All posts tagged: population genetics

New AI model reconstructs human ancestry from DNA

New AI model reconstructs human ancestry from DNA

Published by Jenni Sidey

A stretch of DNA can look static on a screen, just long rows of A, T, C and G. But buried in those letters are small changes that mark where lineages split, rejoined and drifted over time. Researchers at the University of Oregon say they have built an artificial intelligence system that can read those mutation patterns much the way a language model reads text, then use them to estimate when two genes last shared a common ancestor. The tool, called cxt, is described in the Proceedings of the National Academy of Sciences and is aimed at one of population genetics’ hardest jobs: reconstructing the hidden family history inside a genome. Instead of predicting the next word in a sentence, the model predicts what the team calls the next coalescence, an estimate of shared ancestry along a chromosome. Andrew Kern, a computational biologist in the University of Oregon College of Arts and Sciences, said the work draws on ideas behind generative AI but puts them to use in a field that has largely relied on …

Neanderthal males preferred human females, genetic study finds

Neanderthal males preferred human females, genetic study finds

Published by Jenni Sidey

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 …