Technical Reports of the Ins�tute of Cetacean Research (2022)

pp. 1–10

Technical Report

What do we know about whales and ecosystem in the western North
Paciﬁc Ocean? Part 1: summary of results on stock structure in baleen
whale species
Mioko Taguchi*, Mutsuo Goto and Luis A. Pastene
Institute of Cetacean Research, 4–5 Toyomi-cho, Chuo-ku, Tokyo 104–0055, Japan*Contact e-mail: taguchi@cetacean.jp

ABSTRACT

Iden�ﬁca�on of biological stocks within a species is fundamental to appropriately interpret demographic parameters. Informa�on on the temporal-spa�al stock structure is crucial in establishing eﬀec�ve management
and conserva�on strategies of marine living resources. This paper summarizes the recent gene�c studies on
stock structure of four baleen whale species in the North Paciﬁc: right, sei, Brydeʼs and common minke whales.
These studies used a large number of gene�c samples collected mainly in surveys conducted by the Ins�tuteof Cetacean Research since 1994. Results of the studies revealed novel stock structures, and this informa�on
is contribu�ng to stock assessments and conserva�on of each whale species in the North Paciﬁc.

INTRODUCTION
Diﬀerent biological stocks could have diﬀerent demographic characteris�cs and respond in diﬀerent ways toenvironmental stress. For this reason, the iden�ﬁca�onof stocks in a species is fundamental for the appropriate
interpreta�on of abundance es�ma�on and other demographic parameters. Informa�on on the temporal-spa�alstock structure is thus crucial in establishing eﬀec�vemanagement and conserva�on strategies. In this regard, Moritz (1994) deﬁned management units (MUs) as
historically isolated sets of popula�ons and suggested
that gene�c markers be used to deﬁne management
units within species: popula�ons with a signiﬁcant divergence of allele frequencies at nuclear or mitochondrial
loci, regardless of the phylogene�c dis�nc�veness of thealleles.
This paper describes the outline of the recent studies
which examine gene�c diversi�es and stock structure
based on the MUs deﬁned by Moritz (1994) for the four
North Paciﬁc whale species: right (Eubalaena japonica),sei (Balaenoptera borealis), Brydeʼs (B. brydei) and common minke whales (B. acutorostrata).

BACKGROUND ON GENETIC STUDIES ON STOCKSTRUCTURE IN NORTH PACIFIC BALEEN WHALES
North Paciﬁc right whales
LeDuc et al. (2012) was the ﬁrst study that focused on
North Paciﬁc right whaleʼs stock structure and gene�c di-versity. The study using the mitochondrial DNA (mtDNA)
control region and six microsatellite DNA (msDNA) loci,mainly showed the poten�al parentage and gene�c diversity in 24 individual whales (23 from the eastern North
Paciﬁc and one from the western North Paciﬁc). Theirresults inferred that North Paciﬁc right whales could be
isolated to some degree between the western and eastern regions based on paternity analysis. However, it wasnoted that the rela�onship of the eastern North Paciﬁcright whales to those in the western North Paciﬁc waslargely unexamined.
Sei whales
A pioneering work on stock structure of North Paciﬁc sei
whales was carried out on the feeding grounds by Wada
and Numachi (1991) using three polymorphic allozyme
loci, which suggested a single stock in the area eastof 160°E. The most comprehensive gene�c study was
performed by Kanda et al. (2009c) using msDNA genotypes at 17 loci and mtDNA control region sequencesfrom a total of 790 specimens collected on the feeding
grounds between 140°E and 135°W during 1972–1973
and 2002–2007. The study also showed no evidence ofgene�c heterogeneity in the research area. Kanda et al.
(2013) subsequently examined gene�c diﬀerences of thisspecies both spa�ally and temporally. The results of thestudy were consistent with those found by Kanda et al.
(2009). In addi�on, Kanda et al. (2015) examined spa�algene�c diﬀeren�a�on using genotypes at 16 msDNA
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Technical Reports of the Ins�tute of Cetacean Research (2022)

