Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe
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Sequences from two ~120,000-year-old individuals reveal the deep population history of European Neandertals.
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Despite its superior sensitivity, the Peyrégne et al. strategy comes at a cost of reduced accuracy in the mapping of reads containing the reference allele.
“However, despite its superior sensitivity, the Peyrégne et al. strategy comes at a cost of reduced accuracy in the mapping of reads containing the reference allele, as we demonstrate below.”
From Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph (2020) · cites this paper as [15]
The Results (page unavailable) say that aligning to an alternative Neandertal reference recovered additional sequences, supporting the strategy’s increased sensitivity. The Methods (page unavailable) describe excluding reads that aligned to different positions in the two references, but neither passage reports reduced mapping accuracy for reads carrying the reference allele. The citing sentence says that its authors demonstrate that cost below. (LLM, conf=0.85)
Experimental — accuracy not yet measuredRecently proposed approaches modify the reference genome and/or the aDNA sequencing reads to account for alternate alleles at polymorphic sites, and reference bias can be substantially reduced by taking into account non-reference variation in the alignment process.
“Recently proposed approaches modify the reference genome [10, 15] and/or the aDNA sequencing reads [10] in order to account for alternate alleles at polymorphic sites. The authors show that by taking into account non-reference variation in the alignment process, reference bias can be substantially reduced.”
From Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph (2020) · cites this paper as [15]
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredThe Peyrégne et al. workflow was the most sensitive, mapping 99.90% (bwa aln -n0.01 -o2; mapQ ≥ 25; alternate allele fraction = 0.50011 95% CI [0.50011, 0.50011]) and 99.77% (at mapQ ≥ 30; alternate allele fraction = 0.50009 95% CI [0.50009, 0.50009]) of all alternate allele reads vs. 99.69% (at q ≥ 30) and 99.15% (at mapQ ≥ 50) with vg graph.
“This workflow was the most sensitive, mapping 99.90% (bwa aln -n0.01 -o2; mapQ ≥ 25; alternate allele fraction = 0.50011 95% CI [0.50011, 0.50011]) and 99.77% (at mapQ ≥ 30; alternate allele fraction = 0.50009 95% CI [0.50009, 0.50009]) of all alternate allele reads vs. 99.69% (at q ≥ 30) and 99.15% (at mapQ ≥ 50) with vg graph”
From Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph (2020) · cites this paper as [15]
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
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Self-citationSlon, V., Viola, B., Renaud, G., Gansauge, M.-T., Benazzi, S., Sawyer, S., Hublin, J., Shunkov, M. V., Derevianko, A. P., Kelso, J. F., et al. (2017) · Science Advances · doi:10.1126/sciadv.1700186 · Cited by 114 · see citing works
Self-citationExtending the spectrum of DNA sequences retrieved from ancient bones and teethPreprint
Glocke, I., & Meyer, M. (2017) · Genome Research · doi:10.1101/gr.219675.116 · Cited by 112 · see citing works
Self-citationÁrnason, Ú., Xu, X., & Gullberg, A. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02198840 · Cited by 106 · see citing works
Hand to Mouth in a Neandertal: Right-Handedness in Regourdou 1
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scrm: efficiently simulating long sequences using the approximated coalescent with recombination
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Long Bone Shaft Robusticity and Body Proportions of the Saint-Césaire 1 Châtelperronian Neanderthal
Trinkaus, E., Churchill, S. E., Ruff, C. B., & Vandermeersch, B. (1999) · Journal of Archaeological Science · doi:10.1006/jasc.1998.0345 · Cited by 92 · see citing works
A NEW DATE FOR THE NEANDERTHALS FROM EL SIDRÓN CAVE (ASTURIAS, NORTHERN SPAIN)*
Wood, R. E., Higham, T., Torres, T., Tisnérat‐Laborde, N., Valladas, H., Ortíz, J. E., Lalueza‐Fox, C., Moral, S. S., Cañaveras, J. C., Rosas, A., et al. (2012) · Archaeometry · doi:10.1111/j.1475-4754.2012.00671.x · Cited by 92 · see citing works
Sexual differences in Neanderthal limb bones
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Upper Central Incisor and Canine Tooth Crown Size in 47,XXY Males
Alvesalo, L. J., Tammisalo, E. H., & Townsend, G. C. (1991) · Journal of Dental Research · doi:10.1177/00220345910700070801 · Cited by 86 · see citing works
The joint allele frequency spectrum of multiple populations: A coalescent theory approach
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Skoglund, P., Götherström, A., & Jakobsson, M. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq342 · Cited by 73 · see citing works
Anterior tooth root morphology and size in Neanderthals: Taxonomic and functional implications
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Sex discriminatory effectiveness using combinations of root lengths and crown diameters
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Locomotion and body proportions of the Saint-Césaire 1 Châtelperronian Neandertal
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Continuities and Discontinuities in Neandertal Presence: A Closer Look at Northwestern Europe
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Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences
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Self-citationSex- and Age-related Differences in Primary and Secondary Dentin Formation
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Were the Spy fossils evolutionary intermediates between Classic Neandertal and Modern Man?
