DOI: 10.5061/dryad.dz08kps63
title: Reproductive contribution of lake sturgeon transferred upstream of dams on a Great Lakes tributary

description: Dam construction contributes to declines in the abundance and distribution
 of many fishes. Increasing connectivity through adult transfer can be
 demographically/genetically beneficial but assessing the effects resulting
 from transfer can be difficult if resident fish exist upstream. Genotypes
 of adult/larval lake sturgeon (Acipenser fulvescens) were used to quantify
 contributions to larval recruitment from adults transferred upstream of
 dams on the Menominee River, USA. We evaluated whether transfer timing,
 sex, and adult size were associated with the odds of reproduction.
 Elevator transfer operations in Fall 2019/2020, and Spring 2021 resulted
 in 152 male and 81 female lake sturgeon transferred upstream. In 2020 and
 2021, 580 and 518 larvae were genotyped. 86% (201/233) of adults
 reproduced and 62.3% (684/1098) of offspring had transferred parents. 392
 resident adults contributed to offspring production. Mixed matings
 accounted for 53% of offspring genotyped, increasing levels of offspring
 genetic diversity relative to offspring produced from resident-only
 matings. Transferring adults may be a viable restoration alternative for
 other iteroparous fish in river systems where connectivity to spawning
 areas has been impeded.
description: Adult lake sturgeon for upstream transfer were collected from the
 section of the Menominee River below Menominee Dam and were released above
 Park Mill Dam into USF (Fig. 1). Collection of larval sturgeon for
 parentage assignment occurred in the upper portion of USF, just below
 Grand Rapids Dam.Standard D-frame drift nets were used to collect larval
 lake sturgeon dispersing from spawning grounds in 2020 and 2021 (Smith and
 King 2005; Tucker et al. 2021). Genomic DNA was extracted from fin clips
 of all adult and larval tissue using the DNeasy Blood and Tissue kit
 (QIAGEN, Germantown, MD). DNA samples were quantified using a NanoDrop
 1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and diluted
 to 20 ng/µl for use in PCR reactions. Individuals were genotyped at 13
 disomic microsatellite loci as described in Hunter et al. (2020) and
 Scribner et al. (2022).
description: README for: Forsythe et al. 2024. Reproductive contribution of lake
 sturgeon transferred upstream of dams on a Great Lakes tributary. Canadian
 Journal of Fisheries and Aquatic Sciences This repository contains the
 data and code used in the above study which investigated the effects of
 transferring adult lake sturgeon upstream of dams on the Menominee River,
 USA. ### Overview of the Study This study investigated the effects of
 transferring adult lake sturgeon upstream of dams on the Menominee River,
 USA, to mitigate the negative impacts of dam construction on fish
 populations. The study aimed to determine if transferring adult lake
 sturgeon upstream of dams can increase connectivity and improve the
 genetic diversity of the fish population. The researchers used genotypes
 of adult and larval lake sturgeon to infer the contributions of
 transferred adults to larval recruitment. The study also examined the
 effects of transfer timing, sex, and adult size on reproductive success.
