Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate
- Uppsala University, Sweden
- Swedish University of Agricultural Sciences, Sweden
- University of Bergen and the Hjort Center of Marine Ecosystem Dynamics, Norway
- Institute of Marine Research, Norway
- Texas A&M University, United States
Figures
Figure 1 with 1 supplement
Flowchart describing the de novo mutation-calling pipeline.
A schematic illustration of the steps used in calling and filtering the candidate mutations.
Figure 1—figure supplement 1
Sanger sequencing chromatograms of the de novo mutations.
Chromatograms from the identified target offspring and its parents for each region containing a candidate de novo mutation.
Tables
Table 1
Summary of the pedigrees used for whole-genome sequencing.
| No | ID | Pedigree | Sequencing depth (x) | De novo mutations |
|---|---|---|---|---|
| Pedigree 1, Atlantic herring | ||||
| 1 | AM8 | Father | 65.7 | N.A. |
| 2 | AF8 | Mother | 70.2 | N.A. |
| 3 | AA1 | Offspring | 65.6 | 1 |
| 4 | AA2 | Offspring | 70.9 | 2 |
| 5 | AA3 | Offspring | 47.2 | 0 |
| 6 | AA4 | Offspring | 66.9 | 3 |
| 7 | AA5 | Offspring | 64.2 | 4 |
| 8 | AA6 | Offspring | 61.2 | 1 |
| Pedigree 2, Baltic herring | ||||
| 9 | BM19 | Father | 71.8 | N.A. |
| 10 | BF21 | Mother | 65.1 | N.A. |
| 11 | BB1 | Offspring | 74.5 | 2 |
| 12 | BB2 | Offspring | 61.6 | 1 |
| 13 | BB3 | Offspring | 75.0 | 0 |
| 14 | BB4 | Offspring | 69.9 | 2 |
| 15 | BB5 | Offspring | 60.6 | 2 |
| 16 | BB6 | Offspring | 62.6 | 1 |
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N.A. = Not available.
Table 2
Summary of the de novo mutations identified in Atlantic herring.
| SNP position | Mutation | ||||||
|---|---|---|---|---|---|---|---|
| Scaffold:position | Id | Ref | Var | Freq† | Origin‡ | Type§ | Region |
| 1157:174,127 | AA4 | T | A | 1/50 (-) | M | TV | Intergenic |
| 153:2,684,380 | AA2 | T | G | 9/50 (18%) | P | TV | Intronic |
| 241:7,752,158 | AA5 | C | A | 5/50 (10%) | M | TV | Intergenic |
| 4:5,098,858 | AA5 | T | C | 2/50 (4%) | M | TS | Intronic |
| 481:1,927,799 | AA4, AA5* | C | A | 6/50 (12%) | P | TV | 3' UTR |
| 61:815,077 | AA4 | A | T | 3/50 (6%) | N.A. | TV | Intergenic |
| 62:613,919 | AA1, AA6* | C | A | 6/50 (12%) | M | TV | Intergenic |
| 729:1,499,224 | AA2 | C | T | 4/50 (8%) | M | TS | Intronic |
| 887:195,946 | AA5 | G | A | 1/50 (-) | P | TS | Intronic |
| 10:1,443,002 | BB4 | C | T | 1/46 (-) | P | TS | Intronic |
| 151:267,875 | BB5 | A | T | 1/46 (-) | P | TV | Exonic |
| 177:1,045,894 | BB1 | A | G | 1/46 (-) | P | TS | Intronic |
| 194:478,776 | BB6 | A | G | 1/46 (-) | N.A. | TS | Intronic |
| 246:1,890,479 | BB4 | T | C | 1/46 (-) | P | TS | Intergenic |
| 257:380,993 | BB2 | G | A | 1/46 (-) | M | TS | Intergenic |
| 26:2,976,192 | BB1 | T | C | 2/46 (4%) | P | TS | Intronic |
| 37:1,374,669 | BB5 | G | A | 1/46 (-) | M | TS | Intronic |
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*Same mutation detected in two progeny.
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†Number of siblings carrying the de novo mutation; - the frequency of transmission was only estimated when two or more progeny with the de novo mutation was detected.
