DOI: 10.5061/dryad.98sf7m0dm
title: Assessment of fish communities using eDNA: effect of spatial sampling design in lentic systems of different sizes

description: Freshwater fish biodiversity is quickly decreasing and requires effective
 monitoring and conservation. Environmental DNA (eDNA)-based methods have
 been shown to be highly sensitive and cost-efficient for aquatic
 biodiversity surveys, but few studies have systematically investigated how
 spatial sampling design affects eDNA-detected fish communities across
 lentic systems of different sizes. We compared the spatial patterns of
 fish diversity determined using eDNA in three lakes of small (SL; 3 ha),
 medium (ML; 122 ha) and large (LL; 4,343 ha) size using a spatially
 explicit grid sampling method. A total of 100 water samples (including 9,
 17, and 18 shoreline samples and 6, 14, and 36 interior samples from SL,
 ML, and LL, respectively) were collected, and fish communities were
 analyzed using eDNA metabarcoding of the mitochondrial 12S region.
 Together, 30, 35, and 41 fish taxa were detected in samples from SL, ML,
 and LL, respectively. We observed that eDNA from shoreline samples
 effectively captured the majority of the fish diversity of entire
 waterbodies, and pooled samples recovered fewer species than individually
 processed samples. Significant spatial autocorrelations between fish
 communities within 250 m and 2 km of each other were detected in ML and
 LL, respectively. Additionally, the relative sequence abundances of many
 fish species exhibited spatial distribution patterns that correlated with
 their typical habitat occupation. Overall, our results support the
 validity of a shoreline sampling strategy for eDNA-based fish community
 surveys in lentic systems but also suggest that a spatially comprehensive
 sampling design can reveal finer distribution patterns of individual
 species.
description: <strong>01 Rawdata.xlsx</strong>
  <strong>Summary of sequence abundance data generated by the ECOTAG
 program</strong>.<br> Table shows sequence abundance data of
 samples from Weiming Lake (SL), Kunming Lake (ML) and Guanting Reservoir
 (LL) generated by the ECOTAG program, retaining low-frequency sequences
 and negative control sequencing results, including the sample blank (SB),
 filtration blank (FB), extraction blank (EB), and PCR blank (PB). Also
 included are: total read counts of each sequence, taxid, taxonomic
 assignment by the ECOTAG program, taxonomic assignment at the species
 level by BLAST against GenBank nucleotide databases, the identity scores
 and accession numbers of the highest matched sequences, and the query
 sequences. Sequences with an assigned taxon of “NA” and human sequences
 were removed from the table. <strong>02
 Tele02_ngsfilter.txt  File used to assign sequences to samples in the
 OBITOOLS package</strong>.<br> File used to assign sequences
 to each sample in the OBITOOLS package, including the Teleo2 primers and
 primer tags. <strong>03 Tele02_database.fa
  Reference database constructed by in silico PCR with the Teleo2 primers
 using the ECOPCR program</strong>.<br> File shows the in
 silico PCR results using the Teleo2 primers to extract sequences in the
 EMBL database (release 138), which was used as the reference database in
 the ECOTAG program to assign a taxon to each sequence.