Performance of qpAdm-based screens for genetic admixture on admixture-graph-shaped histories and stepping-stone landscapes

Code for simulations and analyses as used in our recent evaluation of the qpAdm tool. Final version published in Genetics:

Olga Flegontova, Ulaş Işıldak, Eren Yüncü, Matthew P. Williams, Christian D. Huber, Jan Kočí, Leonid A. Vyazov, Piya Changmai, Pavel Flegontov (2025): Performance of qpAdm-based screens for genetic admixture on admixture-graph-shaped histories and stepping-stone landscapes. Genetics, 230(1), iyaf047, DOI: https://doi.org/10.1093/genetics/iyaf047

Principal software packages used in this study are:

• slendr v. 0.7.2.9000 (Petr et al. 2023; https://github.com/bodkan/slendr),
• msprime v. 1.1.1 and v. 1.2.0 (Baumdicker et al. 2022; https://github.com/tskit-dev/msprime), and
• ADMIXTOOLS 2 (Maier et al. 2023; https://github.com/uqrmaie1/admixtools).

Other code for generating the simulated genetic data, running qpAdm protocols, and visualization is available in this repository (extensive comments are included within the R scripts). Input data for all the scripts is available in the respective folders here, and larger input files (sets of qpAdm results on simulated data) are available at https://doi.org/10.5281/zenodo.14966948.

The supplementary materials for this study are available at: https://figshare.com/s/8d81948469edfadafba7?file=52105079 (the file includes detailed descriptions of all the materials, supplementary text sections 1 to 6, figures S1 to S40, and tables S1 to S15).