loci by only using samples collected during the summers
in 2010, 2011 and 2012 in order to eliminate temporalnega�ve biases. The study again did not ﬁnd evidence ofmul�ple stocks of sei whales in the North Paciﬁc.
Brydeʼs whales
A series of allozyme studies (Wada and Numachi, 1991;
Wada, 1996) were conducted using Brydeʼs whale
samples collected between 150°E and 160°W, on the
North Paciﬁc feeding grounds. These studies did not ﬁnd
evidence of gene�c heterogeneity in the research area.
A subsequent RFLP analyses inves�gated the pa�ern ofgene�c varia�ons of Brydeʼs whales at intra- and interoceanic levels for mtDNA control region in specimensfrom four loca�ons: western North Paciﬁc, westernSouth Paciﬁc, eastern South Paciﬁc and eastern Indian
Oceans (Pastene et al., 1997). The study showed signiﬁcant gene�c diﬀerences among the four regions, but did
not reveal any signiﬁcant gene�c diﬀerences within thewestern North Paciﬁc Ocean. The most recent popula�ongene�c study was performed by Kanda et al. (2007), using
msDNA genotypes at 17 loci and mtDNA control region
sequences in a sample set used by Pastene et al. (1997),
as well as addi�onal samples from the western North
Paciﬁc feeding grounds. The study conﬁrmed signiﬁcantgene�c diﬀeren�a�ons among oceanic regions, but notwithin the western North Paciﬁc.
Common minke whales
At least two stocks of the common minke whales havebeen historically recognized in the western North Paciﬁc,namely the Okhotsk Sea–West Paciﬁc (known as the Ostock) and the Sea of Japan–Yellow Sea–East China Sea(known as the J-stock). These two stocks are diﬀeren�at-

ed morphologically, reproduc�vely (Omura and Sakiura,
1956; Kato, 1992) and gene�cally (Wada and Numachi,
1991; Goto and Pastene, 1997), which suggests their reproduc�ve isola�on.
Kanda et al. (2009a; b) examined gene�c varia�ons at
16 msDNA loci in a total of 2,542 gene�c samples collected in the waters around Japan and pelagic areas of
the western North Paciﬁc during 1994–2007, and succeeded in the assignment of individual to stocks using a
Bayesian clustering approach, i.e. STRUCTURE analysis.
The study presented the highest likelihood probability at
K=2, which indicated that the samples came from twogene�cally dis�nct popula�ons, i.e. O- and J-stocks.
Pastene et al. (2016a) updated these studies by increasing sample sizes, and showed a ﬁner spa�al distribu�on of each stock (Figure 1): J-stock whales mainly
distributed in the Sea of Japan (sub-areas 6E and 10E), Ostock whales mainly distributed in the oﬀshore North Paciﬁc (east of sub-area 7WR). Both stocks occur along the
Paciﬁc coast of Japan (sub-areas 7CN, 7CS and 2C) and in
the southern Okhotsk Sea (sub-area 11) but sub-area 2C
is mainly occupied by the J-stock whales. Furthermore,
the study showed the temporal distribu�on of the O- andJ-stock whales on the Paciﬁc side of Japan (sub-areas 2C,
7CN and 7CS) as shown in Figure 2: J-stock whales are
predominant throughout the year in sub-area 2C, while
the propor�on of the J-stock whales increases in autumn/
winter and decreases in spring/summer in sub-areas 7CS
and 7CN. The reverse is true for O-stock.
A subsequent study by Pastene et al. (2016b) inves�gated the possibility of addi�onal structure within
O-stock using hypothesis tes�ng and the discriminant
analysis of principal component (DAPC) approach. A
simula�on exercise showed that the sta�s�cal power of

Figure 1. Management sub-areas deﬁned by the IWC for the western North Paciﬁc common minke whales (le�), andspa�al occurrence of O- and J-stocks in sub-areas (right: BC2, BC6, BC7CS, BC7CN, BC10, BC11=bycatches fromthe respec�ve areas; K7CN=coastal JARPNII surveys at Kushiro; S7CS=coastal JARPNII surveys at Sanriku; 7CS,
7CN, 7WR, 7E, 8, 9 and 11=oﬀshore JARPN/JARPNII surveys). Sample sizes are at the top of each bar. Color
indicates stock assignment by STRUCTURE analysis (gray=O-stock, dark gray=J-stock, light gray=unassigned).
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What do we know about whales and ecosystem in the western North Pacific Ocean? Part 1

Figure 2.

