Methodological Changes in the Field of Paleogenetics
Abstract
1. Introduction
2. History of aDNA Research
3. Damage of aDNA
4. Materials, Methods and Contamination
5. Extraction of Ancient DNA
6. Amplification
7. Target Enrichment via Hybridization-Based Capture
8. Sequencing
9. Where Paleogenetic and Forensic Sciences Converge
10. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Year of Discovery | Methods | Sample Material | Result | References |
---|---|---|---|---|
1984 | Molecular cloning, Sanger’s sequencing | Dried muscle tissue, quagga specimen | Two sequenced mitochondrial DNA fragments (117 and 112 bp). First recovered aDNA. | [2] |
1988 | PCR | Dried muscle, quagga specimen | Detected cloning artefacts previously unnoticed in [2] with PCR. | [16] |
1988 | Molecular cloning, PCR | Numerous different ancient samples | Comparing the usefulness of molecular cloning and PCR in aDNA research. | [1] |
1991 | PCR | Human brain tissue, 6990–8130 years old | Sequenced fragments of 6 nuclear genes. | [26] |
1998 | PCR | Coprolite | Amplification of DNA from ancient feces. Analysis of the diet of the specimen and identification of species of the specimen. | [27] |
2003 | PCR | Sediment | First analysis of environmental aDNA | [28] |
2005 | PCR | Bones, teeth | Intact stretches of mitochondrial DNA from 24 Neolithic skeletons. | [29] |
2006 | NGS | Woolly mammoth’s mandible | 28 million bp sequenced, 13 million bp were endogenous. First use of NGS in paleogenetics. Analyses of the metagenomic nature of ancient remains. | [20] |
2008 | NGS | Woolly mammoth’s hair | 4.17 billion bp sequenced, 3.3 billion of which were endogenous | [30] |
2008 | NGS | Neanderthal bone | Fully sequenced Neanderthal mitochondrial genome | [31] |
2010 | NGS | 21 Neanderthal bones, 3 selected for further analysis | First sequenced Neanderthal genome (1.2× coverage), evidence for Neanderthals interbreeding with anatomically modern humans | [22] |
2010 | NGS | Finger bone | Discovery of Denisovans and sequenced Denisovan genome | [23] |
2010 | NGS | Hair | First sequenced ancient human genome (Paleo-Inuit) | [21] |
2011 | NGS | Teeth, bones | First fully sequenced genome of ancient bacterial pathogen | [32] |
2012 | NGS | Finger bone | First high coverage (30×) of Denisovan genome, use of single-stranded library preparation. | [33] |
2012 | NGS | Bone from the mummy of Tyrolean Iceman | Genome of Tyrolean Iceman fully sequenced, analysis of phenotype and metagenome | [34] |
2014 | NGS | Ancient calcified dental plaque | First high-resolution taxonomic and proteomic analysis of ancient oral microbiome from calcified dental plaque | [35] |
2014 | NGS | Bones | Identification of English king Richard III | [36] |
2014 | NGS | Toe phalanx | High-quality sequence of Neanderthal woman genome (coverage ~50×) | [37] |
2015 | NGS | - | Analysis of 230 ancient Eurasian genomes to determine genome-wide patterns of selection | [8] |
2015 | NGS | Molar tooth, soft tissue | Complete high-quality two woolly mammoth genomes, analysis of demographic history | [6] |
2015 | NGS | Auroch bone | 6750-year-old auroch genome, analysis of domestication process and its impact on the genome | [5] |
2017 | NGS | Bone | High-coverage genome (30×) of Neanderthal from Vindija Cave, analysis of gene flow between Neanderthals, Denisovans and anatomically modern humans | [38] |
2020 | NGS | - | Sequencing of 442 genomes from archaeological sites across Europe and Greenland to understand the expansion of the Scandinavian population during the Viking Age | [39] |
2020 | NGS | Finger bone | High coverage (27×) sequencing of a Neanderthal from Chagyrskaya Cave. Detection of selection patterns in Neanderthal lineage | [40] |
2021 | NGS | Loessal permafrost silts | Analysis of ancient sedimentary DNA from a period of 30,000 years from the central Yukon in Canada. | [14] |
2021 | NGS | Mammoth molars | Previous record for the oldest sequenced genome (older than 1 million years). | [25] |
2022 | NGS | Sediment | Current record holder for the oldest sequenced DNA | [24] |
Criterion | Explanation |
---|---|
Physically isolated work area | All work on low-copy number DNA should be carried out in an isolated laboratory where no other genetic research is performed. |
PCR control amplifications | Test laboratory environment for contamination. |
Test the molecular behavior | Check the PCR products for unusual results. aDNA is heavily fragmented, so longer fragments should be increasingly rarer. |
Quantitation | Check the number of starting templates. If below 1000, sporadic contamination cannot be ruled out. |
Reproducibility | Results from the same sample material should be repeatable. |
Clone | After sequencing, the PCR product should be cloned and sequenced in multiple copies to determine the ratio of exogenous sequences and sequencing errors resulting from aDNA damage. |
Independent replication | The results should be reproduced in another independent laboratory. |
Biochemical preservation | Survival of other ancient biomolecules makes the survival of aDNA more believable. |
Associated remains | If target DNA sequences also survive in associated faunal material, it may be used as supporting evidence. |
Phylogenetic sense | Reproducible sequences should be placed in a phylogenetic tree with other known haplotypes. |
Damage patterns | The DNA sequences should show specific damage patterns: a high degree of fragmentation and a high concentration of substitutions on the ends of the fragments (C>T on 5′ and G>A on 3′). |
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Danielewski, M.; Żuraszek, J.; Zielińska, A.; Herzig, K.-H.; Słomski, R.; Walkowiak, J.; Wielgus, K. Methodological Changes in the Field of Paleogenetics. Genes 2023, 14, 234. https://doi.org/10.3390/genes14010234
Danielewski M, Żuraszek J, Zielińska A, Herzig K-H, Słomski R, Walkowiak J, Wielgus K. Methodological Changes in the Field of Paleogenetics. Genes. 2023; 14(1):234. https://doi.org/10.3390/genes14010234
Chicago/Turabian StyleDanielewski, Mikołaj, Joanna Żuraszek, Aleksandra Zielińska, Karl-Heinz Herzig, Ryszard Słomski, Jarosław Walkowiak, and Karolina Wielgus. 2023. "Methodological Changes in the Field of Paleogenetics" Genes 14, no. 1: 234. https://doi.org/10.3390/genes14010234
APA StyleDanielewski, M., Żuraszek, J., Zielińska, A., Herzig, K.-H., Słomski, R., Walkowiak, J., & Wielgus, K. (2023). Methodological Changes in the Field of Paleogenetics. Genes, 14(1), 234. https://doi.org/10.3390/genes14010234