Phenotypic divergence between hatchery pink and coho salmon and their wild counterparts

Interbreeding between hatchery-reared and wild salmon raises concerns that hatchery fish may increase the frequency of maladapted alleles in wild populations, yet divergence between hatchery populations and their original sources remains poorly understood. We explored phenotypic divergence in reproductive traits between hatchery and source populations of pink and coho salmon in Southeast Alaska, hypothesizing that relaxed selection in the hatchery would result in males with smaller snouts and humps and females with larger gonadosomatic indices (GSI) and smaller, less nutrient-dense eggs. Findings partly confirmed these expectations. Our hypotheses were supported in coho salmon females and odd-year pink salmon males, but results from coho salmon males opposed our hypotheses, and we observed no phenotypic divergence in even-year pink salmon, possibly due to high gene flow between hatchery and wild populations. These mixed results indicate significant yet variable phenotypic differences be..., Pink salmon were collected from Sashin Cove and Lovers Creek, and at Port Armstrong Hatchery on south Baranof Island in 2020 and 2021. Coho salmon were collected from Fish Creek (near the Alaska-Canada border of the Taku River) and DIPAC Macaulay Hatchery in Juneau in 2020. The male fish were measured (mid-eye to hypural plate) and photos taken from a camera stand. The female fish were weighed, and the gonads were weighed, and egg samples were collected. Eggs were measured using calipers and ImageJ. The egg samples were processed at NOAA Auke Bay Labs for the lipid and energy density.
Gonadosomatic index (GSI) was calculated for the females.
The datasets were read into R for statistical analyses., , # Phenotypic divergence between hatchery pink and coho salmon and their wild counterparts

## Datasets, organized by topic

### Notes:

The data is separated by species and year: pink 2020, pink 2021, and coho.

The data is also separated by object of interest: GSI, eggs, length, energy, etc.

The data files are named in a specific way to be read specifically into the code for analysis.

Please note that NA in any column indicates an error during field collection and unavailability of that data point. A NA or blank column in the comments column represents the lack of a notable comment.

## Gonadosomatic index datasets:

* FemalePinkGSIotodataadd1_without_gaps copy.csv
*  even-year female pink salmon GSI dataset
* Columns:
* ID: The fish identification number
* Length (mm): The fish's mid-eye to hypural plate length, in millimeters (mm)
* Body depth (mm): A measurement from directly in front of the dorsal fin to the ventral side of the fish, measuring the fish's body dept...,