ArticlebioRxiv : the preprint server for biology2026
Local ancestry inference identifies robust evidence of selection in Neolithic Europe.
Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
During the European Neolithic transition, migrating Anatolian farmers admixed with local hunter-gatherers, coinciding with major shifts in diet, environment, and lifestyle that imposed strong selective pressures. Local ancestry inference is widely used to detect selection following admixture, but most methods were developed and validated on present-day populations. Their performance in ancient DNA, where reference panels are smaller, data sparser, and admixture more ancient, remains unresolved. We benchmark six local ancestry inference methods on 176 imputed Neolithic genomes, comparing ancestry proportions, tract length distributions, and selection signatures. While individual-level ancestry estimates are highly correlated across methods, inferred tract lengths and admixture time estimates vary by over an order of magnitude. Integrating results across methods and replicating across methods and in two independent datasets (n=378 and 1,121) identifies robust ancestry deviations at
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