The DOI matches its Crossref record; 389 of the 389 references it cites were found in a registry or an index; 195 of the 231 sources its claims cite were checked for support.
Ancient DNA analysis
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Integrity signals
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Claims the paper makes
59 Partly supported · 49 No basis given · 21 Supported · 21 Own interpretation · 14 Couldn’t confirm · 13 No full text of the sources · 8 Supported so far · 3 Not checked yet · 2 Own method · 1 Own result · accuracy not yet measured
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“The discovery that particular bone types exhibit better molecular preservation 52,53 has also facilitated the collection of aDNA time-series data at both population and genome-wide scales.”
§ Ancient DNA analysis > [H1] Introduction
What the sources say
- Supportedcites [52] Gamba, C. et al. Genome flux and stasis in a five millennium transect of European prehistory. Nat. Commun. 5, 5257 (2014). This study reports the first matched empirical evidence establishing better DNA preservation rates in petrosal bones, which paved the way for future studies at the population scale, and also presents complete genomes of Mesolithic hunter–gatherers and Neolithic farmers in the Caucasus, supporting direct early contact between both groups. source
The Results section (“The petrous bone and differential DNA yields”; page not available) reports substantially higher endogenous DNA yields from petrous bones than from teeth or other bones. The Discussion links those yields to the feasibility of temporal population genomics and genome-wide analysis, supporting the claim that better-preserving bone types facilitated ancient DNA time-series work. (LLM, conf=0.93)
- Partly supportedcites [53] Damgaard, P. B. et al. Improving access to endogenous DNA in ancient bones and teeth. Sci. Rep. 5, 11184 (2015). sourceExperimental — accuracy not yet measured
The Results section (page unavailable) finds more endogenous DNA in the outer root surface than in the dentine core of 11 of 14 ancient teeth. The Abstract says this targeting method is likely to make more samples suitable for genome-scale characterization. The paper compares parts of teeth rather than particular bone types, and it does not report that the finding facilitated collection of population-scale aDNA time-series data. (LLM, conf=0.83)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“These include dental calculus 26,44 , wood 45,46 , mollusk shells 47 , and sediments 48,49 , as well as biocultural archives such as parchments 50 and textiles 51 .”
§ Ancient DNA analysis > [H1] Introduction
What the sources say
- Supportedcites [26] Warinner, C. et al. Pathogens and host immunity in the ancient human oral cavity. Nat. Genet. 46, 336–344 (2014). This article reports the first metagenomic and paleoproteomic analysis of ancient dental plaque and demonstrates the preservation of oral microbial signatures, diet content and inflammation markers. source
The citation to this paper is attached to “dental calculus,” not to the other materials in the sentence. The Conclusions identify ancient dental calculus as a well-preserved source of DNA and report the recovery of plant and animal DNA from it. (LLM, conf=0.93)
- Supportedcites [44] Adler, C. J. et al. Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and industrial revolutions. Nat. Genet. 45, 450–455, 455e1 (2013). source
The citation to this paper is attached to dental calculus, not to the other materials in the sentence. The Abstract describes extracting and sequencing bacterial DNA from ancient dental calculus, establishing it as a source of ancient DNA. (LLM, conf=0.94)
- Supportedcites [45] Wagner, S. et al. High-throughput DNA sequencing of ancient wood. Mol. Ecol. 27, 1138–1154 (2018). source
The citation is attached to “wood,” not to the other materials in the list. The Introduction describes sequencing ancient DNA from archaeological and subfossil oak wood, and the Discussion identifies waterlogged wood as a source of ancient tree DNA. No page numbers are provided in our copy. (LLM, conf=0.94)
- Supportedcites [46] Lendvay, B. et al. Improved recovery of ancient DNA from subfossil wood—application to the world’s oldest Late Glacial pine forest. New Phytol. 217, 1737–1748 (2018). source
The citation is attached to “wood,” not to the other materials in the list. The Introduction describes ancient DNA recovered from subfossil wood, and the Conclusions report identifying authentic ancient DNA in more than 13,000-year-old pine wood. (LLM, conf=0.94)
- Supportedcites [47] Der Sarkissian, C. et al. Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past. Mol. Ecol. Resour. 17, 835–853 (2017). source
Citation 47 is attached specifically to mollusk shells, not to the other materials in the list. The Conclusion says the authors recovered DNA from ancient marine mollusc shells and validated them as a new ancient DNA reservoir for archaeological and other analyses. (LLM, conf=0.94)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“The rate of such misincorporations increases towards the end of reads when mapped against a reference sequence due to cytosine deamination preferentially occurring in the single-stranded overhanging termini of aDNA fragments 121 .”
§ Ancient DNA analysis > [H2] Post-mortem DNA damage removal
What the sources say
- Partly supportedcites [121] Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA 104, 14616–14621 (2007). This article presents the first statistical model of post-mortem DNA degradation and its impact on nucleotide misincorporation patterns, which provides the basis of important criteria for data authentication. sourceExperimental — accuracy not yet measured
The Results and Discussion report elevated C-to-T misincorporations at 5′ ends and identify cytosine deamination as the principal cause. They suggest that single-stranded overhangs explain the elevated end damage, but also offer DNA breathing as an alternative; the claim presents the overhang mechanism as settled and does not specify the 5′ end. (LLM, conf=0.86)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Small amounts of preserved DNA and extensive DNA fragmentation to lengths <100 bp 109 pose serious challenges for extracting DNA molecules from ancient samples.”
§ Ancient DNA analysis > [H2] DNA extraction
What the sources say
- Partly supportedcites [109] Dabney, J., Meyer, M. & Pääbo, S. Ancient DNA damage. Cold Spring Harb. Perspect. Biol. 5, a012567 (2013). sourceExperimental — accuracy not yet measured
The FRAGMENTATION section says that DNA from almost all ancient remains is degraded into short fragments, citing a range of 40–500 bp in an early study. It does not establish that fragments are typically shorter than 100 bp; the reported range extends well above that threshold. (LLM, conf=0.86)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Partly supported
The sources with a verdict support this claim; the rest weren’t checked yet, have no full text we could read, or their verdicts aren’t rated yet.
In the paper
“Optimizing DNA extraction and library construction to recover fragments as short as 35 bp has been decisive in characterizing DNA from samples showing extensive molecular degradation 39,119 .”
§ Ancient DNA analysis > [H2] DNA extraction
What the sources say
- Not checked — no full text of the sourcecites [39] Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013). This study reports a new DNA extraction method from ancient osseous remains that is tailored to the ultrashort and extensively damaged nature of aDNA molecules. This methodology allowed the retrieval of full mitochondrial genome sequences from 300,000-year-old cave bear specimens preserved in Atapuerca, Spain. source
- Supportedcites [119] Meyer, M. et al. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505, 403–406 (2014). source
The Methods (page unavailable) describe an extraction protocol optimized for very short ancient DNA and a library-preparation protocol developed for highly degraded DNA. They report that fragments with a modal length around 30 bp were efficiently extracted and converted into library molecules, supporting recovery of fragments as short as 35 bp in this hominin analysis. (LLM, conf=0.88)
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“The reduced size of the DNA molecules makes it difficult to separate endogenous DNA of interest from contaminating DNA and from co-extracted small molecules that could act as inhibitors in downstream enzymatic reactions 110,111 .”
§ Ancient DNA analysis > [H2] DNA extraction
What the sources say
- Partly supportedcites [110] Höss, M. & Pääbo, S. DNA extraction from Pleistocene bones by a silica-based purification method. Nucleic Acids Res. 21, 3913–3914 (1993). sourceExperimental — accuracy not yet measured
The paper’s main text (page not given in our copy) says archaeological extracts can contain components that inhibit PCR and that contemporary DNA contamination can yield misleading results. It does not say that reduced DNA size makes endogenous DNA difficult to separate from either contaminants or small inhibitory molecules; that causal explanation is unsupported. (LLM, conf=0.86)
- Partly supportedcites [111] Green, R. E. et al. The Neandertal genome and ancient DNA authenticity. EMBO J. 28, 2494–2502 (2009). sourceExperimental — accuracy not yet measured
The 'Estimates based on fragment size' section (page unavailable) says endogenous and contaminating DNA fragments can overlap in size, making fragment length unreliable for distinguishing them. It does not say that short DNA molecules are difficult to physically separate from contaminants or from co-extracted small molecules, or that those molecules inhibit downstream enzymatic reactions. (LLM, conf=0.84)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“More generally, aDNA data has transformed our understanding of the historical emergence, virulence and spread of major infectious diseases 25 .”
§ Ancient DNA analysis > [H1] Introduction
What the sources say
- Partly supportedcites [25] Key, F. M. et al. Emergence of human-adapted Salmonella enterica is linked to the Neolithization process. Nat. Ecol. Evol. 4, 324–333 (2020). sourceExperimental — accuracy not yet measured
The Abstract and the sections on ancient S. enterica across western Eurasia and genomic architecture show how ancient DNA informs the emergence, geographic distribution and virulence-related genetics of Salmonella. The paper does not establish the broader claim about multiple major infectious diseases; its findings concern S. enterica. (LLM, conf=0.84)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“The next most common hydrolytic degradation reaction is the deamination of cytosines, which are converted into uracils and thereafter sequenced as thymine analogues 121 (FIG.3a).”
§ Ancient DNA analysis > [H2] Post-mortem DNA damage removal
What the sources say
- Partly supportedcites [121] Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA 104, 14616–14621 (2007). This article presents the first statistical model of post-mortem DNA degradation and its impact on nucleotide misincorporation patterns, which provides the basis of important criteria for data authentication. sourceExperimental — accuracy not yet measured
The Results and Discussion (page unavailable) state that cytosine deaminates to uracil and that this damage produces C-to-T substitutions when ancient DNA is sequenced. The paper does not rank deamination as the “next most common” hydrolytic degradation reaction; its frequency conclusion concerns nucleotide misincorporations, not hydrolytic reactions overall. (LLM, conf=0.85)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Partly supported
The sources with a verdict support this claim; the rest weren’t checked yet, have no full text we could read, or their verdicts aren’t rated yet.
In the paper
“PCR, however, does not simply restore sufficient amounts of material for downstream manipulation; it can also significantly alter the library composition as DNA polymerases show various preferences for templates of particular sizes and/or base composition 150 , as well as differing in 'proofreading' capabilities for bypassing post-mortem DNA damage 48,151 .”
§ Ancient DNA analysis > [H2] DNA library amplification
What the sources say
- Not checked — no full text of the sourcecites [150] Dabney, J. & Meyer, M. Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. BioTechniques 52, 87–94 (2012). source
- Not checked — no full text of the sourcecites [48] Pedersen, M. W. et al. Postglacial viability and colonization in North America’s ice-free corridor. Nature 537, 45–49 (2016). source
- Supportedcites [151] Seguin-Orlando, A. et al. Amplification of TruSeq ancient DNA libraries with AccuPrime Pfx: consequences on nucleotide misincorporation and methylation patterns. STAR: Sci. Technol. Archaeol. Res. 1, 1–9 (2015). source
The Introduction says PCR conditions affect library complexity through polymerase-dependent base-composition and length biases. The Results and Discussion show that AccuPrime Pfx cannot amplify uracil-containing, post-mortem-damaged strands, whereas AmpliTaq Gold can bypass uracils, changing the molecules represented in the amplified library. (LLM, conf=0.92)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Parameters maximizing mapping specificity and sensitivity can be identified using aDNA read simulators such as 16 gargammel 180 , and depend on the evolutionary distance to the reference genome used, DNA fragment size and the amount of post-mortem damage 111,181-184 .”
