Population Structure of Todarodes pacificus (Cephalopoda: Ommastrephidae) in the Northwest Pacific: Insights from Integrated Genetic and Statolith Morphology Analyses
Abstract
1. Introduction
2. Materials and Methods
2.1. Population Sampling
2.2. Statolith Sample Collection and Processing
2.2.1. Analysis of Statolith Shape Sampling
2.2.2. Analysis of Statolith Age Identification
2.3. Methods of Population Genetics
3. Results
3.1. Genetic Analysis
3.2. Statolith Morphological Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A

| Gene | Mt/Nu | Primers | PCR Confition | Reference |
|---|---|---|---|---|
| COI | Mt | COI-F: 5′-CCTATCTCGGCAGCACTA-3′ | 95 °C 5 min, (95° C 10 s, 55 °C 20 s, 72 °C 30 s) × 35, 72 °C 5 min | [9] |
| COI-R: 5′-CCAATAAAATCGCTCTAATA-3′ | ||||
| 16S | Mt | 16S-F: 5′-GCCTCGCCTGTTTACCAAAAAC-3′ | [54] | |
| 16S-R: 5′-CGGTCTGAACTCAGATCACGT-3′ | ||||
| ODH | Nu | ODH-F: 5′-ATGAGGGTTACTTTAGAGCCA-3′ | [23] | |
| ODH-R: 5′-GCAGGTCTTCATTGCCATAC-3′ |
References
- Caddy, J.F.; Rodhouse, P.G. Cephalopod and groundfish landings: Evidence for ecological change in global fisheries? Rev. Fish Biol. Fish. 1998, 8, 431–444. [Google Scholar] [CrossRef]
- FAO. The state of world fisheries and aquaculture 2020. In The State of World Fisheries and Aquaculture (SOFIA); FAO: Rome, Italy, 2020; p. 244. [Google Scholar]
- Hohenegger, J. Species as the basic units in evolution and biodiversity: Recognition of species in the recent and geological past as exemplified by larger foraminifera. Gondwana Res. 2014, 25, 707–728. [Google Scholar] [CrossRef]
- Zheng, X.D.; Lv, Y.H.; Lu, C.C. Species diversity of cephalopods in the China seas. J. Ocean Univ. China 2023, 53, 1–18. [Google Scholar]
- Arkhipkin, A.I.; Hendrickson, L.C.; Payá, I.; Pierce, G.J.; Roa-Ureta, R.H.; Robin, J.; Winter, A. Stock assessment and management of cephalopods: Advances and challenges for short-lived fishery resources. ICES J. Mar. Sci. 2020, 78, 714–730. [Google Scholar] [CrossRef]
- Guo, J.Z.; Zhang, C.; Li, Z.X.; Liu, D.; Tian, Y.J. Latitudinal difference in the condition factor of two loliginidae squid (Beka squid and Indian squid) in China seas. Diversity 2023, 15, 812. [Google Scholar] [CrossRef]
- Bower, J.R.; Ichii, T. The red flying squid (Ommastrephes bartramii): A review of recent research and the fishery in Japan. Fish. Res. 2005, 76, 39–55. [Google Scholar] [CrossRef]
- Komai, T.; Kawabata, C.; Amano, M.; Lee, B.R.; Ichishima, E. Todarepsin, a new cathepsin D from hepatopancreas of Japanese common squid (Todarodes pacificus). Comp. Biochem. Physiol. Part B Biochem. Mol. Biol. 2004, 137, 373–382. [Google Scholar] [CrossRef]
- Zhang, Q.; Cao, Y.M.; Lu, H.J.; Liu, Y.; Zhang, Z.; Fang, Z.; Wang, C.C. Genetic variation and genetic structure analysis of Todarodes pacificus based on mitochondrial DNA markers. J. Shanghai Ocean Univ. 2021, 30, 763–769. [Google Scholar]
- Xu, M.; Liu, S.H.; Zhang, H.; Li, Z.G.; Song, X.J.; Yang, L.L.; Tang, B.J. Seasonal Analysis of Spatial Distribution Patterns and Characteristics of Sepiella maindroni and Sepia kobiensis in the East China Sea Region. Animals 2024, 14, 2716. [Google Scholar] [CrossRef] [PubMed]
- Sakurai, Y.; Kiyofuji, H.; Saitoh, S.; Goto, T.; Hiyama, Y. Changes in inferred spawning areas of Todarodes pacificus (Cephalopoda: Ommastrephidae) due to changing environmental conditions. ICES J. Mar. Sci. 2000, 57, 24–30. [Google Scholar] [CrossRef]
