1. Evolutionary Biology
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Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate

  1. Chungang Feng
  2. Mats Pettersson
  3. Sangeet Lamichhaney
  4. Carl-Johan Rubin
  5. Nima Rafati
  6. Michele Casini
  7. Arild Folkvord
  8. Leif Andersson  Is a corresponding author
  1. Uppsala University, Sweden
  2. Swedish University of Agricultural Sciences, Sweden
  3. University of Bergen and the Hjort Center of Marine Ecosystem Dynamics, Norway
  4. Institute of Marine Research, Norway
  5. Texas A&M University, United States
Research Article
Cite this article as: eLife 2017;6:e23907 doi: 10.7554/eLife.23907
1 figure, 3 tables, 1 data set and 3 additional files

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.

https://doi.org/10.7554/eLife.23907.004
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.

https://doi.org/10.7554/eLife.23907.005

Tables

Table 1

Summary of the pedigrees used for whole-genome sequencing.

https://doi.org/10.7554/eLife.23907.003
NoIDPedigreeSequencing depth (x)De novo mutations
Pedigree 1, Atlantic herring
1AM8Father65.7N.A.
2AF8Mother70.2N.A.
3AA1Offspring65.61
4AA2Offspring70.92
5AA3Offspring47.20
6AA4Offspring66.93
7AA5Offspring64.24
8AA6Offspring61.21
Pedigree 2, Baltic herring
9BM19Father71.8N.A.
10BF21Mother65.1N.A.
11BB1Offspring74.52
12BB2Offspring61.61
13BB3Offspring75.00
14BB4Offspring69.92
15BB5Offspring60.62
16BB6Offspring62.61
  1. N.A. = Not available.

Table 2

Summary of the de novo mutations identified in Atlantic herring.

https://doi.org/10.7554/eLife.23907.006
SNP positionMutation
Scaffold:positionIdRefVarFreqOriginType§Region
1157:174,127AA4TA1/50 (-)MTVIntergenic
153:2,684,380AA2TG9/50 (18%)PTVIntronic
241:7,752,158AA5CA5/50 (10%)MTVIntergenic
4:5,098,858AA5TC2/50 (4%)MTSIntronic
481:1,927,799AA4, AA5*CA6/50 (12%)PTV3' UTR
61:815,077AA4AT3/50 (6%)N.A.TVIntergenic
62:613,919AA1, AA6*CA6/50 (12%)MTVIntergenic
729:1,499,224AA2CT4/50 (8%)MTSIntronic
887:195,946AA5GA1/50 (-)PTSIntronic
10:1,443,002BB4CT1/46 (-)PTSIntronic
151:267,875BB5AT1/46 (-)PTVExonic
177:1,045,894BB1AG1/46 (-)PTSIntronic
194:478,776BB6AG1/46 (-)N.A.TSIntronic
246:1,890,479BB4TC1/46 (-)PTSIntergenic
257:380,993BB2GA1/46 (-)MTSIntergenic
26:2,976,192BB1TC2/46 (4%)PTSIntronic
37:1,374,669BB5GA1/46 (-)MTSIntronic
  1. *Same mutation detected in two progeny.

  2. 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.

  3. M:Maternal, P:Paternal, N.A. = Not available

  4. §TV = Transversion, TS = Transition

Table 3

Summary of mutation rates measured to date.

https://doi.org/10.7554/eLife.23907.007
SpeciesTaxonomic groupμMethod*Genome size (Mb) Ne  
Pseudomonas aeruginosaBacteria7.9 × 10−11MA16.32.1 × 108
Burkholderia cenocepaciaBacteria1.3 × 10−10MA28.12.5 × 108
Escherichia coliBacteria2.2 × 10−10MA34.61.6 × 108
Chlamydomonas reinhardtiiUnicellular eukaryotes2.1 × 10−10MA41207.8 × 107
Saccharomyces cerevisiaeUnicellular eukaryotes1.7 × 10−10MA512.21.2 × 107
Schizosaccharomyces pombeUnicellular eukaryotes2.1 × 10−10MA612.61.4 × 107
Arabidopsis thalianaPlants7.1 × 10−9MA71192.8 × 105
Pristionchus pacificusInvertebrates2.0 × 10−9MA81331.8 × 106
Caenorhabditis elegansInvertebrates1.5 × 10−9MA91005.2 × 105
Caenorhabditis briggsaeInvertebrates1.3 × 10−9MA91082.7 × 105
Drosophila melanogasterInvertebrates3.2 × 10−9MA10
PO11
1441.4 × 106
Heliconius melpomeneInvertebrates2.9 × 10−9PO122742.1 × 106
Daphnia pulexInvertebrates5.7 × 10−9MA132508.2 × 105
Atlantic herring (Clupea harengus)Teleosts2.0 × 10−9PO*8504.0 × 105
Collared flycatcher (Ficedula albicollis)Birds4.6 × 10−9PO1411182.0 × 105
Mouse (Mus musculus)Mammals5.4 × 10−9MA15,1628081.8 × 105
Cattle (Bos taurus)Mammals9.7 × 10−9PO1727253.7 × 104
Chimpanzee (Pan troglodytes)Mammals1.2 × 10−8PO1832312.9 × 104
Human (Homo sapiens)Mammals1.2 × 10−8PO1932362.4 × 104
  1. 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).

Data availability

The following data sets were generated

Additional files

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
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
Supplementary file 3

Estimates of generation time for different stocks of herring.

https://doi.org/10.7554/eLife.23907.010

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