§ Ancient DNA analysis > [H1] Results
What the sources say
- Partly supportedcites [111] Green, R. E. et al. The Neandertal genome and ancient DNA authenticity. EMBO J. 28, 2494–2502 (2009). sourceExperimental — accuracy not yet measured
In “Fragment size and divergence to humans” (page unavailable), the paper says that identifying Neandertal fragments by similarity to human or chimpanzee genomes is difficult for short fragments, especially when they contain nucleotide misincorporations. “Fragment size and derived alleles” adds that mismatches with the reference reduce recognition, particularly for short sequences. These passages support the relevance of fragment size, divergence and damage to mapping, but do not establish parameters that maximize both mapping specificity and sensitivity. (LLM, conf=0.83)
- Supportedcites [181] Schubert, M. et al. Improving ancient DNA read mapping against modern reference genomes. BMC Genomics 13, 178 (2012). source
In Results and discussion (Increasing tolerance for higher edit distances; page unavailable), the paper explains that allowed mismatches vary with read length and that post-mortem damage affects recovery of divergent reads, with greater tolerance risking spurious hits. In Divergence estimates (page unavailable), it reports that parameter sets differ in their tolerance for divergent reads and that mapping to a more distant reference misses more of them. These passages support the stated dependence of mapping sensitivity and specificity on fragment size, damage, and reference divergence. (LLM, conf=0.86)
- Partly supportedcites [182] Shapiro, B. & Hofreiter, M. A paleogenomic perspective on evolution and gene function: new insights from ancient DNA. Science 343, 1236573 (2014). sourceExperimental — accuracy not yet measured
In “Hominin Paleogenomics,” the review says very short fragments are difficult to map unambiguously; Fig. 3 says increasing evolutionary distance reduces the proportion of reads mappable to a reference genome. Our copy does not state that mapping parameters maximizing specificity and sensitivity depend on post-mortem damage, or identify such optimal parameters. Page numbers were not supplied for these passages. (LLM, conf=0.84)
- Partly supportedcites [183] Cahill, J. A. et al. Genomic evidence of widespread admixture from polar bears into brown bears during the last ice age. Mol. Biol. Evol. 35, 1120–1129 (2018). sourceExperimental — accuracy not yet measured
In “Mapping and reference bias correction” (page unavailable), the paper compares read-mapping parameters, shows that reference choice changes mappings, and says short reads and high error rates increase mapping bias. It measures fragment lengths and ancient-DNA damage, but does not establish how damage affects the parameters that maximize mapping specificity and sensitivity. (LLM, conf=0.82)
- Partly supportedcites [184] Poullet, M. & Orlando, L. Assessing DNA sequence alignment methods for characterizing ancient genomes and methylomes. Front. Ecol. Evolut. 8, 105 (2020). sourceExperimental — accuracy not yet measured
The Overall Alignment Performance section reports that the best-performing alignment approach varies with DNA fragment size, and the Discussion links performance to post-mortem preservation conditions. The paper does not establish how optimal mapping parameters depend on evolutionary distance to the reference genome; its simulations use a human reference genome (Data Simulation). Page numbers are unavailable in our copy. (LLM, conf=0.87)
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Partly supported
- It may state two separate claims as one. 63
- Probably not a substantial claim. 74
- The quote only partly states this claim. 1
The cited sources that could be checked couldn’t confirm or dispute this claim.
In the paper
“This reagent removes uracils and cleaves the resulting abasic sites, thereby cutting out damage but also shortening the length of the DNA molecule 125 .”
§ Ancient DNA analysis > [H2] Post-mortem DNA damage removal
What the sources say
- Could not verifycites [125] Briggs, A. W. et al. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38, e87 (2010). This article presents an experimental procedure based on enzymatic digestion that eliminates nucleotide misincorporations from ancient sequence data, which provided the basis for robust statistical inference, minimally impacted by spurious allelic variation, and has paved the way to aDNA methylation maps. sourceExperimental — accuracy not yet measured
The Introduction discusses RdgC binding to DNA, and the Oligonucleotide and plasmid binding assays section describes preparing DNA substrates. Neither addresses USER reagent, uracil removal, cleavage at abasic sites, or shortening of DNA molecules (searched for those terms and the reagent’s enzymes). (LLM, conf=0.78)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Could not verify
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Although C-to-T misincorporations provide handy genetic signatures that can be used to authenticate aDNA sequences 54,57 , they can also bias sequence analyses, potentially leading to incorrect conclusions 123,124 .”
§ Ancient DNA analysis > [H2] Post-mortem DNA damage removal
What the sources say
- Partly supportedcites [54] Krause, J. et al. A complete mtDNA genome of an early modern human from Kostenki, Russia. Curr. Biol. 20, 231–236 (2010). This article establishes important criteria for aDNA data authentication, including the presence of post-mortem cytosine deamination signatures and DNA fragmentation through depurination, and reports a complete mitochondrial genome from an approximately 32,000-year-old anatomically modern human from Kostenki, Russia. sourceExperimental — accuracy not yet measured
The Results and Discussion (page not provided) show that C-to-T misincorporations differ between endogenous and contaminating DNA and say that misincorporation patterns can help identify authentic ancient-DNA datasets. The paper does not say that these misincorporations bias sequence analyses or lead to incorrect conclusions; the citing sentence attaches separate citations to that second point. (LLM, conf=0.85)
- Supportedcites [57] Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013). source
The Introduction says cytosine-deamination-driven misincorporation patterns can authenticate ancient DNA sequences. The Conclusion says limiting their impact improves downstream sequence analyses, and the Discussion reports that quality rescaling suggested fewer false-positive SNP calls. Our copy does not provide page numbers for these passages. (LLM, conf=0.91)
- Supportedcites [123] Ho, S. Y. W., Heupink, T. H., Rambaut, A. & Shapiro, B. Bayesian estimation of sequence damage in ancient DNA. Mol. Biol. Evol. 24, 1416–1422 (2007). source
The citation is attached to the claim that misincorporations can bias sequence analyses, not to the separate authentication claim. The Introduction identifies C-to-T transitions as a common type of ancient-DNA damage, and “Effect of Miscoding Lesions on Phylogenetic Analysis” says such errors can distort estimates and mislead phylogenetic inference. Page numbers were not supplied in our copy. (LLM, conf=0.91)
- Supportedcites [124] Axelsson, E., Willerslev, E., Gilbert, M. T. P. & Nielsen, R. The effect of ancient DNA damage on inferences of demographic histories. Mol. Biol. Evol. 25, 2181–2187 (2008). source
The citation to this paper is attached to the claim that misincorporations can bias analyses and lead to incorrect conclusions, not to the preceding authentication claim. The Results report that ancient-DNA miscoding lesions can create spurious signals of population-size change; the Introduction identifies C-to-T miscoding lesions as a form of such damage. (LLM, conf=0.93)
plainconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Partly supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“In order to maximize preservation of the remains' integrity and allow potential further molecular or morphological analyses, minimally-destructive methods have been proposed to sample bones 96 , teeth 97 , insects 98 or plants 99 , for example.”
§ Ancient DNA analysis > [H2] DNA extraction
What the sources say
- Supportedcites [96] Sirak, K. A. et al. A minimally-invasive method for sampling human petrous bones from the cranial base for ancient DNA analysis. BioTechniques 62, 283–289 (2017). source
The Method Summary (Vol. 62, No. 6) describes a minimally invasive method for sampling petrous bone while preserving cranial features needed for anthropological analysis. The paper also says the method enables combined genetic and craniometric study. This supports the bone-sampling example attributed to this citation; the separate teeth, insects, and plants examples have other citations. (LLM, conf=0.93)
- Supportedcites [97] Harney, É. et al. A minimally destructive protocol for DNA extraction from ancient teeth. Preprint at bioRxiv https://doi.org/10.1101/2020.08.19.256412(2020). source
The citation to this paper is attached to “teeth,” not to bones, insects, or plants. The Abstract presents a minimally destructive method for sampling ancient teeth, and the Discussion says it preserves samples for future morphological and biochemical analyses. (LLM, conf=0.94)
- Supportedcites [98] Patzold, F., Zilli, A. & Hundsdoerfer, A. K. Advantages of an easy-to-use DNA extraction method for minimal-destructive analysis of collection specimens. PLoS ONE 15, e0235222 (2020). source
This source supports the insects portion of the sentence, to which citation 98 is attached. The Introduction describes extracting DNA from historic insect specimens while preserving morphological traits, and Material and methods describes a minimal-destructive procedure that leaves the insects’ legs intact. (LLM, conf=0.93)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“These postmortem alterations potentially hinder the manipulation of aDNA and reduce the amount of retrievable genetic information 109,120 .”
§ Ancient DNA analysis > [H2] Post-mortem DNA damage removal
What the sources say
- Supportedcites [109] Dabney, J., Meyer, M. & Pääbo, S. Ancient DNA damage. Cold Spring Harb. Perspect. Biol. 5, a012567 (2013). source
The Abstract says postmortem damage reduces DNA fragment size and creates lesions that block replication, impeding analysis. It also says destructive processes may lead to the loss of all retrievable DNA. Together, these support both parts of the paraphrase. (LLM, conf=0.93)
- Supportedcites [120] Höss, M., Jaruga, P., Zastawny, T. H., Dizdaroglu, M. & Pääbo, S. DNA damage and DNA sequence retrieval from ancient tissues. Nucleic Acids Res. 24, 1304–1307 (1996). source
The Introduction says damage accumulating after burial can prevent ancient DNA from serving as a PCR template, limiting sequence retrieval. The Results and Discussion also suggest that repairing chemical lesions could make more DNA amenable to amplification. The supplied passages do not give page numbers. (LLM, conf=0.91)
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“None of these developments would have been possible without next-generation sequencing (NGS) 30 , which remains thus far the most transformative technology in the history of aDNA research, profoundly affecting wet-lab and dry-lab activities alike (FIG.1).”
§ Ancient DNA analysis > [H1] Introduction
What the sources say
- Partly supportedcites [30] Goodwin, S., McPherson, J. D. & McCombie, W. R. Coming of age: ten years of next-generation sequencing technologies. Nat. Rev. Genet. 17, 333–351 (2016). sourceExperimental — accuracy not yet measured
The Abstract describes NGS as enabling major advances in genome sequencing, and the Closing remarks describe its potential for revolutionary science. But the paper does not address ancient DNA specifically, so it does not establish that the cited aDNA developments depended on NGS or that NGS was the most transformative technology in aDNA research history (searched: ancient DNA, aDNA, ancient). (LLM, conf=0.82)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Postmortem damage can accumulate with the age of the sample 122 , but degradation kinetics are ultimately driven by local environmental conditions 2,45 .”
§ Ancient DNA analysis > [H2] Post-mortem DNA damage removal
What the sources say
- Supportedcites [122] Sawyer, S., Krause, J., Guschanski, K., Savolainen, V. & Pääbo, S. Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PLoS ONE 7, e34131 (2012). source
The source supports the age-related clause attached to citation 122: the Discussion reports a strong positive correlation between sample age and C-to-T nucleotide misincorporations. The environmental-conditions clause is attached to citations 2 and 45, not to this source. (LLM, conf=0.92)
- Not checked — no full text of the sourcecites [2] Orlando, L. et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499, 74–78 (2013). This article presents the oldest sequenced genome to date, from one horse metapodial preserved in permafrost for 560,000–780,000 years. source
- Partly supportedcites [45] Wagner, S. et al. High-throughput DNA sequencing of ancient wood. Mol. Ecol. 27, 1138–1154 (2018). sourceExperimental — accuracy not yet measured
The Results (DNA authenticity and degradation; page unavailable) find that damage increased with thermal age and varied among samples of similar age, possibly because of microenvironmental conditions. The Discussion likewise describes heterogeneous conditions as driving DNA decay, but the paper does not establish that local conditions ultimately determine degradation kinetics; it also identifies thermal age as a factor. (LLM, conf=0.86)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“This may be adequate for relatively recent historical time periods 224 and/or areas such as Europe where many genomes from modern human populations have been collected 222 , but may be underpowered in cases of limited reference panels, as is true for many populations from elsewhere in the world 225 .”
§ Ancient DNA analysis > [H2] Genotype imputation
What the sources say
- Partly supportedcites [224] Antonio, M. L. et al. Ancient Rome: a genetic crossroads of Europe and the Mediterranean. Science 366, 708–714 (2019). sourceExperimental — accuracy not yet measured
Split into 2 atoms — 0 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 1 unverifiable. Expand the claim to see per-atom verdicts.
- Partly supportedcites [222] Cassidy, L. M. et al. A dynastic elite in monumental Neolithic society. Nature 582, 384–388 (2020). sourceExperimental — accuracy not yet measured
Split into 2 atoms — 0 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 1 unverifiable. Expand the claim to see per-atom verdicts.
- Partly supportedcites [225] Sirugo, G., Williams, S. M. & Tishkoff, S. A. The missing diversity in human genetic studies. Cell 177, 26–31 (2019). sourceExperimental — accuracy not yet measured
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Partly supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“Second, allelic drop out, the failure of certain templates to amplify, can occur as a result of the clonal biases inherent in PCR or from length polymorphisms in the target region 133 , both of which are especially problematic when DNA is degraded and template copy number is low, giving rise to low or skewed sequence complexity.”
