Phenotypic divergence between hatchery pink and coho salmon and their wild counterparts
Data files
Apr 15, 2025 version files 148.06 KB
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Data_to_give_to_publication_-_Copy.zip
131.86 KB
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README.md
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Abstract
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 between hatchery and wild salmon in key reproductive traits. Our study provides a rare comparison of how hatchery rearing affects reproductive traits between species with different life histories in Southeast Alaska.
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 depth, in mm
- Fish Weight (g): The weight of the fish in the field, in grams (g)
- Total Egg Mass (g): Measurement of the fish’s egg mass in the field, in grams
- Average egg diameter: The average of 50 individual egg measurements from that fish, in mm.
- Whatman Grid Number: Corresponds to the storage of a fin clip for further genetic analysis
- Date: The date of collection
- Location: The location of the collection
- Otolith results: after the wild fish otolith reading, indication if the fish originated from the wild (no mark), the hatchery (PORT ARMSTRONG), or if the otolith could not be read (unknown). Hatchery fish otoliths were not read but were assumed to originate from PORT ARMSTRONG.
- Wild or Hatchery: indication if the fish is a wild fish or a hatchery fish
- Notes: any notes taken in the field
- Weird: an indicator to identify fish of questionable data collection quality to exclude from data analysis
- Female.p2.Rdata.3.csv
- odd-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 depth, in mm
- Fish Weight (g): The weight of the fish in the field, in grams (g)
- GSI measure 1(g): the total egg mass in grams used for analysis
- GSI measure 2(g) the total egg mass in grams measured by removing more ovarian fluid, experimental, and not used for analysis
- Oto: otolith collection confirmation, y for yes, n for no, 1 for only one, and unknown for a lost sample
- Gen card: reference to the fin clip location for a future genetics study
- Gen grid: reference to a fin clip location for a future genetics study
- Location: field collection location
- Date: date of collection
- NOTES: field notes
- Oto reading: results of the laboratory otolith reading, indicating the fish origin. PORT AMSTRONG indicates the hatchery, No Mark indicates the wild, and No Oto or Overground indicates data collection errors.
- Weird: an indicator if the fish should be left out of analysis due to questionable data quality
- Label: the name of the label in the egg sample
- MASTERFemaleCohoQCwitheggs_copy.csv
- female coho 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 depth, in mm
- Fish Weight (g): The weight of the fish in the field, in grams (g)
- Total Egg Mass (g): Measurement of the fish’s egg mass in the field, in grams
- Average diameter: The average of 50 individual egg measurements from that fish, in mm.
- Genetics grid number: Corresponds to the storage of a fin clip for future genetic analysis
- Date: The date of collection
- Location: The location of the collection
- Wild or Hatch: categorization of wild and hatchery fish
- Tare egg jar (g): the weight of the jar that held the egg samples
- Notes: field notes
- Fish ID: The fish identification number in a more R-friendly form
- Weird: an indicator if the fish should be left out of analysis due to questionable data quality
Egg datasets:
- P1.egg.diameters.csv
- even-year pink salmon egg diameter dataset
- Columns:
- Fish ID: fish identification number
- Egg #: egg identification number (up to 50 per fish)
- Diameter (mm): egg diameter, in millimeters
- Wild or Hatch: wild or hatchery fish identification
- Date: date of egg measurement
- Location: fish collection location
- Results.p2.ImageJ.eggs.csv
- odd-year pink salmon egg diameter dataset
- Columns:
- Label: fish identification code
- Area: area of the egg (millimeters)
- Wild.or.Hatch: wild (W) or hatchery (H) fish designation
- coho.egg.diameters.csv
- Coho salmon egg diameter dataset
- Columns:
- Fish ID: fish identification number
- Egg #: egg identification number (up to 50 per fish)
- Diameter (mm): egg diameter, in millimeters
Other datasets linked to the egg analysis:
- p2.GSI.clean_altdate
- used to test for the significance of Julian date in the odd-year pink GSI analysis
- 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 depth, in mm
- Fish.Weight.g.: The weight of the fish in the field, in grams (g)
- GSI.measure.1.g.: the total egg mass in grams used for analysis
- GSI.measure.2.g.: the total egg mass in grams measured by removing more ovarian fluid, experimental ,and not used for analysis
- Oto: otolith collection confirmation, y for yes, n for no, 1 for only one, and unknown for a lost sample
- Gen.card: reference to the fin clip location for a future genetics study
- Gen.grid: reference to a fin clip location for a future genetics study
- Location: field collection location
- Date: date of collection
- NOTES: field notes
- Oto.reading: results of the laboratory otolith reading, indicating the fish origin. PORT AMSTRONG indicates the hatchery, No Mark indicates the wild, No Oto or Overground indicates data collection errors.
