10.5061/DRYAD.98SF7M0DM
Zhang, Shan
Peking University
Lu, Qi
Peking University
Wang, Yiyan
Peking University
Wang, Xiaomei
Chinese Academy of Fishery Sciences
Zhao, Jindong
Peking University
Yao, Meng
0000-0002-8906-1461
Peking University
Assessment of fish communities using eDNA: effect of spatial sampling
design in lentic systems of different sizes
Dryad
dataset
2019
2019-10-22T00:00:00Z
2019-10-22T00:00:00Z
en
https://doi.org/10.1111/1755-0998.13105
16759168 bytes
2
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
01 Rawdata.xlsx Summary of sequence abundance data generated by the
ECOTAG program. 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. 02
Tele02_ngsfilter.txt File used to assign sequences to samples in the
OBITOOLS package. File used to assign sequences to each sample in the
OBITOOLS package, including the Teleo2 primers and primer tags. 03
Tele02_database.fa Reference database constructed by in silico PCR with
the Teleo2 primers using the ECOPCR program. 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.