Do not cite without written permission from the authors
SC/61/JR5

Update of the analyses on individual identification andmixing of J and O stocks of common minke whalearound Japanese waters examined by microsatellite
analysis
Naohisa Kanda1, Mutsuo Goto1, Toshiya Kishiro2, Hideyoshi Yoshida2, Hidehiro Kato3, and Luis A.
Pastene1
1

The Institute of Cetacean Research, 4-5, Toyomi-cho, Chuo-ku, Tokyo 104-0055, Japan
National Research Institute of Far Seas Fisheries, 2-12-4, Fukuura, Kanazawa-ku, Yokohama,
Kanagawa, 236-8648, Japan
3
Tokyo University of Marine Science and Technology, 1-5-7, Konan, Minato-ku, Tokyo 108-0075, Japan
2

Contact email:kanda@cetacean.jp

ABSTRACTThis paper is the revised version of SC/J09/JR26, which described the results of microsatellite analysis of
the J and O stocks of common minke whales, presented to the Expert Workshop to review the JARPNII
Programme. In this study, we attempted to distinguish sampled common minke whales into geneticallydistinct stocks using a combination of microsatellite analysis and a Bayesian clustering approach. Past
studies indicated that two different stocks of common minke whales existed around the Japanese coast: O
stock in the western North Pacific and the J stock in the Sea of Japan. Samples of 2,542 minke whales
were collected during the offshore component of JARPN and JARPNII from 1994 to 2007, during thecoastal component of JARPNII from 2002 to 2007, and from bycatches in the set net fishery along theJapanese coast from 2001 to 2007, and were analyzed using 16 microsatellite loci. Result of the Bayesianclustering analysis implemented in the computer program STRUCTURE (Pritchard et al., 2000) indicatedthat our samples came from two genetically differentiated groups of minke whales. Approximately 91%
of the individuals were assigned into the either stocks based on their high membership probability (>90%)
obtained from the program. Spatial distribution of these assigned individuals clearly indicated that these
two stocks were the J and O stocks. In addition, it was also found that 1) the O stock individuals appeared
to migrate, although rarely, to the Sea of Japan, 2) the J stock individuals migrated to the 7W of the North
Pacific side and very rarely to further east, and 3) the SA2 (western side of North Pacific coast) was
mainly occupied by the J stock. Temporal distribution of the assigned bycatches collected from the SA7(eastern side of Japan, North Pacific coast) where both the J stock and O stock whales were contained in
the samples in about 50:50 indicated seasonal movement of the whales with the number of the O stockincreased in spring. This study allowed us to better understand the pattern and dynamics of distribution of
the minke whales inhabiting around Japan. The results of this revised version confirmed the main
conclusion in SC/J09/JR26.
KEY WORDS: MINKE WHALE, MICROSATELLITE, O STOCK, J STOCK, JARPN, JARPNII,NORTH PACIFICINTRODUCTION
Common minke whales, Balaenoptera acutorostrata, are the smallest and the most abundant baleen
whales inhabiting major open oceans world-wide. Spatial and temporal separations of the minke whale
populations have occurred (Wada and Numachi, 1991; Bakke et al., 1996; Martinez and Pastene, 1999;
Pastene et al., 2007). They live up to 50 years in age and the adult size is, on average, 6-7m. They feed on
various prey species, such as copepods, Euphausiids, and fish. Their age at first reproduction is five, andthey are thought to reproduce every year. Minke whales undergo seasonal movement from winterbreeding grounds in low latitude to summer feeding grounds in high latitude although their exact breeding1