- Yang, L.L.; Jiang, Y.Z.; Zhang, H.; Yuan, X.W.; Liu, Z.L. Seasonal variations and environmental drivers of suitable habitats of Todarodes pacificus in southern Yellow Sea and East China Sea. Chin. J. Ecol. 2023, 42, 685–693. [Google Scholar]
- Arkhipkin, A.I.; Rodhouse, P.G.K.; Pierce, G.J.; Sauer, W.; Sakai, M.; Allcock, L.; Arguelles, J.; Bower, J.R.; Castillo, G.; Ceriola, L.; et al. World squid fisheries. Rev. Fish. Sci. Aquac. 2015, 23, 92–252. [Google Scholar] [CrossRef]
- Ching, T.Y.; Chen, C.S.; Yagishita, N.; Yamaguchi, A.; Wang, C.H.; Shen, K.N. Variations in life-history traits and statolith shape for Sepioteuthis spp. in the waters off southwestern Japan. Rev. Fish Biol. Fish. 2021, 87, 173–185. [Google Scholar] [CrossRef]
- Raj, N.; Sukumaran, S.; Jose, A.; Nisha, K.; Roul, S.K.; Rahangdale, S.; Kizhakudan, S.J.; Gopalakrishnan, A. Population genetic structure of Randall’s threadfin bream Nemipterus randalli in Indian waters based on mitochondrial and nuclear gene sequences. Sci. Rep. 2024, 14, 7556. [Google Scholar] [CrossRef] [PubMed]
- Xu, R.; Bo, Q.K.; Zheng, X.D. A divergent lineage among Octopus minor (Sasaki, 1920) populations in the northwest Pacific supported by DNA barcoding. Mar. Biol. Res. 2018, 14, 335–344. [Google Scholar] [CrossRef]
- Wang, X.R.; Lv, Y.H.; Zhang, C.; Zheng, X.D. Population genetic structure and phylogenetic relationships reveal cryptic biodiversity in the Uroteuthis (Photololigo) duvaucelii (Cephalopoda: Loliginidae) species complex. Hydrobiologia 2025, 852, 2957–2970. [Google Scholar] [CrossRef]
- Graybeal, A. Evaluating the Phylogenetic Utility of Genes: A Search for Genes Informative About Deep Divergences among Vertebrates. Syst. Biol. 1994, 43, 174–193. [Google Scholar] [CrossRef]
- Arkhipkin, A. Statoliths as ‘black boxes’ (life recorders) in squid. Mar. Freshw. Res. 2005, 56, 573–583. [Google Scholar] [CrossRef]
- Muhammad, F.; Lü, Z.M.; Liu, L.; Gong, L.; Du, X.; Muhammad, S.; Kaleri, H.A. Genetic structure of Octopus minor around Chinese waters as indicated by nuclear DNA variations (Mollusca, Cephalopoda). Zookeys 2018, 775, 1–14. [Google Scholar] [CrossRef]
- Strugnell, J.; Norman, M.; Jackson, J.; Drummond, A.J.; Cooper, A. Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework. Mol. Phylogenet. Evol. 2005, 37, 426–441. [Google Scholar] [CrossRef]
- Arkhipkin, A.I.; Bizikov, V.A. Role of the statolith in functioning of the acceleration receptor system in squids and sepioids. J. Zool. 2000, 250, 31–55. [Google Scholar] [CrossRef]
- Wang, X.R.; Zhang, C.; Zheng, X.D. Integrated genetic and statolith shape analysis reveals the population structure of Loliolus (nipponololigo) uyii (Cephalopoda: Loliginidae) in the coastal waters of China. Diversity 2024, 16, 674. [Google Scholar] [CrossRef]
- Han, P.W.; Wang, Y.; Fang, Z.; Liu, B.L.; Chen, X.J. Review on cephalopoda migration characteristics based on the microchemistry technology of hard tissues. J. Guangdong Ocean Univ. 2021, 41, 142–152. [Google Scholar]
- Markaida, U.; Quiñónez-Velázquez, C.; Sosa-Nishizaki, O. Age, growth and maturation of jumbo squid Dosidicus gigas (Cephalopoda: Ommastrephidae) from the gulf of California, Mexico. Fish. Res. 2004, 66, 31–47. [Google Scholar] [CrossRef]
