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By comparing the sex-specifically inherited X chromosome to the autosomes in ancient genetic samples, we (1) studied sex-specific admixture for two prehistoric migrations. For each migration we used several admixture estimation procedures—including ADMIXTURE model-based clustering (2)—to compare X-chromosomal and autosomal ancestry in contemporaneous Central Europeans and we interpreted greater admixture from the migrating population on the autosomes as male-biased migration. For migration into late Neolithic/Bronze Age Central Europeans (BA) from the Pontic-Caspian Steppe (SP) we inferred male-biased admixture at 5–14 males per migrating female. Lazaridis and Reich (3) contest this male-biased migration claim. For simulated individuals, they claim that ADMIXTURE provides biased X-chromosomal ancestry estimates. They argue that if the bias is taken into account, then X-chromosomal steppe ancestry is similar to our autosomal ancestry estimate, and that hence steppe male and female contributions are similar. Many factors affect ancestry inferences from ADMIXTURE and related programs (2, 4⇓⇓⇓–8). To understand ADMIXTURE inferences for X-chromosomal ancient DNA, we performed simulations examining the effects of multiple variables. First, we used “reference” individuals in ref. 1 to simulate …

Reply to Lazaridis and Reich: Robust model-based inference of male-biased admixture during Bronze Age migration from the Pontic-Caspian Steppe