Do not cite without written permission from the authors
SC/61/JR5
ground is usually unknown. They feed in the fertile cold waters in summer near the poles, and spend theirwinter season in warmer oceans to pair, mate, and give a birth.
Around the ocean off the Japanese coast, at least two different stocks of minke whales are known to exist:
one stock distributes in the western North Pacific (O stock) and the other in the Sea of Japan (J stock)(Omura and Sakiura, 1956; Ohsumi, 1977; Kato, 1992; Wada and Numachi, 1991; Goto and Pastene,
1997; Hatanaka and Miyashita, 1997; Pastene et al., 2007). Whales of the both stocks migrate to the
Okhotsk Sea in spring and stay there until the end of summer. Although they share feeding ground in the
Okhotsk, their temporal distribution in the area slightly differ (Goto and Pastene, 1997). These two stocks
differ from each other in body size, conception dates, allozyme allele frequencies, and mitochondrial
DNA (mtDNA) haplotype frequencies, suggesting their reproductive isolation.
One of the objectives of JARPN II is a systematic monitoring of the occurrence of J stock in sub-area 7 todetermine spatial and temporal dynamics of its occurrence. In a situation of geographical overlap ofmultiple stocks, stock identification at an individual base allows us to directly estimate mixing rates andpattern of temporal and spatial distribution of the stock. The Scientific Committee (SC) has recommended
that the J stock individuals should be excluded from the analyses of the North Pacific common minke
whales. However, the past genetic studies failed to detect diagnostic markers between the two stocks. In
the past genetic studies, the number of the J stock individuals available had been limited and the genetic
markers used (mtDNA and allozymes) might have not been suitable for stock identification due to theirrelatively low resolution power.
The objective of this study was thus to identify stocks of common minke whales collected from around
Japan at an individual level and to gain an understanding of spatial and temporal distribution of the stocks.
We attempted to distinguish samples of minke whales obtained around Japan into the J and O stocks
irrespective their sampling sites by utilizing genetic variation at hypervariable microsatellites with
Bayesian clustering approach. A model based Bayesian approach has been recently developed to defineclusters of individuals based on their genotypes at multiple loci (Pritchard et al., 2000). This approachallows us to treat each individual in the samples as a single operational taxonomic unit in a stock-level
analysis, and Bayesian approach provides relative probability to estimate the number of stocks rather thanreject one of the two hypotheses. An advantage of Bayesian method implemented in the STRUCTURE(Pritchard et al., 2000) used in this study is thus that the obtained results are not affected by arbitrary
chosen sample strata that do not necessarily correspond to real biological stock boundaries.
This paper is a revised version of SC/J09/JR26 to cover the recommendations of the expert panel of theExpert Workshop to review the JARPNII Programme held at Tokyo from 26-30 of January. The panel
recommends that SC/J09/JR26 should provide more details on the analysis involving the STRUCTURE(Pritchard et al., 2000) used for genetic assignment of individuals.
MATERIALS AND METHODS
Sample collections
Eighteen sub-areas were set for management purpose of the western North Pacific common minke whale(Figure1). JARPN and JARPNII surveys were conducted in sub-areas 7, 8, 9, and 11. These sub-areas
were further divided into western and eastern strata for analyses, 7W (140-147°E), 7E (147-150°E), 8W(150-153°E), 8E (153-157°E), 9W (157-162°E), and 9E (162-170°E).
Offshore samples of common minke whales from the western North Pacific were JARPN and JARPNII
samples collected from 1994 to 2007 in SA7, SA8, SA9, and SA11 (Table 1). Each year up to 100
common minke whales were collected. The number of individuals from the SA11 was total 80 collected
in 1995 and 1997. Sampling dates of scientific surveys expand from May to September depending on thesampling plan of a given year. Because of other scientific purposes of the survey (e.g., feeding ecology ofwhales), the sampling locations differed from year by year. Details of offshore component of JARPNII
survey can be found in Tamura et al. (2009). Minke whales obtained from coastal component of JARPNII
were also used in this study (Table 1). Coastal JARPNII surveys were conducted at Sanriku region inspring of 2003, 2004, 2005, 2006, and 2007, and at Kushiro region in fall of 2002, 2004, 2005, 2006, and2007. Sample size per survey was maximum 60 common minke whales. Details of the coastal componentof JARPNII survey can be found in Kishiro et al. (2009). Common minke whales that were bycaught on2