§ Ancient DNA analysis > [H2] Mini-barcode PCR amplification
What the sources say
- Supportedcites [133] Ziesemer, K. A. et al. Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification. Sci. Rep. 5, 16498 (2015). source
The Results section on DNA fragmentation reports that few ancient DNA fragments are long enough to serve as PCR templates, making taxonomic dropout and stochastic amplification effects likely. The Discussion identifies differential PCR amplification of degraded DNA and length polymorphisms as causes of dropout and skewed taxonomic profiles. The copy provides section labels but no page numbers. (LLM, conf=0.90)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“f3 statistics can reveal unambiguous evidence for situations in which one individual (or population) is formed by the admixture of two others 219 , but they can also provide a measure of shared genetic drift when an outgroup is included 220 .”
§ Ancient DNA analysis > [H2] Population ancestry modelling
What the sources say
- Supportedcites [219] Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012). This article describes the statistical methodology forming the core of most subsequent aDNA studies and aims at investigating population structure and admixture patterns. source
The citation follows the first clause, about using f3 to detect admixture. In “The three-population test and introduction of f-statistics” (page not available), the paper says a significantly negative f3(C; A, B) definitively shows a complex history in C, rather than admixture in A or B. It also cautions that admixture does not always produce a negative f3, consistent with the claim’s “can reveal” wording. (LLM, conf=0.92)
- Supportedcites [220] Raghavan, M. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of native Americans. Nature 505, 87–91 (2014). source
Citation 220 is attached to the outgroup clause. The Methods section, “Outgroup f3-statistics,” explains that variation in this statistic reflects how much genetic history two populations share and describes its use with Yoruba as an outgroup. (LLM, conf=0.93)
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“During sequencing preparation, , it is also important to take steps to mitigate index hopping when using Illumina platforms, especially those using patterned flow cells and isothermal cluster generation by exclusion amplification, such as the HiSeq4000, HiSeqX and NovaSeq platforms 173 .”
§ Ancient DNA analysis > [H2] DNA library amplification
What the sources say
- Supportedcites [173] Costello, M. et al. Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms. BMC Genomics 19, 332 (2018). source
The Background identifies HiSeqX, HiSeq 4000 and NovaSeq as Illumina platforms using patterned flow cells and ExAmp chemistry. The Results report index swapping on all three and recommend non-redundant dual indexing to filter swapped reads. Our copy does not provide page numbers for these passages. (LLM, conf=0.94)
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“While PCA results are most often visualized as biplots and in practice analyzed in twodimensional comparisons of two principal components at a time, alternative clustering methods such as those implemented in ADMIXTURE 214 make higher-dimensional assessments possible.”
§ Ancient DNA analysis > [H2] Population ancestry modelling
What the sources say
- Supportedcites [214] Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009). source
The Simulated association studies section (page unavailable) describes ADMIXTURE’s ancestry estimate as a vector with K entries, of which K−1 can be used as predictors. The Discussion (page unavailable) also describes choosing among values of K. Together, these support using ADMIXTURE for assessments beyond two dimensions; the citation need not establish the sentence’s separate observation about how PCA is usually visualized. (LLM, conf=0.88)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Supported
The cited sources that could be checked couldn’t confirm or dispute this claim.
In the paper
“Nevertheless, imputation can also infer false genotype calls 230 , and so care must be exercised when using imputation to investigate the evolutionary history of specific traits.”
§ Ancient DNA analysis > [H2] Genotype imputation
What the sources say
- Could not verifycites [230] Burger, J. et al. Low prevalence of lactase persistence in Bronze Age Europe indicates ongoing strong selection over the last 3,000 years. Curr. Biol. 30, 1–9 (2020). sourceExperimental — accuracy not yet measured
The Principal component analysis section mentions imputing missing entries in a modern reference dataset, but does not say that imputation produced false genotype calls. The Genotype calling section describes calls based on genotype likelihoods, not an imputation error. Searches for false or incorrect imputed genotypes found no passage supporting the attributed caution about studying trait evolution. (LLM, conf=0.74)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Could not verify
Every source the paper cites for this claim was checked and supports it.
In the paper
“Another advantage of the single-stranded preparation method is that it enables the molecular selection of DNA templates carrying evidence of post-mortem DNA damage, which can increase the fraction of endogenous DNA incorporated into sequencing libraries, and thus reduce downstream sequencing costs 43 .”
§ Ancient DNA analysis > [H2] DNA library construction
What the sources say
- Supportedcites [43] Gansauge, M.-T. & Meyer, M. Selective enrichment of damaged DNA molecules for ancient genome sequencing. Genome Res. 24, 1543–1549 (2014). source
The Results section (‘The U selection method’; page not available) describes U selection as an extension of single-stranded library preparation that separates uracil-containing strands. The paper reports an increased proportion of endogenous sequences in some samples, and the Discussion says U selection reduced sequencing costs for samples contaminated with present-day human DNA. (LLM, conf=0.91)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“Finally, f4 statistics test for asymmetries between populations that are indicative of gene flow 219 (FIG.4B).”
§ Ancient DNA analysis > [H2] Population ancestry modelling
What the sources say
- Supportedcites [219] Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012). This article describes the statistical methodology forming the core of most subsequent aDNA studies and aims at investigating population structure and admixture patterns. source
The D-statistics section identifies f4 as a four-population statistic used to provide evidence of admixture. It also defines the corresponding numerator as the difference between BABA and ABBA allele-sharing patterns, supporting the claim that such asymmetries can indicate gene flow. Page numbers are unavailable in our copy. (LLM, conf=0.91)
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Supported
The cited sources that could be checked couldn’t confirm or dispute this claim.
In the paper
“As with PCR-based aDNA approaches used in the 1990s, the authentication of metabarcoding [G] results relies instead on reproducibility across multiple PCR replicates 128 and demonstrating that negative controls are either blank or contain different sequence signatures than that seen within the samples.”
§ Ancient DNA analysis > [H2] Mini-barcode PCR amplification
What the sources say
- Could not verifycites [128] Taberlet, P. et al. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res. 35, e14 (2007). sourceExperimental — accuracy not yet measured
The citation follows the claim about reproducibility across multiple PCR replicates. The Materials and Methods section (‘Robustness of the system for biotechnological applications’; page unavailable) describes multiple extraction and PCR blank controls, but does not say that authentication relies on reproducibility across PCR replicates. Searches for replicate amplification and reproducibility found no passage establishing that point. (LLM, conf=0.72)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Could not verify
Every source the paper cites for this claim was checked and supports it.
In the paper
“Emerging methods such as AuthentiCT 192 , which uses a model of cytosine deamination to estimate contamination, promise to generalize contamination inference across organisms, sex and chromosome types, thereby mitigating the need for the ploidy-based approaches.”
§ Ancient DNA analysis > [H2] Authentication
What the sources say
- Supportedcites [192] Peyrègne, S. & Peter, B. M. AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination. Genome Biol. 21, 246 (2020). source
Split into 2 atoms — 2 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
- Supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“This information is generally digitized in most, if not all, aDNA laboratories, and Laboratory Information Management Systems (LIMS) specifically developed for aDNA such as CASCADE 174 are becoming freely available.”
§ Ancient DNA analysis > [H2] Information management systems
What the sources say
- Supportedcites [174] Dolle, D. et al. CASCADE: a custom-made archiving system for the conservation of ancient DNA experimental data. Front. Ecol. Evol. 8, 185 (2020). source
The Introduction identifies CASCADE as a LIMS tailor-made for ancient DNA processing and says it is available for free. The Discussion likewise describes its aDNA-specific LIMS features and free availability. (LLM, conf=0.93)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Statistical inference of missing genotypes is possible using a process called genotype imputation that assumes that the distribution of haplotypes present in the population is known and that sufficient coverage is available, typically around 1´2 22 .”
§ Ancient DNA analysis > [H2] Genotype imputation
What the sources say
- Partly supportedcites [222] Cassidy, L. M. et al. A dynastic elite in monumental Neolithic society. Nature 582, 384–388 (2020). sourceExperimental — accuracy not yet measured
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- The authors state this as an assumption: The distribution of haplotypes present in the population is known.
- Partly supported
The sources with a verdict support this claim; the rest weren’t checked yet, have no full text we could read, or their verdicts aren’t rated yet.
In the paper
“Although other technologies have been sporadically used (for example, SOLiD 168 , Helicos 2 , BGI-SEQ500 169 , Ion Torrent 170 ), the vast majority of aDNA sequence data have been produced using Illumina instruments, due to their ubiquity, high data output, cost-effectiveness and relatively low error rates.”
§ Ancient DNA analysis > [H2] DNA library amplification
What the sources say
- Supportedcites [168] Keller, A. et al. New insights into the Tyrolean Iceman’s origin and phenotype as inferred by whole-genome sequencing. Nat. Commun. 3, 698 (2012). source
Citation 168 is attached to SOLiD as an example of another technology used for ancient DNA sequencing, not to the subsequent claim about Illumina's prevalence or advantages. The Sequencing section says the Tyrolean Iceman's DNA was sequenced on a SOLiD 4 instrument. (LLM, conf=0.94)
- Not checked — no full text of the sourcecites [2] Orlando, L. et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499, 74–78 (2013). This article presents the oldest sequenced genome to date, from one horse metapodial preserved in permafrost for 560,000–780,000 years. source
- Supportedcites [169] Mak, S. S. T. et al. Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. Gigascience 6, 1–13 (2017). source
Citation 169 is attached to BGISEQ-500 as an example of another technology used for ancient DNA sequencing. The Background describes a direct comparison in which the authors sequenced eight historic and ancient DNA extracts using BGISEQ-500 and Illumina, so the cited paper supports that identification. (LLM, conf=0.94)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Authentication of genomic DNA from single individuals (see below for authentication of microbial DNA) requires both the observation of post-mortem nucleotide misincorporation arising from cytosine deamination 57,120 (FIG.3A-H) and the estimation of contaminating DNA based on heterozygosity levels found in haploid chromosomes 54 (FIG.3I).”
§ Ancient DNA analysis > [H2] Authentication
What the sources say
- Partly supportedcites [57] Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013). sourceExperimental — accuracy not yet measured
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
- Could not verifycites [120] Höss, M., Jaruga, P., Zastawny, T. H., Dizdaroglu, M. & Pääbo, S. DNA damage and DNA sequence retrieval from ancient tissues. Nucleic Acids Res. 24, 1304–1307 (1996). sourceExperimental — accuracy not yet measured
Split into 2 atoms — 0 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 2 unverifiable. Expand the claim to see per-atom verdicts.
- Partly supportedcites [54] Krause, J. et al. A complete mtDNA genome of an early modern human from Kostenki, Russia. Curr. Biol. 20, 231–236 (2010). This article establishes important criteria for aDNA data authentication, including the presence of post-mortem cytosine deamination signatures and DNA fragmentation through depurination, and reports a complete mitochondrial genome from an approximately 32,000-year-old anatomically modern human from Kostenki, Russia. sourceExperimental — accuracy not yet measured
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Partly supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“Performing two successive rounds of enrichment generally increases on-target coverage rates 166 , while the use of short adapters can favor on-target library-to-probe annealing and enhance enrichment efficacy 126 .”
§ Ancient DNA analysis > [H2] DNA library amplification
What the sources say
- Supportedcites [166] Hernandez-Rodriguez, J. et al. The impact of endogenous content, replicates and pooling on genome capture from faecal samples. Mol. Ecol. Resour. 18, 319–333 (2018). source
Citation 166 is attached to the first clause, not the short-adapter claim attributed to citation 126. In Results (Experiment 2; page unavailable), the paper reports that two capture rounds increased capture specificity and enrichment factor relative to one round. It frames the recommendation around complex faecal samples. (LLM, conf=0.90)
- Supportedcites [126] Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil–DNA–glycosylase treatment for screening of ancient DNA. Philos. Trans. R. Soc. Lond. B Biol. Sci. 370, 20130624 (2015). This study reports the first method for DNA library preparation that is compatible with full automation and also describes various approaches aimed at authenticating data while minimizing the impact of post-mortem DNA misincorporation on downstream analyses. source
Citation 126 is attached to the short-adapter clause, not the preceding claim about two enrichment rounds. In the adapter-length results (Table 3 and Additional information; page not provided), short-adapter libraries have higher on-target read percentages than long-adapter libraries, and the authors conclude that short adapters can increase capture specificity. This supports the claim that they can favor on-target hybridization and improve enrichment efficacy. (LLM, conf=0.88)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“This contrasts with methods based on f-statistics [217][218][219] , which leverage covariation of allele frequencies between populations, and can retrieve unbiased admixture proportions.”
