Patterns of damage in genomic DNA sequences from a Neandertal

Briggs, Adrian W.; Stenzel, Udo; Johnson, Philip L.; Green, Edward; Kelso, Janet; Prüfer, Kay; Meyer, Matthias; Krause, Johannes; Ronan, M. T.; Lachmann, Michael; Pääbo, Svante

doi:10.1073/pnas.0704665104

Cited by 813 publications

(926 citation statements)

References 32 publications

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“…As sequences derived from ancient DNA molecules show characteristic nucleotide composition patterns, those can be used to distinguish them from contaminants of modern DNA fragments. In particular, postmortem deamination of cytosine to uracil leads to an increased rate of observed C to T transitions, particularly near the ends of the DNA fragments 7 . Furthermore, postmortem DNA fragmentation occurs at an increased rate at the 3′-end of purine nucleotides due to depurination, leading to a characteristic enrichment in purines at the base preceding the sequencing read 7 .…”

Section: Overall Sequencing Resultsmentioning

confidence: 99%

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

et al. 2012

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The Tyrolean Iceman, a 5,300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Ötztal Alps. Here we report the complete genome sequence of the Iceman and show 100% concordance between the previously reported mitochondrial genome sequence and the consensus sequence generated from our genomic data. We present indications for recent common ancestry between the Iceman and presentday inhabitants of the Tyrrhenian sea, that the Iceman probably had brown eyes, belonged to blood group o and was lactose intolerant. His genetic predisposition shows an increased risk for coronary heart disease and may have contributed to the development of previously reported vascular calcifications. sequences corresponding to ~60% of the genome of Borrelia burgdorferi are indicative of the earliest human case of infection with the pathogen for Lyme borreliosis.

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Section: Overall Sequencing Resultsmentioning

confidence: 99%

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

et al. 2012

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“…The authenticity of the human reads obtained from archaeological dental calculus and dentine was assessed by examining damage patterns typical of ancient DNA (Briggs et al 2007; Ginolhac et al 2011; Jonsson et al 2013). Briefly, authentic ancient DNA is known to exhibit characteristic damage that includes short DNA fragment lengths, a high rate of cytosine deamination at the termini of DNA fragments, and an enrichment of purine bases at DNA breakage sites.…”

Section: Resultsmentioning

confidence: 99%

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

Ozga

Nieves-Colón

Honap

et al. 2016

American J Phys Anthropol

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Objectives Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. Materials and Methods Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing. Results Full mitogenomes (7-34x) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92–100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. Discussion Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains.

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“…The percentage of shotgun reads mapped is significantly lower in herbarium samples than in contemporary samples (mean herbarium = 0.4% mapped, mean contemporary = 1.85%, one-way ANOVA F = 13.71, p = 0.0019). Analyses of potential nucleotide damage patterns suggest that reads from herbarium samples contain C→T and G→A misincorporations that are characteristic of the cytosine deamination process that occurs during DNA degradation (Briggs et al, 2007;Schuenemann et al, 2011). The estimated misincorporation rates were low overall, though, and only marginally higher in the extreme 5' and 3' ends of the reads, making this increase appear less defined than in older vertebrate samples.…”

Section: Sequencing Chloroplast Genomes From Extinct and Ancient Planmentioning

confidence: 99%

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

Welch

Collins

Drautz–Moses

et al. 2016

Molecular Phylogenetics and Evolution

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(2016) 'The quest to resolve recent radiations : plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae).', Molecular phylogenetics and evolution., 99 . pp. 16-33. Further information on publisher's website: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-pro t purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. AbstractThe Hawaiian mints (Lamiaceae), one of the largest endemic plant lineages in the archipelago, provide an excellent system to study rapid diversification of a lineage with a remote, likely paleohybrid origin. Since their divergence from New World mints 4-5 million years ago the members of this lineage have diversified greatly and represent a remarkable array of vegetative and reproductive phenotypes. Today many members of this group are endangered or already extinct, and molecular phylogenetic work relies largely on herbarium samples collected during the last century. So far a gene-by-gene approach has been utilized, but the recent radiation of the Hawaiian mints has resulted in minimal sequence divergence and hence poor phylogenetic resolution. In our quest to trace the reticulate evolutionary history of the lineage, a resolved maternal phylogeny is necessary. We applied a high-throughput approach to sequence 12 complete or nearly complete plastid genomes from multiple Hawaiian mint species and relatives, including extinct and rare taxa. We also targeted 108 hypervariable regions from throughout the chloroplast genomes in nearly all of the remaining Hawaiian species, and relatives, using a nextgeneration amplicon sequencing approach. This procedure generated ~20Kb of sequence data for each taxon and considerably increased the total number of variable sites over previous analyses. Our results demonstrate the potential of high-throughput sequencing of historic material for evolutionary studies in rapidly evolving lineages. Our study, however, also highlights the challenges of resolving relationships within recent radiations even at the genomic level.

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Patterns of damage in genomic DNA sequences from a Neandertal

Cited by 813 publications

References 32 publications

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

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