Do not cite without written permission from the authors
SC/61/JR5
set net fishery conducted along the Japanese coast from 2001 to 2007 were also used (bycatches) (Table
1). As of July 1st 2001, the new regulation governed by the Japanese government has allowed the set net
fishermen to harvest whales found in their set net and to sell these on to the market after DNA registrationof these for individual identification. The bycatches used were obtained from the SA2, SA6, SA7, SA10,
and SA11 year-round.
Microsatellites analysis
We followed the IWC guidelines for DNA data quality (IWC, 2009) as much as possible at the moment.
Genomic DNA was extracted from 0.05g each of the skin or muscle tissues using standard proteinase K,
phenol-chloroform procedure described by Sambrook et al. (1989). Extracted DNA was stored in the TE
buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0).
Microsatellite polymorphisms were analyzed using 16 sets of primers: EV1, EV14, EV21, EV37, EV94,(Valsecchi & Amos, 1996), GT23, GT195, GT211, GT310, GT509, GT575 (Bérubé et al., 2000),
GATA28, GATA98, GATA417, TAA31 (Palsbøll et al., 1997), DlrFCB14 (Buchanan et al., 1996). EV1,
EV14, EV21 were developed from sperm whale (Physeter macrocephalus), EV37, EV94, GT23, GT310,
GT575, GATA28, GATA98, GATA417, TAA31 were from humpback whale (Megaptera novaeanglia),
and DlrFCB14 from beluga whale (Delphinapterus leucas). All GT, EV, and DlrFCB primers are
dinucleotide repeat, TAA31 trinucleotide repeat, and all GATA primers tetranucleotide repeat. Most of theprimers used here were already tested for amplification on common minke whales by these authors.
Primer sequences and PCR profiles follows those of the original authors with slight modifications.
PCR amplifications were performed in 15μl reaction mixtures containing 10-100ng of DNA, 5 pmole ofeach primer, 0.625 units of Ex Taq DNA polymerase (Takara Shuzo), and 2mM of each dNTP, and 10x
reaction buffer containing 20mM MgCl2 (Takara Shuzo). PCR amplifications followed the manufacture’s
instructions for the use of Ex Taq DNA polymerase (Takara Shuzo). Amplified products with internal size
standard (GENESCAN400HD, Applied Biosystems Japan) were run on a 6% polyacrylamide
denaturating gel (Long RangerTM) using an BaseStationTM 100 DNA fragment analyzer (Bio-Rad).
Although alleles were visualized using CartographerTM software specifically designed for the BaseStation,
allelic sizes were determined manually in relation to the internal size standard and minke whale DNA of
known size that were rerun on each gel.
Data analysis
The number of alleles per locus, expected heterozygosity per locus, and Weir and Cockerham estimator of
FST (Weir and Cockerham, 1984) was calculated using the FSTAT 2.9.3 (Goudet, 1995). Statistical tests
for the deviations from expected Hardy-Weinberg genotypic proportions were conducted using the
GENEPOP 4.0 (Rousset, 2008).
The Bayesian clustering approach was implemented with the microsatellite data in the STRUCTURE
version 2.0 (Pritchard et al., 2000) to determine the most likely number of genetically distinct stocks
present in our samples. The program is a model-based clustering method for inferring stock structure (K,the number of stocks in the model) using multilocus genotype data with and without information on
sampling locations. STRUCTURE allowed us to analyze the samples without choosing sample units that
did not necessarily correspond to real biological stock boundaries. Posterior probabilities for K were
estimating from three independent runs for each value of K from one to five with only genetic
information. These data were calculated based on burn-in period of 10,000 iterations and runs of 100,000
iterations. Individual assignment was then conducted for the most plausible K using estimated individual
proportion of membership probability. The ancestry model we used for the simulation was the admixture
model, which assumes individuals may have mixed ancestry. The allele frequency model used was thecorrelated allele frequencies model, which assumes frequencies in the different stocks are likely to be
similar due to migration or shared ancestry.
RESULTS
Multilocus genetic variations for stock numbers and individual assignment
All 16 loci analyzed were polymorphic in overall samples of minke whales we used (Table 2). Total
number of alleles per locus ranged from two at the EV21 to 30 at the EV1 with an average of 13.0.
Expected heterozygosity at each of the loci ranged from 0.330 at EV21 to 0.855 at GT23 with an average3