Monthly occurrence of J- and O-stocks in sub-areas 2C (le�), 7CN (middle) and 7CS (le�). Each bar is expressed as three months moving average. Sample sizes are on the top of each bar. Samples from sub-area
2C and subareas 7CN and 7CS were collected during 2001–2014 and 1994–2014, respec�vely. Color indicates stock assignment by STRUCTURE analysis (dark gray=J-stock, gray=O-stock, light gray=unassigned).

the hypothesis tes�ng was high. Both analyses showedno evidence of sub-structuring within O-stock.
Tiedemann et al. (2017) developed a new maximum
likelihood-based approach to infer Parent–Oﬀspring(P–O) rela�onships using full msDNA data at 16 loci ina total of 4,554 western North Paciﬁc common minke
whales including fetuses. The study iden�ﬁed a total of
49 validated P–O pairs (excluding mother-fetus pairs)
across sub-areas, with J-stock pairs on both sides of Japan
closer to the coast, while O-stock pairs were mostly located to the east of Japan, both close to the coast as well as
far oﬀshore. The study provided no evidence for further
stock structure other than O- and J-stocks.

RECENT GENETIC STUDIES ON STOCK STRUCTURE
IN THE NORTH PACIFIC
Basic laboratory procedures
DNA extraction
Total genomic DNA was extracted from 0.05 g of a �ssue
sample using either the standard phenol-chloroform
method (Sambrook et al., 1989) or Gentra Puregene kits
(QIAGEN) and stored in TE buﬀer (10 mM Tris-HCl, 1 mM
EDTA, pH 8.0).
mtDNA
Approximately 500 base pairs of a variable part of the
mtDNA control region were ampliﬁed by PCR using
primers MT4 (Árnason et al., 1993) and Dlp5R (5ʹ-CCA
TCG AGA TGT CTT ATT TAA GGG GAA C-3ʹ; Pastene
et al., 2022). PCR ampliﬁca�on was carried out in 25 µl
reac�on mixtures containing 10–100 ng of template DNA,0.1 µM of each primer, 0.5 units of Ex Taq DNA polymerase (Takara Bio Inc., Shiga, Japan), 0.2 mM of dNTPs,
and 1× Ex Taq buﬀer. Each reac�on was performed withan ini�al denatura�on step at 95°C for 5 min, followed
by 30 cycles of 30 s at 94°C, 30 s at 50°C and 30 s at 72°C,
with a ﬁnal extension step at 72°C for 10 min. PCR products were puriﬁed using MicroSpin S-400HR Columns(GE Healthcare, Illinois, USA). Cycle sequencing was

performed using BigDye terminator cycle sequence Kit(Applied Biosystems Inc., Massachuse�s, USA), following
the manufacturerʼs instruc�ons. The cycle sequencing
products were puriﬁed using AutoSeq G-50 spin Columns(GE Healthcare). The labeled sequencing fragments wereresolved by ABI gene�c analyzers (Applied Biosystems
Inc.) for Sanger sequencing by capillary electrophoresis.
Both strands of all samples were sequenced using theprimers used for ampliﬁca�on. The nucleo�de sequences
obtained were aligned by using the program MUSCLE
implemented in MEGA ver. 10.0.5 (Kumar et al., 2018) or
the program Sequence Navigator.
msDNA
Diﬀerent nuclear msDNA loci were genotyped according
to the whale species (Table 1). The polymerase chain reac�on (PCR) ampliﬁca�ons were performed in 15 µl reac�on mixtures containing 10–100 ng of DNA, 0.25 µM ofeach primer, 0.35 units of Ex Taq DNA polymerase (Takara
Bio Inc.), 0.2 mM of dNTPs, and 1× Ex Taq buﬀer, with
94°C for 2 min, followed by 30 cycles at 94°C for 20 s/54–
61°C for 45 s/72°C for 1 min, and a post-cycling extension
at 72°C for 10 min. Nega�ve and posi�ve control samples,one of each, were run in parallel with all PCR ampliﬁca�ons. The PCR products were run on a BaseSta�on100
DNA fragment analyzer (Bio-Rad, California, USA) withan internal size standard (GENESCAN400HD, Applied Biosystems Inc.), or on an ABI 3500 DNA Analyzer (Applied
Biosystems Inc.) with a 600 LIZ size standard (Applied Biosystems Inc.). In the former pla�orm, alleles were visualized using Cartographer so�ware speciﬁcally designed for
the BaseSta�on, and the fragment sizes were determinedmanually in rela�on to the internal size standard and aposi�ve control sample of known size that were run oneach gel. In the other pla�orm, each allele was determined by automated binning and assigned to allelic bins
predeﬁned in GeneMapper v. 4.0 (Applied Biosystems
Inc.). Any misassigned scores were corrected by hand.
If msDNA scores generated from both pla�orms were3

