The farther you are, the closer you get: Environmental similarity connects aquatic invertebrate communities across large river networks via ecological convergence
Data files
Sep 08, 2026 version files 2.13 MB
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2022_LCRB_eDNA_Metabarcoding_Pipeline.zip
8.36 KB
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Datasets_for_analysis.zip
2.07 MB
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LCRB_Manuscript_Analysis_UPDATED.R
42.11 KB
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README.md
11.33 KB
Abstract
In freshwater river networks, a key spatial factor affecting biodiversity is the multiple pathways of ecological connectivity and dispersal including the continuous and often sinuous river network and the three-dimensional terrestrial landscape. Differential dispersal of aquatic organisms across both pathways, in combination with environmental factors, can shape aquatic community structure through habitat filtering and dispersal dynamics.
Here, we use the high throughput capacity of environmental DNA (eDNA) metabarcoding to explore the influence of spatial relationships and environmental heterogeneity across an expansive and diverse landscape. We collected invertebrate eDNA samples from 70 lotic habitats ranging from small, free-flowing headwater tributaries to anthropogenically altered high order rivers, spanning five major drainage regions in the Colorado River watershed. Data contained in this repository include the community dataset of OTUs identified at each site, the taxonomic identification of OTUs based on the BOLD reference database, as well as the R code and metadata used for statistical analyses.
Communities displayed high alpha and beta diversity among the drainage regions, structured by a combination of spatial and environmental factors. A novel distance-decay framework adapted from population genetics indicated invertebrate dispersal along terrestrial pathways played a role in structuring communities throughout the network. Consistent with this finding, hierarchical clustering identified patterns of convergent similarity in invertebrate communities of headwater tributaries in two different regions that were geographically proximal but separated by extreme river network distances. These results indicate spatial and environmental metacommunity dynamics in general, and dispersal across the terrestrial landscape specifically, are structuring aquatic invertebrate communities in the Lower Colorado River Basin and can shape convergent patterns of biodiversity in river networks.
Dataset DOI: 10.5061/dryad.573n5tbnp
Description of the data and file structure
Data and R code provided here were used for bioinformatics and analysis of eDNA metabarcoding data from Lower Colorado River Basin aquatic habitats collected in spring 2022, as a part of a manuscript submitted to the journal Ecology and Evolution: The farther you are, the closer you get: Environmental similarity connects aquatic invertebrate communities across large river networks via ecological convergence. eDNA amplicons of aquatic invertebrate COI gene fragments were produced using the fwhF2/EPTDr2n primer set, and sequenced on Illumina NextSeq 2000. Raw sequencing reads can be found at NCBI BioProject **PRJNA1347436: **https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1347436/.
Sequencing reads were processed using the JAMP metabarcoding pipeline (https://github.com/VascoElbrecht/JAMP). Paired end reads were merged and primer sequences trimmed, followed by filtering of sequence length the 142bp +/- 10bp. Reads were then filtered for a max EE of 0.5, and denoised with an alpha value of 5. OTUs were then clustered using a 3% similarity threshold, and OTUs were transformed to presence-absence for further community analysis. Taxonomic identifications were made by aligning OTU consensus sequences to the BOLD reference database of COI barcodes (https://boldsystems.org), using the BOLDigger3 python package (https://github.com/DominikBuchner/BOLDigger3).
Files and variables
File: 2022_LCRB_eDNA_Metabarcoding_Pipeline.zip
Description: ZIP file containing R code used for processing, filtering, and clustering of eDNA metabarcoding sequencing reads. This pipeline was used to create processed and filtered OTU community datasets from demultiplexed Illumina sequencing reads. Raw sequencing reads can be found at NCBI BioProject **PRJNA1347436: **https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1347436/.
File: LCRB_Manuscript_Analysis_UPDATED.R
Description: R code used for statistical analysis and production of figures resulting from the provided data.
Folder structure and instructions for running the code
To run LCRB_Manuscript_Analysis_UPDATED.R, unzip the full archive into a single folder, preserving the subfolder structure below, then open R/RStudio, set the working directory to that folder (e.g., setwd("path/to/unzipped/folder")), and run the script from top to bottom. Figures and result tables are written automatically to an "Output" subfolder created by the script; this folder does not need to be created manually.