- Weird: an indicator if the fish should be left out of analysis due to questionable data quality
- Label: the label from the egg measurement (matches with fish ID)
- X: additional commnets
- GSI.2: the calculated gonadosomatic index, used for analysis
- GSI.1: an alternative method of gonadosomatic index calculation, not used for analysis
- Date_alt: a categorical value that states if the fish was in the earlier or later sampling period
- p2_female_snag.csv
- investigating any differences in the method of fish capture for odd-year pink female salmon
- 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 depth, in mm
- Fish Weight (g): The weight of the fish in the field, in grams (g)
- GSI measure 1(g): the total egg mass in grams used for analysis
- GSI measure 2(g) the total egg mass in grams measured by removing more ovarian fluid, experimental, and not used for analysis
- Oto: otolith collection confirmation, y for yes, n for no, 1 for only one, and unknown for a lost sample
- Gen card: reference to the fin clip location for a future genetics study
- Gen grid: reference to a fin clip location for a future genetics study
- Location: field collection location
- Date: date of collection
- NOTES: field notes
- Oto reading: results of the laboratory otolith reading, indicating the fish origin. PORT AMSTRONG indicates the hatchery, No Mark indicates the wild, and No Oto or Overground indicates data collection errors.
- Green, too ripe, or any other reason to drop this sample?: an indicator if the fish should be left out of analysis due to questionable data quality
- Catch method: weir, snag, seine, or hatchery, a categorical variable of catch method
- p2_male_snag.csv
- Columns:
- ID: fish identification number
- Length(mm): length of the fish, from the mid-eye to hypural plate, in millimeters
- 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 depth, in millimeters
- Snout length(mm): a measurement from the tip of the snout (kype) to the mid-eye, in millimeters
- Weight(g): mass of the fish, in grams
- Photo: yes(y) or no(n), if a morphometric photo was taken of the fish
- Oto: yes(y) or no(n), indicating if the otolith was collected
- Gen card: the identification card on which the fin clip was stored
- Gen grid: fin clip location on the genetics card grid
- Location: fish collection location
- Date: date of sampling
- Otolith reading: No Mark indicating a wild fish, PORT ARMSTRONG indicating a hatchery fish, or Overground, indicating an otolith that could not be read
- Notes: comments on sampling
- Catch method: weir, snag, seine, or hatchery, a categorical variable of catch method
Bomb calorimetry datasets:
- Hatchery egg condition data 1-11-22_modified copy.csv
- Coho salmon egg energy and lipid content data
- Columns:
- SIN: subject identification number
- InvestNo: fish identification number
- SpeciesCode: fish species
- Tissue: type of tissue
- Comments: # of eggs in sample
- %Moisture: moisture content of sample
- BombED(Dry): energy density of sample
- % lipid: percent lipid of sample
- Wild_or_hatch: W for wild fish, H for hatchery fish
- GSI, egg, and morphometric datasets were mutated to work smoothly in the bomb calorimetry analysis
- c_GSI_for_boms copy.csv and c_GSI_clean_for_bomb copy.csv
- 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 depth, in mm
- Fish.Weight..g.: The weight of the fish in the field, in grams (g)
- Total.Egg.Mass..g.: Measurement of the fish’s egg mass in the field, in grams
- Average.Diameter: The average of 50 individual egg measurements from that fish, in mm.
