Data from: Leveraging eDNA metabarcoding to characterize nearshore fish communities in Southeast Alaska: Do habitat and tide matter?

Nearshore marine habitats are critical for a variety of commercially
important fish species, but assessing fish communities in these habitats
is costly and time-intensive. Here, we leverage eDNA metabarcoding to
characterize nearshore fish communities near Juneau, Alaska, USA, a
high-latitude environment with large tidal swings, strong currents, and
significant freshwater input. We investigated whether species richness and
community composition differed across three habitat types (sand beaches,
eelgrass beds, and rocky shorelines) and between high and low tides.
Additionally, we tested whether replication of field samples and PCR
reactions influenced either species richness or composition. We amplified
a 12S mitochondrial locus in our samples and identified 167 fish amplicon
sequence variants (ASVs), which were grouped into 24 unique taxa based on
sequence similarity, with approximately half of these taxa resolved to
single species. Species richness and composition inferred from eDNA
differed substantially among habitats, with rock habitats containing fewer
taxa and fewer overall detections than sand and eelgrass habitats. The
effect of tide was not significant on its own, but a significant
habitat-tide interaction was documented, with the most pronounced
differences in taxa between tides found in sand habitats. Power analyses
indicated that additional field sampling is useful to detect small changes
in species richness such as those due to tide. PCR replicates typically
identified few additional taxa. Our results provide important information
that can be used to guide future studies, most notably, that the influence
of tide on eDNA results appears to be minimal and potentially isolated to
certain habitats. This suggests that replication across tides may not be
vital for future eDNA studies, and that additional replication across
space – particularly across heterogeneous environments – likely is a
better allocation of sampling effort.