- Moustahfid, H. Age and growth of arrow squid Todarodes sagittatus (Cephalopoda: Ommastrephidae) sampled in summer in Atlantic Moroccan waters. Bull. Mar. Sci. 2002, 71, 535–543. [Google Scholar]
- Natsukari, Y.; Nakanose, T.; Oda, K. Age and growth of loliginid squid Photololigo edulis (Hoyle, 1885). J. Exp. Mar. Biol. Ecol. 1988, 116, 177–190. [Google Scholar] [CrossRef]
- Takagi, K.; Kitahara, T. Bias in age estimation of Japanese common squid due to grinding degree of statoliths. Nippon Suisan Gakkaishi 2002, 68, 351–355. [Google Scholar] [CrossRef]
- Shi, Z.; Guo, R.Y.; Lu, H.J.; Sun, T.Z.; Zhao, M.L.; Zhang, B.Q. Growth characteristic of statolith of Todarodes pacificus in the East China Sea in the La Nina year. Chin. J. Appl. Ecol. 2024, 35, 1716–1724. [Google Scholar]
- Sakurai, Y.; Kiyofuji, H.; Saitoh, S.I.; Yamamoto, J.; Goto, T.; Mori, K.; Kinoshita, T. Stock fluctuations of the Japanese common squid, Todarodes pacificus, related to recent climate changes. Fish. Sci. 2002, 68, 226–229. [Google Scholar] [CrossRef] [PubMed]
- Yu, W.; Zhang, Y.; Chen, X.J.; Yi, Q.; Qian, W.G. Response of winter cohort abundance of Japanese common squid Todarodes pacificus to the ENSO events. Acta Oceanol. Sin. 2018, 37, 61–71. [Google Scholar] [CrossRef]
- Rosa, A.L.; Yamamoto, J.; Sakurai, Y. Effects of environmental variability on the spawning areas, catch, and recruitment of the Japanese common squid, Todarodes pacificus (Cephalopoda: Ommastrephidae), from the 1970s to the 2000s. ICES J. Mar. Sci. 2011, 68, 1114–1121. [Google Scholar] [CrossRef]
- Yu, W.; Feng, Z.P.; Chen, B.J.; Wei, Z.H.; Feng, Y.Y. Climate-related variations in autumn cohort of Japanese common squid Todarodes pacificus. J. Ocean Univ. China 2023, 22, 490–500. [Google Scholar] [CrossRef]
- Martinez-Porchas, M.; Villalpando-Canchola, E.; Ortiz Suarez, L.E.; Vargas, A.F. How conserved are the conserved 16S-rRNA regions? PeerJ 2017, 5, e3036. [Google Scholar] [CrossRef]
- Arai, N.; Ikeda, Y.; Kidokoro, H.; Sakamoto, W. Strontium:calcium ratios in statoliths of Japanese common squid Todarodes pacificus (Cephalopoda: Ommastrephidae) as indicators of migratory behavior. Mar. Ecol. Prog. Ser. 2003, 251, 169–179. [Google Scholar] [CrossRef]
- Kidokoro, H.; Goto, T.; Nagasawa, T.; Nishida, H.; Akamine, T.; Sakurai, Y. Impact of a climate regime shift on the migration of Japanese common squid (Todarodes pacificus) in the sea of Japan. ICES J. Mar. Sci. 2010, 67, 1314–1322. [Google Scholar] [CrossRef]
- Liu, Y.; Hu, X.; Lu, H.; Liu, Y.; Wang, C.; Dai, X. Population genetics of Todarodes pacificus (Cephalopoda: Ommastrephidae) in the northwest Pacific Ocean via GBS sequencing. Open Life Sci. 2024, 19, 20220876. [Google Scholar] [CrossRef] [PubMed]
- Dommergues, J.L.; Neige, P.; Boletzky, S.V. Exploration of morphospace using procrustes analysis in statoliths of cuttlefish and squid (Cephalopoda: Decabrachia)—Evolutionary aspects of form disparity. Velige 2000, 43, 265–276. [Google Scholar]
- Yamaguchi, T.; Matsui, H.; Miyahara, H.; Kubota, H.; Hirose, N. Quantitative relationship of Sr:Ca of statoliths of the Japanese flying squid (Todarodes pacificus) with empirical water temperatures. J. Mar. Biol. Assoc. U. K. 2025, 105, e14. [Google Scholar] [CrossRef]
- Libungan, L.A.; Palsson, S. ShapeR: An R package to study otolith shape variation among fish populations. PLoS ONE 2015, 10, e0121102. [Google Scholar] [CrossRef] [PubMed]
