This repository contains code for the R package HybridFindR. The goal of HybridFindR is to identify loci exhibiting signals of differential introgression.

Note: This method has not been validated in distinguishing differential introgression from genetic drift. We recommend pairing this method with demographic modeling (e.g., Moments or dadi) and simulations (e.g., msprime) until it has been validated. Please see Farleigh et al., 2023 and contact Keaka Farleigh ([email protected]) if you have questions.

You can install the development version of HybridFindR from GitHub with:

# install.packages("devtools")
devtools::install_github("kfarleigh/HybridFindR", build_vignettes = TRUE)

A vignette that walks you through differential introgression analysis can be found using:

library(HybridFindR)
vignette(topic = "Differential_Introgression_Analysis", package = "HybridFindR")

There is also an example data file included in the package, which you can load using the command:

data("Anolis")

After referring to the vignette, please direct all questions to [email protected].

If you use HybridFindR in your work please cite:

Farleigh, K., Ascanio, A., Farleigh, M. E., Schield, D. R., Card, D. C., Leal, M., Castoe, T. A., Jezkova, T., & Rodríguez-Robles, J. A. (2023). Signals of differential introgression in the genome of natural hybrids of Caribbean anoles. Molecular Ecology, 32, 6000–6017. https://doi.org/10.1111/mec.17170

You should also cite:

Bailey, R. (2020). gghybrid: R package for evolutionary analysis of hybrids and hybrid zones.

Buerkle, C. A. (2005). Maximum likelihood estimation of a hybrid index based on molecular markers. Molecular Ecology Notes, 5(3), 684-687.