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Evidence for recent, population-specific evolution of the human mutation rate
Open accessAbstract
Significance: Most, but not all, human genetic variation is shared between populations, and whole-genome sequencing is now making it possible to catalogue population-private mutations that occur in only one ethnic group and are especially informative about recent human history. By contrasting frequencies of mutations private to Europe, Asia, and Africa, I have revealed a previously undetected difference between Europeans and other ethnic groups: Europeans experience higher rates of a specific mutation type that has known associations with UV light exposure. Although it is not clear whether the excess mutations are harmful or directly related to the UV sensitivity of light skin, this result demonstrates that the human mutation rate has evolved on a much faster timescale than previously believed.
Overview
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Written from the paper’s full text.
TL;DR
The paper reports that private European SNPs in the 1000 Genomes data are enriched for the C→T transition 5′-TCC-3′→5′-TTC-3′, suggesting a recent population-specific increase in this mutation type after Europeans diverged from Asians. The author argues this implies the human mutation rate has not remained stable over the last tens of thousands of years, though the mechanism and causality remain unresolved.
Key findings
- In the 1000 Genomes phase I data, private European SNPs (462,876) had a higher percentage of C→T transitions (41.01%) than private Asian SNPs (38.99%) and private African SNPs (38.29%).
- The transition 5′-TCC-3′→5′-TTC-3′ plus its reverse-strand complement had frequency 3.32% in private European SNPs, compared with 1.98% in private African SNPs and 2.04% in private Asian SNPs; the abstract reports a 50% frequency increase during the 40,000–80,000 y since Europeans began diverging from Asians, while ARGweaver-based estimates place acceleration between 25,000 and 60,000 y ago.
- TCC→T was the only mutation type with a significant strand-bias difference between populations at P < 0.01: private European TCC→T SNPs showed no discernible strand bias, whereas private Asian and African TCC→T SNPs showed the typical A/C→G/T strand bias.
- European private genic SNPs had higher f(TCC) than intergenic SNPs, while Asian and African private genic sets had lower TCC→T frequencies, suggesting less effective transcription-coupled repair of TCC→T in Europeans; TCC→T is also described as the most common somatic mutation in melanoma and the mutation most frequently induced in vitro by UV.
Methods
- Analyzed 1000 Genomes phase I data from 1,092 human genomes, constructing population-private SNP sets for Europe (PE), Asia (PAs), and Africa (PAf), plus shared European-Asian SNPs (PAsE); singletons and variants with imputation quality RSQ < 0.95 were excluded, and ancestral states were inferred using the UCSC chimp PanTro4 alignment to hg19.
- Used Pearson’s χ² tests to compare mutation-type frequencies between SNP sets, nonparametric bootstrapping in bins of 1,000 consecutive SNPs within chromosomes, and χ² tests for transcription-strand bias using UCSC gene annotations.
- Compared results with Complete Genomics high-coverage genomes and with de novo mutation calls from 82 Icelandic trios.
Limitations
- Stated: The paper says it cannot pinpoint why the TCC→T rate increased and whether UV played a causal role; it cautions that the asymmetry could be confounded by bioinformatic biases, especially because 1000 Genomes phase I is heavily imputed and contains more European than Asian genomes, which could inflate rare European variant ascertainment.
- Stated: The author notes that current data cannot tell whether skin lightening predated TCC→T acceleration, and that the mechanism linking UV to germ-line mutations is unclear.
- Evident from the text: The inference relies on population-private SNPs and ancestral-state calls rather than direct de novo mutation measurement in non-Europeans, and the UV/melanoma connection is correlative rather than causally tested.
