Klamath River renewal project molecular library

The Klamath River Renewal Project (KRRP) is a large dam removal and river restoration project in California and Oregon, United States. With the removal of four large dams in 2024, restoration of connectivity to 640 river kilometers occurred. We created the KRRP molecular library, an environmental specimen bank, for long-term curation of environmental nucleic acids collected from the restoration project area. The library established sampling stations from 45 main stem and tributary sites, as well as pre-dam removal water samples preserved for environmental nucleic acids (eDNA and eRNA) intended to provide long-term use of both raw and extracted molecular material used to track the ecosystem response to dam removal. On a subset of samples, we conducted DNA metabarcoding using next generation sequencing based on the MiFish-U and modified MiFish-U-F primer sets. We used sequence reads to visualize data and calculate diversity metrics to establish a pre-dam removal baseline and proof of conc..., Step 1
On the Klamath River, we selected monitoring locations systematically every 2 km along the river and reservoirs and every 1 km along selected tributaries, with additional sites included near long-term monitoring locations important to the restoration project. Monitoring locations spanned approximately 114 km of mainstem and tributary habitat. Sites were selected along navigable streams and only at locations where long-term continued accessibility was assumed. Sites along the river extend from approximately 3.5 km downstream of the lowermost dam upstream to where the river enters the uppermost reservoir to be removed. Tributary sites extended upstream to fish migration barriers, or as far as the project boundary allowed. Additionally, six “reference” sites in the Scott River basin, a large tributary downstream of the project area, were included to represent habitat not impacted by dams. Having a range of non-treatment reaches from which to compare treatment (i.e., dam removal) eff..., , # Klamath River renewal project molecular library

[https://doi.org/10.5061/dryad.0cfxpnwcn](https://doi.org/10.5061/dryad.0cfxpnwcn)

## Description of the data and file structure

### Files and variables

#### File: Klamath\_Molecular\_Library\_metadata.xml

**Description:** Metadata record of Klamath_ML_Raw.Reads.2023.csv and Klamath_ML_Sample.ID.Metadata.2024.csv following FDGC compliant metadata standards.

#### File: Klamath\_ML\_Raw\.Reads.2023.csv

**Description:** Comma Separated Value (CSV) file containing data.

##### Variables

* MiseqRun: The run identifier code for the DNA next generation sequencing that was conducted on a Illumnina Miseq
* Sample.ID: A unique sample identification code for each sampling site
* ESVseq: \"Exact Sequence Variant\", referring to the unique DNA sequence obtained from metabarcoding.
* ESVsize: ESVsize is the number of reads of the given ESVseq
* CommonName: The common name of the taxon identified from next generation sequencing results.
* Klamath...,