§ Ancient DNA analysis > [H2] Population ancestry modelling
What the sources say
- Could not verifycites [217] Joseph, T. A. & Pe’er, I. Inference of population structure from time-series genotype data. Am. J. Hum. Genet. 105, 317–333 (2019). sourceExperimental — accuracy not yet measured
The Introduction (page unavailable) mentions f- and D-statistics as ways to test hypotheses about population relationships. Searches for allele-frequency covariation and unbiased admixture estimates found no passage explaining that mechanism or making the claimed performance assertion; the Results discuss estimates from DyStruct instead. (LLM, conf=0.75)
- Supportedcites [218] Reich, D., Thangaraj, K., Patterson, N., Price, A. L. & Singh, L. Reconstructing Indian population history. Nature 461, 489–494 (2009). source
The Methods Summary describes using f3 ancestry estimation to infer admixture proportions. The ‘Estimates of mixture proportions in India’ section says the authors developed methods that they verified as accurate despite SNP ascertainment bias and some model inaccuracies, and reports f3-based ancestry estimates. The four-population test passage describes assessing covariation in allele-frequency differences. (LLM, conf=0.88)
- Partly supportedcites [219] Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012). This article describes the statistical methodology forming the core of most subsequent aDNA studies and aims at investigating population structure and admixture patterns. sourceExperimental — accuracy not yet measured
The Abstract says the methods measure allele-frequency correlations among populations and that ratios of f-statistics can provide precise admixture-proportion estimates. The simulations section reports accurate estimates, but the paper’s explicit claim of unbiased estimation concerns f-statistics themselves, not admixture proportions; it does not establish that the latter are unbiased. (LLM, conf=0.86)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Could not verify
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“It is notable that PCA clustering is sensitive to the sample size of different ancestries and also to their amount of genetic drift, which exaggerates principal component distances 207,208,211,212 .”
§ Ancient DNA analysis > [H2] Multivariate analyses
What the sources say
- Partly supportedcites [207] Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006). sourceExperimental — accuracy not yet measured
The Discussion (page unavailable) says sampling strategy can affect apparent population structure, and Results > Cluster Analysis and PCA (page unavailable) relates PCA structure to population divergence and genetic drift. Neither passage establishes that unequal ancestry sample sizes or drift exaggerate distances between clusters on a PCA plot. (LLM, conf=0.81)
- Partly supportedcites [208] McVean, G. A genealogical interpretation of principal components analysis. PLoS Genet. 5, e1000686 (2009). sourceExperimental — accuracy not yet measured
The Results section, “Uneven sampling has a strong influence on PCA projections” (page unavailable), says unequal population sample sizes distort PCA space. The two-population example links PC distance to population divergence, but the retrieved passages do not establish the more specific claim that differing amounts of genetic drift exaggerate those distances. (LLM, conf=0.83)
- Partly supportedcites [211] Engelhardt, B. E. & Stephens, M. Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis. PLoS Genet. 6, e1001117 (2010). sourceExperimental — accuracy not yet measured
The Results section, “Discrete and admixed populations” (page unavailable), reports that removing half the African individuals changed PCA results appreciably, supporting sensitivity to ancestry sample sizes. The passages found do not say that differing amounts of genetic drift exaggerate distances between principal-component clusters. (LLM, conf=0.87)
- Partly supportedcites [212] Skoglund, P., Sjödin, P., Skoglund, T., Lascoux, M. & Jakobsson, M. Investigating population history using temporal genetic differentiation. Mol. Biol. Evol. 31, 2516–2527 (2014). sourceExperimental — accuracy not yet measured
In Results, 'Pitfalls When Comparing Ancient Genomes to Modern Populations' (page unavailable), a simulated population-size reduction changes where an ancient genome clusters in PCA; the authors attribute the misleading relationship to different magnitudes of genetic drift. The cited passages do not establish that unequal sample sizes across ancestries affect PCA clustering, or that drift generally exaggerates principal-component distances. (LLM, conf=0.86)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“However, multiple tools exist for assessing contamination levels in haploid chromosomes, both from mitochondrial DNA data (for example schmutzi 189 ) and using the X-chromosome in males (for example ANGSD 190,191 ).”
§ Ancient DNA analysis > [H2] Authentication
What the sources say
- Supportedcites [189] Renaud, G., Slon, V., Duggan, A. T. & Kelso, J. Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA. Genome Biol. 16, 224 (2015). source
The citation to schmutzi identifies an example of a tool for estimating contamination from mitochondrial DNA; the X-chromosome example is attributed to different citations. The Discussion states that schmutzi can be applied to samples with low or high contamination, and the Results describe contamination estimates obtained using it. (LLM, conf=0.94)
- Partly supportedcites [190] Rasmussen, M. et al. An aboriginal Australian genome reveals separate human dispersals into Asia. Science 334, 94–98 (2011). sourceExperimental — accuracy not yet measured
The paper reports sequencing an Aboriginal Australian male and estimating contamination from X-chromosome heterozygosity (Abstract; page not provided), supporting the X-chromosome method cited here. Our copy does not identify ANGSD as the tool used or describe multiple contamination-assessment tools; the mitochondrial-DNA example is attached to a different citation. (LLM, conf=0.86)
- Could not verifycites [191] Korneliussen, T. S., Moltke, I., Albrechtsen, A. & Nielsen, R. Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data. BMC Bioinforma. 14, 289 (2013). sourceExperimental — accuracy not yet measured
The Methods > Model passage identifies ANGSD as a tool used to calculate genotype likelihoods, not to assess contamination. Searches for contamination and for the male X chromosome found no passage in our copy addressing that use of ANGSD. (LLM, conf=0.76)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Environmental DNA has also provided insights into the spatial and temporal distribution of animal species, including extinct hominins 49 , and the impact of global climatic change 22,48,90,91,328 .”
§ Ancient DNA analysis > [H2] Extinction and climate change
What the sources say
- Supportedcites [49] Slon, V. et al. Neandertal and Denisovan DNA from Pleistocene sediments. Science 356, 605–608 (2017). source
The citation to this paper is attached to the extinct-hominin example, not the separate claim about global climatic change. The Abstract reports Neandertal DNA in eight archaeological layers across four Eurasian caves and Denisovan DNA in a Middle Pleistocene layer, supporting insights into where and when these hominins were present. (LLM, conf=0.92)
- Supportedcites [22] Willerslev, E. et al. Fifty thousand years of Arctic vegetation and megafaunal diet. Nature 506, 47–51 (2014). source
The citation to extinct hominins is separate (49); this source is among those cited for insights into climatic change. In the paper’s Perspectives section (page unavailable), the authors use their ancient-DNA reconstruction of Arctic vegetation to discuss how global warming may have disrupted the vegetation–megafauna relationship after deglaciation. (LLM, conf=0.86)
- Not checked — no full text of the sourcecites [48] Pedersen, M. W. et al. Postglacial viability and colonization in North America’s ice-free corridor. Nature 537, 45–49 (2016). source
- Not checked — no full text of the sourcecites [90] Willerslev, E. et al. Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 300, 791–795 (2003). This article reports the first analysis of environmental DNA prior to the advent of next-generation DNA sequencing and establishes the long-term DNA persistence of paleocommunities within sediments. source
- Partly supportedcites [91] Willerslev, E. et al. Ancient biomolecules from deep ice cores reveal a forested southern Greenland. Science 317, 111–114 (2007). sourceExperimental — accuracy not yet measured
The paper’s Abstract reports that ancient DNA revealed a formerly forested southern Greenland and suggests the forest existed during a period warmer than the present. This supports an insight into past climate and ecology in Greenland, but the paper does not establish the impact of global climatic change. The separate claim about extinct hominins is attached to citation 49, not this source. (LLM, conf=0.83)
- Not checked — no full text of the sourcecites [328] Key, F. M., Posth, C., Krause, J., Herbig, A. & Bos, K. I. Mining metagenomic data sets for ancient DNA: recommended protocols for authentication. Trends Genet. 33, 508–520 (2017). source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“The extent to which quantitative assessments can be obtained is currently unknown, although new biomass proxies aim at this objective 136 .”
§ Ancient DNA analysis > [H2] Extinction and climate change
What the sources say
- Partly supportedcites [136] Gaffney, V. et al. Multi-proxy characterisation of the Storegga tsunami and its impact on the early holocene landscapes of the southern North Sea. Geosciences 10, 270 (2020). sourceExperimental — accuracy not yet measured
Section 4.4 describes a novel sedaDNA-based measure of relative biomass, supporting the claim that a new proxy aims to provide quantitative information. It does not state that the extent to which quantitative assessments can be obtained from eDNA is currently unknown. (LLM, conf=0.84)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Paleogenomic data also do not support the presence of a strong demographic bottleneck during early domestication stages (see 292 for a review in major crops), but rather studies of wheat 293 , sunflowers 294 , and horses 148 support more recent losses of genetic diversity.”
§ Ancient DNA analysis > [H2] Domestication
What the sources say
- Supportedcites [292] Scott, M. F. et al. A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history. Nat. Plants 5, 1120–1128 (2019). source
The wheat citation is attached to the claim about more recent losses, not the separate claim about an early-domestication bottleneck. In the paper’s main text (indexed under Abstract; page unavailable), ancient Egyptian emmer has haplotypes absent from sampled modern emmer, and the authors say it is likely that much ancient Egyptian emmer diversity has been lost since the Roman era. They also note that incomplete modern sampling could explain some of the differences. (LLM, conf=0.88)
- Supportedcites [293] Wales, N. et al. Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement. Evol. Appl. 12, 38–53 (2018). source
The Discussion section, under “Ethnographic and archaeological organellar sequences reveal lost diversity,” attributes diversity absent from modern sunflower cultivars to bottlenecks during 20th-century improvement. That supports the part of the citing sentence attached to the sunflower citation: more recent losses of genetic diversity. The separate claim about early domestication is not the part attributed to this source. (LLM, conf=0.92)
- Partly supportedcites [294] Smith, O. et al. A domestication history of dynamic adaptation and genomic deterioration in sorghum. Nat. Plants 5, 369–379 (2019). sourceExperimental — accuracy not yet measured
The ‘Genetic diversity of sorghum over time’ section reports no measurable diversity loss attributable to an initial domestication bottleneck; the subsequent discussion describes a gradual decline instead. This supports the broader point about paleogenomic evidence, but the paper studies sorghum, not the wheat, sunflowers, or horses named in the citing sentence, and it does not establish recent diversity losses in those species. (LLM, conf=0.84)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“Evidence currently available in bison, horses, reindeer, musk oxen, woolly mammoths, and woolly rhinos, suggest that climate change is a common driver of population size changes, but also that species show individualistic responses in the face of climatic and anthropogenic pressure 20 .”
§ Ancient DNA analysis > [H2] Extinction and climate change
What the sources say
- Supportedcites [20] Lorenzen, E. D. et al. Species-specific responses of late quaternary megafauna to climate and humans. Nature 479, 359–364 (2011). source
Split into 2 atoms — 2 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Both archaic genomes revealed evidence of admixture amongst various hominin lineages 8 , in which Neanderthals and Denisovans contributed significant ancestry to modern non-African populations and modern populations of Australasia and Oceania, respectively 221 , contributing to potential phenotypic and health consequences today 250 .”
§ Ancient DNA analysis > [H2] Human genomics
What the sources say
- Supportedcites [8] Prüfer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014). source
Split into 2 atoms — 2 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
- Partly supportedcites [221] Reich, D. et al. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. Am. J. Hum. Genet. 89, 516–528 (2011). sourceExperimental — accuracy not yet measured
Split into 2 atoms — 1 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 1 unverifiable. Expand the claim to see per-atom verdicts.
- Partly supportedcites [250] Racimo, F., Marnetto, D. & Huerta-Sánchez, E. Signatures of archaic adaptive introgression in present-day human populations. Mol. Biol. Evol. 34, 296–317 (2017). sourceExperimental — accuracy not yet measured
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
plainconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Early analyses relied on molecular cloning of PCR-amplified meta-barcodes, but massively parallel sequencing facilitated access to the entire molecular diversity of individual animals and plants 325 .”
