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Inferring the Demographic History of Japanese Eel (Anguilla japonica) from Genomic Data: Insights for Conservation and Fisheries Management

Leanne Faulks, Prashant Kaushik, Shoji Taniguchi, Masashi Sekino, Reiichiro Nakamichi, Yuki Yamamoto, Hiroka Fujimori, Chiaki Okamoto, Sakie Kodama, Ayu Daryani, Angel Faye Manwong, Ishmerai Galang, Noritaka Mochioka, Kiyo Araki, Motoo Suzuki, Yoshitsugu Kaji, Takumi Ichiki, Tetsuya Matsunaga, Hiroshi Hakoyama
doi: https://doi.org/10.1101/2021.11.18.468312
Leanne Faulks
1Nagano University, Ueda, Japan
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Prashant Kaushik
1Nagano University, Ueda, Japan
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Shoji Taniguchi
1Nagano University, Ueda, Japan
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Masashi Sekino
2National Research Institute of Fisheries Science, Fisheries Research and Education Agency, Yokohama, Japan
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Reiichiro Nakamichi
2National Research Institute of Fisheries Science, Fisheries Research and Education Agency, Yokohama, Japan
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Yuki Yamamoto
2National Research Institute of Fisheries Science, Fisheries Research and Education Agency, Yokohama, Japan
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Hiroka Fujimori
1Nagano University, Ueda, Japan
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Chiaki Okamoto
1Nagano University, Ueda, Japan
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Sakie Kodama
1Nagano University, Ueda, Japan
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Ayu Daryani
1Nagano University, Ueda, Japan
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Angel Faye Manwong
1Nagano University, Ueda, Japan
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Ishmerai Galang
1Nagano University, Ueda, Japan
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Noritaka Mochioka
3Bioresource Sciences, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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Kiyo Araki
4Kumamoto Prefectural Fisheries Research Center, Kamiamakusa, Japan
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Motoo Suzuki
5Shizuoka Prefectural Research Institute of Fishery Hamanako Branch, Hamamatsu, Japan
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Yoshitsugu Kaji
6Wakayama Prefectural Museum of Natural History, Kainan, Japan
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Takumi Ichiki
7Kagoshima Fisheries Technology Development Center
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Tetsuya Matsunaga
8Miyazaki Prefectural Inland Fishery Promotion Center
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Hiroshi Hakoyama
1Nagano University, Ueda, Japan
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  • For correspondence: hiroshi-hakoyama@nagano.ac.jp
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Abstract

  1. Assessing the status or population size of species is a key task for wildlife conservation and the sustainable management of harvested species. In particular, assessing historical changes in population size provides an evolutionary perspective on current population dynamics and can help distinguish between anthropogenic and natural causes for population decline.

  2. Japanese eel (Anguilla japonica) is an endangered yet commercially important catadromous fish species. Here we assess the demographic history of Japanese eel using the pairwise and multiple sequentially Markovian coalescent methods.

  3. The analyses indicate a reduction in effective population size (Ne) from 38 000 to 10 000 individuals between 4 and 1 Ma, followed by an increase to 80 000 individuals, between 1 Ma and 22−30 kya. Approximately 22−30 kya there is evidence for a reduction in Ne to approximately 60 000 individuals. These events are likely due to changes in environmental conditions, such as sea level and oceanic currents, especially around the last glacial maximum (19−33 kya).

  4. The results of this study suggest that Japanese eel has experienced at least two population bottlenecks, interspersed by a period of population growth. This pattern of demographic history may make Japanese eel sensitive to current and future population declines. Conservation management of Japanese eel should focus on practical ways to prevent further population decline and the loss of genetic diversity that is essential for the species to adapt to changing environmental conditions such as climate change.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted November 22, 2021.
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Inferring the Demographic History of Japanese Eel (Anguilla japonica) from Genomic Data: Insights for Conservation and Fisheries Management
Leanne Faulks, Prashant Kaushik, Shoji Taniguchi, Masashi Sekino, Reiichiro Nakamichi, Yuki Yamamoto, Hiroka Fujimori, Chiaki Okamoto, Sakie Kodama, Ayu Daryani, Angel Faye Manwong, Ishmerai Galang, Noritaka Mochioka, Kiyo Araki, Motoo Suzuki, Yoshitsugu Kaji, Takumi Ichiki, Tetsuya Matsunaga, Hiroshi Hakoyama
bioRxiv 2021.11.18.468312; doi: https://doi.org/10.1101/2021.11.18.468312
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Inferring the Demographic History of Japanese Eel (Anguilla japonica) from Genomic Data: Insights for Conservation and Fisheries Management
Leanne Faulks, Prashant Kaushik, Shoji Taniguchi, Masashi Sekino, Reiichiro Nakamichi, Yuki Yamamoto, Hiroka Fujimori, Chiaki Okamoto, Sakie Kodama, Ayu Daryani, Angel Faye Manwong, Ishmerai Galang, Noritaka Mochioka, Kiyo Araki, Motoo Suzuki, Yoshitsugu Kaji, Takumi Ichiki, Tetsuya Matsunaga, Hiroshi Hakoyama
bioRxiv 2021.11.18.468312; doi: https://doi.org/10.1101/2021.11.18.468312

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