Genomic inbreeding and population structure of northern pike (Esox lucius) in Xinjiang, China

• Published in: Ecology and evolution Vol. 11; no. 10; pp. 5657 - 5668
• Main Authors: Luan, Peixian, Huo, Tangbin, Ma, Bo, Song, Dan, Zhang, Xiaofeng, Hu, Guo
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01.05.2021; John Wiley and Sons Inc; Wiley
• Subjects: coancestry coefficient; Commercial fishing; effective population size; Esox Lucius; Fish; Fisheries; Fishing; Gene flow; Genetic diversity; Genomes; Genomics; identity by descent; Inbreeding; Laboratory animals; Lakes; Northern Hemisphere; Original Research; Parameter estimation; Population; Population number; Population statistics; Population structure; River basins; Rivers; Tien Shan Mountains; China; Xinjiang Uighur Autonomous Region China; gene flow; effective population size; Inbreeding; Esox Lucius; identity by descent; coancestry coefficient
• ISSN: 2045-7758; 2045-7758
• DOI: 10.1002/ece3.7469

Northern pike (Esox lucius) was widely distributed in the high latitudes of the northern hemisphere. In China, northern pike was originally distributed only in the upper reaches of the Irtysh River in Xinjiang and has appeared in many water bodies outside the Irtysh River Basin in Northern Xinjiang. A total of four populations were collected from north to south in Xinjiang, including Irtysh River (RIR), Ulungu Lake (LUL), a small lake nearby Ulungu River (LJD), and Bosten Lake (LBO). We estimated population genomic parameters, performed gene flow analysis, and estimated the effective population size of each population. The proportion of individuals with high inbreeding coefficient (F ≥ 0.0625) accounted for 36.4% (44/121) of all sequenced individuals, approximately 4.5% (1/22) in LUL, 25.9% (7/27) in LBO, 42.9% (18/42) in RIR, and 60% (18/30) in LJD. RIR had the highest mean of genomic relatedness (coancestry coefficient = 0.025 ± 0.040, IBD = 0.036 ± 0.078). Gene flow results showed that the population spreading was from RIR into two branches, one was LBO, and the other continued to split into LUL and LJD, and migration signal from LBO to LUL was detected. Our results suggested that the extinction risk of northern pike was very low in Xinjiang of China, and the controlled capture fishery of northern pike could be developed reasonably. Genomic pairwise relatedness of individual pairs within or between populations from the four sampling populations can be identified by coancestry coefficient and IBD, and validated by the consistency of the two parameters. Heat maps for estimates of the genomic pairwise coancestry coefficient and IBD analyses are shown in Figure 4 (coancestry coefficient in Figure 4a, IBD in Figure 4b). Individual pairs within RIR population had the highest mean (p < .05) of genomic relatedness (coancestry coefficient = 0.025 ± 0.040, IBD = 0.036 ± 0.078), and individual pairs within LUL and LJD populations had relatively distant genomic relatedness (p < .05).