Genetic evidence for panmixia of Japanese eel (Anguilla japonica) populations in China

Mitochondrial DNA and Microsatellite Analyses Showed Panmixia between Temporal Samples in Endangered Anguilla japonica in the Pearl River Basin (China)

The Japanese eel (Anguilla japonica) is a commercially important species in East Asia, the abundance of which has rapidly decreased in recent decades. The fishery resource in the Pearl River basin has mainly deteriorated due to overexploitation and habitat degradation. Knowledge on its genetic status is indispensable for resource management. In this study, we explored the temporal genetic structure of A. japonica on the basis of the concatenated sequences of two mitochondrial fragments (mtDNA) and eight microsatellite markers. A total of nine temporal samples (N = 127) were collected during 2019 and 2021 from Jiangmen City, China, which is located in the Pearl River estuary. mtDNA sequence analysis showed a high level of haplotype diversity, and yielded 124 haplotypes with ranging from 9 to 19 in temporal samples. All microsatellite loci were polymorphic among each of the nine temporal samples, with 150 alleles identified across all samples. Pairwise F_ST values were low and nonsignificant according to both mtDNA and microsatellite markers. STRUCTURE analysis showed that all temporal samples were not clearly differentiated from each other. The yielded outcomes supported a panmictic pattern in different temporal A. japonica samples. Therefore, our results call for the management of A. japonica as a single unit and joint conservation strategy of the species, since overexploitation in any region will decrease its global resource.

Whole-Genome Sequencing of 84 Japanese Eels Reveals Evidence against Panmixia and Support for Sympatric Speciation

The Japanese eel (Anguilla japonica), European eel (Anguilla anguilla), and American eel (Anguilla rostrata) are migratory, catadromous, temperate zone fish sharing several common life cycle features. The population genetics of panmixia in these eel species has already been investigated. Our extensive population genetics analysis was based on 1400 Gb of whole-genome sequence (WGS) data from 84 eels. It demonstrated that a Japanese eel group from the Kuma River differed from other populations of the same species. Even after removing the potential adapted/selected single nucleotide polymorphism (SNP) data, and with very small differences (fixation index [Fst] = 0.01), we obtained results consistently indicating that panmixia does not occur in Japanese eels. The life cycle of the Japanese eel is well-established and the Kuma River is in the center of its habitat. Nevertheless, simple reproductive isolation is not the probable cause of non-panmixia in this species. We propose that the combination of spawning area subdivision, philopatry, and habitat preference/avoidance accounts for the non-panmixia in the Japanese eel population. We named this hypothesis the “reproductive isolation like subset mapping” (RISM) model. This finding may be indicative of the initial stages of sympatric speciation in these eels.

Draft genome of the American Eel (Anguilla rostrata)

Freshwater eels (Anguilla sp.) have large economic, cultural, ecological and aesthetic importance worldwide, but they suffered more than 90% decline in global stocks over the past few decades. Proper genetic resources, such as sequenced, assembled and annotated genomes, are essential to help plan sustainable recoveries by identifying physiological, biochemical and genetic mechanisms that caused the declines or that may lead to recoveries. Here, we present the first sequenced genome of the American eel. This genome contained 305 043 contigs (N50 = 7397) and 79 209 scaffolds (N50 = 86 641) for a total size of 1.41 Gb, which is in the middle of the range of previous estimations for this species. In addition, protein-coding regions, including introns and flanking regions, are very well represented in the genome, as 95.2% of the 458 core eukaryotic genes and 98.8% of the 248 ultra-conserved subset were represented in the assembly and a total of 26 564 genes were annotated for future functional genomics studies. We performed a candidate gene analysis to compare three genes among all three freshwater eel species and, congruent with the phylogenetic relationships, Japanese eel (A. japanica) exhibited the most divergence. Overall, the sequenced genome presented in this study is a crucial addition to the presently available genetic tools to help guide future conservation efforts of freshwater eels.