Data and code from: A framework for estimating age and growth using sibship relationships inferred from genomics data
Data files
Jul 03, 2026 version files 685.86 KB
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complete_fsib_lenDate_RTMB.csv
602.90 KB
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growth_simulation_v2026.R
29.87 KB
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README.md
2.12 KB
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sealamprey_age_growth_cluster_v2.R
31.44 KB
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simulation_check_error_in_fg_assign.R
19.53 KB
Abstract
Pedigree reconstruction based on genomics data offers a novel approach for estimating age and growth in wild populations. However, frameworks that use reconstructed pedigrees to parameterize growth models have not been available. We developed a sibship age and growth framework and evaluated the approach using simulation and an empirical application to sea lamprey (Petromyzon marinus) age and growth analysis. Simulation research revealed that the framework may be widely applicable to semelparous fishes. Applicability to iteroparous fishes was constrained to scenarios in which the percentage of multiage sibling groups was low. Age assignment using the framework was unbiased for sibling groups first captured at younger ages. Age assignment for sibling groups first captured at older ages were biased low due to the hierarchical approach we adopted to estimate sibling group age-at-first-capture. However, this did not result in biased growth parameter estimates. Additionally, model output allowed for identification of unreliable age assignments. Finally, the empirical application provided evidence that the framework could address knowledge gaps that have been challenging to address with established age and growth methods.
Dataset DOI: 10.5061/dryad.d7wm37qfv
Description of the data and file structure
Data and code are provided for the simulation study and for the empirical application of the growth model to sea lamprey.
Files and variables
File: growth_simulation_v2026.R
Description: R code for simulating sibship age and growth datasets, running the growth model, and summarizing the results. This code runs all simulations that assume 0 % multi-age full-sibling groups
File: sealamprey_age_growth_cluster_v2.R
Description: R code for the empirical application to sea lamprey
File: simulation_check_error_in_fg_assign.R
Description: R code for simulating sibship age and growth datasets, running the growth model, and summarizing the results. This code runs simulations with variable rates of multi-age full-sibling groups
File: complete_fsib_lenDate_RTMB.csv
Description: sea lamprey sibship dataset
Variables
- Date: date the larval sea lamprey was captured
- ID: a unique ID number
- Station_ID: a unique identifier denoted where in the stream the sample was collected from
- Section: part of the nested survey design (each station has multiple sections)
- Length_mm: length of the larvae (mm)
- collectionGearType: method of collection
- Weight_g: weight of the larvae (grams)
- fullSib_index: full sibling ID (unique by stream)
- FatherID: parent 1 unique ID (unique by stream)
- MotherID: parent 2 unique ID (unique by stream)
- sampling_year: year the larvae was collected
- Stream: stream in which the larvae was collected
Note: "NA" cells are used to denote "Not Applicable" or no data.
Code/software
R is needed to run the .R files. R packages that are required are noted in the R scripts. The analysis was conducted using
R version 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
