Genomics Detects Japanese and Pacific Sardine (Sardinops spp.) Hybrids in the Northeast Pacific Ocean.

Abstract

Sardine (Sardinops spp.) are ecologically important forage fishes distributed globally across temperate, coastal upwelling zones and, when abundant, they support major fisheries. Previous genomic analyses of Pacific Sardine (S. sagax) in the Northeast Pacific detected the presence of Japanese Sardine (S. melanosticta), a species typically found in the Northwest Pacific, along the west coast of North America starting in 2022 over multiple years. To facilitate continued monitoring, we developed a highly accurate species identification Genotyping-in-Thousands-by-sequencing (GT-seq) panel consisting of 88 single nucleotide polymorphisms (SNPs). This panel was constructed by utilizing low-coverage, whole-genome sequence data to identify highly divergent, genome-wide loci between Pacific and Japanese Sardine, enabling unambiguous identification of these morphologically indistinguishable species as well as the detection of hybrids. Using the novel panel, we genotyped 1821 sardine samples from the Northeast Pacific and identified 35 hybrid individuals, which were collected from 2023 to 2025 and are the first known observation of such hybrids. Most were F1 hybrids (33); however, two individuals collected in 2025 appeared to be backcrosses with S. sagax. Our newly developed panel is a powerful resource for the continued monitoring of Japanese Sardine in the Eastern Pacific and is critical for investigating the potential fitness consequences of hybridization with Pacific Sardine.