Joint ancestry inference reveals the landscape of archaic introgression in admixed populations

Studying the evolutionary history of archaic segments in recently admixed individuals requires inferring both continental and archaic ancestry in admixed genomes. Here, we present TRACTINATOR , the first deep-learning method for simultaneous inference of continental and archaic ancestry in admixed human genomes. The model combines SNP sequences, population allele-frequency information, and S* statistics to improve both inference tasks. By learning relationships between haplotypes and population allele frequencies, TRACTINATOR can generalize across genomic regions and even across different genomic datasets. We train our model using both real and synthetic data, and show that augmenting with synthetic data improves accuracy for both continental and archaic ancestry inference. Finally, we apply TRACTINATOR to admixed Latin American populations from the 1,000 Genomes Project, revealing how archaic ancestry is distributed within chromosomal segments of African, European and Indigenous American ancestry in Latin American individuals. For candidates of adaptive introgression, we also infer whether the archaic haplotype was introduced via European or Indigenous American ancestors.