A direct characterization of human mutation based on microsatellites

Journal name:
Nature Genetics
Volume:
44,
Pages:
1161–1165
Year published:
DOI:
doi:10.1038/ng.2398
Received
Accepted
Published online

Mutations are the raw material of evolution but have been difficult to study directly. We report the largest study of new mutations to date, comprising 2,058 germline changes discovered by analyzing 85,289 Icelanders at 2,477 microsatellites. The paternal-to-maternal mutation rate ratio is 3.3, and the rate in fathers doubles from age 20 to 58, whereas there is no association with age in mothers. Longer microsatellite alleles are more mutagenic and tend to decrease in length, whereas the opposite is seen for shorter alleles. We use these empirical observations to build a model that we apply to individuals for whom we have both genome sequence and microsatellite data, allowing us to estimate key parameters of evolution without calibration to the fossil record. We infer that the sequence mutation rate is 1.4–2.3 × 10−8 mutations per base pair per generation (90% credible interval) and that human-chimpanzee speciation occurred 3.7–6.6 million years ago.

At a glance

Figures

  1. Examples of mutations in a trio and in a family.
    Figure 1: Examples of mutations in a trio and in a family.

    The proband is the individual inheriting a mutation, and all other individuals are named relative to the proband. All alleles are given in repeat units and are shifted so that the ancestral allele has length of 0. The mutating allele is underlined. (a) Mutation detected using the trio approach. The mutation was confirmed by multiple genotyping of the trio: the father, mother and proband were genotyped 3×, 3× and 4×, respectively. (b) Mutation detected using the family approach. One ancestral allele was verified by its presence in the proband's sibling, and one mutant allele was verified by its presence in the proband's child. The phasing of alleles from the mutant locus and other loci from the same chromosome shows that the sibling with the (0, −2) alleles did not inherit the ancestral 0 allele but rather the other 0 allele from the father.

  2. Characteristics of the microsatellite mutation process.
    Figure 2: Characteristics of the microsatellite mutation process.

    (a) Paternal (blue) and maternal (red) mutation rates. The x axis shows the parental age at childbirth. Data points are grouped into ten bins (vertical bars show one standard error). The paternal rate shows a positive correlation with age (logistic regression of raw data: P = 9.3 × 10−5; slope = 1.1 × 10−5 mutations per year), with an estimated doubling of the rate from age 20 to 58. The maternal rate shows no evidence of increasing with age (P = 0.47). (b) Mutation length distributions differ for dinucleotide (top) and tetranucleotide (bottom) microsatellites. Whereas the dinucleotide loci experience multistep mutations in 32% of instances, tetranucleotide loci mutate almost exclusively by a single step of 4 bases. (c) Mutation rate increases with allele length. Dinucleotide loci (blue) have a slope of 1.65 × 10−5 mutations per repeat unit (P = 1.3 × 10−3), and tetranucleotide loci (red) have a slope of 6.73 × 10−5 mutations per repeat unit (P = 1.8 × 10−3).(d) Constraints on allele lengths. When the parental allele is relatively short, mutations tend to increase in length, and, when the parental allele is relatively long, mutations tend to decrease in length. Di- and tetranucleotide loci are shown as blue crosses and red circles, respectively. Probit regression of the combined di- and tetranucleotide data show highly significant evidence of an effect (P = 2.8 × 10−18).

  3. Empirical validation of our model with sequence-based estimates of TMRCA.
    Figure 3: Empirical validation of our model with sequence-based estimates of TMRCA.

    Shown in red is the simulation of ASD as a function of TMRCA for the standard random walk (GSMM) model. In blue is the simulation of our model in which the nonlinearity compared to GSMM is primarily due to the length constraint that we empirically observed in microsatellites. In black is the empirically observed ASD at microsatellites in 23 HapMap individuals as a function of sequence-based estimates of TMRCA, which is estimated using qseq/2mseq, where qseq is the local sequence diversity surrounding each microsatellite locus and mseq is 1.82 × 10−8 (obtained from Table 2). The close match of the empirical curve to our model simulations indicates that our model is consistent with the data and motivates the analysis in which we use the sequence substitution rate in small windows around the microsatellites to make inferences about evolutionary parameters such as the sequence mutation rate.

  4. Human-chimpanzee speciation date inferred without calibration with the fossil record.
    Figure 4: Human-chimpanzee speciation date inferred without calibration with the fossil record.

    The 90% Bayesian credible interval for human-chimpanzee speciation time (gray) for a range of values of the ratio of speciation time to divergence time (τHC/tHC). The blue histogram shows our Bayesian prior distribution for τHC/tHC, justified in the Supplementary Note. The red horizontal lines are the dates of fossils that are candidates for being on the hominin lineage after the speciation of humans and chimpanzees. Australopithecus anamensis, Orrorin tugenensis and Ardipithecus kadabba are within our plausible speciation times, whereas Sahelanthropus tchadensis predates the inferred speciation time for all plausible values of τHC/tHC. Bottom histogram, our Bayesian prior distribution for τHC/tHC; left histogram, our posterior distribution of human-chimpanzee speciation time. MYA, million years ago.

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Author information

Affiliations

  1. Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • James X Sun
  2. Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.

    • James X Sun,
    • Heng Li,
    • Swapan Mallick &
    • David Reich
  3. deCODE Genetics, Reykjavik, Iceland.

    • Agnar Helgason,
    • Gisli Masson,
    • Sigríður Sunna Ebenesersdóttir,
    • Augustine Kong &
    • Kari Stefansson
  4. Department of Anthropology, University of Iceland, Reykjavik, Iceland.

    • Agnar Helgason
  5. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.

    • Heng Li,
    • Sante Gnerre,
    • Nick Patterson &
    • David Reich
  6. Faculty of Medicine, University of Iceland, Reykjavik, Iceland.

    • Kari Stefansson

Contributions

J.X.S., A.H., G.M. and D.R. conceived and performed the research. A.H., G.M., A.K., D.R. and K.S. jointly supervised the study, with A.H. acting as the coordinator at deCODE Genetics and D.R. at Harvard Medical School. A.H. and G.M. prepared the raw microsatellite data. J.X.S., A.H. and S.S.E. designed and analyzed the regenotyping, resequencing and electropherogram re-examination experiments; and A.H. analyzed next-generation sequencing data to independently validate mutations. J.X.S., A.H., N.P., A.K. and D.R. designed and analyzed the microsatellite modeling and the statistics. S.M., H.L. and J.X.S. processed and extracted sequence data for the 23 HapMap individuals. S.M., S.G. and D.R. performed the analyses of human-chimpanzee genetic divergence and developed the Bayesian prior distributions relevant to human-chimpanzee speciation. The manuscript was written primarily by J.X.S., A.H. and D.R. The supplementary information was prepared by J.X.S. and D.R.

Competing financial interests

The authors at deCODE Genetics (A.H., G.M., S.S.E., A.K. and K.S.) work for a for-profit company carrying out genetic research and thus declare competing financial interests.

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