SC/F16/JR51

A note on mismatch distributions of mtDNA control region
sequences in baleen whales from the western North Pacific
Luis A. Pastene1, Mutsuo Goto1 and Toshihide Kitakado2
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Institute of Cetacean Research, 4-5 Toyomi-cho, Chuo-ku, Tokyo 104-0055, JapanTokyo University of Marine Science and Technology, 1-5-7 Konan, Minato-ku, Tokyo 108-0075, Japan

ABSTRACTThis study examined the distribution of the number of nucleotide substitutions between all pairs ofindividuals within western North Pacific O and J stock common minke, Bryde’s, sei and right whales, toinvestigate whether the pattern of distribution is indicative of exponential population growth (inevolutionary terms), and thus of non-equilibrium. According to Slatkin and Hudson (1991), unimodalityof the frequency distribution is indicative of exponential population growth, and this pattern was found in
the O stock common minke and sei whales. In contrast multimode pattern in the frequency distribution
was found in the J stock common, Bryde’s and right whales, which is inconsistent with exponential
population expansion.
INTRODUCTION
The 2009 JARPNII review workshop noted that the genetic analyses conducted under JARPNII assumed
mutation-drift-migration equilibrium but that some evidences suggested exponentially expanding
population, and thus non-equilibrium (IWC, 2010). Consequently the workshop recommended that tests
for population genetic equilibrium should be undertaken. Furthermore it recommended that estimation ofdivergence between sample partitions should be undertaken using non-equilibrium approaches, andsuggested the IM approach by Hey and Nielsen (2004).
As a starting point to respond the workshop recommendation above, the distribution of pairwisedifferences among mtDNA control region sequences were estimated (Slatkin and Hudson, 1991) for
several western North Pacific baleen whale species. Previous analyses suggested that the mismatch
distributions in population samples from North Pacific O stock common minke whales were consistent
with exponential population expansion (and thus non-equilibrium) however the sample of J stock
common minke whale had multiple mismatch distributions, which was inconsistent with exponential
population expansion (Pastene et al., 2007).
In this study we used all the available sequences till 2014 to estimate the mismatch distributions insamples of western North Pacific O and J stocks common minke, sei, Bryde’s and right whales, toinvestigate whether the pattern of distribution is indicative of exponential population growth, and thus ofnon-equilibrium.
MATERIALS AND METHODS
Samples and DNA extraction
Samples and DNA extraction procedures used in this study for J and O stocks common minke, Bryde’s,
sei and North Pacific right whales were the same as in the studies in Pastene et al. (2016a: SC/F16/JR38,
2016b: SC/F16/JR40; 2016c: SC/F16/JR44, 2016d: SC/F16/JR46, 2016e: SC/F16/JR50).
mtDNA control region sequencing analysis
Sequencing procedures for J and O stocks common minke, Bryde’s, sei and North Pacific right whales
were the same as in the studies in Pastene et al. (2016a: SC/F16/JR38, 2016b: SC/F16/JR40; 2016c:

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SC/F16/JR44, 2016d: SC/F16/JR46, 2016e: SC/F16/JR50). The lengths of the mtDNA control region
segments used in those species were 487bp, 487bp, 299bp, 487bp and 275bp, respectively.
Mismatch distribution analysis
The distribution of the number of nucleotide substitutions between all pairs of individuals of common
minke (J and O stocks), Bryde’s, sei and right whales within the western North Pacific, was computedand compared to the Poisson distribution (Slatkin and Hudson, 1991) expected if the population had
undergone exponential growth. We used the computer program Arlequin ver. 3.01. A total of 10,000
simulations were made. The agreement of the observed distribution with the expected distribution wasevaluated using the chi-square test.
RESULTS AND DISCUSSION
Figure 1 shows the observed distribution of pairwise differences compared with the number of expecteddistributions assuming a Poisson distribution for O stock common minke (A), J stock common minke (B),
Bryde’s (C), sei (D) and right (E) whales. All observed distributions were significantly different than theexpected Poisson distribution. However, unimodality (as opposed to more than two modes) of thefrequency distribution is indicative of exponential population growth (Slatkin and Hudson, 1991). This
was the case of the O stock common minke and sei whales (Figures 1 A and D, respectively). It was not
the case of the J stock common minke, Bryde’s, and North Pacific right whales (Figures 1B, C and E).
In the case of the Bryde’s whale when total samples were used, there is a mode at zero and then a steadydecline, which is similar to what Excoffier (2004) shows for scenarios where there is a range expansion,
but more recent.
As noted earlier the 2009 JARPNII review workshop recommended that estimation of divergence
between sample partitions should be undertaken using non-equilibrium approaches, and suggested the IM
approach by Hey and Nielsen (2004). This could be the case for O stock common minke, sei and possibly
Bryde’s whales. The IM approach estimates the divergence time and the migrations having occurred in
the ancestry of two populations. It reports the posterior distributions of the ancestral population size, thedivergence time, the relative initial population sizes, the growth rates and potentially asymmetricalmigration rates between populations and the approach can use DNA sequence and microsatellite data. It
should be noted, however, that this and other similar approaches face real difficulties when genetic
differentiation among populations is low (Fst<0,01) (Gaggiotti, pers. communication).
ACKNOWLEDGEMENTS
We gratefully acknowledge the researchers and crew members that participated in JARPN/JARPNII,
IWC/POWER and Japanese dedicated sighting surveys for the collection of genetic samples. We thank H.
Oikawa and S. Azumi (ICR) who collaborated in the process of DNA extraction.
REFERENCES
Excoffier, L. 2004. Patterns of DNA sequence diversity and genetic structure after a range expansion:
lessons from the infinite-island model. Molecular Ecology 13: 853-864.
Hey, J. and Nielsen, R. 2004. Multilocus methods for estimating population sizes, migration rates anddivergence time, with applications to the divergence of Drosophila pseudoobscura and D.
persimilis. Genetics. 167:747-760.
International Whaling Commission. 2010. Report of the Expert Workshop to Review the Ongoing
JARPN II Programme. J. Cetacean Res. Manage. 11 (suppl. 2):405-449.
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.
Pastene, L.A., Goto, M., Taguchi, M. and Kitakado, 2016a. T. Temporal and spatial distribution of the ‘J’and ‘O’ stocks of common minke whale in waters around Japan based on microsatellite DNA. Paper

2SC/F16/JR38 presented to the JARPNII special permit expert panel review workshop, Tokyo,February 2016 (unpublished). 14pp.
Pastene, L.A., Goto, M., Taguchi, M. and Kitakado, T. 2016b. Updated genetic analyses based on
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 the JARPNII special permit
expert panel review workshop, Tokyo, February 2016 (unpublished). 19pp.
Pastene, L.A., Goto, M., Taguchi, M. and Kitakado, T. 2016c. Updated genetic analyses based on mtDNAand microsatellite DNA suggest possible stock differentiation of Bryde’s whales between management
sub-areas 1 and 2 in the North Pacific. Paper SC/F16/JR44 presented to the JARPNII special permit
expert panel review workshop, Tokyo, February 2016 (unpublished). 17pp.
Pastene, L.A., Goto, M., Taguchi, M. and Kitakado, T. 2016d. Genetic analyses based on mtDNA control
region sequencing and microsatellite DNA confirmed the occurrence of a single stock of sei whales inoceanic regions of the North Pacific. Paper SC/F16/JR46 presented to the JARPNII special permit
expert panel review workshop, Tokyo, February 2016 (unpublished). 10pp.
Pastene, L.A., Goto, M., Taguchi, M., Nishiwaki, S. and Kitakado, T. 2016e. A note on the genetic
diversity and phylogeny of western North Pacific and southern right whales based on mitochondrialand microsatellite DNA. Paper SC/F16/JR50 presented to the JARPNII special permit expert panel
review workshop, Tokyo, February 2016 (unpublished). 8pp.
Slatkin, M. and Hudson, R.R. 1991. Pairwise Comparisons of Mitochondrial DNA Sequences in Stable
and Exponentially Growing Population. Genetics. 129: 555-562.

3A)

B)

4C)

5D)

6E)

Figure1. Observed distributions of pairwise difference (blue line) compared with the number of expecteddistributions assuming a Poisson distribution (orange line) for each baleen whale species in the western
North Pacific. The x axis is the number of substitutions, the y axis, the frequencies of the pairwise. A= O
stock common minke whale; B= J stock common minke whale; C= Bryde’s whale; D= Sei whale; E=North Pacific right whale.

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