Quantitative genetics of extreme insular dwarfing: The case of red deer on Jersey

This repository contains codes of the paper published in the Journal of Biogeography.

How to cite

Diniz-Filho, J.A.F., Santos, A.M.C., Barreto, E., Naves, F., Santos, W., Souza, K.S., Santos-Silva, R., Dobrovolski, R., Soares, T.N., Tidon, R., Spigoloni, Z.A., Rangel, T.F., Raia, P., Hortal, J. and Jardim, L. (2021), Quantitative genetics of extreme insular dwarfing: The case of red deer on Jersey. J Biogeogr. https://doi.org/10.1111/jbi.14109

Data

This study simulates an individual-based quantitative genetics model parameterized with red deer life-history data gathered from the literature (more details). All data are available in DRYAD.

Analyses

The folders contain files to reproduce each simulation scenarios (1) Baseline, (2) constant_k, (3) no_plasticity, (4) no_recolonization and (5) no_reproduction_system. There is also a file named island_area.txt, which contains data of the island area (Kisl) and isolation (migr) changes through time.

Repository structure

Jersey_cervus/
├── R
│   ├── baseline  
│   │ # The baseline model includes non-constant carrying capacity,phenotypic plasticity, island recolonization,
│   │ # and sexual dimorphism.
│   │   ├── AdaptSS_cervus_K.R
│   │   └── parallel_function_cervus.R
│   │
│   ├── constant_k
│   │   # Scripts to run baseline models with constant carrying capacity through time.
│   │   ├── AdaptSS_cervus_K.R
│   │   └── parallel_function_cervus.R
│   │
│   ├── no_plasticity
│   │   # Scripts to run baseline models without phenotypic plasticity.
│   │   ├── AdaptSS_cervus_K_no_plasticity.R
│   │   └── parallel_function_cervus.R
│   │
│   ├── no_recolonization
│   │   # Scripts to run baseline models without island recolonization.
│   │   ├── AdaptSS_cervus_K_no_recolonization.R
│   │   └── parallel_function_cervus.R
│   │
│   └── no_reproduction_system
│       # Scripts to run baseline models without sexual dimorphism.
│       ├── AdaptSS_cervus_no_reproduction_system.R
│       └── parallel_function_cervus.R
│
├── data
│   └── island_area.txt
├── tests
│   ├── test-AdaptSS_constant_k.R
│   ├── test-AdaptSS_no_plasticity.R
│   ├── test-AdaptSS_no_recolonization.R
│   ├── test-AdaptSS_no_reproduction.R
│   ├── test-AdaptSS.R
│   ├── test-run_generation_constant_k.R
│   ├── test-run_generation_no_plasticity.R
│   ├── test-run_generation_no_recolonization.R
│   ├── test-run_generation_no_reproduction.R
│   └── test-run_generation.R
│
├── LICENSE
└── README.md

• AdaptSS_cervus_(scenario).R - Scripts to run adaptation through generations. The function AdaptSS runs a simulation of trait adaptation for each generation step and the function run_generation updates simulation's parameters for each generation and calls AdaptSS.

• parallel_function_cervus.R - Set simulation parameters and run simulations.

Glossary

• h2 - heritability

• cv - phenotypic coefficient of variation

• vm - mutational variance

• Ancestral - Initial trait

• meanK - mean carrying capacity

• Ni - initial population size

• Nrecol - number of recolonization

• Precol - probability of colonization

• w2 - Length of adaptive landscape

• time_adap - time until adaptation

• selgrad - selection gradient

• meanG - mean genotype

• varG - genotypic variance

• N_end - Final population size

• F_Peak - adaptive landscape optimum (optimum trait)

• meanP - Final mean trait

• bp.max - maximum phenotypic plasticity

• bp - phenotypic plasticity

Contributing

Contributions are welcome. Open an issue to discuss the changes.

Funding

• Ministério da Ciência, Tecnologia e Inovações

• Conselho Nacional de Desenvolvimento Científico e Tecnológico

• Fundação de Amparo à Pesquisa do Estado de Goiás

• Spanish MICIU Juan de la Cierva-Incorporación