§ Ancient DNA analysis > [H2] Extinction and climate change
What the sources say
- Partly supportedcites [325] Murchie, T. J. et al. Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set. Quat. Res. https://doi.org/10.1017/qua.2020.59 (2020). sourceExperimental — accuracy not yet measured
The PCR metabarcoding section describes amplification of genetic barcodes, and the Introduction says high-throughput sequencing can identify diverse organisms from one sample. The paper does not say early analyses relied on molecular cloning. Its Introduction also says environmental DNA generally precludes genomic reconstruction of single individuals, so it does not support access to the entire molecular diversity of individual animals and plants. Page numbers are unavailable in our copy. (LLM, conf=0.85)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Partly supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“More recently, NGSbased methods have resulted in the successful recovery of authenticated pathogen genomes from not only Mycobacterium tuberculosis and Mycobacterium leprae, but also many pathogens that leave no visible evidence in the skeleton, such as Yersinia pestis, Helicobacter pylori, Vibrio cholera, Salmonella enterica Paratyphi C, Variola virus, human parvovirus, and hepatitis B virus (see”
§ Ancient DNA analysis > [H2] Pathogens and microbiomes
What the sources say
- Supportedcites [13] Spyrou, M. A., Bos, K. I., Herbig, A. & Krause, J. Ancient pathogen genomics as an emerging tool for infectious disease research. Nat. Rev. Genet. 20, 323–340 (2019). source
The Introduction states that NGS enabled recovery of ancient pathogen genomes, and Table 1 lists genome data for the named pathogens, including Vibrio cholerae. ‘The sweet spot for ancient pathogen DNA’ explains that acute infections may leave no diagnostic skeletal changes and describes recovery from teeth and other preserved tissues. Pages are not specified in our copy. (LLM, conf=0.91)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Large-scale population replacement occurred in dogs 278 , wolves 196,279,280 , horses 148,281 , pigs 282 and crops such as potato 283 .”
§ Ancient DNA analysis > [H2] Domestication
What the sources say
- Supportedcites [278] Ní Leathlobhair, M. et al. The evolutionary history of dogs in the Americas. Science 361, 81–85 (2018). source
The citation to this paper is attached to dogs, not to the other species or potato. The Abstract reports that European dogs almost completely replaced indigenous American dog lineages, supporting large-scale population replacement in dogs. (LLM, conf=0.92)
- Partly supportedcites [196] Skoglund, P., Ersmark, E., Palkopoulou, E. & Dalén, L. Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds. Curr. Biol. 25, 1515–1519 (2015). sourceExperimental — accuracy not yet measured
In Results and Discussion (page not specified), the paper reports mitochondrial DNA evidence for a Holocene replacement of European gray wolves. It also proposes, as a hypothesis, that a distinct wolf population ancestral to dogs was subsequently replaced. This supports the wolf-related part of the citing sentence, but not its unqualified assertion that large-scale replacement occurred; the paper does not address replacement in horses, pigs, or potato. (LLM, conf=0.84)
- Partly supportedcites [279] Frantz, L. A. F. et al. Genomic and archaeological evidence suggest a dual origin of domestic dogs. Science 352, 1228–1231 (2016). sourceExperimental — accuracy not yet measured
The paper reports clear turnover in European dogs’ mitochondrial ancestry and says ancient dog lineages were partially replaced (passage [2]). It presents the broader population-replacement scenario as hypothetical, however, so the unqualified claim that large-scale replacement occurred is stronger than the source supports. This citation is attached to dogs, not to the other species and crops in the sentence. (LLM, conf=0.85)
- Could not verifycites [280] Sinding, M.-H. S. et al. Arctic-adapted dogs emerged at the Pleistocene–Holocene transition. Science 368, 1495–1499 (2020). sourceExperimental — accuracy not yet measured
Citation 278 is attached to the claim about dogs, not the other animals or potato. The paper’s discussion of genetic continuity in Arctic sled dogs and admixture in some sled dogs (indexed section labeled Abstract; page unavailable) does not establish large-scale population replacement in dogs. A search for replacement and for replacement of indigenous dogs found no passage in our copy that establishes that claim. (LLM, conf=0.72)
- Supportedcites [148] Fages, A. et al. Tracking five millennia of horse management with extensive ancient genome time series. Cell 177, 1419–1435.e31 (2019). source
The Results section (‘Influence of Persian Lines Post C7th–C9th’; page unavailable) describes the introduction of new horse lineages in Europe and says the population shift was mirrored in Central Asia and Mongolia. The Discussion adds that most modern breeds investigated clustered with a group related to Sassanid Persian horses. This supports the horse portion of the citing sentence; the other species have separate citations. (LLM, conf=0.86)
- Supportedcites [281] Gaunitz, C. et al. Ancient genomes revisit the ancestry of domestic and Przewalski’s horses. Science 360, 111–114 (2018). source
The citation to Gaunitz et al. is attached to the claim about horses, not the other species or potato. The Abstract reports a “massive genomic turnover” associated with the expansion of the horse stock that gave rise to modern domestic horses. (LLM, conf=0.92)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“For example, analyses of the victims of both the Plague of Justinian and the Black Death have shown that Y. pestis was indeed the cause of both pandemics 65,303 , and further genomic analysis has provided insight into the course of these pandemics over time, including parallel changes in the pathogen itself [304][305][306] .”
§ Ancient DNA analysis > [H2] Pathogens and microbiomes
What the sources say
- Partly supportedcites [65] Bos, K. I. et al. A draft genome of Yersinia pestis from victims of the Black Death. Nature 478, 506–510 (2011). This article reports the first complete genome of an ancient bacterial pathogen, Y. pestis, from osseous human remains of individuals who died from the Black Death in 1347–1348. sourceExperimental — accuracy not yet measured
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
- Supportedcites [303] Spyrou, M. A. et al. Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes. Nat. Commun. 10, 4470 (2019). source
Split into 2 atoms — 2 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
- Supportedcites [304] Keller, M. et al. Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the first Pandemic (541–750). Proc. Natl Acad. Sci. USA 116, 12363–12372 (2019). source
Split into 2 atoms — 2 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
- Supportedcites [305] Susat, J. et al. Yersinia pestis strains from Latvia show depletion of the pla virulence gene at the end of the second plague pandemic. Sci. Rep. 10, 14628 (2020). source
Split into 2 atoms — 2 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
- Could not verifycites [306] Bos, K. I. et al. Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature 514, 494–497 (2014). sourceExperimental — accuracy not yet measured
Split into 2 atoms — 0 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 2 unverifiable. Expand the claim to see per-atom verdicts.
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“However, bisulfite conversion is also extremely harmful to DNA and, thus, generally not recommended for aDNA, despite a few successes on limited numbers of samples 244,245 .”
§ Ancient DNA analysis > Two main experimental methods have been applied to map DNA methylation [G]
What the sources say
- Partly supportedcites [244] Llamas, B. et al. High-resolution analysis of cytosine methylation in ancient DNA. PLoS ONE 7, e30226 (2012). sourceExperimental — accuracy not yet measured
The Results section (page unavailable) reports successful bisulphite sequencing in only one of six ancient DNA samples; the other five, with lower DNA integrity, could not be amplified despite different treatment protocols. This supports the limited-success qualifier, but the paper does not say that bisulphite conversion itself is extremely harmful to DNA or generally not recommended for ancient DNA. Its Introduction instead says methylation patterns can be resolved when nuclear DNA can be amplified. (LLM, conf=0.85)
- Partly supportedcites [245] Smith, R. W. A., Monroe, C. & Bolnick, D. A. Detection of cytosine methylation in ancient DNA from five Native American populations using bisulfite sequencing. PLoS ONE 10, e0125344 (2015). sourceExperimental — accuracy not yet measured
The Discussion (page unavailable) says sodium bisulfite can reduce viable DNA molecules by 90% or more, supporting the claim that conversion is harmful to aDNA. But the paper reports successful methylation recovery in large numbers of ancient remains, and its Conclusions say bisulfite sequencing may be useful for well-preserved aDNA; it does not generally advise against the method or characterize its successes as limited to a few samples. (LLM, conf=0.88)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“While the analyses of ancient pathogen genomes have shown plague to be older than expected, they suggest that the origins of the tuberculosis complex (M.tuberculosis and related strains) in humans may have evolved more recently (~3,000-6,000 years ago) [307][308] .”
§ Ancient DNA analysis > [H2] Pathogens and microbiomes
What the sources say
- Partly supportedcites [307] Sabin, S. et al. A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex. Genome Biol. 21, 201 (2020). sourceExperimental — accuracy not yet measured
The Discussion dates the common ancestor of known tuberculosis-complex diversity to approximately 2,000–6,000 years before present, supporting the claim of a relatively recent emergence but not its 3,000-year lower bound. The Discussion also cautions that a closely related ancestor may have infected humans before 6,000 years ago, so the estimate does not establish when tuberculosis-like infections in humans began. (LLM, conf=0.84)
- Could not verifycites [308] Shillito, L.-M., Blong, J. C., Green, E. J. & van Asperen, E. N. The what, how and why of archaeological coprolite analysis. Earth Sci. Rev. 207, 103196 (2020). sourceExperimental — accuracy not yet measured
Sections 5 (Non-dietary inclusions) and 6.2 (DNA and ancestral gut microbiomes) discuss parasites and ancient microbial DNA, but do not address when plague or the human tuberculosis complex originated. Searches for “tuberculosis,” “plague,” and “6,000 years ago” found no passage supporting the claimed comparison or the 3,000–6,000-year estimate. (LLM, conf=0.76)
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Partly supported
The cited sources that could be checked couldn’t confirm or dispute this claim.
In the paper
“As for the extinct huia birds of New Zealand, the drastic reduction of forest cover and the translocation of mammal predators during the European settlement may have been fatal to these endemic passerines 316 .”
§ Ancient DNA analysis > [H2] Extinction and climate change
What the sources say
- Could not verifycites [316] Li, H. & Durbin, R. Inference of human population history from whole genome sequence of a single individual. Nature 475, 493–496 (2011). sourceExperimental — accuracy not yet measured
The Abstract discusses human population history and genetic exchange, not huia extinction. Searches for huia, New Zealand forest loss, and introduced mammalian predators found no passage addressing the claim; no page number is provided in our copy. (LLM, conf=0.78)
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
- Could not verify
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“The sensitivity and specificity of taxonomic assignment largely depends on the representation characteristics of the comparative database but are robust to post-mortem DNA damage 238,239 .”
§ Ancient DNA analysis > [H2] Microbiota profiling
What the sources say
- Partly supportedcites [238] Velsko, I. M., Frantz, L. A. F., Herbig, A., Larson, G. & Warinner, C. Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research. mSystems 3, e00080-18 (2018). sourceExperimental — accuracy not yet measured
The Discussion (page not available) says database biases strongly affect profiling of abundant species and that ancient-DNA damage does not substantially affect which dominant taxa are identified. But it also reports that damage increases false-positive assignments, particularly for low-abundance taxa. Thus, describing taxonomic assignment as broadly robust to post-mortem damage omits an important qualification. (LLM, conf=0.88)
- Partly supportedcites [239] Eisenhofer, R. & Weyrich, L. S. Assessing alignment-based taxonomic classification of ancient microbial DNA. PeerJ 7, e6594 (2019). sourceExperimental — accuracy not yet measured
The Results section, “Reference database choice strongly influences taxonomic classification” (page unavailable), reports that database choice changed false positives, false negatives, and the number of reads assigned. The Results section, “Deamination minimally affects alignment-based classification” (page unavailable), finds little effect from deamination under most tested conditions, but a loss of assignments for heavily deaminated 30-bp reads. The claim's broader assertion of robustness to post-mortem DNA damage is not established: the paper tested deamination, not every form of damage. (LLM, conf=0.86)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Current approaches build on shotgun metagenomics 48 and more economical techniques involving target-enrichment 49,326 .”
