Failure to replicate

Just in at bioRxiv:

We fail to replicate a genetic signal for sex bias in the steppe migration to central Europe after ~5,000 years proposed by Goldberg et al. PNAS 114(10):2657-2662. Estimation of X-chromosome steppe ancestry in the Bronze Age central European population with the qpAdm method (Haak et al. Nature 522, 207-11) does not indicate lower steppe ancestry on the X-chromosome than in the autosomes. We perform a simulation which indicates presence of estimation bias of -19.5% in the inference of X-chromosome admixture proportions using the method used by Goldberg et al., largely eliminating the observed sex bias.

Iosif Lazaridis, David Reich, Failure to Replicate a Genetic Signal for Sex Bias in the Steppe Migration into Central Europe, bioRxiv, Posted March 14, 2017, doi: https://doi.org/10.1101/114124

Update 04/04/2017: Goldberg et al. reply:

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), comparing X-chromosomal and autosomal ancestry in contemporaneous Central Europeans, interpreting 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 & 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. We conduct simulations of ancient and modern data under a range of conditions. We conclude that our inference of male-biased Pontic-Caspian steppe migration, seen using ADMIXTURE, STRUCTURE, mechanistic simulations, and X/autosomal FST, is robust. Our analysis further illuminates the impact of small haploid reference samples on ADMIXTURE; we look forward to refining sex-specific migration estimates as larger, higher-coverage ancient samples become available.

Goldberg et al., Reply To Lazaridis And Reich: Robust Model-Based Inference Of Male-Biased Admixture During Bronze Age Migration From The Pontic-Caspian Steppe, bioRxiv, Posted April 3, 2017, doi: https://doi.org/10.1101/122218