Evaluation of genetic diversity in an endangered fish Gnathopogon caerulescens using environmental DNA and its potential use in fish conservation

Abstract

AbstractGnathopogon caerulescens, an endemic fish of Lake Biwa, Japan, is one of the most important fishes for lake fisheries. It has been listed as an endangered species following its population decline in the 1990s and thus needs conservation. An increasing number of studies have recently stressed on the importance of incorporating genetic diversity for conservation purposes. In this study, we aimed to evaluate the mitochondrial DNA haplotype composition of G. caerulescens using environmental DNA (eDNA) to determine the genetic diversity of this species. We developed an eDNA‐based haplotyping approach using high‐throughput sequencing (HTS), which can accurately detect and eliminate erroneous HTS reads, even when the target sequences are differentiated by a single or a few mismatches. Field surveys using the developed method successfully revealed the genetic structure of local G. caerulescens populations. We found star‐shaped haplotype networks with two major haplotypes accompanied by several rare haplotypes for all local populations except one, which suggested that the G. caerulescens population had undergone a historical expansion, and its population size did not shrink to the extent that rare haplotypes were eliminated during the population decline in the 1990s. We also observed that the genetic diversity was lower in the northern populations in terms of haplotype number and haplotype diversity (h), suggesting that the decline in population was more severe in the north than in the south. We demonstrated the practical use of eDNA analysis in population genetics of endangered species. Continuous monitoring using this approach would facilitate the conservation and management of fish resources.