 The study found that the majority of transferred adults reproduced and
 contributed significantly to the next generation of lake sturgeon. The
 results suggest that transferring adults may be an effective restoration
 strategy for other iteroparous fish species in river systems where dam
 construction has disrupted connectivity to spawning areas. ### Description
 of the Folders Each subfolder (analysis) contains an "Input"
 folder with all the data required for the R scripts in that directory. All
 R scripts include a detailed "About" section describing their
 purpose. All figures and analytical output were written to the
 subfolder's associated "Output" folder. Software
 Requirements for analyses described below: R (version 4.1.2 or later) and
 the following R packages were used: tidyverse, readxl, stringr ####
 Subfolder 1) Actual Data Analysis: This folder contains the data and
 scripts used to analyze the biological characteristics of the lake
 sturgeon population and assess reproductive success. R scripts: fitness
 evaluation both years.R: This script evaluates the fitness of the lake
 sturgeon population over both years of the study, considering factors
 associated with reproductive success. Mate pair randomization tests and
 stats with NoS19.R: This script conducts mate pair randomization tests and
 calculates statistics related to mate pair types. Input folder file: ALL
 ADULT DATA sex and biodata.xlsx: This file contains biological data for
 adult lake sturgeon, including: sample.id: Unique identifier for each
 individual sex: M = male, F = female collection: Date of specimen
 collection (MM/DD/YY) release: Date of specimen release upstream
 (MM/DD/YY) reintro.year: simplified cohort description to connect to
 offspring collected in subsequent year rs.20: To be filled with counts of
 offspring assignments in 2020 rs.21: To be filled with counts of offspring
 assignments in 2021 ms.20: To be filled with counts of mates in 2020,
 based on reconstructed pedigree ms.21: To be filled with counts of mates
 in 2021, based on reconstructed pedigree tl (mm): Total length in inches
 girth (mm): Thorax girth in inches season: Season specimen was transfered
 about the dam Output folder files: All adults bio data.txt: This file
 contains the same biological data as "ALL ADULT DATA sex and
 biodata.xlsx" but in a plain text format. The "rs" and
 "ms" columns are filled in with non-NAs integers that represent
 the counts of offspring and mates assigned to each parent in each cohort
 (2020 and 2021). In addition, tl has been converted in millimeters. suc.20
 and suc.21 were used in the logistic regression analysis to identify if a
 given adult successfully spawned based on if they were assigned to at
 least one offspring (1) or not (0). relyear and season2 were just columns
 describing what year the fish was transferred and what season and year
 (e.g., S19 - Spring 19). Both relyear and season2 information is
 represented in other columns as well. mp randomization tests 2019.txt:
 This file contains the results of mate pair (mp) randomization tests
 conducted for 2020 pedigree. These tests assessed whether the observed
 count of mate pair types differs significantly from a random distribution.
 mp randomization tests 2021 NoS19.txt: This file contains the results of
 mate pair randomization tests conducted for the 2021 reconstructed
 pedigree. mate pair breakdown both years NoS19.tiff: This file shows a
 breakdown of counts of offspring for each mate pair type
 (resident-resident, resident-migratory, migratory-migratory) for both
 years of the study, along with statistical significant based on the
 randomization procedure. repeat spawners.txt: This file lists the lake
 sturgeon that spawned multiple times during the study, along with their
 spawning years and other relevant information. reproductive success
 table.txt: This file contains summary statistics describing the
 reproductive success of the lake sturgeon population. successful spawning
 table.txt: This file provides details on successful spawning events,
 similar to the reproductive success table described above. #### Subfolder
 2) Relatedness Randomization: This folder contains the data and scripts
 used to randomize the relatedness of the lake sturgeon population and
 evaluate the impact of adult transfers on offspring genetic diversity. R
 scripts: relatedness simulations 2020.R: This script conducts the
 relatedness randomization tests for the lake sturgeon population in 2020.
 relatedness simulations 2021.R: This script conducts the relatedness
 randomization tests for the lake sturgeon population in 2021. cleaning up
 relatedness tables.R: This script organizes and prepares the relatedness
 tables for analysis. Input folder files:
 F19Adults_2020Kids2.BestConfig.txt and NoS19V1.BestConfig.txt: These files
 are Best Configuration pedigree reconstructions inferred by Colony, which
 infer which offspring were produced by which adults transferred above the
 dam, as well as which were produced by resident lake sturgeon above the
 dam. 2020 Offspring disomic loci.xlsx: This file contains disomic loci
 data (microsatellite markers) for the 2020 offspring, which were used to
 estimate rxy for all possible offspring dyads in 2020. Each row represents
 an individual, and each column represents an allele for a specific locus.
 2021 Offspring disomic loci.xlsx: This file contains disomic loci data
 (microsatellite markers) for the 2021 offspring, which were used to
 estimate rxy for all possible offspring dyads in 2020. Data are structured
 the same as the 2020 offspring file. Output folder files: 2020 offspring
 pairwise relatedness values.txt: This file contains pairwise relatedness
 values for the 2020 offspring, which were inferred based on disomic loci
 in the program Coancestry using the trio-ML method. 2021 offspring
 pairwise relatedness values.txt: This file contains pairwise relatedness
 values for the 2021 offspring. output summary 2020.txt: This file
 summarizes the 2020 simulation output that tested is the ratio of the
 median rxy the two groups were expected by chance alone. See supplemental
 file for more details. output summary 2020 ordered.txt: This file
 summarizes the 2020 simulation output, ordered by the pairs of parental
 categories being compared. output summary 2021.txt: This file summarizes
 the 2021 simulation output, similar to the 2020 summary file. output
 summary 2021 ordered.txt: This file summarizes the 2021 simulation output,
 ordered by the pairs of parental categories being compared. Randomization
 tables.xlsx: This file contains the randomization tables used in the study
 to summarize median ratios and statistical significance for both cohorts
 of offspring produced. #### Subfolder 3) Simulating Colony Dat Files: This
 folder contains the data and scripts used to simulate colony dat files,
 which are used for pedigree reconstructions. R script: colony inputPar
 simulations RESrandDRAW.R: This script simulates the colony input
 parameters for the RESrandDRAW simulation, which is used to reconstruct
 pedigrees using genotypic information. Input folder files 2020 Menominee R
 Af genotyping data 121721_FINAL.xlsx: This file contains genotyping data
 both disomic and polysomic microsatellite markers for the Menominee River
 adult lake sturgeon population. Each row represents an individual, and
 each column represents an allele for a specific locus. Output folder files
 Scenarios representing when 25%, 50%, or 75% of transferred adults
 successfully reproduced. Read more about the simulations in the
 "About" part of the associated R script. Importantly, the Output
 folder has three subfolders associated with these three different
 simulated scenarios: sims_adults25successful, sims_adults50successful, and
 sims_adults75successful. Within each, there are three additional folders:
 breeding matrices, colony_dat, and input_par - these three folders contain
 output files, of the same name, for each simulation. Also, a .txt file
 contains summary statistics associated with each simulation for each
 scenario - again, see the R script's ABOUT section (and below) for
 more details. The four remaining folders are empty and were used for
 copy/pasting the subfolder structure multiple times. #### Subfolder 4)
 Simulation Analysis: This folder contains the data and scripts used to
 analyze the simulations, assess the accuracy of parentage assignments, and
 evaluate the performance of different simulation scenarios. R scripts:
 Step 1 - sim.analysis.Bestconfig.summaries.R: This script performs the
 first step in the simulation analysis, focusing on summarizing results
 from the "best configuration" pedigrees inferred by Colony for
 each simulation. Step 2 - sim.analysis.adding.confit.output.summaries.R:
 This script integrates results from other configuration output summaries
 with all possible assignment rates between offspring, providing a more
 comprehensive view of the simulation results. Step 3 -
 sim.analysis.graphics.pubs.R: This script generates the graphics (plots
 and visualizations) used in the publication. Step 4 -
 expected.false.assignments.R: This script calculates or estimates the
 expected number of false parentage assignments in the simulations, helping
 to assess the accuracy of the parentage analysis. Input folder files AND
 folders: sim.info_mom0.25_dad0.25.txt: This file contains information
 about a simulation with a 25% successful spawning rate for both females
 and males. This information was used in the Simulation analysis to compare
 true number of transferred adults and resident adults that produced
 offspring used in pedigree constructued to the number inferred by Colony.