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Claims the paper makes
31 Own result · 19 Not checked yet · 17 Own interpretation · 6 No basis given · 2 Own method · 1 Partly supported · accuracy not yet measured
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
“The TCC → T frequency difference holds genome-wide, evident on every chromosome except for chromosome Y, which has too little population-private variation to yield accurate measurements of context-dependent SNP frequencies (Fig. 1E).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
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In the paper
“To rule out the possibility that TCC → T excess in Europe is a bioinformatic artifact specific to the 1000 Genomes data, I reproduced Fig. 1 A and B in a set of human genomes sequenced at high coverage using Complete Genomics technology (SI Appendix, section 3) (23).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
What the sources say
- Not checked yetcites [23] source
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In the paper
“A comparison of SNPs private to Africa, Asia, and Europe in the 1000 Genomes data reveals that private European variation is enriched for the transition 5′-TCC-3′ → 5′-TTC-3′.”
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“TCC → T and a few other C → T transitions exhibit the clearest evidence of European rate acceleration, but other mutation types might have experienced smaller rate changes within Europeans or other human populations.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Discussion
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In the paper
“As predicted by this logic, f ðTCCÞ is higher among private genic European SNPs than among private intergenic European SNPs (Fig. 3F).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
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- The authors state this as an assumption: The TCC to T mutation rate is the same in genic and intergenic regions in Europeans because transcription-coupled repair is ineffective at preventing TCC to T mutations in Europeans.
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
“By contrasting frequencies of mutations private to Europe, Asia, and Africa, I have revealed a previously undetected difference between Europeans and other ethnic groups: Europeans experience higher rates of a specific mutation type that has known associations with UV light exposure.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“In contrast, genomic regions that differ in GC content and/or sequencing depth show little consistency as to which mutation types show the most frequency differentiation between Africa and Asia.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
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In the paper
“In contrast, when PAs and PAf are partitioned into genic and intergenic SNPs, the genic SNP sets have lower TCC → T frequencies, suggesting that TCR of this mutation type is relatively efficient in non-Europeans.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
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In the paper
“Within Europe, Fig. 2 shows a slight f ðTCCÞ gradient running from north to south; the median f ðTCCÞ is lowest in the Finns and highest in the Spanish and Italians.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
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In the paper
“Three other C → T transitions (TCT → TTT, ACC → ATC, and CCC → CTC) are also more abundant in Europe than in Africa across a broad range of GC contents and sequencing depths.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
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In the paper
“C → T transitions may not be the only mutations that experienced recent rate change; for example, TTA → TAA mutations seem to be less abundant in Europe than in Africa.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“TCC → T is the only mutation type that exhibits a significant strand bias difference between populations at the level P < 0:01.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“All of these populations have elevated TCC → T frequencies, suggesting that the European mutation rate changed before subpopulations diversified across the continent.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Several other C → T transitions are also moderately more abundant in PE than PAf, in most cases flanked by either a 5′ T or a 3′ C.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
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In the paper
“As shown in Fig. 1A, the strongest candidate for mutation rate change is the transition 5′-TCC-3′ → 5′-TTC-3′ (hereafter abbreviated as TCC → T).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
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In the paper
“In contrast, the four admixed populations ASW (African Americans), MXL (Mexicans), PUR (Puerto Ricans), and CLM (Colombians) display broader ranges of f ðTCCÞ with extremes overlapping both the European and non-European distributions.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“In the 1000 Genomes data, TCC → T frequency differentiation is greatest for private alleles of frequency less than 0.02 (SI Ap- pendix, Fig. S6B).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
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In the paper
“Here, I present evidence that the rate of a particular mutation type has recently increased in the European population, rising in frequency by 50% during the 40,000-80,000 y since Europeans began diverging from Asians.”
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“When singletons are included they create spurious between-population differences that are not reproducible with nonsingleton SNPs (SI Appendix, section 8).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
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In the paper
“In contrast, private European TCC → T SNPs exhibit no discernible strand bias; the C → T change affects the sense strand about 50% of the time (Fig. 3E).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
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“For each 1000 Genomes population P, Fig. 2 shows the distribution of f h ðTCCÞ across all haplotypes h sampled from P, and it can be seen that the distribution of f ðTCCÞ values found in Europe does not overlap with the distributions from Asia and Africa.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
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In the paper
“One notable feature of PE is the percentage of SNPs that are C → T transitions, which is higher (41.01%) than the corresponding percentages in PAs (38.99%) and PAf (38.29%).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
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In the paper
“In this way, TCC → TTC frequency seems to correlate negatively with recent Asian coancestry (SI Appendix, section 2).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
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In the paper
“The slightly admixed African Americans and more strongly admixed Latin American populations have intermediate f ðTCCÞ values reflecting partial European ancestry.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Statistical Analysis of Frequency Differences.
