2.1 Sample collection and whole-genome sequencing
In the invasive range, a total of 62 C. auratus juveniles with an average weight of 2.9 g were collected in 2019 from the Lala (LL) and Chabalang (CBL) wetlands within the Yarlung Zangbo River basin in Tibet (Table 1). In the native range, 73 C. auratus adults were collected in 2015-2021 from 11 sites belonging to five river systems, including the Yangtze River (SC, Sichuan; SS, Shishou; ZDL, Zhangdu lake; CL, Chao lake; TH, Tai lake), Yellow River (NX, Ningxia), Huai River (RR, Ru River; HZL, Hongze lake), Songhua River (DQ, Daqing; JPL, Jingpo lake) and Pearl River (WR, You River). As the Ningxia and Sichuan regions assumed to be the sources of goldfish introduced into Tibet, samples were collected from these two regions across a wide geographical range; the coordinate of each sample can be found in Table S1. Here populations and individuals sampled from invasive and native ranges are denoted “invasive” and “native” populations and individuals, respectively. A small piece of fin tissue was sampled from each fish individual and stored in absolute ethanol until DNA extraction.
Genomic DNA was extracted from fin clips using a phenol-chloroform method (Taggart et al., 1992). At least 0.5 μg of genomic DNA from each sample was used to construct the resequencing library with an insert size of ~350 bp using the NEBNext Ultra DNA Library Prep Kit for 150 bp paired-end sequencing on the Illumina X Ten platform (Illumina USA). Sequencing was outsourced to Biomarker Technologies Corporation (Beijing, China). In addition, resequencing data of 16 individuals from the native range were downloaded from a previous study (Chen et al., 2020). A total of 151 goldfish genomes were included in this study. Additional information of each sample is shown in Table S1.