Environmental DNA provides quantitative estimates of Pacific hake abundance and distribution in the open ocean

All species inevitably leave genetic traces in their environments, and the resulting environmental DNA (eDNA) reflects the species present in a given habitat. It remains unclear whether eDNA signals can provide quantitative metrics of abundance on which human livelihoods or conservation successes depend. Here, we report the results of a large eDNA ocean survey (spanning 86,000 km2 to depths of 500m) to understand the abundance and distribution of Pacific hake Merluccius productus, the target of the largest finfish fishery along the west coast of the United States. We sampled eDNA in parallel with a traditional acoustic-trawl survey to assess the value of eDNA surveys at a scale relevant to fisheries management. Despite local differences, the two methods yield comparable information about the broad-scale spatial distribution and abundance. Furthermore, we find depth and spatial patterns of eDNA closely correspond to acoustic-trawl estimates for hake. We demonstrate the power and efficacy..., There are two main datasets for this paper. Both were collected during the 2019 U.S.-Canada Integrated Ecosystem & Acoustic-Trawl Survey for Pacific hake aboard the NOAA Ship Bell M. Shimada from July 2 to August 19. The first is data associated hake DNA concentrations as identified in water samples collected and analyzed using qPCR analysis. The second dataset is estimates of hake biomass derived from analysis of the acoustic-trawl information. Refer to the primary manuscript for detailed information on data collection and processing protocols., We provide scripts for reading in and manipulating data as well as estimating statistical models and visualizing results from the raw data. Please refer to scripts in the repository for manipulations of the raw data.
, , # Data from: Environmental DNA provides quantitative estimates of Pacific hake abundance and distribution in the open ocean

Dataset DOI: [10.5061/dryad.n2z34tmzf](https://doi.org/10.5061/dryad.n2z34tmzf)

## Description of the data and file structure

This repository supports the publication, \"Environmental DNA provides quantitative estimates of Pacific hake abundance and distribution in the open ocean\" by Shelton et al. It contains raw data, scripts for processing that data, code for estimating statistical models from that data, and code for post-processing those model fits.

The primary scripts are found in the \"Scripts.zip\" and begin with the numbers 01 to 05:

* 01_qPCR_analysis.R reads in qPCR data and estimates statistical models of hake qPCR.
* 02_acoustics_analysis.R reads in acoustic estimates of biomass density and estimates statistical models for hake biomass.
* 03_post_process_acoustics_Output.R processes the fitted MCMC object from the eDNA models, calculates summary stati..., **Changes after Mar 31, 2022:** 

Added two compressed files. One containing all of the data used in the analysis and one providing all of the scripts and model outputs files. Added an improved read me file to direct readers to the necessary folders.

Removed file 6038706 because it contained absolutely nothing useful.
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