Do not cite without written permission from the authors
SC/61/JR5of 0.692. Eleven out of 16 loci showed significant deviation from the expected Hardy-Weinberg
genotypic proportions even after correction for the multiple tests. This deviation suggested existence ofindividuals from multiple stocks in our samples.
Bayesian clustering analyses conducted on the total samples (2,542 individuals) without information on
their geographic origins presented the highest likelihood probability at K=2 (Table 3). Figure 2 shows
estimated stock structure at K=2 and K=3. At K=3, the second and third stocks were indistinguishable.
These results strongly indicated that our samples came from two genetically distinct groups of common
minke whales. Same individuals were grouped into the same groups over the three runs. Assignment
probabilities of the same individuals to the groups were quite consistent at the different runs (Figure 3)
with very low CV (average CV =0.014). These observations allowed us to assign the individuals into thedifferent groups on the basis of their membership probabilities at arbitrary chosen level. In this study, theindividuals with the membership probability of over 90% for either of the two groups at each of the runs
were assigned as pure individuals. All other individuals with the membership probability less than 90% to
the either groups were assigned as individuals of unknown origin. Even with this relatively strict criterion,
2,302 individuals (91%) were assigned as the pure individuals to the either stocks (770 to stock 1 and
1,532 to stock 2). FST between the two pure groups was 0.049, which was significantly larger than zero.
Spatial distribution of the two genetically different stocks along the Japanese coast
Both of the assigned and unassigned individuals were grouped based on their sampling origins (offshore,coastal, and bycatch) as well as locations (IWC sub-areas) (Table 4; Figure 4). In this way, distribution of
the pure individuals that were genetically assigned to the different stock was clearly separated
geographically. Almost all of the individuals collected from the Sea of Japan side belonged to the Stock 1,
whereas almost all of the individuals from the offshore North Pacific (east of the SA7E) belonged to thestock 2. Intermediate areas (SA7W and SA11) contained the individuals from the both stocks. The results
indicated that the Stock 1 and Stock 2 were the J and O stock. Hereafter, we named the Stock 1 and 2 as
the J and O stock, respectively. The SA2 was mainly occupied by the J stock, and the SA7W was by thetwo stocks. Two individuals collected from the 9W (N=260) were assigned as the J sock individual, whilefour individuals from the SA6 (N=387) was assigned as the O stock individual. Sighting locations of theassigned individuals from the JARPN and JARPNII samples were plotted in Figure 5a and coastal area
was closed up in Figure 5b. The individuals of unknown origins also distributed widely.
Temporal distribution of the two genetically different stocks along the Japanese coast of North
Pacific side of Japan
The proportion of the J stock and O stock individuals in the bycatches from the SA7 were approximately
50:50 (93 J and 90 O). In addition to that, the sampling dates of the bycatches expand year around.
These things allowed us to depict temporal distribution of the J and O stocks along the Japanese coast of
the North Pacific side. Because the sample sizes were relatively small in a single month base, we
calculated the proportion of the J stock, O stock, and unknowns from a three months moving average(Figure 6). The result revealed that the proportion of the O stock increased in spring and decreased toward
winter season although both the J and O stock individuals stayed year round. At the SA2, total of 168
individuals was assigned to 114 J and 24 O individuals, and temporal distribution of these individuals
showed similar, but less clear, pattern to that observed at the 7W.
DISCUSSION
Delineation of the samples into geographic groups for analyses is often arbitrary based on cultural,political jurisdictions, or simply sampling locations. The arbitrary predefined groups, however, may notnecessarily correspond to real biological stock boundaries. This is especially the case for thegeographically widely distributed species that are capable of long distance migration. They may not haveclear stock boundaries or may be genetically structured through unidentified barriers of gene flow.
In this study, combined use of the hypervariable microsatellite markers and Bayesian clustering approachsuccessfully distinguished most of the individuals in the samples into the J and O stocks. One notableaspect of this study was that the number of samples used, especially from the Sea of Japan side, was muchlarger than the previous genetic studies. Past genetic studies dealing with the J and O stocks used only
small amount of the samples taken from past commercial whaling operated in coastal areas of Korea in1982 as the J sock (Wada and Numachi, 1991; Goto and Pastene, 1997). In addition to that, this paper4

