This repository contains scripts, supporting data, and resources supporting the manuscript:
Spatiotemporal stability of fish communities in a regulated stream: Insights from environmental DNA.
✅ Open Science Compliance
This repository includes working versions of research materials for transparency and internal organization only. It is not a formal archive.
- Final versions of scripts, supporting data, and resources will be archived via Zenodo ([DOI to be added]) following the Ecological Society of America’s Open Research Policy.
- Raw sequencing data is archived via Dryad Digital Repository ([DOI to be added]).
🔗 DOI links will be added upon manuscript acceptance.
This is a community ecology study of freshwater fishes in Putah Creek (California, US), a remnant habitat for formerly abundant native freshwater and anadromous fishes (Moyle et al. 1998) and model system for stream restoration (Kiernan et al. 2012; Jacinto et al. 2023). The objectives of this study are to (1) elucidate spatiotemporal trends in fish assemblages along the longitudinal profile of a stream where flows are managed to benefit native anadromous fishes; (2) compare eDNA results with long-term standardized monitoring techniques at a subset of sites; and (3) assess how eDNA might be used to inform stream management to benefit native fishes. This work demonstrates the value of eDNA as a complement to conventional sampling for understanding community assembly dynamics in streams, including responses to ecosystem rehabilitation and flow management.
Figures, tables, and supplementary files, in the following subfolders:
1_sites_and_sequencing/– Sampling site metadata, sequencing summaries, and diversity metrics (e.g., richness, Shannon diversity)2_community_and_spatiotemporal_dynamics/– Community composition, NMDS ordination, and PERMANOVA analyses3_comparison_with_conventional_sampling/– Comparisons eDNA and conventional fish sampling results4_reordering_and_species_responses/– Gradient forest model, rank abundance curves (Whittaker plots) and exploratory mean rank shift
R scripts used in bioinformatic processing, statistical analysis, and figure generation.
Core processed data and resources, in the following subfolders:
1_reference_sequence_database/– Custom regional reference database used for taxonomic assignment, based on Nagarajan, Holmes, & Schreier (2023) and GenBank records This is an open access resource, see citation information below2_analysis_data/– Processed eDNA data including ASV tables, taxonomy, metadata, and eDNA index3_conventional_sampling/– Fish count and biomass data from electrofishing and traps at sites paired with eDNA sampling
- Scripts, data, and resources will be formally archived with a DOI via Zenodo (upon manuscript acceptance [DOI to be added]).
- Raw Illumina sequencing data will be archived with a DOI via Dryad ([DOI to be added]).
- Materials in this GitHub repository are provided as working versions for transparency and internal organization only, not as a formal archive.
If you use materials from this study, please cite the published manuscript when available:
Holmes, A., et al. (in prep). Spatiotemporal stability of fish communities in a regulated stream: Insights from environmental DNA. ([DOI to be added]).
If you use the custom 12S rRNA gene reference sequence database, please also cite this foundation resource:
Nagarajan, R., Holmes, A., & Schreier, A. (2023). Reference sequence database for eDNA metabarcoding of San Francisco estuary fishes and invertebrates [Dataset]. Dryad. https://doi.org/10.5061/dryad.0p2ngf25z
- Manuscript preprint (when available) ([DOI to be added]).
This repository was created by Ann Holmes
🔗 ORCID: 0000-0003-4775-868X
🌐 Personal research website: www.drannholmes.com
✉️ Contact: aholmes@ucdavis.edu