Joint monitoring of species' richness and genetics diversity in fish communities using long-reads metabarcoding

Understanding how fluctuations in marine fish population abundances affect the levels of genetic diversity is key in current times when abrupt environmental changes are expected at sea, owing to climate change. Loss of genetic diversity could lead to a loss of adaptive potential to environmental changes threatening species populations to extinction, especially in exploited fish, where synergies between harvest and environmental changes are still unclear. Here, we performed a small experiment using a mock fish community from an ichthyoplankton sample to test the potential of long-reads metabarcoding for monitoring changes in the genetic diversity of fish communities. The ichthyoplankton sample contained 17 fish species with different abundances of individuals. The results indicate that PacBio SMRT long reads metabarcoding could identify all species with abundance higher than 5% according to the visual taxonomic assignation in the meta-sample. Long-reads hybrids correction (Salmela & Rivals, 2014) and the SWARM (Mahé et al. 2022) algorithm for clustering Amplicon Sequence Variants (ASVs) were used to produce non-sample-size-frequency-based genetic diversity estimates for the three unambiguously assigned species with abundances higher than six individuals. This statistic is calculated as the ratio of the number of detected polymorphic mutations (i.e., number of segregating sites, S) to the number of detected haplotypes (H), i.e., S/H, as a first approach to monitoring changes in the genetic diversity of wild fish populations. These genetic diversity estimates correlated at more than 90% with frequency-based estimates (i.e. nucleotide diversity) obtained by analysing the reference Sanger sequences of the same individuals. The method implies that haplotypic diversity of the monitored species populations should be known, and that these species are unambiguously taxonomically assigned by using the COI barcode (i.e. 640bp). In summary, the results indicated the potential of PacBio long-read metabarcoding for monitoring fish community health. Keywords: PacBio, fisheries, adaptive potential, population genetics, biodiversity monitoring. Files: lordec_filteredbylength.fasta: fasta file containing corrected PacBIO Long-read sequences. Hygophum_hygomii_sanger_align.fasta, Lampanyctus_ater_sanger_align.fasta, Paralepis_coregonoides_sanger_align.fasta: fasta files containing Sanger sequences (i.e. real haplotypes) of the three species unambiguously assigned, and with more than five individuals in the ichthyoplankton metasample.