Do not cite without written permission from the authors
SC/61/JR5
used the samples of minke whales collected from along the Japanese coast of both sides of Japan andoffshore North Pacific at a similar time frame. This allowed us to minimize potential large temporal
influence, if it exists, on describing present day stock structure, although no samples had been obtained in
winter in the western North Pacific due to logistic constraints.
According to the probability for each of K, our data was not supported at all by K=1, 3, 4, and 5. Veryhigh membership probabilities and great geographic concordance indicated that K=2 was appropriate
choice for our data. When we lower our membership probability criteria from 90% to 75%, 97% of theindividuals in the samples are assigned to either the two stocks and the additional assigned individuals
does not change the general picture of spatial distribution of the two stocks. Status of the unassigned
individuals especially those with the membership probability of less than 75% (82 individuals) are
difficult to be identified at this moment. They could be either individuals of interbreeding origins or pureindividuals simply with low power to be assigned by the current markers and analyses. The clear genetic
difference between the two stocks with moderate level of the FST value and the observation from the past
ecological and biological studies of minke whales suggests that the interbreeding between them isprobably a rare event.
The individual assignments by the microsatellites had good agreements with that by mtDNA haplotype
analysis. It has been known that some of the mtDNA haplotypes were unshared by the individuals fromthe Sea of Japan and North Pacific and these unshared haplotypes with a few shared ones made an
independent cluster in a phylogenetic tree (Goto et al., 2000). Based on the specific nucleotide sequences
common to the haplotypes in that cluster, Goto et al. (2000) identified 25 of the 80 minke whales from theSA11 as the J stock individuals. Our microsatellite assignments of the same SA 11 individuals were very
well consistent to those in Goto et al. (2000). By our method, 23 of the 80 were assigned as the pure J
stock, and 22 of them were identified as the J stock by the method of Goto et al. (2000). In the remaining
three J stock individuals from the mtDNA identification, two were the J stock individuals with themembership probability over 75%, and one was the O stock individual with the membership probability
over 90%. Although the microsatellite markers we used are not complete diagnostic in the common minke
whales samples, all of these findings suggest that assignments of the individuals is very reliable.
Spatial and temporal distributions of the assigned individuals depicted a pattern and dynamics ofgeographic overlap of the two stocks around Japan. As predicted, main distribution areas of the J and O
stock were clearly separated. The J stock occupied the Sea of Japan and the O stock offshore did theNorth Pacific. Other important findings that should be raised are 1) the O stock individuals appeared tooccasionally, but rarely, migrate to the Sea of Japan, 2) the J stock individuals migrated to the 7W of theNorth Pacific side and very rarely to further east, and 3) the SA2 was mainly occupied by the J stock.
The third finding suggests that the Kuroshio Current, which is one of the strongest west-boundary
currents of the subtropical gyre, is working as the stock boundary between the two stocks. Temporal
distribution of the assigned whales indicated seasonal differences in the movement of the two stocks
along the Japanese coast of North Pacific (SA7 and SA2). The number of the O stocks increased in spring
although both stocks appeared to distribute there year around.
It is important to note that the individuals from the JARPN/JARPNII and those from the bycatch samples
differ in their body length. Average body length of the all JARPN and JARPNII samples including boththe offshore and coastal components was 6.95m (s.d.=0.992) and that of the all bycatch sample was 4.92
m (s.d.=0.942). Kato (1992) estimated mean body length at the sexual maturity of the North Pacificcommon minke whales to be 6.3m for males and 7.1m for females, so that the bycatch sample in thispaper consisted of mostly, if not all, immature whales. The observation that the number of the immature O
stock individuals increased in spring along the Japanese coast of the North Pacific side was thus wellconsistent to that illustrated by Hatanaka and Miyashita (1997). The observed difference in the maturity
status between the individuals from the bycatch and JARPN/JARPNII samples, however, could indicatethat the patterns of the temporal and spatial distributions we illustrated with the bycatches for the SA2 andSA7 may be different at some extent from those of adults. In regard to the SA2, minke whales from theoffshore area have not been available yet. Related concern can be also seen in the SA11. The number of
the J stock individuals in the SA11 differed between the bycatch and JARPN samples. Average bodylength of the 14 bycatches from the SA11 was 4.5m and 13 of the 14 were collected from late fall
(September to November). This difference we observed between the bycatch and JARPN samples could
be due to the immature/mature, temporal, or both factors, but we were not able to distinguish which one

