Ancient plant DNA in the genomic era

Estrada, Oscar; Breen, James; Richards, Stephen M.; Cooper, Alan

doi:10.1038/s41477-018-0187-9

Cited by 28 publications

(19 citation statements)

References 33 publications

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“…As for individuals-based tests, only the D-statistic analysis conducted on the contiguous genome revealed gene flow between the Saqqara leaf and P. sylvestris (with D[Saqqara, P. atlantica; P. sylvestris, P. reclinata] = Z < -5.7; Table S5). Discussion Generating genomic data from plant archaeological remains of known origin and unequivocal age provides a unique window into the timing and sequence of plant crop domestication and diffusion processes (Estrada et al, 2018;Gutaker et al, 2017;Swarts et al, 2017;Scott et al, 2019). Archaeological evidence thus far has not informed us about the occurrence and timing of genetic exchanges between date palms and their wild relatives, and whether their distribution overlapped in the past (Flowers et al, 2019).…”

Section: Phylogenetic Placement Of the Saqqara Leaf And Detection Of mentioning

confidence: 99%

Archaeogenomics of a ~2,100-year-old Egyptian leaf provides a new timestamp on date palm domestication

Bellot

Gros-Balthazard

et al. 2020

Preprint

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The date palm (Phoenix dactylifera) has been a cornerstone of Middle Eastern and North African agriculture for millennia. It is presumed that date palms were first domesticated in the Persian Gulf and subsequently introduced into North Africa, where their evolution in the latter region appears to have been influenced by gene flow from the wild relative P. theophrasti, which is restricted to Crete and Turkey. However, the timing of gene flow from P. theophrasti to P. dactylifera remains unknown due to the limited archaeobotanical evidence of P. theophrasti and their exclusion from population genomic studies.We addressed this issue by investigating the relatedness and ancestry of a ~2,100-year-old P. dactylifera leaf from Saqqara (Egypt), combining genome sequencing of this ancient specimen with a broad sample of date palm cultivars and closely related species.The ancient Saqqara date palm shares close genetic ancestry with North African date palm populations. We find clear genomic admixture between the Saqqara date palm, P. theophrasti and the closest known relative P. sylvestris.Our study highlights that gene flow from P. theophrasti and P. sylvestris to North African date palms had already occurred at least ~2,100 years ago, providing a minimum timestamp for hybridisation between species.

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Section: Phylogenetic Placement Of the Saqqara Leaf And Detection Of mentioning

confidence: 99%

Archaeogenomics of a ~2,100-year-old Egyptian leaf provides a new timestamp on date palm domestication

Bellot

Gros-Balthazard

et al. 2020

Preprint

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“…Generating DNA sequences from historical material has been a major challenge, but the advent of high-throughput parallel sequencing and ancient or trace DNA (aDNA) approaches have fundamentally altered the situation. Although still not routine, generating historical DNA data has become feasible on a large scale 3–6 . DNA sequencing of name-bearing type specimens is thus regarded as the gold standard for taxonomy 7 , because it enables unambiguous assignment of extant populations to the named entity or enables a clear distinction between newly discovered forms and those that have already been described.…”

Section: Introductionmentioning

confidence: 99%

Mitogenomics of historical type specimens of Australasian turtles: clarification of taxonomic confusion and old mitochondrial introgression

Kehlmaier

Zhang

Georges

et al. 2019

Sci Rep

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Diagnosability is central to taxonomy as are type specimens which define taxa. New advances in technologies and the discovery of new informative traits must be matched with previous taxonomic decisions based on name-bearing type specimens. Consequently, the challenge of sequencing highly degraded DNA from historical types becomes an inevitability to resolve the very many taxonomic issues arising from, by modern standards, poor historical species descriptions leading to difficulties to assign names to genetic clusters identified from fresh material. Here we apply high-throughput parallel sequencing and sequence baiting to reconstruct the mitogenomes from 18 type specimens of Australasian side-necked turtles (Chelidae). We resolve a number of important issues that have confused the taxonomy of this family, and analyse the mitogenomes of the types and those of fresh material to improve our understanding of the phylogenetic relationships of this morphologically conservative group. Together with previously published nuclear genomic data, our study provides evidence for multiple old mitochondrial introgressions.

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“…Ancient DNA studies focusing on plant remains have made significant contributions to the fields of anthropology and biology (Palmer et al, 2012;Allaby et al, 2015;Brown et al, 2015;Estrada et al, 2018;Brunson and Reich, 2019;Pont et al, 2019), with important projects reconstructing the genomic history of maize, grape, and barley domestication (Fonseca et al, 2015;Mascher et al, 2016;Ramos-Madrigal et al, 2016Vallebueno-Estrada et al, 2016;Swarts et al, 2017;Kistler et al, 2018). The findings reported here suggest that the ever-increasing amounts of sequencing data underlying such projects will soon open for an evaluation of the epigenetic impact of domestication.…”

Section: Discussionmentioning

confidence: 83%

Uncovering Signatures of DNA Methylation in Ancient Plant Remains From Patterns of Post-mortem DNA Damage

2020

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The ultra-short DNA molecules still preserved in archeological remains can provide invaluable genetic information about past individuals, species, and communities within the half to 1-million-year time range. The sequence data are, however, generally affected by post-mortem DNA damage and include specific patterns of nucleotide misincorporations, which can help data authentication. Recent work in ancient mammals has shown that such patterns can also help assess past levels of DNA methylation in CpG contexts. Despite pioneering work in barley and sorghum, ancient epigenetic marks have received limited attention in plants and it remains unknown whether ancient epigenetic signatures can be retrieved in any of the three main sequence contexts (CG, CHG, and CHH). To address this question, we extended a statistical methylation score originally proposed to trace cytosine methylation in mammal sequence data to accommodate the three methylation contexts common in plants. We applied this score to a range of tissues (wood, cobs, and grains) and species (oak, maize, and barley), spanning both desiccated and waterlogged archeological samples. Ancient sequence data obtained for USER-treated DNA extracts yielded methylation scores on par with DNA methylation levels of modern organellar and nuclear genomes. At the quantitative level, scores were (1) positively correlated to post-mortem cytosine deamination, and (2) replicated relative contributions of CG, CHG, and CHH contexts to DNA methylation assessed by bisulfite DNA sequencing of modern plant tissues. This demonstrates that genuine DNA methylation signatures can be characterized in ancient plant remains, which opens new avenues for investigating the plant evolutionary response to farming, pollution, epidemics, and changing environmental conditions.

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Ancient plant DNA in the genomic era

Cited by 28 publications

References 33 publications

Archaeogenomics of a ~2,100-year-old Egyptian leaf provides a new timestamp on date palm domestication

Archaeogenomics of a ~2,100-year-old Egyptian leaf provides a new timestamp on date palm domestication

Mitogenomics of historical type specimens of Australasian turtles: clarification of taxonomic confusion and old mitochondrial introgression

Uncovering Signatures of DNA Methylation in Ancient Plant Remains From Patterns of Post-mortem DNA Damage

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