§ Ancient DNA analysis > [H2] Extinction and climate change
What the sources say
- Not checked — no full text of the sourcecites [48] Pedersen, M. W. et al. Postglacial viability and colonization in North America’s ice-free corridor. Nature 537, 45–49 (2016). source
- Partly supportedcites [49] Slon, V. et al. Neandertal and Denisovan DNA from Pleistocene sediments. Science 356, 605–608 (2017). sourceExperimental — accuracy not yet measured
The Enrichment of mammalian mtDNA section (page not provided) describes hybridization capture with probes targeting mammalian and human mitochondrial DNA in sediment samples, supporting the target-enrichment part of the claim. The Main Text discusses limitations of shotgun sequencing, but our copy does not establish that target enrichment is more economical. (LLM, conf=0.84)
- Partly supportedcites [326] Haile, J. et al. Ancient DNA reveals late survival of mammoth and horse in interior Alaska. Proc. Natl Acad. Sci. USA 106, 22352–22357 (2009). sourceExperimental — accuracy not yet measured
In “Sequence Retrieval and Determination” (page not specified), the paper describes using species-specific primers and PCR to obtain selected mitochondrial DNA sequences from sediment samples, supporting it as an example of a targeted eDNA approach. Our copy does not say that this approach is more economical than shotgun metagenomics; citation 326 is attached to the target-enrichment part of the sentence, not the shotgun-metagenomics part. (LLM, conf=0.82)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Studies of west Eurasia have revealed that the genetic diversity of present-day Europeans is primarily formed by three major ancestry components 210 , consisting first of early huntergatherers 194,265 who later admixed with farmers leaving Anatolia approximately 9,000 years ago, and who brought with them agricultural innovations such as domesticated crops and livestock and introduced the Neolithic”
§ Ancient DNA analysis > [H2] Human genomics
What the sources say
- Partly supportedcites [210] Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014). sourceExperimental — accuracy not yet measured
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
- Not checked — no full text of the sourcecites [194] Skoglund, P. et al. Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science 336, 466–469 (2012). source
- Partly supportedcites [265] Sánchez-Quinto, F. et al. Genomic affinities of two 7,000-year-old Iberian hunter-gatherers. Curr. Biol. 22, 1494–1499 (2012). sourceExperimental — accuracy not yet measured
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
- Partly supportedcites [266] Lipson, M. et al. Parallel palaeogenomic transects reveal complex genetic history of early European farmers. Nature 551, 368–372 (2017). sourceExperimental — accuracy not yet measured
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Partly supported
The cited sources that could be checked couldn’t confirm or dispute this claim.
In the paper
“Whether seemingly rapid shifts in ancestry detected in aDNA data were the result of sudden massive population replacements and/or long-term individual human mobility due to institutions such as patrilocality has also been a matter of discussion and debate 333,334 .”
§ Ancient DNA analysis > [H2] Dry-lab
What the sources say
- Not checked — no full text of the sourcecites [333] Zarrillo, S. et al. The use and domestication of Theobroma cacao during the mid-Holocene in the upper Amazon. Nat. Ecol. Evol. 2, 1879–1888 (2018). source
- Could not verifycites [334] Hendy, J. et al. Proteomic evidence of dietary sources in ancient dental calculus. Proc. Biol. Sci. 285, 20180977 (2018). sourceExperimental — accuracy not yet measured
Split into 2 atoms — 0 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 2 unverifiable. Expand the claim to see per-atom verdicts.
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The sources with a verdict support this claim; the rest weren’t checked yet, have no full text we could read, or their verdicts aren’t rated yet.
In the paper
“Moreover, the often unreflected use of problematic terms and the simplistic equivalence of genetic and cultural groupings (BOX 1) have found major criticism 104,107 .”
§ Ancient DNA analysis > [H2] Dry-lab
What the sources say
- Supportedcites [104] Eisenmann, S. et al. Reconciling material cultures in archaeology with genetic data: the nomenclature of clusters emerging from archaeogenomic analysis. Sci. Rep. 8, 13003 (2018). source
The Introduction reports archaeologists’ criticism of studies they interpreted as simplistically equating people with culture. The section on archaeological cultural designations also warns that using the same names for genetic and archaeological groups conflates distinct kinds of evidence, while the Conclusions call for carefully considered terminology. (LLM, conf=0.91)
- Not checked — no full text of the sourcecites [107] Hakenbeck, S. E. Genetics, archaeology and the far right: an unholy Trinity. World Archaeol. 51, 517–527 (2019). source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
- Supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“The list of factors to consider extends far beyond the minimal data requirement for specific analyses 330 and includes: platform-specific sequence error profiles 169 ; the magnitude of post-mortem DNA damage and contamination and their impact on downstream inference 55 ; base quality rescaling 57 ; read alignment parameters 180,182 ; database selection and taxonomic classifier parameters 27,238 ;”
§ Ancient DNA analysis > H2] Possible confounding factors
What the sources say
- Supportedcites [330] Skourtanioti, E. et al. Genomic history of Neolithic to bronze age Anatolia, Northern Levant, and Southern Caucasus. Cell 181, 1158–1175.e28 (2020). source
The Human genome enrichment section reports measuring DNA damage and applying damage-related quality-control thresholds before further analysis. The Quality control and test of kinship section reports estimating contamination in individuals selected for downstream population-genetic analysis; the PMDtools section also describes using damage profiles to evaluate reads from a genetic outlier. These passages support the part of the citing sentence attached to this source, not the other separately cited factors. (LLM, conf=0.86)
- Supportedcites [169] Mak, S. S. T. et al. Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. Gigascience 6, 1–13 (2017). source
The Analyses and Discussion section (page unavailable) compares sequence accuracy across BGISEQ-500 and HiSeq2500 and reports a small but significant difference in the background rate of differences from the reference genome. It also cautions that library amplification or low coverage may explain the observed differences, so it does not establish that the platform itself caused them. This supports considering platform-associated error profiles in ancient genomic analyses. (LLM, conf=0.88)
- Supportedcites [55] Skoglund, P. et al. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proc. Natl Acad. Sci. USA 111, 2229–2234 (2014). source
The citation to this paper is attached to the magnitude of post-mortem DNA damage and contamination and their impact on downstream inference, not to the other factors in the list. The Abstract describes characteristic damage patterns and says modern human contamination can impose major biases on population-genetic and phylogenetic analyses; the Results (Model Outline) also quantify a damage-associated mismatch pattern. (LLM, conf=0.92)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“For example, while petrosal bones are generally preferred for retrieving genome-scale data from host species, their metagenomic potential for pathogen studies is limited 330 .”
§ Ancient DNA analysis > [H1] Limitations and optimizations [H2] Wet-lab
What the sources say
- Partly supportedcites [330] Skourtanioti, E. et al. Genomic history of Neolithic to bronze age Anatolia, Northern Levant, and Southern Caucasus. Cell 181, 1158–1175.e28 (2020). sourceExperimental — accuracy not yet measured
The Preparation of aDNA section describes sampling the inner-ear portion of petrous bones for human DNA analysis, and the Human genome enrichment section describes targeting genome-wide human SNPs. This supports their use for host genomic data, but the paper does not assess whether petrous bones are generally preferred or whether their metagenomic potential for pathogen studies is limited. (LLM, conf=0.84)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Partly supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“For highly degraded or contaminated material, analyses may be conditioned on reads showing evidence of post-mortem DNA damage 55,189,192 and/or limited to transversions 7 so as to mitigate both rampant contamination and damage-related nucleotide misincorporation.”
§ Ancient DNA analysis > [H2] Dry-lab
What the sources say
- Supportedcites [55] Skoglund, P. et al. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proc. Natl Acad. Sci. USA 111, 2229–2234 (2014). source
The Abstract describes selecting fragments likely to be ancient using postmortem-damage scores, and the Results report that applying a score threshold reduced contamination to negligible levels. The Discussion notes that damage-related errors in the selected reads can be alleviated by error correction. The separate proposal to limit analyses to transversions is attached to citation 7, not this source. (LLM, conf=0.91)
- Supportedcites [189] Renaud, G., Slon, V., Duggan, A. T. & Kelso, J. Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA. Genome Biol. 16, 224 (2015). source
The Discussion (page unavailable) explicitly describes approaches that reduce contamination by using only deaminated fragments to call the consensus. The Methods section on contDeam (page unavailable) also explains why deamination helps distinguish endogenous fragments from contaminants. The transversion restriction has a separate citation in the citing sentence and is not attributed to this paper. (LLM, conf=0.89)
- Supportedcites [192] Peyrègne, S. & Peter, B. M. AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination. Genome Biol. 21, 246 (2020). source
The citation is attached to conditioning analyses on reads showing post-mortem damage, not to the separate transversions restriction. In Results, ‘Separating ancient DNA and present-day DNA sequences’ (page not provided), the paper evaluates a filter requiring C-to-T substitutions and reports that it identifies ancient sequences with few false positives. The Discussion (page not provided) also explicitly describes filtering for ancient-DNA sequences. (LLM, conf=0.90)
- Supportedcites [7] Green, R. E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010). This article reports the first Neanderthal genome obtained from the DNA extracts of three paleontological bones, establishing the Neanderthal genetic legacy within modern human genomes and describing important wet-laboratory and dry-laboratory methodologies that have shaped the following decade of aDNA research. source
Citation 7 is attached to the transversion restriction. In “Average DNA divergence between Neandertals and humans” (page unavailable), the paper says it restricted divergence estimates to transversions because many apparent substitutions were damage-related transitions. Its contamination analysis also uses transversion sites, although the paper does not claim that this restriction itself removes contamination. (LLM, conf=0.91)
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“For example, a minimal threshold of 10,000-30,000 SNPs is commonly used for assessing genetic relationships of human individuals at intra-continental scales 331,332 but molecular sexing of mammal species and identification of first-generation hybrids generally requires no more than 1,000-10,000 mapped reads 200 .”
§ Ancient DNA analysis > [H2] Dry-lab
What the sources say
- Partly supportedcites [200] Schubert, M. et al. Zonkey: a simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages. J. Archaeol. Sci. 78, 147–157 (2017). sourceExperimental — accuracy not yet measured
The Methods validation section reports that Zonkey achieved maximal sensitivity and specificity for identifying equine F1 hybrids with approximately 10,000 equine reads, and the Introduction reports high specificity with as few as 1,000 mapped sequences. The Hybridization report describes molecular sex estimation but gives no 1,000–10,000-read threshold for it. The Conclusions discuss extending hybrid identification to other mammals as a possibility, not an established general requirement. (LLM, conf=0.87)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Large-scale projects can benefit from nascent automation procedures both for the preparation of DNA libraries and their capture 49,126,144 .”
§ Ancient DNA analysis > [H1] Limitations and optimizations [H2] Wet-lab
What the sources say
- Partly supportedcites [49] Slon, V. et al. Neandertal and Denisovan DNA from Pleistocene sediments. Science 356, 605–608 (2017). sourceExperimental — accuracy not yet measured
In “Enrichment of mammalian mtDNA” (page unavailable), the paper reports using automated liquid handling to generate 102 DNA libraries, supporting automation of library preparation. It also reports hybridization capture, but does not say that capture was automated or assess a benefit for large-scale projects. (LLM, conf=0.85)
- Partly supportedcites [126] Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil–DNA–glycosylase treatment for screening of ancient DNA. Philos. Trans. R. Soc. Lond. B Biol. Sci. 370, 20130624 (2015). This study reports the first method for DNA library preparation that is compatible with full automation and also describes various approaches aimed at authenticating data while minimizing the impact of post-mortem DNA misincorporation on downstream analyses. sourceExperimental — accuracy not yet measured
The Introduction describes a library-preparation protocol optimized for high-throughput target enrichment, and the Target capture methods describe semiautomated capture in 96-well plates that reduces hands-on time. The cited paper does not establish automation of library preparation itself, so it supports the capture portion but not both procedures as claimed. Page numbers are unavailable in our copy. (LLM, conf=0.84)
- Not checked — no full text of the sourcecites [144] Gansauge, M.-T., Aximu-Petri, A., Nagel, S. & Meyer, M. Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA. Nat. Protoc. 15, 2279–2300 (2020). source
plainconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“In ancient human genome studies, this approach typically queries 1.2 million positions known to be polymorphic amongst a worldwide panel of contemporary human populations 160 , leaving other positions and other DNA material present in the extracts, like those from pathogens or microbiota, unexplored.”
§ Ancient DNA analysis > [H2] Long-term legacy
What the sources say
- Partly supportedcites [160] Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499–503 (2015). sourceExperimental — accuracy not yet measured
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Partly supported
The cited sources that could be checked couldn’t confirm or dispute this claim.
In the paper
“New advances in de novo genomic and metagenomic assembly likewise hold promise for moving beyond reference-based mapping and towards a more accurate and complete reconstruction of ancient microbial genomes and metagenomes 238 , including improved strain separation, genomic architecture reconstruction, and the identification and recovery of novel genes.”
§ Ancient DNA analysis > [H2] Future directions
What the sources say
- Could not verifycites [238] Velsko, I. M., Frantz, L. A. F., Herbig, A., Larson, G. & Warinner, C. Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research. mSystems 3, e00080-18 (2018). sourceExperimental — accuracy not yet measured
The Introduction and Discussion address taxonomic classification of ancient microbiome reads and biases in reference databases, not advances in de novo assembly. Searches for de novo assembly, strain separation, genomic architecture, and novel genes found no passage supporting the claimed improvements in ancient genome reconstruction. (LLM, conf=0.72)
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Could not verify
The cited sources that could be checked couldn’t confirm or dispute this claim.