5Do not cite without written permission from the authors
SC/61/JR5
accounted for at this moment. Although we definitely gained our understanding of common minke
whales’ distribution around the Japanese water substantially from this study, our samples are still missing
some pieces to depict whole picture of it.
The IWC SC completed the RMP Implementation for the western North Pacific common minke whales
during the 2003 Annual Meeting and adopted four stock scenarios in the western North Pacific at the final
stage of the Implementation process (IWC, 2004). Three of the four baselines assumed the third stock
other than the J and O in the SA7, 8, and 9. This study denied that possibility because it showed that theNorth Pacific side of Japan was occupied by the O stock with some J stock individuals migrated into nearcoastal line area. Detailed analyses on this matter can be seen in Kanda et al. (2009).
This study is the first one that shed the light on the dynamics of geographic overlap between the twostocks at the individual base. We believe that the results of this study are also quite useful for the effective
management of the two stocks. Another usefulness of the individual identification by the genetic markers
is it can be used to look for stock differences in other traits, such as morphometry, pollutant levels, andbiological parameters.
ACKNOWLEDGEMENTS
We thank researchers and crewmembers participating in the JARPN and JARPNII surveys for their effort
in collecting the samples used in this study. Our sincere gratitude also goes to H. Oikawa and S. Azumi
for their assistance in DNA extraction, and H. Hatanaka and the expert panel of the Expert Workshop to
review the JARPNII Programme for valuable comments on the paper.
REFERENCES
Bakke, I., Johansen, S., Bakke, O., and El-Gewely, R. 1996. Lack of population subdivision among theminke whales (Balaenoptera acutorostrata) from Icelandic and Norwegian waters based on
mitochondrial DNA sequences. Mar. Biol. 125:1-9.
Bérubé, M., Jørgensen, H., Mcewing, R., and Palsbøll, P.J. 2000. Polymorphic di-nucleotide
microsatellite loci isolated from the humpback whale, Megaptera novaeanglliae. Mol. Ecol.
9:2181-2183.
Buchanan, F.C., Friesen, M.K., Littlejohn, R.P., and Clayton, J.A. 1996. Microsatellites from beluga
whale Delphinapterus leucas. Mol. Ecol. 5:571-575.
Goto, M. and Pastene, L.A. 1997. Population structure of the western North Pacific minke whale based on
an RFLP analysis of the mtDNA control region. Rep. int. Whal. Commn. 47:531-537.
Goto, M., Kim, Z.G.., Abe, H., and Pastene, L.A. 2000. A note on the possibility of identifying individual
J stock animals from a mixed assemblage based on mitochondrial DNA analysis. Paper SC/F2K/J28
presented to the IWC Scientific Committee Workshop to Review the Japanese Whale Research
Programme under Special Permit for North Pacific Minke Whales (JARPN), Tokyo, 7-10 February
2000 (unpublished). 9pp.
Goudet, J. 1995. FSTAT, version 1.2: a computer program to calculate F-statistics. J. Hered. 86:485-486.
Hatanaka, H. and Miyashita, T. 1997. On the feeding migration of the Okhotsk Sea-West Pacific stock ofminke whales, estimates based on length composition data. Rep. int. Whal. Commn. 47: 557-564.
International Whaling Commission. 2004. Report of the sub-committee on the Revised Management
Procedure. J. Cetacean Res. Manage. 67:75-184.
International Whaling Commission. 2009. Report of the Scientific Committee, Annex I. Report of theworking group on stock definition. J. Cetacean Res. Manage. (Suppl.) 11: in press.
Kanda, N., Goto, M., Kishiro, T., Yoshida, H., Kato, H., and Pastene, L.A. 2009. Microsatellite analysis ofminke whales in the western North Pacific. Paper SC/J09/JR30 presented to the JARPN II Review
Workshop, Tokyo, January 2009 (unpublished). 14pp.
Kato, H. 1992. Body length, reproduction and stock separation of minke whales off northern Japan. Rep.
int. Whal. Commn. 42:443-453.
Kishiro, T., Yoshida, H., Goto, M., Bando, T., and Kato, H. 2009. Methodology of whale sampling
surveys in the 2002-2007 coastal components under the JARPNII. Paper SC/J09/JR3 presented to the
JARPN II Review Workshop, Tokyo, January 2009 (unpublished). 27pp.
Martinez, I. and Pastene, L.A. 1999. RAPD-typing of Central and Eastern North Atlantic and Western
North Pacific minke whales, Balaenoptera acutorostrata. ICES J. Marine Sci. 56: 640-651.

