Abstract
Delimiting ichthyoplankton is fundamental work for monitoring the recruitment process and identifying the spawning and nursing grounds of fishes. Nevertheless, it is extremely difficult to identify the fish during the early stages at the species level based on morphological characters because of the paucity of diagnostic features. In this study, we investigated the fish larval community through large-scale ecosystemic sampling in South China Sea (SCS) during 2013 and 2017 using DNA barcodes. To maintain the morphologies of fish larvae, we preserved the larvae in formalin and developed a technique to recover their DNA. Among the 3,500 chosen larvae, we successfully extracted DNA from 2,787 larval samples and obtained 1,006 high-quality sequences. Blast searches showed that 408 larvae (i.e., 40.5%) could be unambiguously identified to species, 413 larvae (i.e., 41.1%) were ambiguously species delimitation, and 185 larvae (i.e., 18.4%) showed a low match similarity with target sequences. A total of 101 species were identified, among which 38 and 33 species corresponded to demersal and reef-associated species, whereas the remaining 30 species corresponded to benthopelagic, pelagic-oceanic, bathypelagic, and pelagic-neritic species. High-quality larval photographs of the 101 diagnosed species showed intact morphological characters and thus provided a reference for identifying fish species during the early stages based on morphological characters. Our study highlighted the possibility of recovering and amplifying DNA from formalin-fixed samples and provided new insight into the fish larval community in the SCS.
Highlights
Perennial and continuous anthropogenic impacts, for example, global warming, water extraction, species invasions, overfishing, and habitat degradation, have been documented to severely decrease fish diversity in both the sea and inland water bodies (Olden et al, 2007; Rahel et al, 2008)
Given that formalin fixation can lead to DNA corrosion and damage and hamper amplification of the target c oxidase I (COI) gene, especially in fragile larvae, we developed a formalin-based preservation and fixation technique for ocean fish larvae
Three criteria similar to those used in Hubert et al (2015) were adopted in our study: (i) sequences with greater than 99% similarity and exhibiting greater than 1% divergence between sequences and the nearest neighbor species were unambiguously tagged with that species name; (ii) if the genetic divergence was less than the 1% threshold, we considered identification to species uncertain; and (iii) sequences with matches less than 99% were deemed unidentified samples
Summary
Perennial and continuous anthropogenic impacts, for example, global warming, water extraction, species invasions, overfishing, and habitat degradation, have been documented to severely decrease fish diversity in both the sea and inland water bodies (Olden et al, 2007; Rahel et al, 2008). The early phase of fish without initiative migration potential, offer an ideal opportunity to obtain important information on reproductive biology, preferred reproduction sites and times, and population recruitment success rates (Bialetzki et al, 2005; Cao et al, 2007; Reynalte-Tataje et al, 2012). This information is comparatively important for ecological monitoring and developing management and conservation plans. A reliable and efficient approach that can identify fish larvae to species is urgently needed
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