Datasets_for_analysis/
community/
2022_LowCol_all_OTU_table_PA_USETHIS.csv
2022_LowCol_taxonomy_bysite.csv
env/
lowcol_all_env_ppt_elev_coord.csv
lowcol_lcd_dist.csv
gis/
rivnet_cleaned.rdata
OD_matrix_symmetric.csv
LCRB_Manuscript_Analysis_UPDATED.R
Note: the file Datasets_for_analysis/env/lowcol_all_riv_dist.csv is generated automatically by the script (pairwise in-stream distances calculated from rivnet_cleaned.rdata) and does not need to be provided separately.
File: Datasets_for_analysis.zip
Description: Compressed folder containing the data required to perform the analysis described in LCRB_Manuscript_Analysis_UPDATED.R. The compressed directory contains a file structure dividing datasets into community, environmental (env), and GIS categories. The file structure is as follows:
Datasets_for_analysis/
community/
2022_LowCol_all_OTU_table_PA_USETHIS.csv
2022_LowCol_taxonomy_bysite.csv
env/
lowcol_all_env_ppt_elev_coord.csv
lowcol_lcd_dist.csv
gis/
rivnet_cleaned.rdata
OD_matrix_symmetric.csv
Below is a description of files contained within the directory:
File: community/2022_LowCol_all_OTU_table_PA_USETHIS.csv
Description: Presence-absence community matrix of OTUs identified at each sampling location.
Variables
- OTU: Operational Taxonomic Unit
- SCL_R: Sycamore Canyon, Lower Riffle
- VRSC: Verde River above Sycamore Canyon
- SCU_R: Sycamore Canyon, Upper Riffle
- VRWC: Verde River above West Clear Creek
- WBC_LR: Wet Beaver Creek, Lower Riffle
- VROC: Verde River above Oak Creek
- WFOC_U: West Fork Oak Creek, Upper Riffle
- WFOC_LR: West Fork Oak Creek, Lower Riffle
- WCC_LR: West Clear Creek, Lower Riffle
- WCC_U: West Clear Creek, Upper Riffle
- WBC_U: Wet Beaver Creek, Upper Riffle
- VRHW: Verde River Headwaters
- VRBH: Verde River below Horseshoe Dam
- VRBB: Verde River below Bartlett Dam
- SRUV: Salt River above Verde
- SRRS: Salt River at Rio Salado Park
- GRGD: Gila River below Gillespie Dam
- GRY: Gila River above Colorado River confluence
- CRUG: Colorado River above Gila
- CRPV: Colorado River below Palo Verde Dam
- CRPD: Colorado River below Parker Dam
- CRDD: Colorado River below Davis Dam
- CRBH: Colorado River below Hoover Dam
- PAR: Paria River
- Nank: Nankoweap Creek
- LCR: Little Colorado River
- CLR: Clear Creek
- BA: Bright Angel Creek
- Her: Hermit Creek
- Bou: Boucher Creek
- Cry: Crystal Creek
- Shi: Shinumo Creek
- RAC: Royal Arch Creek
- Tap: Tapeats Creek
- Deer: Deer Creek
- Kan: Kanab Creek
- Mat: Matkatamiba Creek
- Hav: Havasu Creek
- VW: Vulvan's Well
- Spr: Spring Creek
- TS: Three Springs Creek
- Dia: Diamond Creek
- Tra: Travertine Canyon
- Spe: Spencer Creek
- Col: Colombine Creek
- CR01: Colorado River Mile 01
- CR19: Colorado River Mile 19
- CR52: Colorado River Mile 52
- CR61: Colorado River Mile 61
- CR76: Colorado River Mile 76
- CR84: Colorado River Mile 84
- CR88: Colorado River Mile 88
- CR95: Colorado River Mile 95
- CR97: Colorado River Mile 97
- CR98: Colorado River Mile 98
- CR109: Colorado River Mile 109
- CR117: Colorado River Mile 117
- CR134: Colorado River Mile 134
- CR136: Colorado River Mile 136
- CR144: Colorado River Mile 144
- CR148: Colorado River Mile 148
- CR157: Colorado River Mile 157
- CR175: Colorado River Mile 175
- CR180: Colorado River Mile 180
- CR205: Colorado River Mile 205
- CR215: Colorado River Mile 215
- CR226: Colorado River Mile 226
- CR229: Colorado River Mile 229
- CR246: Colorado River Mile 246
- CR275: Colorado River Mile 275
File: community/2022_LowCol_taxonomy_bysite.csv
Description: Output from BOLDigger alignment of aquatic invertebrate OTUs (derived from eDNA metabarcoding sequences) to the BOLD reference database of COI barcodes, and OTU detections by site. Only OTUs with >85% similarity to a reference sequence were retained.