In the paper
“The comparison of our genome and that of archaic hominins has, for example, provided a preliminary list of the genetic changes that made us humans, and attempts to understand their consequences on human brain development have already started 347 .”
§ Ancient DNA analysis > [H2] Future directions
What the sources say
- Could not verifycites [347] Jun, G. et al. Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data. Am. J. Hum. Genet. 91, 839–848 (2012). sourceExperimental — accuracy not yet measured
The Introduction describes methods for detecting contamination in human DNA samples, not comparisons with archaic hominins. Searches for archaic hominins, genetic changes in humans, and brain development found no passage in our copy addressing the attributed claim. (LLM, conf=0.75)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
- Could not verify
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Quantitative assessment of damage and contamination followed by explicit simulation 180 can help establish the robustness of the conclusions.”
§ Ancient DNA analysis > [H2] Dry-lab
What the sources say
- Partly supportedcites [180] Renaud, G., Hanghøj, K., Willerslev, E. & Orlando, L. gargammel: a sequence simulator for ancient DNA. Bioinformatics 33, 577–579 (2017). sourceExperimental — accuracy not yet measured
The Methods describe simulations with specified contamination rates and damage models, and the Features section says these simulations can evaluate the robustness of analyses. The paper does not describe a prior quantitative assessment of damage and contamination followed by simulation as a distinct workflow. (LLM, conf=0.82)
plainconditional- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“An increasing body of work has shown that genetic data in tandem with archaeological and paleopathological data can illuminate social rules governing past societies, including marital patrilocality and social inequality 205 , consanguinity 222 , inbreeding avoidance 255 , and care for individuals with genetic disorders.”
§ Ancient DNA analysis > [H2] Future directions
What the sources say
- Not checked — no full text of the sourcecites [205] Mittnik, A. et al. Kinship-based social inequality in Bronze Age Europe. Science 366, 731–734 (2019). source
- Partly supportedcites [222] Cassidy, L. M. et al. A dynastic elite in monumental Neolithic society. Nature 582, 384–388 (2020). sourceExperimental — accuracy not yet measured
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
- Supportedcites [255] Sikora, M. et al. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science 358, 659–662 (2017). source
Split into 2 atoms — 2 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The cited sources that could be checked couldn’t confirm or dispute this claim.
In the paper
“Over the past decade, short read high throughput DNA sequencing technologies have fundamentally changed the field of ancient DNA, but even now new sequencing technologies are on the horizon 343 .”
§ Ancient DNA analysis > [H2] Future directions
What the sources say
- Could not verifycites [343] Li, H. L., Gee, P., Ishida, K. & Hotta, A. Efficient genomic correction methods in human iPS cells using CRISPR–Cas9 system. Methods 101, 27–35 (2016). sourceExperimental — accuracy not yet measured
The Introduction discusses CRISPR–Cas9 genome editing in human iPS cells, while the assay table in section 6 mentions deep sequencing only as a way to measure editing outcomes. Searches for ancient DNA, the impact of short-read sequencing, and emerging sequencing technologies found no passage addressing the citing sentence. (LLM, conf=0.78)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
- Could not verify
The cited sources that could be checked couldn’t confirm or dispute this claim.
In the paper
“For example, a minimal threshold of 10,000-30,000 SNPs is commonly used for assessing genetic relationships of human individuals at intra-continental scales 331,332 but molecular sexing of mammal species and identification of first-generation hybrids generally requires no more than 1,000-10,000 mapped reads 200 .”
§ Ancient DNA analysis > [H2] Dry-lab
What the sources say
- Could not verifycites [331] Burmeister, S. Archaeological research on migration as a multidisciplinary challenge. medieval worlds 4, 42–64 (2016). sourceExperimental — accuracy not yet measured
The ‘Genetics of Anglo-Saxon migration’ section discusses using DNA to investigate ancestry and migration, but gives no minimum SNP count for assessing relationships. Searches for ‘10,000–30,000 SNPs’ and genetic-marker thresholds found no passage addressing the claimed threshold or its use at intra-continental scales. (LLM, conf=0.77)
- Could not verifycites [332] Knipper, C. et al. Female exogamy and gene pool diversification at the transition from the final Neolithic to the early bronze age in central Europe. Proc. Natl Acad. Sci. USA 114, 10083–10088 (2017). sourceExperimental — accuracy not yet measured
The Sex assignment and Ancient DNA Analysis sections describe genetic-distance comparisons using mitochondrial DNA, but neither states a minimum SNP count for assessing relationships. Searches for “10,000–30,000 SNPs” and genome-wide SNP thresholds found no passage addressing the claimed commonly used threshold. The “-l 10000” value in Ancient DNA Analysis is a read-alignment parameter, not an SNP count. (LLM, conf=0.74)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Could not verify
The cited sources that could be checked couldn’t confirm or dispute this claim.
In the paper
“some dentine samples show evidence of being decomposed by the dental plaque bacteria”
§ Ancient DNA analysis > Additional information
What the sources say
- Could not verifycites [349] Librado, P. & Orlando, L. Detecting signatures of positive selection along defined branches of a population tree using LSD. Mol. Biol. Evol. 35, 1520–1535 (2018). sourceExperimental — accuracy not yet measured
The Empirical Data Set section discusses genetic adaptations, and the other retrieved passages concern population genetics rather than dental samples. Searches for dentine decomposition and dental plaque bacteria found no passage in our copy addressing the claim. (LLM, conf=0.78)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Could not verify
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Genome editing technologies such as CRISPR-Cas9 344 , pluripotent iPS stem cells 345 and miniaturized organoid systems mimicking simplified organs 346 now offer the possibility to investigate the functional consequences of virtually any change in the sequence of a given genome.”
§ Ancient DNA analysis > [H2] Future directions
What the sources say
- Partly supportedcites [344] Muchnik, S. K., Lorente-Galdos, B., Santpere, G. & Sestan, N. Modeling the evolution of human brain development using organoids. Cell 179, 1250–1253 (2019). sourceExperimental — accuracy not yet measured
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
- Partly supportedcites [345] Kanton, S. et al. Organoid single-cell genomic atlas uncovers human-specific features of brain development. Nature 574, 418–422 (2019). sourceExperimental — accuracy not yet measured
The paper’s Abstract describes stem-cell-derived cerebral organoids used to study human brain development and gene-regulatory differences, supporting citation 346’s identification of organoids as a model system. It does not establish that organoids can be used to investigate the functional consequences of virtually any genome-sequence change; the study examines particular differences among primates, not that general capability. (LLM, conf=0.83)
- Could not verifycites [346] Racimo, F., Renaud, G. & Slatkin, M. Joint estimation of contamination, error and demography for nuclear DNA from ancient humans. PLoS Genet. 12, e1005972 (2016). sourceExperimental — accuracy not yet measured
The Discussion (page not provided) describes DICE, a method for estimating contamination, sequencing error and demographic parameters in ancient DNA. Searches for CRISPR-Cas9, iPS cells, organoids and functional consequences of genome edits found no passage addressing the attributed claim. (LLM, conf=0.75)
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Partly supported
In the paper
“The methods may also be combined 42 , but both approaches also result in varying degrees of endogenous aDNA loss, and therefore aggressive cleaning should be viewed as a trade-off that is subject to diminishing returns.”
§ Ancient DNA analysis > [H2] DNA extraction
What the sources say
- Not checked — no full text of the sourcecites [42] Boessenkool, S. et al. Combining bleach and mild predigestion improves ancient DNA recovery from bones. Mol. Ecol. Resour. 17, 742–751 (2017). source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Ancient DNA fragments are typically ultrashort molecules and carry extensive amounts of chemical damage accumulated after death.”
§ Ancient DNA analysis > Abstract
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
In the paper
“Because it is highly fragmented, aDNA behaves differently than high molecular weight genomic DNA from fresh specimens, and it requires custom protocols for efficient recovery 39 .”
§ Ancient DNA analysis > [H2] DNA extraction
What the sources say
- Not checked — no full text of the sourcecites [39] Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013). This study reports a new DNA extraction method from ancient osseous remains that is tailored to the ultrashort and extensively damaged nature of aDNA molecules. This methodology allowed the retrieval of full mitochondrial genome sequences from 300,000-year-old cave bear specimens preserved in Atapuerca, Spain. source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Regardless of sample origins, the extraction and manipulation of aDNA must be carried out in dedicated clean lab facilities to minimize further contamination risks.”
§ Ancient DNA analysis > [H2] Ancient DNA facilities
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Optimization at every experimental and computational step of the aDNA pipeline has significantly increased the sensitivity of aDNA methods, thereby decreasing the amounts of sampled material necessary for successful analyses.”
§ Ancient DNA analysis > [H2] DNA extraction
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Analyzing aDNA requires the destruction of irreplaceable, finite subfossil material that is part of humanity's bio-cultural heritage.”
§ Ancient DNA analysis > [H1] Experimentation
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper may give no reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, the need to build multiple libraries per sample can dramatically increase costs.”
§ Ancient DNA analysis > [H2] Post-mortem DNA damage removal
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“While having the beneficial effect of reducing sequencing errors, USER treatment also has the negative effect of eliminating the damage patterns that are needed to authenticate aDNA sequences and differentiate them from contaminating; however, in the case of mammalian nuclear DNA, this damage signal can still be observed by examining CpG dinucleotides (FIG.3c).”
§ Ancient DNA analysis > [H2] Post-mortem DNA damage removal
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“These strict procedures are necessary to minimize modern DNA entering the facilities through reagents, ventilation and staff personnel.”
§ Ancient DNA analysis > [H2] Ancient DNA facilities
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“NGS also importantly allows the study of DNA in its entirety, a cornerstone in modern authentication approaches of aDNA data.”
§ Ancient DNA analysis > [H1] Introduction
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Ancient DNA data help to address an entire array of questions in anthropology, evolutionary biology, and the environmental and archaeological sciences.”
§ Ancient DNA analysis > Abstract
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper may give no reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In addition, degradation processes are best studied in mineralized tissues, and are less well understood in other kinds of remains.”
§ Ancient DNA analysis > [H2] Post-mortem DNA damage removal
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
In the paper
“More than three decades later, the time range amenable to DNA analysis extends to over a half million years (560,000-780,000 years ago 2 )”
§ Ancient DNA analysis > [H1] Introduction
What the sources say
- Not checked — no full text of the sourcecites [2] Orlando, L. et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499, 74–78 (2013). This article presents the oldest sequenced genome to date, from one horse metapodial preserved in permafrost for 560,000–780,000 years. source
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In the paper
“Their extraction, manipulation and authentication require specific experimental wet-lab and dry-lab procedures before patterns of genetic variation present in past individuals, populations and species can be confidently interpreted.”
§ Ancient DNA analysis > Abstract
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In the paper
“The data have revealed a considerably more dynamic past than previously appreciated and have revolutionized our understanding of many major prehistoric and historic events.”
§ Ancient DNA analysis > Abstract
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In the paper
“Preserved aDNA is often limited in quantity and has a high degree of degradation, which can be compounded by contamination with modern DNA.”
§ Ancient DNA analysis > [H2] Ancient DNA facilities
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In the paper
“However, these approaches are sensitive to (and thus can be biased by) genetic drift between time periods and differences in relative sample size between ancestries.”
§ Ancient DNA analysis > [H2] Population ancestry modelling
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In the paper
“Increasing PCR cycle number drives the formation of PCR duplicates [G], resulting in clonality, and must be mitigated to avoid saturation during sequencing unless target-enrichment is performed.”
§ Ancient DNA analysis > [H2] DNA library amplification
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In the paper
“Culture-free NGS DNA libraries provide a substantially less labor-intensive solution as they can be virtually immortalized by PCR for unlimited reuse prior to sequencing.”
§ Ancient DNA analysis > [H2] DNA library construction
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In the paper
“Reconstructed ancient genomes generally contain sequences with both genuine and artefactual variants, which may impact population-level analyses of allelic sharedness and genetic distances.”
§ Ancient DNA analysis > [H2] Error rates
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In the paper
“The total number of nucleotide misincorporations present in a reconstructed genome depends on the amount of sequencing data produced, the amount of post-mortem DNA damage that has accumulated and whether or not USER treatment was used in the experimental workflow.”
§ Ancient DNA analysis > [H2] Error rates
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In the paper
“Further rounds of enrichment are generally not beneficial, as they tend to increase library clonality and therefore lead to diminishing returns.”
