DOI: 10.5061/dryad.8kprr4xmm
title: Large‐scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north‐western Australia

description: Aim: Environmental DNA (eDNA) metabarcoding has demonstrated its
 applicability as a highly sensitive biomonitoring tool across small
 spatial and temporal scales in marine ecosystems. However, it has rarely
 been tested across large spatial scales, or biogeographical barriers.
 Here, we scale up marine eDNA metabarcoding, test its ability to detect a
 major marine biogeographic break, and evaluate its use as a regional
 biomonitoring tool in Australia. Location: North-western Australia (NWA)
 Methods: We applied metabarcoding assays targeting the mitochondrial 16S
 rRNA and CO1 genes to 284 surface seawater eDNA samples collected from 71
 mid-shelf, inshore, coastal and nearshore estuarine sites over 700 km of
 the NWA coastline. Results: Metabarcoding detected a wide range of bony
 fish (404 taxa), elasmobranchs (44) and aquatic reptiles (5). We detected
 bioregional and depth differentiation within inshore bony fish
 communities. These findings support the presence of a marine biogeographic
 break, which is purported to occur in the vicinity of Cape Leveque,
 demarcating the border between the Kimberley and Canning bioregions.
 Inshore bony fish and elasmobranch communities, as well as coastal bony
 assemblages, were additionally found to differ between the South and North
 Kimberley regions suggesting previously unrecognised subregional
 differentiation among these taxa. The overall compositional data has been
 used to update distribution information for a number of endangered,
 elusive and data-deficient taxa, including sawfish (family: Pristidae),
 northern river shark (Glyphis garricki) and wedgefish (genus:
 Rhynchobatus). Main conclusions: eDNA metabarcoding demonstrated a high
 level of sensitivity that was able to discern fine-scale patterns across
 the large-scale, remote and oceanographically complex region of
 North-western Australia. Importantly, this study highlights the potential
 of integrating broad-scale eDNA metabarcoding alongside other baseline
 surveys and long-term monitoring approaches, which are crucial for the
 sustainable management and conservation of marine biodiversity in this
 unique marine region.
description: Four one-litre water replicates were sampled from 71 sites across
 the Canning/Kimberley bioregions in September 2017 and July/September
 2018, totaling 284 samples over 700 km<sup> </sup>of
 coastline. Samples were taken on a transect line traversing a purported
 biogeographic break and more widely across the Kimberley region in
 mid-shelf, inshore, coastal and nearshore estuarine habitats. Samples were
 immediately stored on ice and were individually filtered across Pall
 0.45mm Supor®
 polyethersulfone
 membranes using a Pall Sentino® Microbiology pump
 (Pall Corporation, Port Washington, USA) within five hours of
 collection. DNA
 was extracted from half of the filter membranes using a DNeasy Blood and
 Tissue Kit (Qiagen; Venlo, Netherlands) with modifications. DNA was
 amplified using three previously published PCR assays (16S and COI) to
 target bony fish, elasmobranchs and aquatic reptiles from our mixed
 seawater samples (see Diversity and Distributions publication for more
 information).  Libraries were sequenced on 300
 cycle (for unidirectional sequencing of the 16S & COI amplicons)
 MiSeq® V2 Standard Flow Cells on an Illumina MiSeq platform (Illumina, San
 Diego, USA), housed in the TrEnD Laboratory at Curtin University, Western
 Australia. Sequencing reads were demultiplexed and quality filtered in
 OBITools (v1.2.9;
 Boyer et al.,
 2014) and in R (v3.5.3;
 RStudio Team, 2015) using the DADA2 (v1.10.1)
 bioinformatics package (Callahan et al.,
 2016).
description: We have uploaded demultiplexed (unfiltered) data for public use.
 This is in a fastq format and corresponds to sample IDs (see Diversity and
 Distributions publication for more information). We have also uploaded a
 taxonomic (read abundance) matrix that has gone through our quality
 filtering (DADA2) pipeline and has been blasted against NCBI's
 GenBank (2019). This can be directly used for multivariate statistical
 analyses.