SC/66b/DNA

A note with an estimate of microsatellite genotyping
error rate for common minke whales
Mutsuo Goto1, Hideyoshi Yoshida2 and Luis A. Pastene11Institute of Cetacean Research, Toyomi-cho 4-5, Chuo-ku, Tokyo 104-0055 Japan
National Research Institute of Far Seas Fisheries, 2-12-4 Fukuura, Kanazawa-ku, Yokohama 236-8648,
Japan
2Contact email: goto@cetacean.jp
ABSTRACTThe JARPNII review workshop provided three short-term analytical recommendations on the genetic
analyses of stock structure. This paper responds to the recommendation of estimating genotyping error
rates. For this aim, a total of 200 common minke whales from JARPN/JARPNII (approximately 8% of
the total available samples) were randomly selected and newly genotyped at the same16 loci (repeatgenotyping). The genotyping error rate combined over all loci and all samples was low, 0.0044 perreaction or 0.0025 per allele. These rates were similar to the rates estimated for fur seals and lower than
the rates estimated for bowhead whales
KEYWORDS: PACIFIC OCEAN; COMMON MINKE WHALE; GENETICSINTRODUCTION
The procedures to ensure data quality at the genetic laboratory of the Institute of Cetacean Research(ICR), in accordance with IWC guidelines for DNA quality, was presented and discussed at the IWC SCin 2014 (Kanda et al., 2014). The IWC SC welcomed this document and agreed that it responded
appropriately to previous recommendations from the JARPAII review workshop (IWC, 2015: p. 59).
The JARPNII review workshop noted that information on genotyping and DNA sequencing errors rates
were not provided in Kanda et al. (2014) and consequently recommended that ‘more explicit informationon quality checks be provided in each study as well as study-specific estimates of genotyping and DNA
sequencing error rates’ (IWC, 2016).
The authors consider that providing information on quality check in each study is not necessary as thelaboratory and analytical procedures at ICR are very similar and consistent through different case studies.
Here the authors respond to the recommendation from the JARPNII review workshop by providing
estimates of genotyping error based on a sub-sample of common minke whales from the western NorthPacific.

MATERIAL AND METHOD
A total of 200 common minke whale individuals sampled by JARPN/JARPNII in coastal andoffshore waters off Japan were randomly selected from the total samples. These samples weregenotyped with the same 16 microsatellite loci employed for common minke whales in previous
study (repeat-genotyping) (Pastene et al., 2016). Discrepancies between the two sets ofgenotypes were then examined based on the following classification: (i) adjacent allele
heterozygote scoring error, resulting from confusion between homozygote and adjacent allele
heterozygote genotypes; (ii) miss-scoring in either set; (iii) data input, where mistake was made1

in transcribing genotypes into the excel spread sheet; and (iv) unknown, where the error could
not be attributed to any of the above cases.
To enable comparison with other studies (Hoffman and Amos, 2005; Morin et al., 2007), error
rates were expressed wherever possible as both the number of errors per allele and per reaction,and summarized for each locus individually and across all loci. Consequently, error rate perreaction was calculated as the number of incorrect genotypes divided by the total number ofreactions used for comparison. Similarly, error rate per allele was calculated as the number ofincorrect alleles divided by the total number of alleles.
RESULTS AND DISCUSSION
A total of 200 common minke whales were re-genotyped successfully at all 16 loci. The

genotyping error rate combined over all loci and all samples was low, 0.0044 per reaction or0.0025 per allele. The breakdown being 28 reactions mistyped, accounting for 32 incorrect
alleles out of 12,800 alleles (Table 1). Seven (21.9%) were categorized as adjacent allele
heterozygote scoring error, 12 (37.5%) were miss-scoring, nine (28.1%) were data input error,
and the remaining four (12.5%) were found as unknown.
The genotyping error rates estimated in this study were similar to those estimated for fur seals of
0.0038 per reaction or 0.0022 per allele (Hoffman and Amos, 2005), and lower than thoseestimated for bowhead whales of 0.010 per allele (Morin et al., 2007).
REFERENCES

Hoffman, J.I. and Amos, W. 2005. Microsatellite genotyping errors: detection approaches,common sources and consequences for paternal exclusion. Molecular Ecology 14:599-612.
International Whaling Commission. 2015. Report of the Scientific Committee. J. Cetacean
Res. Manage. 16 (suppl.): 1-87.
International Whaling Commission. 2016. Report of the Expert Panel of the final review on thewestern North Pacific Japanese Special Permit programme (JARPN II). Paper
SC/66b/Rep06 presented to the IWC Scientific Committee, June 2016. 96pp.
Kanda, N., Goto, M., Oikawa, H. and Pastene, L.A. 2014. Update of note on sampling andlaboratory procedure protocols of the genetic work at the Institute of Cetacean Research(SC/F14/J27rev). Paper SC/65b/DNA1 presented to the IWC Scientific Committee, May2014 (unpublished). 6pp.
Morin, P.A., LeDuc, R.G., Archer, E., Martien, K.K. and Taylor, B.L. 2007. Estimatedgenotype error rates from bowhead whale microsatellite data. Paper SC/59/BRG15
presented to the IWC Scientific Committee. 10pp.
Pastene, L.A., Goto, M., Taguchi, M. and Kitakado, T. 2016. Updated genetic analyses basedon mitochondrial and microsatellite DNA indicated no sub-structure of the ‘O’ stock
common minke whale in the western North Pacific. Paper SC/F16/JR40 presented to theJARPNII special permit expert panel review workshop, Tokyo, February 2016
(unpublished). 19pp.

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Table 1. Locus-specific and overall genotyping error rates estimated from concordance among
duplicate genotypes.
Locus
EV37
EV1
GT310
GATA28
GT575
EV94
GT23
GT509
GATA98GATA417
GT211
EV21
DlrFB14
EV14
GT195
TAA31
Overall

Number ofreactions
400
400
400
400
400
400
400
400
400
400
400
400
400
400
400
400
6400

Number of
mistyped reactions
110
121
2012501001128

Number of
mistyped alleles1
10
141301250
10021323

Error rate perreaction
0.00250.002500.0300
0.00250.005000.00250.00500.012500.0025000.0025
0.00250.0044

Error rate perallele0.00130.001300.01750.00130.003800.00130.00250.006300.0013000.0025
0.00130.0025