Fig 1.
Sampling locations for eDNA collection and MOCNESS trawls.
eDNA sampling (closed circles) and MOCNESS trawls (green asterisks) were performed within the Southern California Current Ecosystem, mostly at designated CalCOFI stations (open circles). MOCNESS trawls were conducted at three stations representing distinct pelagic habitats. Three zones (numbered within each green square) are indicated where eDNA samples were collected in proximity to MOCNESS samples. Within these three zones, we compared animal assemblage diversity between sampling methods. Map includes bathymetry data from NOAA National Centers for Environmental Information [35] and coastline data from Natural Earth; all data are in the public domain.
Table 1.
Sampling location, depth, and volume for eDNA samples and MOCNESS trawls.
Table 2.
Summary of sampling characteristics for eDNA sequencing and MOCNESS trawls.
Fig 2.
Simplified phylogenetic tree of taxonomic groups detected by eDNA methods.
Groups identified using 12S are indicated in orange (Vertebrates: Phylum Chordata (1); Classes Actinopterygii (2), Mammalia (3), Aves (4), and Chondrichthyes (5); Hemichordates: Phylum Enteropneusta) and groups identified using COI are indicated in purple (Invertebrates: Phyla Ctenophora, Mollusca (6), Echinodermata (7), Cnidaria (9); Subphylum Crustacea (8); Classes Anthozoa (10), Scyphozoa (11), Hydrozoa (12), Polychaeta; Genus Membranipora). Branch lengths are not to scale.
Fig 3.
eDNA sampled a higher diversity of taxonomic groups than MOCNESS.
(a) Mean proportional occurrence (± SD) of taxonomic groups in co-located MOCNESS (n = 27 nets) and eDNA samples from 0–1,750 m for vertebrate (n = 211 12S samples) and invertebrate groups (n = 244 COI samples). Bar charts include taxonomic orders with mean proportional occurrences greater than 0.01. (b) Venn diagrams show a higher richness of taxonomic groups sampled by eDNA than MOCNESS for both primers, but a higher number of vertebrate species were detected by MOCNESS. Number pairs describe total and species-level taxonomic richness for each method (number of ASVs for eDNA and unique taxonomic assignments for MOCNESS, number of species). Taxonomic group type key: Fi = bony fish, Ch = cartilaginous fish, Ma = mammal, Bi = bird; Cn = cnidarian, Cr = crustacean, Mo = mollusc, Br = bryozoan, Wo = worm, Ec = echinoderm.
Fig 4.
Species were often represented by multiple ASVs, with large variations across taxonomic groups.
Bar plots display the mean number of ASVs per species within each taxonomic group, with error bars representing one standard deviation. Taxonomic group type key: Fi = bony fish, Ch = cartilaginous fish, Ma = mammal, Bi = bird, He = hemichordate, Cn = cnidarian, Cr = crustacean, Mo = mollusc, Br = bryozoan, Wo = worm, Ec = echinoderm.
Fig 5.
eDNA sample characteristics with respect to primer and sampling depth.
(a) The concentration of DNA per sample decreased with depth (n = 433). For samples with more than 1,000 reads, the number of reads per mL (b,e) and total ASVs per mL of seawater (c,f) were not meaningfully variable across depth bins. The proportion of ASVs assigned to species (d,g) decreased with depth for COI samples (n = 331), with 12S samples (n = 231) having higher proportions of species-level identifications than COI across depths. Statistical differences among depth bins (Games-Howell, p <0.05) are indicated by the number of asterisks. Results of global and post hoc tests describing the effects of depth bin on each eDNA metric are given in Table 3.
Table 3.
Summary of the effect of sampling depth on eDNA metrics.
Fig 6.
Hierarchical clustering of 12S samples reflects three spatially variable fish assemblages dominated by either coastal pelagic or mesopelagic migrator species.
(a) Clustering was performed on 126 12S samples collected at night and only included species present in at least three samples. (b) Up to 10 of the most frequently occurring species are displayed for each cohesive cluster (average silhouette width >0.1). (c) Fifty percent probability density contours (“50% density”) demonstrate that nearshore clusters had the highest occurrences coastal forage species, and intermediate to offshore clusters were generally dominated by mesopelagic migrator species for both deep and shallow samples. Silhouette plots and additional probability density contour maps are given for each cluster in S5 and S6 Figs in S1 File, respectively.
Fig 7.
Hierarchical clustering of COI samples reflects three spatially variable invertebrate assemblages dominated by copepod and cnidarian species.
(a) Clustering was performed on 120 COI samples collected at night and only included species present in at least three samples. (b) Up to 10 of the most frequently occurring species are displayed for each cohesive cluster (average silhouette width >0.1). (c) Fifty percent probability density contours (“50% density”) depict horizontal and vertical variability in the distribution of invertebrate assemblages. Silhouette plots and additional probability density contour maps are given for each cluster in S5 and S6 Figs in S1 File, respectively.