Dataset DOI: 10.5061/dryad.9p8cz8wvr

Description of the data and file structure

The data were collected as part of an environmental DNA (eDNA) monitoring study aimed at assessing the distribution and community structure of the endangered Redside Dace (Clinostomus elongatus) in urban streams. Field sampling involved the collection of water samples from multiple sites across the Greater Toronto Area, followed by metabarcoding analyses to detect Redside Dace presence and characterize associated fish communities.

Files and variables

File: R_script_for_processing_blast_results.R

• R script created to process blast results and create tables to analyze the data

File: RSD_habitat_eDNA_2020.xlsx

• File created to assign standardized site codes to water bodies for consistent reference throughout the study
• Site_Code: site code that was given to waterbody
• Waterbody: waterbody where water samples were collected for eDNA sampling
• Type: type of waterbody
• Sample: each site had a field blank and 3 replicates taken

File: PS1RSDSitesReads.csv

• File created to isolate Redside Dace reads from data created using PS1 primer
• Site: name that was given to the corresponding location
• Replicate: the replicate number of that specific site
• Clinostomus.elongatus: Redside Dace reads detected for that replicate at that specific site.

File: PS1Siteblanks.csv

• File created to isolate field blanks from data created using PS1 primer
• Site: name that was given to the corresponding location
• Replicate: specifying that it is the field blank replicate we are focused on
• The rest of the columns: species the primer detected, and how many reads were detected in the field blank

File: PS1PCRblanks.csv

• File created to isolate PCR blanks from data created using the PS1 primer
• Site: name that was given to the corresponding location
• Replicate: specifying that it is the PCR blank replicate we are focused on
• The rest of the columns: the species the primer detected, and how many reads were detected in the PCR blank

File: PS1MeanRSDReads.csv

• File created to average Redside Dace reads across replicates within a site from data created using the PS1 primer
• Site: name that was given to the corresponding location
• Mean.Reads: Mean reads of Redside Dace of replicates for that site

File: PS1EBblanks.csv

• File created to isolate extraction blank reads from data created using the PS1 primer
• Site: name that was given to the corresponding location
• Replicate: specifying that it is the field blank replicate we are focused on
• The rest of the columns: the species the primer detected, and how many reads were detected in the PCR blank

File: MMitoSiteBlanks.csv

• File created to isolate field blank reads from data created using M-Mito primer
• Site: name that was given to the corresponding location
• Replicate: specifying that it is the PCR blank replicate we are focused on
• The rest of the columns: the species the primer detected, and how many reads were detected in the PCR blank

File: MMitoRSDReads.csv

• File created to isolate Redside Dace reads from data created using M-Mito primer
• Site: name that was given to the corresponding location
• Replicate: the replicate number of that specific site
• Clinostomus.elongatus: Redside Dace reads detected for that replicate at that specific site.

File: MMitoMeanRSDReads.csv

• File created to average Redside Dace reads across replicates within a site from data created using M-Mito primer
• Site: name that was given to the corresponding location
• Mean.Reads: Mean reads of Redside Dace of replicates for that site

File: MMitoPCRBlanks.csv

• File created to isolate PCR blank reads from data created using M-Mito primer
• Site: name that was given to the corresponding location
• Replicate: specifying that it is the PCR blank replicate we are focused on
• The rest of the columns: the species the primer detected, and how many reads were detected in the PCR blank

File: MMitoEBBlanks.csv

• File created to isolate extraction blank reads from data created using M-Mito primer
• Site: name that was given to the corresponding location
• Replicate: specifying that it is the field blank replicate we are focused on
• The rest of the columns: the species the primer detected, and how many reads were detected in the PCR blank

File: PS1MetabarcodingData.csv

• File created to show all reads from fish species known to be in these habitats using the PS1 primer
• Site: name that was given to the corresponding location
• Replicate: the replicate number of that specific site
• The rest of the columns: the species the primer detected, and how many reads were detected for that species

File: MMitoMetabarcodingData.csv

• File created to show all reads from fish species known to be in these habitats using the M-Mito primer
• Site: name that was given to the corresponding location
• Replicate: the replicate number of that specific site
• The rest of the columns: the species the primer detected, and how many reads were detected for that species

File: PS1MetabarcodingDataNoContamination.csv

• File created to account for potential contamination biases by doubling the contamination values and subtracting them from the corresponding field site data (PS1). This adjusted dataset was then subjected to a second co-occurrence analysis to assess the impact of contamination on species associations.
• Site: name that was given to the corresponding location
• Replicate: the replicate number of that specific site
• The rest of the columns: the species the primer detected, and how many reads were detected for that species

File: MMitoMetabarcodingDataNoContamination.csv

• File created to account for potential contamination biases by doubling the contamination values and subtracting them from the corresponding field site data (M-Mito). This adjusted dataset was then subjected to a second co-occurrence analysis to assess the impact of contamination on species associations.
• Site: name that was given to the corresponding location
• Replicate: the replicate number of that specific site
• The rest of the columns: the species the primer detected, and how many reads were detected for that species

File: Sampling_Map_Rounded.csv

• File with long and lat of sampling sites to create a map
• Waterbody: waterbody that was sampled
• Lat: latitude
• Long: longitude

File: Mapping_Combined.qgz

• File used to create maps on QGIS

File: R_script_for_cooccurance_analysis.R

• R script to create species co-occurrence table 

Code/software

R Studios, QGIS, and some sort of spreadsheet application with the up-to-date software are needed to view the files.