§ Ancient DNA analysis > [H2] DNA library amplification
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In the paper
“They also work optimally on relatively short DNA sequences (<300 bp) and are well suited to sequence DNA in the 50-150 bp range, which characterizes most aDNA.”
§ Ancient DNA analysis > [H2] DNA library amplification
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In the paper
“The exact sources of eDNA fragments and the conditions governing their preservation remain largely unknown.”
§ Ancient DNA analysis > [H2] Extinction and climate change
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In the paper
“Extinctions can also have many indirect causes that can be difficult to disentangle, such as human-mediated habitat disturbance or introduction of pathogens or predators.”
§ Ancient DNA analysis > [H2] Extinction and climate change
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In the paper
“The retrieval of animal and plant DNA from sediments, ice and lake cores, commonly known as environmental DNA [G] (eDNA), is probably the only research area that traces its origins to the field of aDNA itself rather than being adopted from contemporary genetics.”
§ Ancient DNA analysis > [H2] Extinction and climate change
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In the paper
“Taxonomic resolution is, however, limited due to the extensive fragmentation of eDNA, and it varies with the completeness of comparative sequence databases.”
§ Ancient DNA analysis > [H2] Extinction and climate change
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In the paper
“At first glance, long read sequencers such as PacBio and Oxford Nanopore seem to have little relevance for highly degraded ancient DNA; however, concatenating ancient DNA fragments separated by spacers within single library templates may offer new opportunities for aDNA sequencing, including the direct detection of base modifications.”
§ Ancient DNA analysis > [H2] Future directions
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Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Regardless of approach, however it is also possible to create from the original extracted aDNA an immortal DNA sequencing library that can serve as a longterm genetic archive of the sample, and which could be stored in a museum or laboratory cryofacility.”
§ Ancient DNA analysis > [H2] Long-term legacy
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In the paper
“Library pooling prior to sequencing helps to reduce sequencing costs but requires that the base composition is balanced, especially for Illumina platforms, as a balanced base composition within the first six nucleotides is instrumental for calibrating the fluorescence measurement of nucleotide bases.”
§ Ancient DNA analysis > [H1] Limitations and optimizations [H2] Wet-lab
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In the paper
“In studies of humans, aDNA research has been thus far most successful when reconstructing ancestry profiles of past individuals and their population affinities.”
§ Ancient DNA analysis > [H2] Future directions
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“New developments in inferring function from ancient genetic sequences are also afoot.”
§ Ancient DNA analysis > [H2] Future directions
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In the paper
“It has moved forward in parallel with technological and computational advances in the life sciences, and it has grown and matured in response to new developments in the social sciences and humanities.”
§ Ancient DNA analysis > [H2] Future directions
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The discovery that a vast and invisible molecular past survives in the archaeological record has had a transformative effect on the field of archaeology, and promises many new and unexpected findings to come.”
§ Ancient DNA analysis > [H2] Future directions
plaindirect- Asserted: passes — The authors put it forward as true.
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“More often, the selection of programs and parameters is research groupbased, with publications reporting different analytical approaches and criteria.”
§ Ancient DNA analysis > H2] Possible confounding factors
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“The inherent complexity of relevant terms such as culture, migration or people in the social sciences was insufficiently acknowledged, in part due to different disciplinary publishing norms and to the strict limitations on word count and number of references imposed by high-profile journals”
§ Ancient DNA analysis > Additional information
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“which resulted in very negative feedback by the archaeological community.”
§ Ancient DNA analysis > Additional information
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In the paper
“However, several early publications did not fully appreciate the related history of research in archaeology.”
§ Ancient DNA analysis > Additional information
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In the paper
“Outlook of aDNA is that it offers access to a wealth of biological information that can help shape and test working hypotheses about the past in a quantitative manner.”
§ Ancient DNA analysis > [H2] Dry-lab
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Genetic hypotheses generated using PCA can be formally tested using f-statistics.”
§ Ancient DNA analysis > Additional information
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“While more expensive to generate and more demanding to analyze, this un-targeted approach can reveal new informative variants and produce data that are applicable to future research questions.”
§ Ancient DNA analysis > [H2] Long-term legacy
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In the paper
“Such efforts would facilitate DNA analyses into the Upper Paleolithic and Middle Pleistocene, and possibly beyond the current record for the oldest genome around 560,000-780,000 years ago 2 .”
§ Ancient DNA analysis > [H2] Future directions
What the sources say
- Not checked — no full text of the sourcecites [2] Orlando, L. et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499, 74–78 (2013). This article presents the oldest sequenced genome to date, from one horse metapodial preserved in permafrost for 560,000–780,000 years. source
hedgedconditional- Asserted: passes — The authors put it forward as true.
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“In the last decade, archaeogenetic studies have provided radically new insights into prehistory worldwide.”
§ Ancient DNA analysis > Additional information
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Common caveats include the impact of contamination and post-mortem DNA damage and of read alignment parameters.”
§ Ancient DNA analysis > [H2] Dry-lab
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The destructive sampling underpinning ancient genomic work has raised severe concerns pertaining to the long-term viability of the data produced.”
§ Ancient DNA analysis > [H2] Long-term legacy
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“For example, most aDNA work to date has focused on big picture studies comprising large temporal and spatial scales.”
§ Ancient DNA analysis > [H2] Dry-lab
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Over almost forty years, aDNA research has taught us surprising things about the human story and life on this planet.”
§ Ancient DNA analysis > [H2] Future directions
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“As a fast-evolving and inherently interdisciplinary field, ancient DNA research is where these distinct disciplinary approaches mix and meet -to both great effect and occasional mutual misunderstanding.”
§ Ancient DNA analysis > [H2] Dry-lab
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The last decade has shown that aDNA researchers can be extremely creative in developing innovative solutions to harness the full power of available high throughput sequencing technologies.”
§ Ancient DNA analysis > [H2] Future directions
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“This approach, however, differs from that of archaeologists, whose research is primarily grounded within the epistemological frameworks of the social sciences and humanities.”
§ Ancient DNA analysis > [H2] Dry-lab
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Rates of aDNA preservation also vary at microscopic scales.”
§ Ancient DNA analysis > [H1] Limitations and optimizations [H2] Wet-lab
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In the paper
“Current approaches are mainly based on whole-genome shotgun sequencing or targeted SNP capture.”
§ Ancient DNA analysis > [H2] Long-term legacy
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“This can be achieved by spiking library pools with sufficient amounts of a PhiX DNA library prior to sequencing.”
§ Ancient DNA analysis > [H1] Limitations and optimizations [H2] Wet-lab
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, now that studies have created a basic overview of the population genomic developments in many regions of the world, it is possible to zoom into more local contexts.”
§ Ancient DNA analysis > [H2] Dry-lab
hedgeddirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“While necessary for delineating major trends and new working hypotheses, such studies have sometimes divided the archaeological community, as they necessarily over-simplified the inherent complexity of past societies and the archaeological record itself.”
§ Ancient DNA analysis > [H2] Dry-lab
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The amount of sequence data necessary for a given analysis depends on the underlying population history and genetic diversity present in a species.”
§ Ancient DNA analysis > [H2] Dry-lab
plaindirect- Asserted: passes — The authors put it forward as true.
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Adopting such a hypothesis-testing framework comes naturally for evolutionary biologists who share similar methodologies, including phylogenetic reconstruction and population genetics.”
§ Ancient DNA analysis > [H2] Dry-lab
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“With genome-scale sequence data, the number of possible statistical analyses is virtually limitless.”
§ Ancient DNA analysis > [H2] Dry-lab
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Library pooling prior to sequencing helps to reduce sequencing costs but requires that the base composition is balanced, especially for Illumina platforms, as a balanced base composition within the first six nucleotides is instrumental for calibrating the fluorescence measurement of nucleotide bases.”
§ Ancient DNA analysis > [H1] Limitations and optimizations [H2] Wet-lab
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper relies on this without support.
Illumina platforms are not devoid of problems, and the assessment of possible batch effects may be required.
“Illumina platforms are not devoid of problems, however, and the assessment of possible batch effects may be required.”
The authors state this as an assumption.
The distribution of haplotypes present in the population is known.
“Statistical inference of missing genotypes is possible using a process called genotype imputation that assumes that the distribution of haplotypes present in the population is known and that sufficient coverage is available, typically around 1´2 22 .”
The authors state this as an assumption.
A five-population history of a specific topology can be assumed.
“If a five-population history of a specific topology can be assumed, a ratio of two f4 statistics can be used to estimate ancestry proportions unbiased by genetic drift 219 .”
The paper relies on this without support.
Single haploid genomes provide only one version of the structural and sequence diversity present in a species.
“Single haploid genomes provide only one version of the structural and sequence diversity present in a species.”
The authors state this as an assumption.
eDNA derives from skin cells, feces, urine and microfossils.
“eDNA is assumed to derive from skin cells, feces, urine and microfossils, and various mineral particles have been suggested to favor its preservation within sediments 90 .”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools.”
From Unravelling reference bias in ancient DNA datasets (2024) · cites this paper as Orlando et al. 2021
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“Without employing proper data quality control checks, downstream analyses and the reliability of the results obtained from ancient genomes can become significantly biassed (Günther and Nettelblad 2019, Orlando et al. 2021).”
From Unravelling reference bias in ancient DNA datasets (2024) · cites this paper as Orlando et al. 2021
The cited source says what the claim attributes to it.
In the citing paper
“but also poses analytical challenges due to the degraded nature of aDNA and the presence of environmental contaminants (Orlando et al. 2021).”
From Unravelling reference bias in ancient DNA datasets (2024) · cites this paper as Orlando et al. 2021
Citations
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Self-citationRapid range shifts and megafaunal extinctions associated with late Pleistocene climate change
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Coprolites as a source of information on the genome and diet of the cave hyena
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High-Resolution Analysis of Cytosine Methylation in Ancient DNA
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Did Neandertals and anatomically modern humans coexist in northern Italy during the late MIS 3?
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Metadata
- Authors
- Orlando, L., Allaby, R., Skoglund, P., Der Sarkissian, C., Stockhammer, P. W., Ávila-Arcos, M. C., Fu, Q., Krause, J., Willerslev, E., Stone, A. C., & Warinner, C.
- Affiliations
- Université Toulouse III - Paul Sabatier (FR)
- University of Warwick (GB)
- The Francis Crick Institute (GB)
- Max Planck Institute of Geoanthropology (DE)
- Chinese Academy of Sciences (CN)
- University of Copenhagen (DK)
- Arizona State University (US)
- Harvard University (US)
- Corresponding author
- Orlando, Ludovic
- ORCID
- Venue
- Nature Reviews Methods Primers
- Published
- 2021-02-11
- Volume
- 1
- Issue
- 1
- Pages
- 60 pages
- ISSN
- 2662-8449 (ISSN-L)
- OpenAlex
- W3129075539
- Cited by
- 411
- References
- 378
- Citations by year
- 2026: 82 · 2025: 82 · 2024: 110 · 2023: 76 · 2022: 41 · 2021: 20
- FWCI
- 9.53
- Type
- journal article
- Language
- en
- Open access
- green
- hal.science
- Licence
- Locations
- Nature Reviews Methods Primers (publishedVersion)
- HAL (submittedVersion, other-oa)
- University of Southern Denmark Research Portal (University of Southern Denmark) (submittedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, cc-by)
- Warwick Research Archive Portal (University of Warwick) (submittedVersion)
- Funders
- Vallee Foundation (FC001595, 852558, 217223/Z/19/Z)
- Wellcome Trust (852558, FC001595, 217223/Z/19/Z)
- Francis Crick Institute (852558, 217223/Z/19/Z, FC001595)
- Cancer Research UK (217223/Z/19/Z, FC001595, 852558)
- European Commission (ERC-2017, ERC-2018-StG, 217223, HORIZON2020, 681605)
- Deutsche Forschungsgemeinschaft (EXC 2051—, 390713860)
- Agence Nationale de la Recherche (2017-)
- Max-Planck-Gesellschaft
- Medical Research Council (217223/Z/19/Z, FC001595, 852558)
- H2020 European Research Council (678901)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Social Sciences › Arts and Humanities › Archeology (arts and humanities) › Paleopathology and ancient diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- ancient DNA, ancient genomes, DNA extraction, DNA damage, DNA authentication, next-generation sequencing, prehistoric humans, human evolution, ethical considerations, stakeholder engagement, descendant communities, archaeological samples
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.
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