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In the paper
“Overrepresentation of 5′-TCC-3′ → 5′-TTC-3′ within Europe.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Statistical Analysis of Frequency Differences.
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In the paper
“There is a clear division between the low f ðTCCÞ values of African and Asian genomes and the high f ðTCCÞ values of European genomes.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Statistical Analysis of Frequency Differences.
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In the paper
“The most parsimonious explanation is that Europeans experienced a genetic change increasing the rate of TCC → T mutations.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
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In the paper
“The African American f ðTCCÞ values are only slightly higher on average than the nonadmixed African values, but a few African American individuals have much higher f ðTCCÞ values in the middle of the admixed American range, presumably because they have more European ancestry than the other African Americans who were sampled.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
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In the paper
“Although the data presented here do not reveal a clear mechanism, they leave little doubt that the European population experienced a recent mutation rate increase.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Discussion
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In the paper
“However, it is not likely to be the sole cause of the observed TCC → T rate acceleration because this acceleration is evident in both genic and intergenic regions.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
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In the paper
“Although it is not clear whether the excess mutations are harmful or directly related to the UV sensitivity of light skin, this result demonstrates that the human mutation rate has evolved on a much faster timescale than previously believed.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
boosteddirect- Asserted: passes — The authors put it forward as true.
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In the paper
“All of these populations have elevated TCC → T frequencies, suggesting that the European mutation rate changed before subpopulations diversified across the continent.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
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In the paper
“An attempt to date the origin of this allele yielded a 95% confidence interval of 6,000-38,000 y ago (26), which overlaps with the time interval when the TCC → T rate seems to have accelerated.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
What the sources say
- Not checked yetcites [26] source
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In the paper
“This TCR differential alone could modestly elevate the European TCC → T mutation rate.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
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In the paper
“A 7,000-y-old Early European farmer was found to be homozygous for the skinlightening SLC24A5 allele (25), suggesting that light skin was relatively prevalent by 7,000 y ago and could have originated much earlier.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
What the sources say
- Not checked yetcites [25] source
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In the paper
“However, there is some reason to suspect that mutation rates might have changed owing to recent regional adaptations affecting DNA repair.”
§ Evidence for recent, population-specific evolution of the human mutation rate > UV damage
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In the paper
“By this measure, the Icelandic mutations resemble PE more closely than PAs, as expected for European trios.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
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In the paper
“In contrast, when PAs and PAf are partitioned into genic and intergenic SNPs, the genic SNP sets have lower TCC → T frequencies, suggesting that TCR of this mutation type is relatively efficient in non-Europeans.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
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In the paper
“Prüfer et al. (22) used a similar technique to quantify divergence between archaic and modern genomes and found that branch length differences between sequencing batches often exceeded branch length differences between populations.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
What the sources say
- Not checked yetcites [22] source
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In the paper
“The mutation types CCC → CTC and TCT → TTT, two other candidates for rate acceleration in Europe, are also prominent in the spectrum of melanoma (SI Appendix, section 11).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Discussion
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In the paper
“This is not surprising given that high CpG mutation rates makes these sites especially susceptible to ancestral state miscalls (21).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
What the sources say
- Not checked yetcites [21] source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“It was once assumed that the human lineage's mutation rate had changed little since we shared a common ancestor with chimpanzees, but this assumption is losing credibility owing to the conflict between direct mutation rate estimates and molecular-clock-based estimates (8,9).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Discussion
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.
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
“Even if the overall European mutation rate increase was small, it adds to a growing body of evidence that molecular clock assumptions break down on a faster timescale than generally assumed during population genetic analysis.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Discussion
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.
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
“This is true of both the low-coverage 1000 Genomes dataset and the smaller, higher-coverage Complete Genomics dataset, suggesting that singletons are error-prone even in highcoverage genomes.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
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.
