Marine animals possess genomes of considerable complexity and heterozygosity. Their unique reproductive system, characterized by high fecundity and substantial early mortality rates, increases the risk of inbreeding, potentially leading to severe inbreeding depression during various larval developmental stages. In this study, we established a set of inbred families of Fenneropenaeus chinensis, with an inbreeding coefficient of 0.25, and investigated elimination patterns and the manifestations of inbreeding depression during major larval developmental stages. Reduced-representation genome sequencing was utilized to explore the genotype frequency characteristics across two typical elimination stages. The results revealed notable mortality in hatching and metamorphosis into mysis and post-larvae stages. Inbreeding depression was also evident during these developmental stages, with depression rates of 24.36%, 29.23%, and 45.28%. Segregation analysis of SNPs indicated an important role of gametic selection before hatching, accounting for 45.95% of deviation in the zoea stage. During the zygotic selection phase of larval development, homozygote deficiency and heterozygote excess were the main selection types. Summation of the two types explained 82.31% and 89.91% of zygotic selection in the mysis and post-larvae stage, respectively. The overall distortion ratio decreased from 22.37% to 12.86% in the late developmental stage. A total of 783 loci were identified through selective sweep analysis. We also found the types of distortion at the same locus could change after the post-larvae stage. The predominant shifts included a transition of gametic selection toward normal segregation and other forms of distortion to heterozygous excess. This may be attributed to high-intensity selection on deleterious alleles and genetic hitchhiking effects. Following larval elimination, a greater proportion of heterozygous individuals were preserved. We detected an increase in genetic diversity parameters such as expected heterozygosity, observed heterozygosity, and polymorphic information content in the post-larvae stage. These findings suggest the presence of numerous recessive deleterious alleles and their linkage and suggest a major role of the partial dominance hypothesis. The results provide valuable insights into the mechanisms of inbreeding depression in marine animals and offer guidance for formulating breeding strategies in shrimp populations.

The Indian Ocean is globally significant in terms of capture fisheries, and understanding the species composition of fish in the Indian Ocean is of great importance for the protection and development of its fishery resources. While coastal fish communities in the Indian Ocean are relatively well-documented, studies on pelagic zones remain sparse, especially for non-target species constituting fishery bycatch. Traditional biodiversity surveys rely on labor-intensive, inefficient trawling methods. To address these limitations, this study aims to apply environmental DNA (eDNA) metabarcoding for a species diversity survey in the Western Indian Ocean, offering a more reliable, efficient, and non-invasive alternative to traditional methods. The results will provide important insights into the region’s fish biodiversity, supporting sustainable management and conservation of fisheries resources in the area. Samples were collected from 130 stations in different water layers in the Western Indian Ocean, and species diversity was analyzed through 12S rRNA gene amplicon sequencing. The results showed that 98 fish species were detected from 176 seawater eDNA samples, belonging to two classes (Actinopteri and Chondrichthyes), 20 orders, 35 families, and 60 genera. Within a depth range of 300 m, there were no significant differences in species diversity parameters among samples from different depths. The orders with the highest relative abundance detected include Scombriformes, Aulopiformes, and Myctophiformes. The species with the highest relative abundance include Thunnus albacares, Alepisaurus ferox, Xiphias gladius, Diaphus fragilis, Decapterus macarellus, Thunnus maccoyii, and Platycephalus cultellatus. The species composition and relative abundance of economic species observed in this study showed, as expected, differences from fishery catch statistics. These results suggest that eDNA technology can not only monitor marine fish diversity more efficiently but also complement the lack of fisheries data. Integrating eDNA technology into routine monitoring in the Western Indian Ocean in the future could promote sustainable management of fisheries resources in the region.