DOI: 10.5068/d1qd5m
title: Data from: eDNA metabarcoding bioassessment of endangered fairy shrimp (Branchinecta spp.) - Part A

description: 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 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 both state and 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 overlap of B. sandiegonensis with a common (non-threatened) sister
 species, B. lindahli. 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 had a sensitivity of 99% and specificity 98% for B.
 sandiegonensis while dip net samplings had a sensitivity of 96.5% and
 specificity of 93.6%. For B. lindahli, dip net sampling had a sensitivity
 of 97.4% and specificity of 85.9% while eDNA methods had a specificity of
 86.8% and sensitivity of 72.6%. 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 or decaying individuals. Together these results provide
 resource managers a simple cost effective and non-invasive method for
 biomonitoring endangered fairy shrimp species.
description: eDNA metabarcoding data of <em>16S</em> invertebrate
 reads were collected from 11 vernal pools is 2017. Samples were sequenced
 twice on MiSeq PE 2x300. Raw sequences were processed using the
 <em>Anacapa Toolkit </em>with standard parameters.  Taxonomy
 was assigned using CRUX-generated <em>16S </em>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.
description: 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 <i>16S</i> 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/D1DW95. Database files require Bowtie (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml).