DOI: 10.5061/dryad.8931zcs16
title: Phenotypic divergence between hatchery pink and coho salmon and their wild counterparts

description: 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.
description: 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.
description: # 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 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 ## 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](https://github.com/alexgreich/2023_relaxed_selection_project).