Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

Supplemental Information for: Suchan, T., Kusliy, M.A., Khan, N., Chauvey, L., Tonasso-Calvière, L., Schiavinato, S., Southon, J., Keller, M., Kitagawa, K., Krause, J., Bessudnov, A.N., Bessudnov, A.A., Graphodatsky, A.S., Lamas, S.V., Wilczyński, J., Pospuła, S., Tunia, K., Nowak, M., Moskal-delHoyo, M., Tishkin, A.A., Pryor, A.J.E., Outram, A.K., Orlando, L. (2021) Performance and automation of ancient DNA capture with RNA hyRAD probes. Molecular Ecology Resources, doi: 10.1111/1755-0998.13518

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Correction for Stiller et al., Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0607610103 ◽

2006 ◽

Vol 103 (40) ◽

pp. 14977-14977 ◽

Cited By ~ 1

Keyword(s):

Ancient Dna ◽

Large Scale ◽

Enzymatic Amplification

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Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0605327103 ◽

2006 ◽

Vol 103 (37) ◽

pp. 13578-13584 ◽

Cited By ~ 123

Author(s):

M. Stiller ◽

R. E. Green ◽

M. Ronan ◽

J. F. Simons ◽

L. Du ◽

...

Keyword(s):

Ancient Dna ◽

Large Scale ◽

Enzymatic Amplification

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A geostatistical approach to modelling human Holocene migrations in Europe using ancient DNA

10.1101/826149 ◽

2019 ◽

Cited By ~ 1

Author(s):

Fernando Racimo ◽

Jessie Woodbridge ◽

Ralph M. Fyfe ◽

Martin Sikora ◽

Karl-Göran Sjögren ◽

...

Keyword(s):

Bronze Age ◽

Ancient Dna ◽

Large Scale ◽

Local Fauna ◽

Population Replacement ◽

European Continent ◽

The Holocene ◽

Geostatistical Approach ◽

Broad Leaf ◽

Westward Movement

AbstractThe European continent was subject to two major migrations of peoples during the Holocene: the northwestward movement of Anatolian farmer populations during the Neolithic and the westward movement of Yamnaya steppe peoples during the Bronze Age. These movements changed the genetic composition of the continent’s inhabitants, via admixture and population replacement processes. The Holocene was also characterized by major changes in vegetation composition, which altered the environment occupied by the original hunter-gatherer populations. Here, we use a combination of paleogenomics and geostatistical modelling to produce detailed maps of the movement of these populations over time and space, and to understand how these movements impacted the European vegetation landscape. We find that the dilution of hunter-gatherer ancestries and the Yamnaya steppe migration coincided with a reduction in the amount of broad-leaf forest and an increase in the amount of pasture lands in the continent. We also show that climate played a role in these vegetational changes. Additionally, we find that the spread of Neolithic farmer ancestry had a two-pronged wavefront, in agreement with similar findings based on patterns of the cultural spread of farming from radiocarbon-dated archaeological sites. With thousands of ancient genomes publicly available and in production, we foresee that the integration of ancient DNA with geostatistical techniques and large-scale archaeological datasets will revolutionize the study of ancient populations movements, and their effects on local fauna and flora.

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HOPS: Automated detection and authentication of pathogen DNA in archaeological remains

10.1101/534198 ◽

2019 ◽

Cited By ~ 1

Author(s):

Ron Hübler ◽

Felix M. Key ◽

Christina Warinner ◽

Kirsten I. Bos ◽

Johannes Krause ◽

...

Keyword(s):

High Throughput ◽

Ancient Dna ◽

High Throughput Screening ◽

Large Scale ◽

Sequence Data ◽

Evolutionary Relationship ◽

Molecular Data ◽

Clinical Samples ◽

Archaeological Remains ◽

Archaeological Material

AbstractHigh-throughput DNA sequencing enables large-scale metagenomic analyses of complex biological systems. Such analyses are not restricted to present day environmental or clinical samples, but can also be fruitfully applied to molecular data from archaeological remains (ancient DNA), and a focus on ancient bacteria can provide valuable information on the long-term evolutionary relationship between hosts and their pathogens. Here we present HOPS (HeuristicOperations forPathogenScreening), an automated bacterial screening pipeline for ancient DNA sequence data that provides straightforward and reproducible information on species identification and authenticity. HOPS provides a versatile and fast pipeline for high-throughput screening of bacterial DNA from archaeological material to identify candidates for subsequent genomic-level analyses.

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The Justinianic Plague: An inconsequential pandemic?

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1903797116 ◽

2019 ◽

Vol 116 (51) ◽

pp. 25546-25554 ◽

Cited By ~ 13

Author(s):

Lee Mordechai ◽

Merle Eisenberg ◽

Timothy P. Newfield ◽

Adam Izdebski ◽

Janet E. Kay ◽

...