6

Do not cite without written permission from the authors
SC/61/JR5
Ohsumi, S. 1977. Minke whales in the coastal waters of Japan. Rep. int. Whal. Commn. 27:164-166.
Omura, H. and H. Sakiura. 1956. Studies on the little piked whale from the coast of Japan. Science Rep.
Whal. Res. Inst. Tokyo 11:1-37.
Palsbøll, P.J., Bérubé, M., Larsen, A.H., and Jørgensen, H. 1997. Primers for the amplification of tri-and
tetramer microsatellite loci in baleen whales. Mol. Ecol. 6:893-895.
Pastene, L.A., Goto, M., Kanda, N., Zerbini, A.N., Kerem, D., Watanabe, K., Bessho, Y., Hasegawa, M.,
Nielsen, R., Larsen, F., Palsboll, P.J. 2007. Radiation and speciation of pelagic organisms during
periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata. Mol.
Ecol. 16: 1481-1500.
Pritchard, J.K., Stephens, M., and Donnelly, P. 2000. Inference of population structure using multilocus
genotype data. Genetics 155:945-959.
Rousset, F. 2008. Genepop'007: a complete re-implementation of the genepop software for Windows
and Linux. Molec. Ecol. Resources 8:103-106.
Sambrook, J., Fritsch, E.F., and Maniatis, T. 1989. Molecular cloning: A laboratory manual. 2nd Ed.,
Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
Tamura, T., Matsuoka, K., and Fujise, Y. 2009. General methodology and survey procedure under the
JARPNII, offshore component. Paper SC/J09/JR4 presented to the JARPN II Review Workshop,
Tokyo, January 2009 (unpublished). 16pp.
Valsecchi, E., and Amos, W. 1996. Microsatellite markers for the study of cetacean populations. Mol. Ecol.
5:151-156.
Wada, S. and Numachi, K. 1991. Allozyme analyses of genetic differentiation among the populations andspecies of the Balaenoptera. Rep. int. Whal. Commn. (special issue 13) :125-154.
Weir, B. S. and Cockerham, C.C. 1984. Estimating F-statistics for the analysis of population structure.
Evolution 38: 1358–1370.

7

Do not cite without written permission from the authors
SC/61/JR5
Table 1. Number of individuals used in this study.
Survey area
Total
JARPN and JARPNII
Offshore (‘94-‘07)
Coastal (‘02-‘07)
Bycatch (‘01-‘07)

1231
480
831

2

183

6

7W

7E

8W

8E

9W

9E

47

86

139

291

174

411

414
480
212

10

11
80

9

16

Table 2. The number of alleles (A), expected heterozygosity (He), and test result for the expected
Hardy-Weinberg genotypic proportions (HW) at 16 microsatellite loci analyzed in the JARPNII samplesof minke whales. n.s. = not significant
MarkerA

He

HW

DlrFCB14
EV1
EV14
EV21
EV37
EV94
GATA28GATA417
GATA98
GT195
GT211
GT23
GT310
GT509
GT575
TAA31

5
30
6
2
12
8
24
13
7
13
17
16
14
23
13
5

0.405
0.785
0.543
0.330
0.709
0.638
0.830
0.737
0.610
0.857
0.874
0.885
0.833
0.881
0.809
0.349

p<0.01p<0.01p<0.001
n.s.
n.s.
n.s.
p<0.001n.s.
n.s.
p<0.001p<0.001p<0.001p<0.001p<0.001p<0.001p<0.001

Table 3. Results of Bayesian clustering method analyzed for overall samples.
K

Log P(k/x)*

variance*Pr(k/x)**

1
2
3
4
5

-128869.8-123973.8-124376.2-125643.1-127277.0

95.3
613.1
2243.85312.39061.4

~0.0
~1.0
~0.0
~0.0
~0.0

* log likelihood of the data for different values of K and the variance.
** Probability for each of K.

8

Do not cite without written permission from the authors
SC/61/JR5
Table 4. Number of individuals assigned to each of the categories based on the assignment probabilities
obtained from STRUCTURE.
SourceArea

Bycatch2

6

Coastal*Offshore

7

10

11

CK CS

11 7W

7E

8W 8E 9WJ
144 383 93
O
24
4 90
Unknown 15
24 29
Total
183 411 212

7
0
2
9

15
0
1
16

38 41
190 16425 22
253 227

23 24
49 3468 43
80 413

0
46
2
48

0
0
2
0
75 125 258 161
11 13 32 13
86 138 292 174* CK7=Kushiro coastal component, CS7=Sanriku coastal component

Figure 1. The 18 sub-areas designated by the IWC for North Pacific common minke whales.