 Information in the columns are as follows: n.par: The number of parents in
 the simulation. n.mom: The number of mothers in the simulation. n.dad: The
 number of fathers in the simulation. sex.ratio: The sex ratio of the
 parents (dads/moms). noff: The number of offspring in the breeding matrix.
 female.rs: The mean number of offspring produced per female.
 females.mates: The mean number of mates per female. male.rs: The mean
 number of offspring produced per male. male.mates: The mean number of
 mates per male. mp.count: The total number of mate pairs. mp.rs: The mean
 number of offspring produced per mate pair. type: Whether the breeding
 matrix "Before" any subsampling happened or "After"
 the 580 offspring were sampled randomly. lost: The number successful mate
 pairs where none of there offspring were sampled in the 580 collected.
 sim: The simulation replicate number. tot.mom: The total number of
 potential transferred mothers (including unsampled). tot.dad: The total
 number of potential transferred fathers (including unsampled). mom.prob:
 The probability that a transfered mother was successful at reproduction.
 dad.prob: The probability that a transfered mother was successful at
 reproduction. unsampled: The number of unsampled parents after randomly
 sampling 580 offspring. res.mom: The number of resident mothers in the
 original breeding matrix. res.dad: The number of resident fathers in the
 original breeding matrix. sim.info_mom0.5_dad0.5.txt: This file contains
 similar information to the previous file but for a simulation with a 50%
 successful spawning rate for both females and males.
 sim.info_mom0.75_dad0.75.txt: This file contains similar information to
 the previous files but for a simulation with a 75% successful spawning
 rate for both females and males. BestConfigs subfolder: This folder
 contains the "best configuration" pedigrees inferred by COLONY
 software for each simulated dataset in each simulation scenario.
 Confit.summaries subfolder: This folder contains text files that summarize
 confusion matrices associated with each simulations BestConfiguation file
 inferred by COLONY. The number of known (real.type) full-siblings (FS),
 half-siblings (HS), and unrelated (UR) offspring dyads. The FS, HS, and UR
 columns are what were inferred by COLONY. The real.type column rows
 represent known FS, HS, and UR dyads. The counts are summed rowwise in the
 total column. And pFS, pHS, and pUR. Are just the proportions of counts
 divided by the total column. Output.summaries subfolder: This folder
 contains summaries statistics based on the best configuration pedigree
 (estimated - est) inferred by COLONY and what was known based by
 simulation information embedded in offspring names (real) for the number
 of mate pairs (mp), the number of fullsiblins (nFS), number of maternal
 and paternal halfsiblings (nMHS and n PHS). The number of parents, as well
 as the mean and variance in reproductive success (counts of offspring
 assigned to each parent in the pedigree). Output folder files:
 confusion.matrix.jpeg: This file shows a confusion matrix that visualizes
 the accuracy of parentage assignments in the simulations.
 confusion.matrix.pub.tiff: This file contains the same confusion matrix as
 the JPEG version but in a higher-resolution format suitable for
 publication. expected_migartory_parent_distributions_bothsexes.jpeg: This
 file shows the expected distributions of migratory parents (both sexes) in
 the simulations.
 expected_migartory_parent_distributions_bothsexes.pub.tiff: This file
 contains the same distributions as the JPEG version but in a
 higher-resolution format suitable for publication.
 inferred2known_ratio_bothsexes.jpeg: This file visualizes the ratio of
 inferred to known parents for both sexes in the simulations.
 inferred2known_ratio_bothsexes.pub.tiff: This file contains the same
 visualization as the JPEG version but in a higher-resolution format
 suitable for publication. inferred2known_relationship_bothsexes.jpeg: This
 file visualizes the relationship between inferred and known parents for
 both sexes. inferred2knownresidents_dads.jpeg: This file visualizes the
 relationship between inferred and known resident fathers.
 inferred2knownresidents_moms.jpeg: This file visualizes the relationship
 between inferred and known resident mothers.
 inferred2knownresidents_parents.pub.tiff: This file contains a
 visualization of the relationship between inferred and known resident
 parents in a higher-resolution format suitable for publication.
 simulation.bestconfig.info.txt: This file contains information
 specifically from the simulations using the "best configuration"
 pedigree and is effectively an intermediate file created before adding in
 the confit and output.summary information for each simulation.
 simulation.all.info.txt: This file contains comprehensive information from
 all the simulations, including the number of offspring,the number of
 parents, the proportion of migratory parents, and the accuracy of
 parentage assignments.