Variables
- OTU_ID: OTU number
- Class: Class of top COI barcode ID
- Order: Order of top COI barcode ID (>85%)
- Family: Family of top COI barcode ID (>90%)
- Genus: Genus of top COI barcode ID (>95%)
- Species: Species of top COI barcode ID (>97%)
- Similarity: Percent similarity of OTU consensus sequence to top COI barcode
- Columns BA – WFOC_U: Site codes. See description of 2022_LowCol_all_OTU_table_PA_USETHIS.csv for further details.
File: env/lowcol_all_env_ppt_elev_coord.csv
Description: Environmental and experimental variables and measurements that correspond with sampling locations in the Lower Colorado River Basin
Variables
- SiteCode: Unique code to identify site
- Site: Full site name
- Basin: Regional basin designation of site (Grand Canyon, Lower Colorado, or Verde/Wilderness Canyons)
- Streamtype: Identity of site as Mainstem or Tributary
- River: Broad river-network grouping used for regional comparisons (Colorado, GC_Trib, Headwaters, Salt/Gila, or Verde)
- River_Name: Specific river or tributary from which the sample was taken
- Sample_Date: Date of eDNA sample collection
- Dataset: Sampling collection the site belongs to (2022_GC_eDNA = Grand Canyon eDNA collection; 2022_LowCol_eDNA = Lower Colorado eDNA collection)
- Longitude
- Latitude
- DRNAREA_sqmi: Drainage area of basin upstream from sampling location, in square miles
- RELIEF_ft: Vertical relief of drainage basin from sampling location to highest elevation upstream, in feet
- FLOOD_1: Magnitude of the estimated 100-year interval flood, in feet³/second
- annual_precip: Annual precipitation at site, mm
- Elevation: Elevation of site, meters above sea level
File: env/lowcol_lcd_dist.csv
Description: Pairwise least-cost distance (LCD) matrix (km) between all sampling sites, representing the cumulative cost of movement across a landscape resistance/friction surface rather than straight-line or in-stream network distance. Distances were calculated using a slope-derived cost surface from a digital elevation model (DEM) with the R package gdistance (Van Etten, 2017). Row and column headers are site codes, matching those in 2022_LowCol_all_OTU_table_PA_USETHIS.csv.
File: gis/rivnet_cleaned.rdata
Description: Cleaned river-network object (class "rivernetwork", riverdist R package) representing the Lower Colorado River Basin stream network. Used to snap sampling site coordinates to the network and calculate pairwise in-stream (river-course) distances between sites. The process to create this river network is commented out in LCRB_Manuscript_Analysis_UPDATED.R (lines 77-80), but the process is time- and computation-intensive and therefore a pre-calculated network is used.
File: gis/OD_matrix_symmetric.csv
Description: Symmetric origin-destination (OD) cost-distance matrix giving the network path distance (meters) between every pair of sampling sites along the Lower Colorado River Basin stream network, calculated using the “OD Matrix from Layers as Table (m:n)” tool in the QGIS package QNEAT3 with sites snapped directly onto network nodes (entry_cost and exit_cost = 0). A symmetric version of the directed output was created so it could be used as an undirected connectivity graph. Blank rows in the dataset correspond with self-comparisons of the distance matrix, which have no distance value.
Variables
- origin_id: Site code for the origin site of the pair
- destination_id: Site code for the destination site of the pair
- entry_cost: Cost of travel from the origin point onto the network, in meters (0, as sites are snapped directly onto network nodes)
- network_cost: Cost (path distance, in meters) of travel along the network between the origin and destination locations
- exit_cost: Cost of travel from the network to the destination point, in meters (0, as sites are snapped directly onto network nodes)
- total_cost: Sum of entry_cost, network_cost, and exit_cost — the total network path distance between sites, in meters
Access information
Other publicly accessible locations of the data:
- Raw sequencing reads can be found at NCBI BioProject PRJNA1347436: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1347436/.