- Breiman, L.; Last, M.; Rice, J. Random forests: Finding quasars. In Statistical Challenges in Astronomy; Springer: New York, NY, USA, 2003; pp. 243–254. [Google Scholar]
- Winnepenninckx, B.; Backeljau, T.; De Wachter, R. Extraction of high molecular weight DNA from molluscs. Trends Genet. 1993, 9, 407. [Google Scholar] [CrossRef]
- Swindell, S.R.; Plasterer, T.N. Seqman. In Sequence Data Analysis Guidebook; Springer: New York, NY, USA, 2003; pp. 75–89. [Google Scholar]
- Tamura, K.; Stecher, G.; Kumar, S. MEGA11: Molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 2021, 38, 3022–3027. [Google Scholar] [CrossRef]
- Rozas, J.; Ferrer-Mata, A.; Sánchez-DelBarrio, J.C.; Guirao-Rico, S.; Librado, P.; Ramos-Onsins, S.E.; Sánchez-Gracia, A. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol. Biol. Evol. 2017, 34, 3299–3302. [Google Scholar] [CrossRef] [PubMed]
- Leigh, J.W.; Bryant, D. Popart: Full-feature software for haplotype network construction. Methods Ecol. Evol. 2015, 6, 1110–1116. [Google Scholar] [CrossRef]
- Lv, H.Y.; Wang, J.T.; Zhang, C. Stock assessment of the winter-born group of Todarodes pacificus based on sea surface temperature at spawning grounds. J. Shanghai Ocean Univ. 2022, 31, 650–657. [Google Scholar]
- Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989, 123, 585–595. [Google Scholar] [CrossRef]
- Fu, Y.X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 1997, 147, 915–925. [Google Scholar] [CrossRef]
- Excoffier, L.; Lischer, H.E. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under linux and windows. Mol. Ecol Resour. 2010, 10, 564–567. [Google Scholar] [CrossRef]
- Kalyaanamoorthy, S.; Minh, B.Q.; Wong, T.K.F.; von Haeseler, A.; Jermiin, L.S. ModelFinder: Fast model selection for accurate phylogenetic estimates. Gondwana Res. 2017, 14, 587–589. [Google Scholar] [CrossRef]
- Nguyen, L.T.; Schmidt, H.A.; von Haeseler, A.; Minh, B.Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 2015, 32, 268–274. [Google Scholar] [CrossRef]
- Ronquist, F.; Teslenko, M.; van der Mark, P.; Ayres, D.L.; Darling, A.; Höhna, S.; Larget, B.; Liu, L.; Suchard, M.A.; Huelsenbeck, J.P. MrBayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 2012, 61, 539–542. [Google Scholar] [CrossRef]
- Palumbi, S.; Martin, A.; Romano, S.; McMillan, W.O.; Stice, L.; Grabowski, G. The Simple Fool’s Guide to PCR; Department of Zoology Special Publication; University of Hawaii: Honolulu, HI, USA, 1991. [Google Scholar]





| Region | Number of Analyzed Individuals | Cohort Composition (Summer:Autumn) | Sampling Time | Mantle Length Range/mm | |
|---|---|---|---|---|---|
| Statolith samples | NYS | 48 | 48:0 | November 2019 | 162~204 |
| 26 | 26:0 | November 2023 | 235~305 | ||
| 68 | 68:0 | November 2024 | 160~320 | ||
| NECS | 51 | 0:51 | December 2024 | 150~317 | |
| 24 | 0:24 | March 2024 | 205~280 | ||
| 49 | 49:0 | November 2024 | 215~296 | ||
| SECS | 60 | 0:60 | March 2024 | 165~283 | |
| Genetic samples | NYS | 20 | 20:0 | November 2023 | 235~305 |
| 20 | 20:0 | November 2024 | 160~320 | ||
| 20 | 0:22 | December 2024 | 150~317 | ||
| NECS | 20 | 0:20 | March 2024 | 216~296 | |
| 20 | 20:0 | November 2024 | 215~296 | ||
| SECS | 20 | 0:20 | March 2024 | 165~284 |
