kristinmlee/dmc

Distinguishing among modes of convergent adaptation using population genomic data: statistical inference method, extensions, and examples

dmc

Distinguishing among modes of convergent adaptation using population genomic data

This repository contains code associated with Lee and Coop (2017) and for extension myAdIDAS.

1. Scripts to run DMC

• A fully worked example for how to use DMC can be found at dmc_example.md

• Short descriptions of the scripts needed to run DMC found in this repository.

  See individual files for more details and example for their usage in context.

  • calcNeutralF.R contains code to generate and save F as an R object.

  • genSelMatrices_individualModes.R contains functions to generate F^(S) for single modes of convergent adaptation.

  • genSelMatrices_multipleModes.R contains functions to generate F^(S) for multiple modes of convergence.

  • calcInvDetSelMatrices_all.R contains scripts to generate all the possible inverses and determinants.

  • calcCompositeLike.R contains functions for calculating the composite log-likelihoods for all models.

  • getMCLE.R contains functions to get the maximum composite likelihood estimates of parameters for all convergence models.

2. Scripts associated with the Mimulus and killifish analyses in Lee and Coop (2017)

3. Modified version of mssel, a version of ms [1] that allows for the incorporation of selection at a single site, modified by KL to allow for multiple independent origins of beneficial lineages.

4. MYAdIDAS extension

• Code for extension MYAdIDAS by Sivan Yair and Kristin Lee, associated with Oziolor et al. (2019) and modified for cases of adaptive introgression, can be found in folder myAdidas. This also includes modifications for deletions, strong selection coefficients, and differences in effective population sizes among populations. See folder for complete details.

[1] Hudson, R. R. (2002). Generating samples under a Wright–Fisher neutral model of genetic variation. Bioinformatics 18, 337–338.