Revealing elasmobranch distributions in turbid coastal waters: insights from environmental DNA and particle tracking
Data files
Jan 15, 2025 version files 12.95 GB
-
Data_Run_1.zip
2.36 GB
-
Data_Run_2.zip
2.04 GB
-
Data_Run_3.zip
2.83 GB
-
Data_Run_4.zip
2.33 GB
-
Data_Run_7.zip
1.94 GB
-
Museum_Run_1.zip
1.06 GB
-
Museum_Run_2.zip
390.41 MB
-
README.md
3.70 KB
Abstract
Many sharks, rays, and skates are highly threatened and vulnerable to overexploitation, as such reliable monitoring of elasmobranchs is key to effective management and conservation. The mobile and elusive nature of these species makes monitoring challenging, particularly in temperate waters with low visibility. Environmental DNA (eDNA) methods present an opportunity to study these species in the absence of visual identification or invasive techniques. However, eDNA data alone can be difficult to interpret for species monitoring, particularly in a marine setting where its distribution can be influenced by water currents. In this study, we investigated the spatial and temporal distribution of elasmobranch species in two Special Areas for Conservation (SAC) off the coast of Wales. We took monthly eDNA samples for one year (starting September 2020 and March 2022 for the northern and southern SACs, respectively), and used metabarcoding to reveal the presence of elasmobranch species. We combined these data with hydrodynamic modelling and particle tracking methods to simulate the potential origins of the detected eDNA. We detected 11 elasmobranch species, including the Critically Endangered angelshark (Squatina squatina) and tope (Galeorhinus galeus). Most detections were in the spring and fewest in the autumn. The particle tracking simulations predicted that eDNA was shed, on average, approximately 7 km and 15 km (in the northern and southern SACs, respectively) from the sampling stations at which it was detected. These results show that the two SACs represent important areas for elasmobranchs in the United Kingdom and demonstrate that eDNA methods combined with particle tracking simulations can represent a new frontier for monitoring marine species.
README: Revealing elasmobranch distributions in turbid coastal waters: insights from environmental DNA and particle tracking
https://doi.org/10.5061/dryad.m0cfxppcx
Description of the data and file structure
Revealing elasmobranch distributions in turbid coastal waters: insights from environmental DNA and particle tracking
Raw sequence FASTQ data from 8 experimental run files from Illumina MiSeq paired-end sequencing of the Elas02 barcode.
Files are named according to the sample location and date; "Site-Date_Sequencer information.fastq
" i.e. AB-1020_S22_L001_R1_001.fastq is the data from site AB in October 2020
Where the Site is replaced by NegExt/NEG and NTC, it means negative extraction controls (DNA extraction control) and negative template controls (PCR control) respectively.
All samples were processed with a corresponding negative control, designated with a 0 after the sample location ID e.g. "AB0_..."
Sample locations are as follows:
Location | Site | Latitude | Longitude |
---|---|---|---|
PLAS | AB | 52.5292 | -4.0492 |
PLAS | BA | 52.7177 | -4.0531 |
PLAS | BL | 52.9112 | -4.1906 |
PLAS | BO | 52.4802 | -4.0528 |
PLAS | CA | 52.8728 | -4.449 |
PLAS | DY | 52.7853 | -4.126 |
PLAS | HA | 52.8618 | -4.1275 |
PLAS | PE | 52.908 | -4.316 |
PLAS | PO | 52.8083 | -4.5508 |
PLAS | TY | 52.5823 | -4.1004 |
CBAE | TS | 51.6674 | -4.7014 |
CBAE | SA | 51.7112 | -4.6966 |
CBAE | PE | 51.7402 | -4.5586 |
CBAE | FE | 51.7692 | -4.3705 |
CBAE | SI | 51.7372 | -4.3565 |
CBAE | PB | 51.6742 | -4.3146 |
CBAE | BU | 51.6789 | -4.2359 |
CBAE | LL | 51.5941 | -4.2953 |
CBAE | PO | 51.5435 | -4.2072 |
CBAE | CA | 51.5683 | -4.0325 |
PLAS: Pen Llŷn a'r Sarnau
CBAE: Carmarthen Bay and Estuaries
Data runs 5 and 6 did not produce results that were used in the analysis and are therefore not included here.
Files and variables
File: Data_Run_1.zip
Description: FASTQ files from PLAS samples September to December 2020
File: Data_Run_2.zip
Description: FASTQ files from PLAS samples January to April 2021
File: Data_Run_3.zip
Description: FASTQ files from PLAS samples May to August 2021
File: Data_Run_4.zip
Description: FASTQ files from CBAE samples March to June 2022
File: Data_Run_7.zip
Description: FASTQ files from CBAE samples January to February 2022
File: Museum_Run_1.zip
Description: Rerun FASTQ files from CBAE samples July to December 2022
File: Museum_Run_2.zip
Description: FASTQ files from CBAE samples November and December 2022
Code/software
Analysed using the SimpleMetaPipeline (Williams et al. 2024) J-Cos/SimpleMetaPipeline: 2.0.2
Access information
Other publicly accessible locations of the data:
- Particle tracking and analysis scripts are available here: https://zenodo.org/records/14391532
Data was derived from the following sources:
- environmental DNA samples from filtered water and MiSeq sequencing