| Mt/Nu | Gene | Length/bp | T/% | C/% | A/% | G/% | A + T/% | G + C/% | S | Proportion of Variable Sites/% |
|---|---|---|---|---|---|---|---|---|---|---|
| Mt | COI | 439 | 43.20 | 20.86 | 21.49 | 15.36 | 63.79 | 36.22 | 15 | 3.36 |
| Mt | 16S | 458 | 26.58 | 0.00 | 48.42 | 25.00 | 75.00 | 25.00 | 4 | 0.88 |
| Nu | ODH | 517 | 28.13 | 31.30 | 26.63 | 13.93 | 54.76 | 45.23 | 106 | 20.58 |
| Group | COI | 16S | ODH | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| N | Hap | Hd | π | N | Hap | Hd | π | N | Hap | Hd | π | |
| summer | 59 | 9 | 0.4610 | 0.0014 | 55 | 3 | 0.2300 | 0.0005 | 57 | 12 | 0.6020 | 0.0020 |
| autumn | 58 | 11 | 0.4740 | 0.0013 | 55 | 4 | 0.1090 | 0.0002 | 56 | 13 | 0.6070 | 0.0059 |
| total | 117 | 18 | 0.4650 | 0.0013 | 110 | 6 | 0.1710 | 0.0004 | 113 | 21 | 0.6010 | 0.0053 |
| Gene | Source of Variation | df | Sum of Squares | Variance Component | Percentage of Variation (%) | F Statistic |
|---|---|---|---|---|---|---|
| COI | Among populations | 2 | 0.463 | −0.00280 Va | −0.85 | FST: −0.00853 (p-value = 0.83187 ± 0.01114) |
| Within populations | 114 | 37.811 | 0.33167 Vb | 100.85 | ||
| Total | 116 | 38.274 | 0.32887 | 100.00 | ||
| 16S | Among populations | 2 | 0.203 | −0.00066 Va | −0.54 | FST: −0.00537 (p-value = 0.57478 ± 0.01351) |
| Within populations | 107 | 13.251 | 0.12385 Vb | 100.54 | ||
| Total | 109 | 13.455 | 0.12385 Vb | 100.00 | ||
| ODH | Among populations | 2 | 1.133 | 0.00080 Va | 0.15 | FST: 0.00148 (p-value = 0.37634 ± 0.01613) |
| Within populations | 111 | 59.815 | 0.53887 Vb | 99.85 | ||
| Total | 113 | 60.947 | 0.53967 | 100.00 |
| Groups | Autumn | Summer | |
|---|---|---|---|
| COI | autumn | 0.00000 | |
| summer | 0.00291 | 0.00000 | |
| 16S | autumn | 0.00000 | |
| summer | 0.03191 | 0.00000 | |
| ODH | autumn | 0.00000 | |
| summer | 0.00075 | 0.00000 | |
| Season | Autumn | Summer | Classification Success Rate (%) |
|---|---|---|---|
| autumn | 119 | 21 | 85.00 |
| summer | 10 | 182 | 94.79 |
| Groups | p | Sw/Sl | Ssa |
|---|---|---|---|
| autumn | 0.5710 | 1763.0060 | |
| summer | 0.5483 | 1706.8217 | |
| summer vs. autumn | 1.351 × 10−10 * | 5.342 × 10−6 * | 0.09057 |
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Liu, X.; Zhang, C.; Phuynoi, S.; Li, J.; Zheng, X. Population Structure of Todarodes pacificus (Cephalopoda: Ommastrephidae) in the Northwest Pacific: Insights from Integrated Genetic and Statolith Morphology Analyses. Diversity 2026, 18, 123. https://doi.org/10.3390/d18020123
Liu X, Zhang C, Phuynoi S, Li J, Zheng X. Population Structure of Todarodes pacificus (Cephalopoda: Ommastrephidae) in the Northwest Pacific: Insights from Integrated Genetic and Statolith Morphology Analyses. Diversity. 2026; 18(2):123. https://doi.org/10.3390/d18020123
Chicago/Turabian StyleLiu, Xiaoyun, Chi Zhang, Sonthaya Phuynoi, Jing Li, and Xiaodong Zheng. 2026. "Population Structure of Todarodes pacificus (Cephalopoda: Ommastrephidae) in the Northwest Pacific: Insights from Integrated Genetic and Statolith Morphology Analyses" Diversity 18, no. 2: 123. https://doi.org/10.3390/d18020123
APA StyleLiu, X., Zhang, C., Phuynoi, S., Li, J., & Zheng, X. (2026). Population Structure of Todarodes pacificus (Cephalopoda: Ommastrephidae) in the Northwest Pacific: Insights from Integrated Genetic and Statolith Morphology Analyses. Diversity, 18(2), 123. https://doi.org/10.3390/d18020123

