ArchIE2: A software package for robust inference of introgressed local ancestry

Introgression is a pervasive feature of human and non-human evolutionary history, and methods that identify introgressed loci have become central to studying its biological impact. We present ArchIE2, an enhanced and more robust version of the reference-free local ancestry framework introduced by ArchIE. ArchIE2 replaces ArchIE’s high-dimensional, sample-size–dependent feature set with a compact collection of summary statistics that generalize across demographic settings. This redesign removes dependency to sample size while preserving predictive accuracy and improving model stability. Across simulations, ArchIE2 matches or exceeds the performance of existing approaches, demonstrating a flexible and scalable framework for detecting introgressed segments, including in scenarios lacking reference genomes from source populations.