Genetic architecture of long-distance migration and population genomics of the endangered Japanese eel

Yan-Fang Liu; Yu-Long Li; Teng-Fei Xing; Dong-Xiu Xue; Jin-Xian Liu

doi:10.1016/j.isci.2024.110563

Genetic architecture of long-distance migration and population genomics of the endangered Japanese eel

iScience. 2024 Jul 22;27(8):110563. doi: 10.1016/j.isci.2024.110563. eCollection 2024 Aug 16.

Authors

Yan-Fang Liu^{1

2

3}, Yu-Long Li^{1

2}, Teng-Fei Xing^{1

2}, Dong-Xiu Xue^{1

2}, Jin-Xian Liu^{1

2}

Affiliations

¹ CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
² Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China.
³ University of Chinese Academy of Sciences, Beijing 100049, China.

Abstract

The Japanese eel (Anguilla japonica), a flagship anguillid species for conservation, is known for its long-distance-oriented migration. However, our understanding of the genetic architecture underlying long-distance migration and population genomic characteristics of A. japonica is still limited. Here, we generated a high-quality chromosome-level genome assembly and conducted whole-genome resequencing of 218 individuals to explore these aspects. Strong signals of selection were found on genes involved in long-distance aerobic exercise and navigation, which might be associated with evolutionary adaptation to long-distance migrations. Low genetic diversity was detected, which might result from genetic drift associated with demographic declines. Both mitochondrial and nuclear genomic datasets supported the existence of a single panmictic population for Japanese eel, despite signals of single-generation selection. Candidate genes for local selection involved in functions like development and circadian rhythm. The findings can provide insights to adaptative evolution to long-distance migration and inform conservation efforts for A. japonica.

Keywords: Ecology; Evolutionary biology; Genetics; Molecular biology; Nature conservation.