library preparation for Illumina sequencing (Variant of 3.2, with partial damage removal treatment from Rohland et al. 2015 Philos Trans R Soc Lond B Biol Sci) Full-UDG Treated double-stranded ancient DNA library preparation for Illumina sequencing (Variant of 3.2, with complete damage removal treatment from Briggs et al. 2010 Nucleic Acids Res) Dual-Indexing of aDNA libraries for Illumina Sequencing (based on Meyer and Kircher 2010 Cold Spring Harb. Protoc. protocol) 4. Preparation for Sequencing Amplification and Pooling for dual-indexed Illumina library for sequencing

Ancient DNA

10.17504/protocols.io.bj8nkrve

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Citations (2)

Papers

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H-Index

i-10 index

Papers

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H-Index

i-10 index