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 slightly admixed African Americans and more strongly admixed Latin American populations have intermediate f ðTCCÞ values reflecting partial European ancestry.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Statistical Analysis of Frequency Differences.
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. 25
- The quote only partly states this claim. 1
- Probably not a substantial claim. 12
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Based on these estimates, TCC → T rate acceleration seems to have occurred between 25,000 and 60,000 y ago, not long after Europeans diverged from Asians (SI Appendix, section 4).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
What the sources say
- Partly supportedcites [24] sourceExperimental — accuracy not yet measured
The Results (Analysis of Real Data; page unavailable) state that ARGweaver produced allele-age estimates from human genomes, supporting the basis named in the claim. Our copy does not report a TCC → T rate acceleration, date it to 25,000–60,000 years ago, or relate it to European–Asian divergence; that appears to be the citing authors’ inference rather than a finding of this source. (LLM, conf=0.85)
hedgedcorrelational- 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
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
“Combined with its reverse strand complement 5′-GGA-3′ → 5′-GAA-3′, TCC → T has frequency 3.32% in PE compared with 1.98% in PAf and 2.04% in PAs.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
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.
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
“The results suggest that many mutation types occur at slightly higher rates in Europe compared with Asia, with C → T transitions, particularly TCC → T, showing the strongest signal of rate differentiation.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
hedgedcorrelational- 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 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 African American f ðTCCÞ values are only slightly higher on average than the nonadmixed African values, but a few African American individuals have much higher f ðTCCÞ values in the middle of the admixed American range, presumably because they have more European ancestry than the other African Americans who were sampled.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
hedgedcorrelational- 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.
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
“In PE, TCC → TTC and its complement GGA → GAA are the 16th and 17th most common SNP types, respectively, whereas they are only ranked 27th and 32nd in PAs.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
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.
In the paper
“Private Asian and African TCC → T SNPs were found to exhibit the strand bias that is typical of A/C → G/T mutations (28), with the C → T change usually affecting the antisense strand and the G → A change usually affecting the sense strand.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
What the sources say
- Not checked yetcites [28] source
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.
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
“there remain 462,876 private European SNPs (PE) that are variable in Europe but fixed ancestral in all nonadmixed Asian and African populations, as well as 265,988 private Asian SNPs (PAs) that are variable in Asia but fixed ancestral in Africa and Europe.”
- Also stated in: § Significance · plain
“I compared PE and PAs to the set of 3,357,498 private African SNPs (PAf) that are variable in the Yorubans (YRI) and/or Luhya (LWK) but fixed ancestral in Europe and Asia.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
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. The quote only partly states this claim.
- Also stated in: § Significance · plain
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
“Several CpG transitions including ACG → ATG seem to have higher frequencies in Asia than in Africa, but these differences disappear when the spectrum is folded to, for instance, identify ACG → ATG with the inverse mutation ATG → ACG (SI Appendix, section 5).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
hedgedcorrelational- 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.
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
“At the P = 0:01 significance level (gray dashed line), only TCC → T has a significant strand bias difference between Europe and Africa, whereas no mutation type significantly differs in strand bias between Asia and Africa.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Statistical Analysis of Frequency Differences.
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.
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
“Regardless of its causality, this change indicates that DNA replication fidelity has not remained stable even since the origin of modern humans and might have changed numerous times during our recent evolutionary history.”
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.
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
“A 7,000-y-old Early European farmer was found to be homozygous for the skinlightening SLC24A5 allele (25), suggesting that light skin was relatively prevalent by 7,000 y ago and could have originated much earlier.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Antiquity of the European Mutation Rate Change.
hedgedSingle case- 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.
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
“This could produce a false overall excess of European-derived alleles but seems unlikely to elevate the discovery rate of TCC → T in Europe relative to other mutation types.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
hedgedconditional- 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.
In the paper
“Excess C → T transitions are characteristic of several different mutagenic processes including UV damage and cytosine deamination (19).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
What the sources say
- Not checked yetcites [19] source
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.