Keyword(s):

Middle Ages ◽

Ancient Dna ◽

Large Scale ◽

Causal Factor ◽

Late Antique ◽

Mortuary Archaeology ◽

Mediterranean World ◽

Economic Trends ◽

Mortality Estimates ◽

Written Sources

Existing mortality estimates assert that the Justinianic Plague (circa 541 to 750 CE) caused tens of millions of deaths throughout the Mediterranean world and Europe, helping to end antiquity and start the Middle Ages. In this article, we argue that this paradigm does not fit the evidence. We examine a series of independent quantitative and qualitative datasets that are directly or indirectly linked to demographic and economic trends during this two-century period: Written sources, legislation, coinage, papyri, inscriptions, pollen, ancient DNA, and mortuary archaeology. Individually or together, they fail to support the maximalist paradigm: None has a clear independent link to plague outbreaks and none supports maximalist reconstructions of late antique plague. Instead of large-scale, disruptive mortality, when contextualized and examined together, the datasets suggest continuity across the plague period. Although demographic, economic, and political changes continued between the 6th and 8th centuries, the evidence does not support the now commonplace claim that the Justinianic Plague was a primary causal factor of them.

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Human mobility at Tell Atchana (Alalakh) during the 2nd millennium BC: integration of isotopic and genomic evidence

10.1101/2020.10.23.351882 ◽

2020 ◽

Author(s):

Tara Ingman ◽

Stefanie Eisenmann ◽

Eirini Skourtanioti ◽

Murat Akar ◽

Jana Ilgner ◽

...

Keyword(s):

Bronze Age ◽

Ancient Dna ◽

Large Scale ◽

Near East ◽

Eastern Mediterranean ◽

Human Mobility ◽

Isotope Data ◽

Individual Mobility ◽

Non Local ◽

Trade And Exchange

AbstractThe Middle and Late Bronze Age Near East, a period roughly spanning the second millennium BC (ca. 2000-1200 BC), is frequently referred to as the first ‘international age’, characterized by intense and far-reaching contacts between different entities from the eastern Mediterranean to the Near East and beyond. In a large-scale tandem study of stable isotopes and ancient DNA of individuals excavated at Tell Atchana (Alalakh), situated in the northern Levant, we explore the role of mobility at the capital of a regional kingdom. We generated strontium isotope data for 53 individuals, oxygen isotope data for 77 individuals, and added ancient DNA data from 9 new individuals to a recently published dataset of 28 individuals. A dataset like this, from a single site in the Near East, is thus far unparalleled in terms of both its breadth and depth, providing the opportunity to simultaneously obtain an in-depth view of individual mobility and also broader demographic insights into the resident population. The DNA data reveals a very homogeneous gene pool, with only one outlier. This picture of an overwhelmingly local ancestry is consistent with the evidence of local upbringing in most of the individuals indicated by the isotopic data, where only five were found to be ‘non-local’. High levels of contact, trade, and exchange of ideas and goods in the Middle and Late Bronze Ages, therefore, seem not to have translated into high levels of individual mobility detectable at Tell Atchana.

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Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir

Scientific Data ◽

10.1038/s41597-021-00816-y ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

James A. Fellows Yates ◽

Aida Andrades Valtueña ◽

Åshild J. Vågene ◽

Becky Cribdon ◽

Irina M. Velsko ◽

...

Keyword(s):

Ancient Dna ◽

Large Scale ◽

Data Retrieval ◽

Data Sources ◽

Valuable Data ◽

Dna And Rna ◽

Metagenomic Sample ◽

Wide Range ◽

Evolutionary Studies ◽

Meta Analyses

AbstractAncient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual taxa and communities of both microbes and eukaryotes. AncientMetagenomeDir (archived at 10.5281/zenodo.3980833) is a collection of annotated metagenomic sample lists derived from published studies that provide basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These tables are community-curated and span multiple sub-disciplines to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks facilitate compatibility with established sequence-read archives and term-ontologies, and ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies.

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hyRAD RNA probes preparation and capture v1

10.17504/protocols.io.rzqd75w ◽

2018 ◽

Author(s):

Tomasz Suchan ◽

Ludovic Orlando

Keyword(s):

Ancient Dna ◽

Molecular Ecology ◽

Rna Probes ◽

Dna Capture

Supplemental Information for: Suchan, T., Kusliy, M.A., Khan, N., Chauvey, L., Tonasso-Calvière, L., Schiavinato, S., Southon, J., Keller, M., Kitagawa, K., Krause, J., Bessudnov, A.N., Bessudnov, A.A., Graphodatsky, A.S., Lamas, S.V., Wilczyński, J., Pospuła, S., Tunia, K., Nowak, M., Moskal-delHoyo, M., Tishkin, A.A., Pryor, A.J.E., Outram, A.K., Orlando, L. (2021) Performance and automation of ancient DNA capture with RNA hyRAD probes. Molecular Ecology Resources, accepted.

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