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‡M:Maternal, P:Paternal, N.A. = Not available
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§TV = Transversion, TS = Transition
Table 3
Summary of mutation rates measured to date.
| Species | Taxonomic group | μ | Method* | Genome size (Mb) | Ne† |
|---|---|---|---|---|---|
| Pseudomonas aeruginosa | Bacteria | 7.9 × 10−11 | MA1 | 6.3 | 2.1 × 108 |
| Burkholderia cenocepacia | Bacteria | 1.3 × 10−10 | MA2 | 8.1 | 2.5 × 108 |
| Escherichia coli | Bacteria | 2.2 × 10−10 | MA3 | 4.6 | 1.6 × 108 |
| Chlamydomonas reinhardtii | Unicellular eukaryotes | 2.1 × 10−10 | MA4 | 120 | 7.8 × 107 |
| Saccharomyces cerevisiae | Unicellular eukaryotes | 1.7 × 10−10 | MA5 | 12.2 | 1.2 × 107 |
| Schizosaccharomyces pombe | Unicellular eukaryotes | 2.1 × 10−10 | MA6 | 12.6 | 1.4 × 107 |
| Arabidopsis thaliana | Plants | 7.1 × 10−9 | MA7 | 119 | 2.8 × 105 |
| Pristionchus pacificus | Invertebrates | 2.0 × 10−9 | MA8 | 133 | 1.8 × 106 |
| Caenorhabditis elegans | Invertebrates | 1.5 × 10−9 | MA9 | 100 | 5.2 × 105 |
| Caenorhabditis briggsae | Invertebrates | 1.3 × 10−9 | MA9 | 108 | 2.7 × 105 |
| Drosophila melanogaster | Invertebrates | 3.2 × 10−9 | MA10 PO11 | 144 | 1.4 × 106 |
| Heliconius melpomene | Invertebrates | 2.9 × 10−9 | PO12 | 274 | 2.1 × 106 |
| Daphnia pulex | Invertebrates | 5.7 × 10−9 | MA13 | 250 | 8.2 × 105 |
| Atlantic herring (Clupea harengus) | Teleosts | 2.0 × 10−9 | PO* | 850 | 4.0 × 105 |
| Collared flycatcher (Ficedula albicollis) | Birds | 4.6 × 10−9 | PO14 | 1118 | 2.0 × 105 |
| Mouse (Mus musculus) | Mammals | 5.4 × 10−9 | MA15,16 | 2808 | 1.8 × 105 |
| Cattle (Bos taurus) | Mammals | 9.7 × 10−9 | PO17 | 2725 | 3.7 × 104 |
| Chimpanzee (Pan troglodytes) | Mammals | 1.2 × 10−8 | PO18 | 3231 | 2.9 × 104 |
| Human (Homo sapiens) | Mammals | 1.2 × 10−8 | PO19 | 3236 | 2.4 × 104 |
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*MA = Mutation Accumulation, PO = Parent-Offspring. The values are from the following sources: 1. Dettman et al. (2016); 2. Dillon et al. (2015); 3. Lee et al. (2012); 4. Ness et al. (2012); 5. Zhu et al. (2014); 6. Farlow et al. (2015); 7. Ossowski et al. (2010); 8. Weller et al. (2014); 9. Denver et al. (2012); 10. Keightley et al. (2009); 11. Keightley et al. (2014); 12. Keightley et al. (2015); 13. Keith et al. (2016); 14. Smeds et al. (2016); 15. Lindsay et al. (2016); 16. Uchimura et al. (2015); 17. Harland et al. (2016); 18. Venn et al. (2014); 19. Kong et al. (2012).
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†Ne is calculated as π/4μ. The underlying π estimates are all from Lynch et al. (2016) except for herring (present study), collared flycatcher (Ellegren et al., 2012) and cattle (Daetwyler et al., 2014).
Additional files
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Supplementary file 1
Estimated population size of major stocks of Atlantic herring in the North East Atlantic Ocean including the Baltic Sea.
- https://doi.org/10.7554/eLife.23907.008
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Supplementary file 2
Summary statistics of the SNP calls underlying the estimation of the false negative rate by means of simulation.
- https://doi.org/10.7554/eLife.23907.009
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Supplementary file 3
Estimates of generation time for different stocks of herring.
- https://doi.org/10.7554/eLife.23907.010
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Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate
eLife 6:e23907.
https://doi.org/10.7554/eLife.23907