- Genetics.Grid.Number: Corresponds to the storage of a fin clip for future genetic analysis
- Date: The date of collection
- Location: The location of the collection
- Wild.or.Hatch: categorization of wild and hatchery fish
- Tare.egg.jar..g.: the weight of the jar that held the egg samples
- Notes: field notes
- Fish.ID: The fish identification number in a more R-friendly form
- Weird: an indicator if the fish should be left out of analysis due to questionable data quality
- GSI: gonadosomatic index of the fish
- c_all_eggs_bomb copy.csv
- Columns:
- Fish.ID: the fish identification number
- Egg..: the egg identification number (50 or fewer per fish)
- Diameter..mm.: the egg diameter, in millimeters
- Columns:
Male morphometric datasets:
- Coho_morpho_data.csv:
- the coho male salmon dataset
- Columns:
- ID: fish identification number
- length: length of the fish, in millimeters, from the mid-eye to the hypural plate
- snout: length of the tip of the fish’s snout (kype) to mid-eye, in millimeters
- Wild.or.hatch: categorical variable indicating if the fish is of wild (W) or hatchery (H) origin
- depth: a measurement from directly in front of the dorsal fin to the ventral side of the fish, measuring the fish’s body depth, in millimeters
- pink_morpho_data.csv:
- the even-year pink male salmon dataset
- Columns:
- ID: fish identification number
- length: length of the fish, in millimeters, from the mid-eye to the hypural plate
- snout: length of the tip of the fish’s snout (kype) to mid-eye, in millimeters
- Wild.or.hatch: categorical variable indicating if the fish is of wild (W) or hatchery (H) origin
- depth: a measurement from directly in front of the dorsal fin to the ventral side of the fish, measuring the fish’s body depth, in millimeters
- Male.p2.Rdata.2.csv
- male odd-year pink salmon data
- 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 depth, in mm
- Snout length(mm): length of the tip of the fish’s snout (kype) to mid-eye, in millimeters
- Weight(g): The weight of the fish in the field, in grams
- Photo: indicates if a field photo was taken, yes (y) or no (n)
- Oto: indicates if an otolith was collected, yes (y) or no (n)
- Gen card, Gen grid: Corresponds to the storage of a fin clip for future genetic analysis
- Location: The location of the collection
- Date: The date of collection
- Otolith results: the reading of the otolith, indicating wild (No Mark), hatchery (PORT ARMSTRONG), or unidentified origin (Overground) fish. Otoliths from fish collected at the hatchery were not read, and were assumed to be hatchery origin.
- Notes: field notes, if any
- p2.males2_dateadj.csv
- male odd-year pink salmon date data
- 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 depth, in mm
- Snout.length.mm.: length of the tip of the fish’s snout (kype) to mid-eye, in millimeters
- Weight.g.: The weight of the fish in the field, in grams
- Photo: indicates if a field photo was taken, yes (y) or no (n)
- Oto: indicates if an otolith was collected, yes (y) or no (n)
- Gen.card, Gen.grid: Corresponds to the storage of a fin clip for future genetic analysis
- Location: The location of the collection
- Date: The date of collection
- Otolith.results: the reading of the otolith, indicating wild (No Mark), hatchery (PORT ARMSTRONG), or unidentified origin (Overground) fish. Otoliths from fish collected at the hatchery were not read, and were assumed to be hatchery origin.
- Notes: field notes, if any
- Date_adj: a categorical value of the run time of fish collection (early, middle, or late)
Analysis files
Masters_thesis_organization.R
- This R file analyzes GSI and egg diameter for the pink 2020, pink 2021, and full coho datasets. It spits out two CSVs into the results folder, one for GSI and the other for egg. It also spits out the GSI/EGG graph into the Plots folder and results into the results folder.
Bomb_final_simple_dec2023.Rmd
- This RMD analyzes the bomb data. There’s some excess exploratory stuff in there, but essentially the file spits out one combined egg energy and lipid csv into the Results folder and a two plots into the Plots folder: a boxplot (for the supplement) and a violin plot (we chose not to use this one, but it exists).
Male_morpho_analysis_basics_nogeomorph.R
- This code runs the analysis for the male linear morphometrics. This is a simplified version of Male_morpho_analysis_cleanup_dec_2023.R, with the geometric morphometric analysis removed. I plan to publish the geometric morphometric results in a later paper.
The code was run using R version 4.1.0.
The code is also available on my GitHub: https://github.com/alexgreich/2023_relaxed_selection_project.
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.