None of the sources cited for this claim have been checked yet.
In the paper
“Melanoma incidence in admixed Hispanics is strongly correlated with European ancestry (33)(34)(35).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Discussion
What the sources say
boostedcorrelational- 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 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
“Despite the strong evidence that UV causes TCC → T mutations, the question remains how UV could affect germ-line cells that are generally shielded from solar radiation.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Discussion
boosteddirect- 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.
None of the sources cited for this claim have been checked yet.
In the paper
“Incidentally, melanoma is not only associated with UV light exposure but also with European ancestry, occurring at very low rates in Africans, African Americans, and even light-skinned Asians (32)(33)(34).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Discussion
What the sources say
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. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Although this conflict might have arisen from a gradual decrease in the rate of germ-line mitoses per year as our ancestors evolved longer generation times (12,13), the results of this paper indicate that another force may have come into play: change in the mutation rate per mitosis.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Discussion
What the sources say
- Not checked yetcites [12]
- Not checked yetcites [13] source
hedgedconditional- 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.
In the paper
“In the Icelandic trios, TCC → TTC and GGA → GAA are ranked 20th and 18th.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
What the sources say
- Not checked yetcites [10] source
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.
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 addition, because the 1000 Genomes phase I dataset is heavily imputed and contains more European genomes than Asian genomes, rare European variants might be ascertained more completely than rare Asian variants.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Significance
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.
None of the sources cited for this claim have been checked yet.
In the paper
“The association of TCC → T mutations with UV exposure is not well understood, but two factors seem to be in play: (i) the propensity of UV to cross-link the TC into a base dimer lesion and (ii) poorer repair efficacy at TCC than at other motifs where UV lesions can form (36,37).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Discussion
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.
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
“Most human trios that have been sequenced are European in origin (SI Appendix, section 9), meaning that there exist few measurements of de novo mutation patterns on diverse genetic backgrounds.”
§ Evidence for recent, population-specific evolution of the human mutation rate > UV damage
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.
None of the sources cited for this claim have been checked yet.
In the paper
“Melanoma somatic mutations consist almost entirely of C → T transitions, 28% of which are TCC → T mutations (19,31).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Discussion
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.
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
“Although it is not clear whether UV played a causal role in changing the European mutational spectrum, 5′-TCC-3′ → 5′-TTC-3′ is known to be the most common somatic mutation present in melanoma skin cancers, as well as the mutation most frequently induced in vitro by UV.”
boosteddirect- 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.
None of the sources cited for this claim have been checked yet.
In the paper
“In the mid-1990s, Drobetsky et al. (29) and Marionnet et al. (30) observed that TCC → T dominated the mutational spectra of single genes isolated from UV-irradiated cell cultures.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Discussion
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.
In the paper
“A study of the California Cancer Registry found that the annual age-adjusted incidence of melanoma cases per 100,000 people was 0.8-0.9 for Asians, 0.7-1.0 for African Americans, and 11.3-17.2for Caucasians (35).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Discussion
What the sources say
- Not checked yetcites [35] 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.
In the paper
“SNPs that affect gene expression in DNA damage response pathways show evidence of recent diversifying selection, exhibiting geographic frequency gradients that seem to be correlated with environmental UV exposure (7).”
§ Evidence for recent, population-specific evolution of the human mutation rate > UV damage
What the sources say
- Not checked yetcites [7] source
hedgedcorrelational- 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.
In the paper
“Drobetsky et al. (29) compared the incidence of UV lesions to the incidence of mutations in irradiated cells and found that TCC motifs were not hotspots for lesion formation but instead were disproportionately likely to have lesions develop into mutations rather than undergoing error-free repair.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Discussion
What the sources say
- Not checked yetcites [29] source
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.
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 definitions are meant to select for mutations that have been confined to a single continent for most of their history except for possible recent transmission to the Americas.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Materials and Methods
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.
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
“Singletons are excluded to minimize the impact of possible sequencing error, and variants with imputation quality lower than RSQ = 0:95 are excluded to minimize erroneous designation of shared SNPs as population-private.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Materials and Methods
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.
