Archaic coverage tracts on chromosome X are longer than those on an autosome in our simulation studies.

All results shown reflect an additive model of dominance. A Tract length spectra from simulations of an archaic introgression scenario under autosomal or chromosome X inheritance; note log scale. Points indicate frequencies of archaic coverage tracts within length bins of 3000 bp. Simulated chromosomes shared a variable recombination rate landscape (see Methods for details). Solid lines indicate expected archaic coverage lengths under a simple, neutral model with constant recombination rate equal to the mean rate of the simulated recombination landscape. B Average recombination rate within each simulated archaic coverage tract, plotted against length of the tract. Note log scale. C Proportion of archaic coverage tracts that are a given length or shorter; proportions are calculated within each inheritance type. Arrow indicates 95th percentile of tract lengths, illustrated in panel D alongside sex-biased scenarios. D Distribution of 95th percentiles of archaic coverage tract lengths found on either an autosome or chromosome X, across degrees of introgressor sex-bias. Each box reflects the length distributions from ten simulation replicates. (TIF)