SSR Analysis of Logged and Unlogged Forest Plots in French Guiana
This repository contains R scripts used to analyze nuclear SSR data from two forest plots managed by the French National Forest Office (ONF) near Régina, French Guiana. One plot was selectively logged 12 years ago, whereas the second plot remains unlogged, providing a paired design to assess the long-term genetic effects of forest exploitation.
Objectives
The main goal of this study is to quantify and compare genetic diversity, spatial genetic structure, and gene dispersal patterns between logged and unlogged tropical forest plots. Specifically, the analyses focus on:
- genetic diversity and inbreeding,
- spatial genetic structure (SGS),
- seed and pollen dispersal inferred from parentage analyses,
- reproductive success and its inequality (Gini index, Lorenz curves),
- the legacy effects of selective logging on contemporary gene flow.
Repository Content
The repository includes R scripts for:
- data preprocessing and formatting of SSR and parentage outputs,
- genetic diversity and SGS analyses,
- parentage-based seed and pollen dispersal analyses,
- spatial visualisation of parent–offspring relationships,
- reproductive success analyses (counts, distances, Gini index, Lorenz curves),
- statistical comparisons between plots and disturbance contexts.
All scripts are written in R and rely on commonly used packages such as tidyverse, adegenet, sf, ggplot2, and ineq.
Contact For further information or questions related to the analyses, please contact: Julien Bonnier julien.bonnier@inrae.fr