DOI: 10.5061/dryad.hq229kc
title: Data from: Cobble community DNA as a tool to monitor patterns of biodiversity within kelp forest ecosystems

description: Kelp forest ecosystems dominate 150,000 km of global temperate coastline,
 rivalling the coastal occurrence of coral reefs. Despite the astounding
 biological diversity and productive ecological communities associated with
 kelp forests, patterns of species richness and composition are difficult
 to monitor and compare. Crustose coralline algae are a critically
 important substrate for propagule settlement for a range of kelp forest
 species. Coralline covered cobbles are home to hundreds of species of
 benthic animals and algae and form a replicable unit for ecological
 assays. Here, we use DNA metabarcoding of bulk DNA extracts sampled from
 cobbles to explore patterns of species diversity in kelp forests. The data
 from 98 cobbles within kelp forest ecosystems at three sites in Central
 California show the presence of 2,037 Molecular Operational Taxonomic
 Units (MOTUs) and 79 MOTUs assigned up to the species level with
 &gt;95% similarity to current databases. We are able to detect spatial
 patterns of important management targets such as abalone recruits, and
 localized abundance of sea stars in 2012. Comparison of classic ecological
 surveys of these sites reveals large differences in species targets for
 these two approaches. In order to make such comparisons more quantitative,
 we use Presence/Absence Metabarcoding (PAM), using the fraction of
 replicate cobbles showing a species as a measure of its local abundance.
 This approach provides a fast and repeatable survey method that can be
 applied for biodiversity assessments across systems to shed light on the
 impact of different ecological disturbances and the role played by marine
 protected areas.
description: Cobble_2012_COITable including the taxonomic assignment (using ecotag), the abundances of MOTUs of each sample per site and the sequence generated using COI found in cobble substrate collected from three sites across four depths (10, 20, 30 and 40 foot) at Hopkins Marine Life Refuge, Lovers Point and Point Pinos along the Monterey Peninsula, California, November 2012 . Ordered in the following columns: (A) id, (B) rank, (C) scientific_name, (D) best_identity, (E) superkingdom_name, (F) kingdom_name, (G) phylum_name, (H) class_name, (I) order_name, (J) family_name, (K) genus_name, (L) species_name, (M to DV) abundances of each sample at different sites including filtration blanks, positive and negative controls [HMS: Hopkins Marine Station; LovP: Lovers Point; Pt.Pinos: Point Pinos], (DW) sequence.Obitools demultiplexing of each sampleFile used to demultiplex samples using the Obitools bioinformatic pipeline including barcode combinations and COI forward and reverse primers.ngsfilter_cobble2012.txtObitools_pipeline_ScriptsScript used to process Illumina COI sequence reads using Obitools in SLURM manager; QC; demultiplexing; filtering; chimera detection (vsearch); clustering (swarm d=13); taxinomic assignment (ecotag); reformatting (custom R scripts, ref Owen WANGENSTEEN - https://github.com/metabarpark/R_scripts_metabarpark)obi_cobble.jobsubmit_parallel_ecotagScript to split sequences for ecotag assignment in parallelsubmit_parallel_ngsfilterScript to split sequences for ngsfilter demultiplexing in parallelSupplementaryInformation_PISCOdatasetPISCO SWATH sampling of kelp forest organisms 1999-2017, see https://search.dataone.org/dataiTOLFiles needed to reproduce Figure 2. Maximum likelihood tree and three annotation files for iTOL, Identity, Phyla and bar chart.