Technical Reports of the Ins�tute of Cetacean Research (2022)
Table 1
msDNA markers used in the recent studies on four North Paciﬁc baleen whales.
Norht Paciﬁc right whale

Sei whale

Brydeʼs whale

Common minke whale

EV1
EV14
EV21
EV37
EV94
GT023
GT211
GT310
GATA028
DlrFCB17
TR3G2
TR2G5
TR3F2

EV94
EV1
GT211
EV14
EV21
GGAA520
GATA53GT23
GT575
GATA417GT310
EV104
GATA28
GT271
GT011
DlrFCB17
GATA98

DlrFCB14
EV1
EV104
EV14
EV21
EV94
GATA28GATA417
GATA53
GATA98GGAA520
GT011
GT23
GT310
GT575
TAA31

EV1
EV14
EV21
EV37
EV94
GATA28GATA98GATA417
TAA31
GT23
GT195
GT211
GT310
GT509
GT575
DlrFCB14

Table 2Gene�c analyses used in the recent studies on four North Paciﬁc baleen whales.
Analysis
Gene�c diversity indices
HWE test
Hypothesis test
FST es�mates
G'ST es�mates
AMOVA
Mantel test
STRUCTUREDAPCsPCAGENELANDBAPS
TESS
Phylogene�c analyses
PO analysis

North Paciﬁc right whale

Sei whale

Common minke whale

mtDNA

msDNA

mtDNA

msDNA

mtDNA

msDNA

mtDNA

msDNA

●
●
●
●

●
●

●
●
●
●

●
●
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●

●
●
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●

●
●
●
●

●
●
●
●

●

●

●

●
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●
●
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●

●
●

●

contained in a single dataset, then all msDNA scores generated by the ABI 3500 DNA Analyzer were standardized
to those by the BaseSta�on100 DNA fragment analyzer.
Basic analy�cal procedures
The analy�cal procedures used in the recent gene�c studies on popula�on structure are shown in Table 2 for eachwhale species.
This sec�on brieﬂy explains these analy�cal procedures.
4

Brydeʼ s whale

●
●
●
●
●
●

●
●

Genetic diversity indices
mtDNA haplotype (h) and nucleo�de (π) diversi�es(Nei, 1987) were es�mated with sample standard devia�ons. The number of alleles (A), inbreeding coeﬃcient(FIS) and expected heterozygosity (HE) were es�mated per
msDNA locus and across loci. The departure from Hardy–
Weinberg equilibrium (HWE) was also tested for each
msDNA locus and across loci.

What do we know about whales and ecosystem in the western North Pacific Ocean? Part 1

Genetic diﬀerentiation
The gene�c diﬀerence between popula�ons was examined by several sta�s�cal tests for diﬀerences in allele/
haplotype frequencies between popula�ons, as well as
by pairwise FST es�mates and GʼST values (Hedrick, 2005).
The Analysis of Molecular Variance (AMOVA) (Excoﬃer
et al., 1992) was used to examine the hierarchical gene�cstructure. A Mantel test was performed between a matrixof pairwise Edwardʼs gene�c distances and a matrix of
Euclidian geographic distances to examine the pa�ern of
isola�on by distance (IBD).
Genetic clustering and stock assignment approaches
Es�ma�on of the most likely number of clusters and/or
individual-based stock assignment were performed usinga Bayesian clustering analysis with an admixture model
assuming correlated allele frequencies implemented in
STRUCTURE program (Pritchard et al., 2000).
To iden�fy and describe clusters of gene�cally related
individuals, a Discriminant Analysis of Principal Components (DAPC; Jombart et al., 2010), which relies on datatransforma�on using Principal Components Analysis as aprior step to discriminant analysis, was performed with orwithout a priori group assignments for msDNA genotype
set. A priori group was determined based on geographic
sampling site.
The spa�ally explicit clustering approaches, e.g. spa�al Analysis of Principal Components (sPCA; Jombart
et al., 2008), GENELAND (Guillot et al., 2005), TESS(François et al., 2006; Chen et al., 2007) and BAPS (Corander et al., 2008), have been also used to inves�gate
gene�c structure and stock assignment.
Phylogeographic analysis
A sta�s�cal parsimony network (Clement et al., 2000)
was generated to infer the phylogene�c rela�onships
among mtDNA haplotypes.
Parent–oﬀspring analysis
Parent–Oﬀspring (P–O) rela�onships were inferred
based on a maximum-likelihood approach (Tiedemannet al., 2017). mtDNA haplotypes and biological informa�on, e.g. sex, sexual maturity and sampling posi�on,were used to interpret the inferred P–O pairs. The geographical distribu�on of the pairs was discussed from theview point of stock structure.

Main results
North Paciﬁc right whales
Dataset
Pastene et al. (2022) summarized and analyzed all available gene�c data for North Paciﬁc right whales. A�erremoving all duplicates (i.e. samples that were collectedfrom the same individual) and one sample from eachmother and calf pair, a single dataset was generated forthe mtDNA sta�s�cal analyses, which consisted of 30
samples each in the western North Paciﬁc (WNP: 27 newsamples, one from LeDuc et al. [2012] and two historicalbaleen samples) and the eastern North Paciﬁc (ENP: 21
samples from LeDuc et al. [2012], three historical baleensamples and six new samples), respec�vely (Figure 3);
the sample size for the msDNA analysis was 19 whales
for WNP.
Main results and discussion
The study found a total of 16 haplotypes among 60
individual whales. Only four haplotypes were shared between WNP and ENP right whales. The FST between WNP
and ENP right whales was high (0.128) and sta�s�callysigniﬁcant, and the heterogeneity test resulted in sta�s�-

Figure 3.

Approximate core distribu�on of North Paciﬁc rightwhales in summer (July–August) based on 19th
century whaling records and 20th century sigh�ng
and whaling catch data compiled by Clapham et al.
(2004). The pa�ern of distribu�on shows high density in the western and eastern sides of the North
Paciﬁc (purple) and low density in the central area
(white). The monthly plots of right whale sigh�ngs
and catches by Clapham et al. (2004) suggesteda pa�ern of south–north migratory movement inspring (March–May) to summer (June–August)on both sides of the North Paciﬁc. The ﬁgure also
shows the distribu�on of gene�c samples examinedin the recent study (Pastene et al., 2022). Mostof the samples from the eastern side are from
LeDuc et al. (2012). Symbol color indicates sexes(red=female, blue=male, black=uniden�ﬁed).
5Technical Reports of the Ins�tute of Cetacean Research (2022)

cally signiﬁcant diﬀerences between whales on both sidesof the North Paciﬁc; however, there was no concordance
between geography and haplotype network pa�ern.
The number of msDNA alleles per locus ranged from
2 to 7 (4.08 on average), and the HE ranged from 0.285
to 0.787 (0.593 on average). The FIS in each locus ranged
from 0.045 to 0.350 with 0.032 on average. The study
found no signiﬁcant devia�ons from HWE across loci.
The mtDNA results, sugges�ng some degree of popula�on structuring, were consistent with the pa�ern of catchand sigh�ng data showing higher densi�es on either sideof the North Paciﬁc, but li�le in between as shown in Figure 3 (Clapham et al., 2004). These ﬁndings support the
hypothesis of diﬀerent popula�ons occurring in the eastern and western sides of the North Paciﬁc. The authors
also suggested the possibility of incomplete lineage sorting of ancestral polymorphisms from a lack of structure in
haplotype network.
An alterna�ve interpreta�on on these results was that
there is a single interbreeding popula�on in the North
Paciﬁc that is exhibi�ng mtDNA structuring as a result of
matrilineally driven seasonal site ﬁdelity. Although theauthors could not rule out the alterna�ve interpreta�on,they considered, as the more plausible, the hypothesisof two discrete breeding popula�ons of right whales onboth sides of the North Paciﬁc since such hypothesis is
supported also by the pa�ern of catches and sigh�ng
distribu�on, and diﬀerent catch and recovery histories(Brownell et al., 2001; Clapham et al., 2004).
Sei whales
DatasetA single dataset consis�ng of mtDNA control region
sequences (n=1,733) and msDNA genotypes at 17 loci(n=1,729) was generated from specimens of sei whales
collected from diﬀerent sources (Figure 3: Appendix 7
in Tamura et al., 2019). The gene�c data generated fromthese samples were divided into three areas for the purpose of data analyses (Figure 4).
Main results and discussion
Pairwise FST es�mates between areas showed noevidence of gene�c heterogeneity in North Paciﬁc sei
whales for both gene�c markers. These results were also
supported by AMOVA and STRUCTURE analyses, whichshowed a lack of gene�c structuring of this species in theoceanic areas of the North Paciﬁc. These ﬁndings werealso consistent with results of comparable gene�c diversi�es among areas as well as the results from the tests of
HWE and FIS es�mates. Overall, the recent reﬁned analyses supported a single stock hypothesis as suggested
6

