Illuminating Genetic Mysteries of the Dead Sea Scrolls

Anava, Sarit; Neuhof, Moran; Gingold, Hila; Sagy, Or; Munters, Arielle R.; Svensson, Emma; Afshinnekoo, Ebrahim; Danko, David; Foox, Jonathan; Shor, Pnina; Riestra, Beatriz; Huchon, Dorothée; Mason, Christopher E.; Mizrahi, Noam; Jakobsson, Mattias; Rechavi, Oded

doi:10.1016/j.cell.2020.04.046

Cited by 11 publications

(11 citation statements)

References 67 publications

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“…Ancient DNA (aDNA) studies are particularly prone to problems with missing data, since long‐degraded samples often cannot yield full SNP coverage. Recent aDNA studies have included samples with as much as 40% (Marcus et al, 2020) or 50% missing data (Anava et al, 2020), while others removed SNPs with missingness >10% (Sikora et al, 2014), leading to a greatly reduced genomic coverage. Since these studies are particularly challenging to replicate given the barriers to sample collection, it is especially concerning that missing data may interfere with conclusions.…”

Section: Discussionmentioning

confidence: 99%

Alignment‐free methods for polyploid genomes: Quick and reliable genetic distance estimation

VanWallendael

Álvarez

2021

Molecular Ecology Resources

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Polyploid genomes pose several inherent challenges to population genetic analyses.While alignment-based methods are fundamentally limited in their applicability to polyploids, alignment-free methods bypass most of these limits. We investigated the use of Mash, a k-mer analysis tool that uses the MinHash method to reduce complexity in large genomic data sets, for basic population genetic analyses of polyploid sequences. We measured the degree to which Mash correctly estimated pairwise genetic distance in simulated haploid and polyploid short-read sequences with various levels of missing data. Mash-based estimates of genetic distance were comparable to alignment-based estimates, and were less impacted by missing data. We also used Mash to analyse publicly available short-read data for three polyploid and one diploid species, then compared Mash results to published results. For both simulated and real data, Mash accurately estimated pairwise genetic differences for polyploids as well as diploids as much as 476 times faster than alignment-based methods, though we found that Mash genetic distance estimates could be biased by per-sample read depth.Mash may be a particularly useful addition to the toolkit of polyploid geneticists for rapid confirmation of alignment-based results and for basic population genetics in reference-free systems or those with only poor-quality sequence data available.

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Section: Discussionmentioning

confidence: 99%

Alignment‐free methods for polyploid genomes: Quick and reliable genetic distance estimation

VanWallendael

Álvarez

2021

Molecular Ecology Resources

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“…Ancient DNA studies are particularly prone to problems with missing data, since long-degraded samples often cannot yield full SNP coverage. Recent aDNA studies have included samples with as much as 40% (Marcus et al 2020) or 50% missing data (Anava et al 2020), while others removed SNPs with missingness >10% (Sikora et al 2014), leading to a greatly reduced genomic coverage. Since these studies are particularly challenging to replicate given the barriers to sample collection, it is especially concerning that missing data may interfere with conclusions.…”

Section: Genomics Of Ancient and Degraded Samplesmentioning

confidence: 99%

Alignment-free methods for polyploid genomes: quick and reliable genetic distance estimation

VanWallendael

Álvarez

2020

Preprint

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Polyploid genomes pose several inherent challenges to population genetic analyses. While alignment-based methods are fundamentally limited in their applicability to polyploids, alignment-free methods bypass most of these limits. We investigated the use of Mash, a k-mer analysis tool that uses the MinHash method to reduce complexity in large genomic datasets, for basic population genetic analyses of polyploid sequences. We measured the degree to which Mash correctly estimated pairwise genetic distance in simulated diploid and polyploid short-read sequences with various levels of missing data. Mash-based estimates of genetic distance were comparable to alignment-based estimates, and were less impacted by missing data. We also used Mash to analyze publicly available short-read data for three polyploid and one diploid species, then compared Mash results to published results. For both simulated and real data, Mash accurately estimated pairwise genetic differences for polyploids as well as diploids as much as 476 times faster than alignment-based methods, though we found that Mash genetic distance estimates could be biased by per-sample read depth. Mash may be a particularly useful addition to the toolkit of polyploid geneticists for rapid confirmation of alignment-based results and for basic population genetics in reference-free systems with poor quality DNA.

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“…However, there is also a more indirect way to study human history, especially when ancient human remains are absent: animal DNA from artifacts manufactured by humans, such as tools, clothing, ornaments, and parchments. In this issue of Cell, Anava et al (2020) combine the full power of modern ancient DNA laboratory methods with state-of-the-art bioinformatic analyses to explore the origin of a set of parchments with fundamental historical, religious, and linguistic significance: the Dead Sea Scrolls.…”

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confidence: 99%

“…Early efforts of obtaining DNA from the DSS were already tailored at discerning which animals had been used for parchment production in the region and sorting out which fragments could be grouped into a manuscript by identifying similar DNA signals between them (Woodward et al, 1996). In Anava et al (2020), the authors extracted ancient DNA and used high-throughput DNA sequencing to recover vast amounts of data from multiple samples of DSS parchments. The results show that most of the DSS fragments were made of sheepskin and only a few of cowskin (Figure 1).…”

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confidence: 99%

“…For example, both ancient microbiomes and DNA from plants recovered from the parchments could yield information about the environment of the time the scrolls were written. Also, it is intriguing to think that DNA from the DSS's original authors could be hiding somewhere among the 2.6 billion DNA sequences generated by Anava et al (2020). Unfortunately, separating the authentic ancient microbial and plant DNA, as well as the authors' DNA sequences, from modern contamination could be exceedingly difficult, if not outright impossible.…”

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confidence: 99%

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Unroll Please: Deciphering the Genetic Code in Scrolls and Other Ancient Materials

Díez-del-Molino

Dalén

2020

Cell

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The unrelenting development of ancient DNA methods now allows researchers to obtain archaeogenetic data from increasingly diverse sources. In a new study in this issue of Cell, researchers apply the latest DNA technologies to unravel the mysteries of the Dead Sea Scrolls, one of the world's most famous and influential sets of ancient parchments. Figure 1. Genetic Characterization of ParchmentsAncient DNA allows for species identification of the animal skins that parchments of the Dead Sea Scrolls were made from.

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Illuminating Genetic Mysteries of the Dead Sea Scrolls

Cited by 11 publications

References 67 publications

Alignment‐free methods for polyploid genomes: Quick and reliable genetic distance estimation

Alignment‐free methods for polyploid genomes: Quick and reliable genetic distance estimation

Alignment-free methods for polyploid genomes: quick and reliable genetic distance estimation

Unroll Please: Deciphering the Genetic Code in Scrolls and Other Ancient Materials

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