DOI: 10.5061/dryad.9p8cz8wvr
title: Using environmental DNA metabarcoding to determine endangered Redside Dace occurrence and associated community composition in urban streams

description: Redside Dace, an endangered fish native to the Greater Toronto Area (GTA),
 faces significant threats from urbanization, which has degraded its
 habitat and water quality. Understanding its current distribution is
 essential for guiding conservation efforts, identifying critical habitats
 for protection, and targeting degraded areas for restoration. We collected
 water samples from streams previously inhabited by Redside Dace in the GTA
 and used eDNA metabarcoding to determine its contemporary distribution and
 the associated fish communities. As expected, Redside Dace was less
 frequently detected in heavily urbanized streams, highlighting the
 negative impact of urbanization. Co-occurrence analysis identified nine
 positive associations with other fish species, many of which inhabit cool
 water streams and build nests, suggesting possible shared habitat
 preferences or reliance on these species as nest hosts. This study
 emphasizes the value of eDNA metabarcoding in assessing urbanization’s
 effects on Redside Dace and freshwater ecosystems, reinforcing the
 importance of focused conservation strategies to protect this endangered
 species and restore critical habitats.
description: # Using environmental DNA metabarcoding to determine endangered Redside
 Dace occurrence and associated community composition in urban streams
 Dataset DOI: [10.5061/dryad.9p8cz8wvr](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.