None of the sources cited for this claim have been checked yet.
In the paper
“Given such a general challenge to the molecular clock assumption, it may be wise to infer demographic history from mutations such as CpG transitions that accumulate in a more clocklike way than other mutations (8,20).”
§ Evidence for recent, population-specific evolution of the human mutation rate > Discussion
hedgedcorrelational- 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.
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
“If the mutagenic spectrum was able to change during the last 60,000 y of human history, it might have changed numerous times during great ape evolution and beforehand.”
§ Evidence for recent, population-specific evolution of the human mutation rate > Discussion
hedgedconditional- 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. It may state two separate claims as one.
The authors state this as an assumption.
The TCC to T mutation rate is the same in genic and intergenic regions in Europeans because transcription-coupled repair is ineffective at preventing TCC to T mutations in Europeans.
“If we assume that the TCC → T mutation rate is the same in genic and intergenic regions because TCR is ineffective at preventing TCC → T mutations in Europeans, we should expect the frequency f ðTCCÞ to be slightly higher among private genic SNPs than among private intergenic SNPs.”
The paper relies on this without support.
The observed European excess of TCC to T mutations is not explained by demographic events such as a population bottleneck.
“This asymmetry cannot be explained by a demographic event such as a population bottleneck; however, it should be interpreted with caution because many bioinformatic biases have the potential to confound this test.”
The paper relies on this without support.
Previous studies have presented no evidence of mutation rate evolution on a timescale as recent as the human migration out of Africa.
“To my knowledge, previous studies have presented no evidence of mutation rate evolution on a timescale as recent as the human migration out of Africa.”
The paper relies on this without support.
The private SNPs used in the analysis are enriched for young mutations that arose after humans left Africa and began adapting to temperate latitudes.
“These SNPs should be enriched for young mutations that arose after humans had already left Africa and begun adapting to temperate latitudes.”
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 check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Evidence indicates that both Denisovan and Neanderthal aSNPs, especially those within protein coding and conserved non-coding elements, are mostly deleterious and negatively selected in modern humans [14, 61].”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [61]
Experimental — accuracy not yet measured
Citations
Cites
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Genetic drift, selection and the evolution of the mutation rate
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Detection of human adaptation during the past 2000 years
Field, Y., Boyle, E. A., Telis, N., Gao, Z., Gaulton, K. J., Golan, D., Yengo, L., Rocheleau, G., Froguel, P., McCarthy, M. I., et al. (2016) · Science · doi:10.1126/science.aag0776 · Cited by 383
Variation in the molecular clock of primates
Moorjani, P., Amorim, C. E. G., Arndt, P. F., & Przeworski, M. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1600374113 · Cited by 248
Metadata
- Authors
- Harris, K.
- Affiliations
- University of California, Berkeley (US)
- Corresponding author
- Harris, Kelley
- ORCID
- Harris, Kelley
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2015-03-02
- Volume
- 112
- Issue
- 11
- Pages
- 3439-3444
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC4371947
- OpenAlex
- W2115741580
- Semantic Scholar
- 43a60e7b197d8f860145743b4fc95a6b8ec0cbbe
- Cited by
- 165
- References
- 47
- Citations by year
- 2026: 8 · 2025: 10 · 2024: 10 · 2023: 15 · 2022: 19 · 2021: 20 · 2020: 19 · 2019: 14 · 2018: 9 · 2017: 11 · 2016: 21 · 2015: 8
- FWCI
- 11.23
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (1000078615)
- HHS | National Institutes of Health (IR01GM109454-01)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- mutation spectrum, UV mutagenesis, DNA replication fidelity, local adaptation, European populations, melanoma, DNA damage response, human dispersal out of Africa, 1000 Genomes Project
- MeSH terms
- Europe, Biological Evolution, Genetics, Population, Humans, Mutation, Transcription, Genetic, Genetic Variation, Computational Biology, Mutation Rate
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.
A language model drew the claims from the paper on 2026-10-08, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-08 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Cited sources are checked with a language model’s help (gpt-6-sol).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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