Thin stretches of the human X chromosome look oddly empty when you scan for Neanderthal DNA. Geneticists even have a name for the gaps: “Neanderthal deserts.” They sit there like blank tape in an otherwise crowded recording. For years, the standard story went like this: Neanderthal DNA landed in our ancestors’ genomes. However, some of it was harmful, especially on the X chromosome. Natural selection, the thinking said, gradually stripped those “toxic” variants away. A new analysis from Sarah Tishkoff’s lab at the University of Pennsylvania argues that the emptiness may say more about who paired with whom than which genes were dangerous. In Science, the team reports a mirror-image pattern inside Neanderthal genomes. Neanderthals carried unusually high levels of modern human DNA on their X chromosomes compared with the rest of their genome. That reversal, they say, makes simple “toxicity” a much harder explanation to defend. The deserts and the old assumption “Along our X chromosomes, we have these missing swaths of Neanderthal DNA we call ‘Neanderthal deserts,’” says Alexander Platt, a senior research …