Figure 4.

Sampling posi�on of sei whales used in the recent gene�c analyses (Appendix 7 in Tamura
et al., 2019). Color indicates sample source; yellow:
historical commercial whaling during 1972–1973,
red: JARPNII during 2002–2016, and blue: POWER
during 2010–2013. Solid red line shows subareas.
The gene�c data was stra�ﬁed according to thethree areas, i.e. western, central and eastern, fordata analyses.

Figure 5.

Sampling posi�on of Brydeʼs whales used in thegene�c analysis in Taguchi et al. (in press). Color
indicates sample source; yellow: historical commercial whaling operated in 1979 and 1983–1984,
red: JARPNII during 2000–2016, blue: POWER during 2013–2016, green: dedicated sigh�ng survey
in 2012 and 2014, and gray: bycatch in 2010. Areas
enclosed by solid and dashed lines are sample
stra�ﬁca�on according to management areas forthe western North Paciﬁc Brydeʼs whales deﬁned
by the IWC scien�ﬁc commi�ee (IWC, 2008; 2018).
Mul�ple gene�c samples that were collected outside of these areas were assigned to the longitudinally closest area, i.e. area 2.

previously.
Brydeʼs whales
DatasetIn the most recent study (Taguchi et al., in press), a total of
1,182 msDNA genotype sets at 17 loci and 1,195 mtDNA
control region sequences were analyzed (Figure 5). These
data were divided into the three management areas forthe purpose of data analyses (Figure 5).

What do we know about whales and ecosystem in the western North Pacific Ocean? Part 1

Main results and discussion
According to Taguchi et al. (in press), gene�c diversi�eswere similar among areas and a haplotype network did
not show any geographic structure. However, an AMOVA
found evidence of gene�c structure in this species. Pairwise FST and GʼST es�mates, as well as heterogeneity tests,a�ributed this gene�c structure to weak, but signiﬁcantdiﬀeren�a�on between areas 1W and 2. Furthermore,
a Mantel test and a high-resolu�on analysis of gene�cdiversity sta�s�cs showed a weak spa�al cline of gene�c
diﬀeren�a�on.
Given that this study focused on whales in their feeding grounds, these ﬁndings could be reconciled by two
possible scenarios: (1) the occurrence of a single popula�on with kin-associa�on being responsible for feeding
ground preference, and (2) the occurrence of two popula�ons, with feeding ground preference for either area 1Wor area 2; both popula�ons mix geographically througharea 1E. The results from the DAPC were not inconsistent
with these scenarios. Given an es�mated dispersal rateof less than 2% between areas 1W and 2, which indicatessome demographic independency among whales in these
two areas, both scenarios should be considered based on
the precau�onary principle in stock assessments.
Common minke whales
Recent gene�c works have focused on reﬁning the twostock hypothesis, O- and J-stocks, as well as inves�ga�ngwhether addi�onal structure exists within each stock.
DatasetRecent studies have been based on mtDNA control region
sequences (n=4,706) and msDNA genotype sets at 16 loci(n=4,707). The gene�c samples were collected during theJapanese Whale Research Programs under Special Per-

