Genetic diversity of T. ichikawai
The genome-wide SNP heterozygosity of Tachysurus ichikawai (1.6 × 10–4/bp) estimated from the individual of the reference genome was considerably lower than its congeneric speciesT. fulvidraco (4.5 × 10–3/bp; Gong et al., 2018). Additionally, the heterozygosity of T. ichikawai was much lower than that of some critically endangered teleost species listed on the IUCN Red List, such as large yellow croaker (3.58 × 10–3/bp; Wu et al., 2014) or European eel (1.48–1.59 × 10–2/bp; Jansen et al., 2017). However, it remains uncertain whether the reduction in genetic diversity is a recent consequence of declining population size or has historical origins. Furthermore, approximately 54% of the SNPs determined in this study for a group of 20 individuals including F0 and F1 generations, were singletons. Singleton SNPs exhibit mutations in only one allele among all individuals examined, so they do not provide useful information for kinship inference. Thus, despite our acquisition of a substantial number of SNPs, we estimated that approximately half of them were uninformative loci for kinship analysis.
Despite the challenge posed by limited genetic diversity, frequent occurrence of singleton SNPs, and high level of inbreeding demonstrated by frequent HS and FS occurrence among F0s (Table S8-9), we successfully accomplished a kinship analysis by employing whole-genome resequencing. An alternative method incorporating reduced genome analysis, such as RAD-seq, would have yielded an insufficient quantity of SNPs to facilitate a comprehensive kinship analysis. Although it is imperative to carefully select suitable loci for kinship analysis, we deem the use of whole-genome resequencing for pedigree analysis in wild animals exhibiting low genetic diversity and inbreeding to be effective.