10.5068/D1DW95
Gold, Zachary
0000-0003-0490-7630
University of California Los Angeles
Wall, Adam R.
0000-0002-2223-6757
Natural History Museum of Los Angeles County
Curd, Emily E.
0000-0003-0336-6852
Los Angeles Mission College
Kelly, Ryan P.
0000-0001-5037-2441
University of Washington
Pentcheff, N. Dean
0000-0002-4049-3941
Natural History Museum of Los Angeles County
Ripma, Lee
San Diego State University
Barber, Paul H.
0000-0002-1486-8404
University of California Los Angeles
Wetzer, Regina
0000-0003-2674-5150
Natural History Museum of Los Angeles County
Data from: eDNA metabarcoding bioassessment of endangered fairy shrimp
(Branchinecta spp.) - Part B
Dryad
dataset
2020
University of California Office of the President
https://ror.org/00dmfq477
CA-16-376437
National Science Foundation
https://ror.org/021nxhr62
1650604
2020-08-25T00:00:00Z
2020-08-25T00:00:00Z
en
https://doi.org/10.1007/s12686-020-01161-9
https://doi.org/10.5068/D1QD5M
5758263172 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Fairy shrimp are integral components of vernal pool ecosystems, providing
key food resources for migratory birds and amphibians. However, habitat
degradation and land use change severely threaten the health of both
vernal pools and the survival of fairy shrimp species. Branchinecta
sandiegonensis Fugate, 1993 has been particularly affected by urban and
agricultural development in its small native range within San Diego
County, California, USA. It is listed as an endangered species under
federal laws and is actively managed for its conservation. However,
despite its legal protections, current methods of population assessment
require the capture and sacrifice of individuals of B. sandiegonensis in
order to identify specimens to species level through microscopy.
Furthermore, accurate species-level identification is especially important
given the overlap of B. sandiegonensis with a common (non-threatened)
sister species, B. lindahli Packard, 1883. Thus non-invasive methods to
definitively distinguish these species are desirable. Here we demonstrate
that eDNA metabarcoding methods are an effective non-invasive technique
for monitoring fairy shrimp. We sampled a series of vernal pools with both
eDNA and traditional dip net methods, finding that eDNA metabarcoding with
16S rDNA provides species-level resolution. eDNA metabarcoding for B.
sandiegonensis had a sensitivity of 99% and a specificity of 99% while dip
net sampling had a sensitivity of 98.8% and a specificity of 89.2%. We
found that the two methods were concordant within the early hydroperiod of
pools. Additionally, the eDNA method detected fairy shrimp in vernal pools
up to 2 months after dip nets detected any adult individuals, suggesting
eDNA methods detect fairy shrimp eggs, newly hatched larvae, or decaying
individuals. Together these results provide resource managers a simple,
cost effective, and non-invasive method for biomonitoring endangered fairy
shrimp species.
eDNA metabarcoding data of 16S invertebrate reads were collected from 11
vernal pools is 2017. Samples were sequenced twice on MiSeq PE 2x300. Raw
sequences were processed using the Anacapa Toolkit with standard
parameters. Taxonomy was assigned using CRUX-generated 16S rDNA
metabarcode reference database. The CRUX reference database was generated
from EMBL and NCBI repositories downloaded in May 2019. Please see Gold et
al. 2020 for detailed description of the methods.
VP_meta_data has a list of all sample names and associated metadata needed
to process and analyze the raw sequencing files. Raw sequence data
includes two demultiplexed MiSeq PE 2x300 zipped
fastq files. CRUX-generated 16S reference database has a bowtie-2
formatted reference database as well as a corresponding fasta file of all
sequences and matching taxonomy text file. Metabarcode generated
sequencing data are in the two parts, attached
and at https://doi.org/10.5068/D1QD5M.