99E

Do not cite without written permission from the authors
SC/61/JR5

Offshore

CoastalBycatch

SA11*

1.0

1.0

0.8

0.8

0.6

0.6

run 3

run 2

Figure 2. Plot of membership probabilities at K=2 (above) and K=3 (blow). Each individuals is characterized by a thin vertical line, which is divided into K colored
segments on the basis of the individual’s membership fractions in K clusters. *: Samples only from the JARPN.

0.4

0.4

0.2

0.2
0.0

0.0
0.0

0.2

0.4

0.6

run 1

0.8

1.0

0.0

0.2

0.4

0.6

0.8

1.0

run 1

Figure 3. Relationship between the membership probabilities from different runs (run 1~3) for each of the individuals at K=2.

10

Do not cite without written permission from the authors
SC/61/JR5

Stock 1

Stock 2

unknown

100%

80%

60%

40%

20%

0%
BC6

BC10

BC2

BC11

11

BC7

CK7

CS7

7W

7E

8W

8E

9W

9E

Figure 4. Spatial distribution of the whales assigned to the Stock 1, Stock 2, and unknown categories. See text for assignment criteria. BC2, BC6, BC7, BC10,
BC11 = bycatches from the SA2, SA6, SA7, SA10, and SA11. CK7 and CS7 = individuals from coastal survey of JARPNII at Kushiro and Sanriku region,
respectively. 7W, 7E, 8W, 8E, 9W, 9E and 11 = individuals collected from offshore survey of JARPN and JARPNII.

11

Do not cite without written permission from the authors
SC/61/JR5

48N

48N

43N

43N

38N

38N

33N
135E

33N
145E

155E

165E

Figure 5a. Locations of the minke whales that were assigned to O stock (◆), J stock (▲), and unknown origin (+) based on STRUCTURE.

12

Do not cite without written permission from the authors
SC/61/JR5

42N

42N

37N
140E

37N

Figure 5b. Zoomed into the coastal area of the Fig. 2a. ◆: O stock, ▲: J stock, +: unknown13

Do not cite without written permission from the authors
SC/61/JR5

JO

unknown

MayJul.

Jun.Aug.

Jul.Sep.

100%

80%

60%

40%

20%

0%
Jan.Mar.

Feb.Apr.

Mar.May

Apr.Jun.

Aug.Oct.

Sep.Nov.

Oct.Dec.

Nov.Jan

Dec.Feb.

Figure 6. Temporal distribution of the bycatches assigned to the J, O, and unkwon categories in the SA7. Each bar was expressed as three months moving average.

14

Do not cite without written permission from the authors

SC/61/JR5
COLOR FIGURES

Update of the analyses on individual identification and mixing of the J and O stocks around
Japanese waters examined by microsatellite analysis
Naohisa Kanda1, Mutsuo Goto1, Toshiya Kishiro2, Hideyoshi Yoshida2, Hidehiro Kato3, and Luis A. Pastene1
1

The Institute of Cetacean Research, 4-5, Toyomi-cho, Chuo-ku, Tokyo 104-0055, Japan
National Research Institute of Far Seas Fisheries, 2-12-4, Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
3
Tokyo University of Marine Science and Technology, 1-5-7, Konan, Minato-ku, Tokyo 108-0075, Japan
2

Offshore

CoastalBycatchSA11*

Fig. 2. Plot of membership probabilities at K=2 (above) and K=3 (blow). Each individuals is characterized by a thin vertical line, which is divided into K colored
segments on the basis of the individual’s membership fractions in K clusters. *: Samples only from the JARPN.

1

Do not cite without written permission from the authors

SC/61/JR5
COLOR FIGURES

48N

48N

43N

43N

38N

38N

33N
135E

33N
145E

155E

165E

Fig. 5a. Locations of the minke whales that were assigned to O stock (◆), J stock (▲), and unknown origin (+) based on STRUCTURE.

2

Do not cite without written permission from the authors

SC/61/JR5
COLOR FIGURES

42N

42N

37N
140E

37N

Fig 5b. Zoomed into the coastal area of the Fig. 2a.

◆: O stock, ▲: J stock, +: unknown.

3