DOI: 10.5061/dryad.cfxpnvxjd
title: Detection of a non-indigenous marine macroalga (<em>Acanthophora spicifera</em>) with environmental DNA from surface seawater

description: Non-indigenous species (NIS) have far-reaching economic, ecological, and
 cultural impacts to native biota. Early detection of nuisance species is
 crucial for preventing their widespread establishment and conserving
 threatened ecosystems. Acanthophora spicifera is a red alga that has
 successfully colonized coral reefs around the globe, out-competing native
 flora and fauna, and is among the most common non-indigenous algae of
 shallow Hawaiian coral reefs. To assist early detection and eradication
 efforts of NIS, we developed a qPCR assay for the non-indigenous A.
 spicifera. Assay sensitivity and specificity was validated with
 species-specific primers targeting a 131 base-pair region of the
 ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene.
 Using environmental DNA (eDNA) collected from surface seawater samples, we
 then estimated A. spicifera site occupancy across sites where its presence
 was visually confirmed, as well as a large number of sites where its
 presence is unknown. Through occupancy modeling of eDNA and opportunistic
 visual survey data, A. spicifera eDNA was estimated to be present at 17%
 of surveyed sites, including one in the remote Papahānaumokuākea Marine
 National Monument (PMNM), a world heritage site that is home to numerous
 endemic species. Thorough investigation of control samples,
 high-throughput sequencing data, and visual surveys suggests that the
 presence of A. spicifera eDNA within PMNM is associated with an emerging
 colonization front in the region. Our results indicate that the eDNA assay
 is sensitive to the presence of A. spicifera and is a cost-effective
 method for monitoring its distribution on impacted coral reefs.
description: # Detection of a non-indigenous marine macroalga (*Acanthophora
 spicifera*) with environmental DNA from surface seawater Quantitative PCR
 (qPCR) data includes: * **qPCR metadata** (2qPCR_metadata.csv) - Project
 metadata includes site IDs, date of sample collection, region, island,
 site depth (meters), *Acanthophora spicifera* presence from visual
 surveys, and GPS coordinates (Lat./Long.) * **quantification amplification
 results** (2qPCR_amplification_data.csv) - raw qPCR data used to visualize
 amplification curves (cycle number, relative fluorescence units
 "value", detection threshold as calculated by the CFX96 and
 efficiency "E", as calculated using the CFX Manager software)
 merged with sample metadata * **melt curve derivative results**
 (2qPCR_melt_data.csv) - raw qPCR data used in the melt curve analysis
 (cycle temperature C, negative first derivative of the melting-curve,
 -dF/dT "value", detection threshold as calculated by the CFX96
 and efficiency "E", as calculated using the CFX Manager
 software) merged with sample metadata * **quantification Cq results**
 (2Cq_data.csv) - raw qPCR detection data used for modeling of site
 occupancy (quantification cycle Cq, detection threshold as calculated by
 the CFX96, efficiency "E", as calculated using the CFX Manager
 software, efficiency-corrected eDNA starting quantities "SQ.E")
 merged with sample metadata * **standard curve data** (2standards.csv) -
 Cq values from standards formatted for plotting standard curve for rbcL
 marker (quantification cycle Cq and expected starting quantities
 "SQ") using tenfold serial dilutions of synthetic DNA gBlocks
 for *Acanthophora spicifera* High-throughput sequence data run on an
 Illumina MiSeq includes: * **raw sequence data** (2sequence_data.zip)- Raw
 sequence data (fastq.gz) from environmental DNA of surface seawater
 samples highlighted in the study * **sequence metadata**
 (2sequence_metadata.csv) - sample IDs, plate IDs, forward reads filename,
 reverse reads filename * **curated OTU table** (2OTU_table.csv) - OTU
 table constructed using the methods outlined in the paper with annotations
 from NCBI blastn database search Entries marked "NA" are absent.