Recovering signatures of archaic hominin introgression using ancestral recombination graphs

Abstract

Introduces TRACE, a method for detecting archaic ancestry that needs neither reference archaic genomes nor an unadmixed outgroup, working instead from features of ancestral recombination graphs. Simulations indicate high precision and a low false discovery rate. On 1000 Genomes data it recovers the known Neanderthal and Denisovan signals and also detects ghost admixture from uncharacterised hominins in both African and non-African populations. Ghost ancestry is found within Neanderthal and Denisovan ancestry deserts, which complicates reading those regions as Homo sapiens–specific; in Oceanians, deep lineages are enriched in Denisovan relative to Neanderthal regions, consistent with super-archaic introgression.