Data and code from: Variety is the spice of life: nongenetic variation in life histories influences population growth and evolvability
Data files
Oct 03, 2024 version files 5.29 MB
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FixedG1000P4Juv1.RDS
1.68 MB
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FixedG1000P4Juv10.RDS
1.68 MB
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README.md
3.21 KB
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UncorrelatedG1000P4Juv1.RDS
916.97 KB
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UncorrelatedG1000P4Juv10.RDS
1.01 MB
Abstract
Individual vital rates, such as mortality and birth rates, are key determinants of lifetime reproductive success, and variability in these rates shapes population dynamics. Previous studies have found that this vital rate heterogeneity can influence demographic properties including population growth rates. However, the explicit effects of the amount of variation within and the covariance between vital rates that can also vary throughout the lifespan on population growth remains unknown. Here, we explore the analytical consequences of nongenetic heterogeneity on long-term population growth rates and rates of evolution by modifying traditional age-structured population projection matrices to incorporate variation among individual vital rates. The model allows vital rates to be permanent throughout life ("fixed condition”) or to change over the lifespan ("dynamic condition”). We reduce the complexity associated with adding individual heterogeneity to age-structured models through a novel application of matrix collapsing ("phenotypic collapsing"), showing how to collapse in a manner that preserves the asymptotic and transient dynamics of the original matrix. The main conclusion is that nongenetic individual heterogeneity can strongly impact the long-term growth rate and rates of evolution. The magnitude and sign of this impact depends heavily on how the heterogeneity covaries across the lifespan of an organism. Our results emphasize that nongenetic variation cannot simply be viewed as random noise, but rather that it has consistent, predictable effects on fitness and evolvability.
Code prepared for the following article: Forsythe, A.B., S.P. Otto, W.A. Nelson, and T. Day. 2024. Variety is the spice of life: nongenetic
variation in life histories influences population growth and evolvability. Journal of Evoluionary Biology.
All code performed in R (version 4.3.1, R Core Team 2023).
There are 3 code files (prepared as R Markdown files) and 4 data files
(prepared as .RDS files) for this manuscript:
1. "Code for Genotype Simulations - Fixed Condition.Rmd" -This file
provides the code used to simulate genotypes with nongenetic
heterogeneity that is permanent throughout life ("fixed condition")
-Packages used: mvtnorm (version 1.2-4), Matrix (version 1.6-5) - for
multivariate normal distributions and sparse matrices, respectively -The
output of this code produces the data contained in two .RDS files:
"FixedG1000P4Juv1.RDS" and "FixedG1000P4Juv10.RDS"
2. "Code for Genotype Simulations - Uncorrelated Condition.Rmd" -This file
provides the code used to simulate genotypes with nongenetic
heterogeneity that allows vital rates to change randomly throughout life
("uncorrelated condition") -Packages used: mvtnorm (version 1.2-4), Matrix
(version 1.6-5) - for multivariate normal distributions and sparse
matrices, respectively -The output of this code produces the data
contained in two .RDS files: "UncorrelatedG1000P4Juv1.RDS" and
"UncorrelatedG1000P4Juv10.RDS"
3. "Code for Genotype Simulations - Plots.Rmd" -RUN LAST -This file
provides the code to make the figures (main text and supplementary),
using the data from the simulations in the above two files. -Packages
used: ggplot2 (version 3.4.4), ggpubr (version 0.6.0)
4. The 4 data (.RDS) files contain the simulation outputs that were
used to generate the plots in the main text and supplemental PDF of the
manuscript. There are 3 columns in each .RDS file: 1) "fits" - the fitness of a genotype, 2) "scalar" - the ratio of nongenetic:genetic variation for that genotype, 3) "type" - the genetic covariance structure, followed by the nongenetic covariance (0 = none, + = positive covariance, - = negative covariance)
Citations:
Douglas Bates, Martin Maechler, Mikael Jagan. (2024). Matrix: Sparse and Dense
Matrix Classes and Methods. R package version 1.6-5. URL
https://CRAN.R-project.org/package=Matrix
Alan Genz, Frank Bretz, Tetsuhisa Miwa, Xuefei Mi, Friedrich Leisch,
Fabian Scheipl, Bjoern Bornkamp, Martin Maechler, Torsten Hothorn. (2023). mvtnorm: Multivariate Normal and
t Distributions. R package version 1.2-4. URL
http://CRAN.R-project.org/package=mvtnorm
Alboukadel Kassambara. (2023). ggpubr: 'ggplot2' Based Publication
Ready Plots. R package version 0.6.0. URL
https://CRAN.R-project.org/package=ggpubr
R Core Team. 2023. R: a language and environment for statistical
computing. R Foundation for Statistical Computing, Vienna.
H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag
New York, 2016.
These files contain all R code used for performing simulations and generating plots in: "Variety is the spice of life: nongenetic variation in life histories influences population growth and evolvability" (Forsythe et al. 2024, Journal of Evolutionary Biology). The code is provided as RMarkdown (.RMD) files. The .RDS files contain the ouput data from the simulations that were used to generate the plots. The README.md provides information about each file and the packages required (for code files).
- Forsythe, Amy B.; Otto, Sarah P.; Nelson, William A.; Day, Troy (2024). Data and code from: Variety is the spice of life: nongenetic variation in life histories influences population growth and evolvability. Zenodo. https://doi.org/10.5281/zenodo.8162155
- Forsythe, Amy B.; Otto, Sarah P.; Nelson, William A.; Day, Troy (2024). Data and code from: Variety is the spice of life: nongenetic variation in life histories influences population growth and evolvability. Zenodo. https://doi.org/10.5281/zenodo.8162154
- Forsythe, Amy B.; Otto, Sarah P.; Nelson, William A.; Day, Troy (2024). Variety is the spice of life: nongenetic variation in life histories influences population growth and evolvability [Preprint]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.03.02.583100
- Forsythe, Amy B; Otto, Sarah P; Nelson, William A; Day, Troy (2024). Variety is the spice of life: nongenetic variation in life histories influences population growth and evolvability. Journal of Evolutionary Biology. https://doi.org/10.1093/jeb/voae107