Figure 6.

mit in the western North Paciﬁc, Phases I and II (JARPN/
JARPNII) conducted systema�cally in the western North
Paciﬁc during spring–summer from 1994 to 2016, as well
as from bycatches which occurred along the Japanese
coast from 2001 to 2016.
Main results and discussion
P–O inferences and their geographical distribu�on
Goto et al. (2019) updated the analysis by Tiedemannet al. (2017), and iden�ﬁed a total of 40 and 13 P–O
pairs for O- and J-stocks, respec�vely. The O-stock pairs
were found between coastal and oﬀshore waters, while
J-stock pairs were distributed within and between the Sea
of Japan and the Paciﬁc side of Japan (Figure 6). These
results provided no evidence for further stock structureother than O- and J-stocks.
Spa�ally explicit clustering analyses
The results of sPCA in conjunc�on with those of DPAC
suggested the occurrence of the O- and J-stocks but
provided no evidence for addi�onal structure in eachstock (Taguchi et al., 2019a), which was also supportedby the mtDNA analyses. These ﬁndings indicated a low
possibility that mul�ple stocks exist (other than the J- andO-stocks) in the study area with overlapping geographic
ranges.
A study by de Jong and Hoelzel (2019) using threeother spa�ally explicit clustering tools including GENELAND, TESS and BAPS showed diﬀerent pa�erns of clustering, and the authors stated that the most informa�ve
approach was GENELAND using the mixture model withcorrelated allele frequency model which supported K=4.
However, an addi�onal work subsequently undertaken by
Taguchi et al. (2019b) examined the correspondence ofthe four clusters by GENELAND with the available gene�cand non-gene�c informa�on, and concluded that theDistribu�on of parent–oﬀspring pairs of O- (le�) and J-stocks (right) in western North Paciﬁc common
minke whale (blue square: parent, orange circle: mature oﬀspring, red cross: immature or unknown oﬀspring).
7

Technical Reports of the Ins�tute of Cetacean Research (2022)

most plausible scenario was for two popula�ons (O- andJ-stocks) with complex spa�al and temporal mixing along
the Paciﬁc coast of Japan. de Jong and Hoelzel (2019)
further noted that some of the analyses conducted wereconsistent with a scenario of coastal areas containing gene�cally admixed individuals, and recommended further
analyses under the GENELAND as well under the TESS
and BAPS.

CONCLUDING REMARKSOver the last two decades, many gene�c studies focusedon stock iden�ﬁca�on and structure in western North
Paciﬁc baleen whales have been undertaken. The driving force behind these analyses was to obtain informa�on to assist in determining eﬀec�ve conserva�on andmanagement. Of necessity, these studies were based ongene�c samples collected on feeding grounds and migratory corridors. In this context, they are based on theconcept of MUs described by Moritz (1994). The recent
studies summarized in this paper used several increasingly sophis�cated clustering approaches for the purposeof iden�fying stocks, which showed sta�s�cal results
consistent with this criterion for deﬁning stocks and contributed to their stock assessment. It is also important tomake eﬀort to inves�gate the stock structure of baleen
whales distributed in unsurveyed areas including breeding grounds, and the gene�c rela�onship of them withwhales distributed around Japan.

FUTURE WORKS
Gene�c samples for other baleen whale species in thewestern North Paciﬁc (i.e. humpback whales, ﬁn whales
and blue whales) are also available at the ICR. The gene�cdata generated from these samples will be analyzed in
the near future to inves�gate their stock structure.
The development of a new gene�c marker, which isless error-prone than msDNA, i.e. SNP (Single Nucleo�dePolymorphism) is on-going at the ICR. This marker will be
used to perform the gene�c analyses for all whale species
of interest. Such analyses will aid in a be�er understanding of stock structure of baleen whales in the western
North Paciﬁc.

ACKNOWLEDGEMENTS
We thank all of the whalers and researchers who contributed to the collec�on of samples. We are grateful to
all technicians for their laboratory works at the ICR. We
would also like to thank Naohisa Kanda who organized
most of the msDNA data used in the studies summarized
in this paper. We thank the Editorial Team of TEREP-ICR
8

for the editorial work on this manuscript.

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