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Spy and Scladina Caves: A Neandertal’s Story
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Die magdalénienzeitlichen Menschenfunde von Oberkassel bei Bonn
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Flagged first, then by citations
Research works printed but not linked: 3
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- [83]S. Pirson, M. Toussaint, D. Bonjean, K. Di Modica, in Landscapes and Landforms of Belgium and Luxembourg, A. Demoulin, Ed. (Springer International Publishing, 2018), pp. 357–383.
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Cited by
Sorted by citations
A high-coverage Neandertal genome from Chagyrskaya Cave
Mafessoni, F., Grote, S., de Filippo, C., Slon, V., Kolobova, K. A., Viola, B., Markin, S. V., Chintalapati, M., Peyrégne, S., Skov, L., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2004944117 · Cited by 309 · see citing works
Self-citationMartiniano, R., Garrison, E., Jones, E. R., Manica, A., & Durbin, R. (2020) · Genome Biology · doi:10.1186/s13059-020-02160-7 · Cited by 128 · see citing works
Systematic benchmark of ancient DNA read mapping
Oliva, A., Tobler, R., Cooper, A., Llamas, B., & Souilmi, Y. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab076 · Cited by 63 · see citing works
The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals
Peyrégne, S., Kelso, J., Peter, B. M., & Pääbo, S. (2022) · eLife · doi:10.7554/elife.75464 · Cited by 24 · see citing works
Self-citation
- Authors
- Peyrégne, S., Slon, V., Mafessoni, F., de Filippo, C., Hajdinjak, M., Nagel, S., Nickel, B., Essel, E., Le Cabec, A., Wehrberger, K., Conard, N. J., Kind, C. J., Posth, C., Krause, J., Abrams, G., Bonjean, D., Di Modica, K., Toussaint, M., Kelso, J., Meyer, M., Pääbo, S., & Prüfer, K.
- Affiliations
- Max Planck Institute for Evolutionary Anthropology (DE)
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany.
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig04103, Germany.
- Museum Ulm, Marktplatz 9, Ulm89073, Germany.
- University of Tübingen (DE)
- State Office for Cultural Heritage Baden-Württemberg Berliner Strasse 12, Esslingen 73728 Germany.
- Max Planck Institute of Geoanthropology (DE)
- Scladina (BE)
- Scladina Cave Archaeological Center, Sclayn, Belgium.
- Ouffet, Belgium.
- Corresponding author
- Peyrégne, Stéphane
- Prüfer, Kay
- ORCID
- Peyrégne, Stéphane
- Slon, Viviane
- Mafessoni, Fabrizio
- de Filippo, Cesare
- Hajdinjak, Mateja
- Essel, Elena
- Le Cabec, Adeline
- Wehrberger, Kurt
- Conard, Nicholas J.
- Kind, Claus Joachim
- Posth, Cosimo
- Krause, Johannes
- Abrams, Grégory
- Bonjean, Dominique
- Di Modica, Kévin
- Toussaint, Michel
- Kelso, Janet
- Meyer, Matthias
- Pääbo, Svante
- Prüfer, Kay
- Venue
- Science Advances
- Published
- 2019-06
- Volume
- 5
- Issue
- 6
- Pages
- eaaw5873-eaaw5873
- ISSN
- 2375-2548 (ISSN-L)
- PMC
- PMC6594762
- OpenAlex
- W2955983787
- Cited by
- 82
- References
- 110
- Citations by year
- 2026: 8 · 2025: 10 · 2024: 12 · 2023: 10 · 2022: 12 · 2021: 11 · 2020: 14 · 2019: 4 · 2018: 1
- FWCI
- 47.22
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by-nc
- Locations
- Science Advances (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Ghent University Academic Bibliography (Ghent University) (publishedVersion)
- Leiden Repository (Leiden University) (submittedVersion, cc-by-nc)
- ArTS Archivio della ricerca di Trieste (University of Trieste https://www.units.it/) (submittedVersion, cc-by-nc)
- HAL (submittedVersion, other-oa)
- MPG.PuRe (Max Planck Society) (submittedVersion, cc-by-nc)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Funders
- European Research Council (694707)
- Max-Planck-Gesellschaft
- Topics
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- Neanderthals, nuclear DNA, genetic continuity
- MeSH terms
- Animals, Cell Nucleus, DNA, Europe, Fossils, Germany, Mitochondria, Genome, Cell Lineage, Evolution, Molecular, Neanderthals
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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