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Only Haplotype A (with CCR5delta32) was under positive selection.
This suggests the deletion conferred an adaptive advantage—possibly by modulating immune tolerance in denser Neolithic populations.
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Importantly, we benchmarked HAPI against GATK and vg graph-genomes:
✅ HAPI called 63% more ancient genomes
✅ Maintained high precision even at 0.3× coverage
👉 This enables robust indel detection in challenging aDNA datasets.
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Applying HAPI to 934 ancient genomes revealed we identified CCR5delta32
CCR5Δ32 originated once in the Western Steppe ~6,700–9,000 years ago.
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Our spatiotemporal model estimates a rapid westward diffusion of CCR5delta32, covering 60–100 km² per generation.
Its spread likely paralleled the expansion of Steppe-related ancestry into Europe in the Early Bronze Age.
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Its frequency rose rapidly during the Late Neolithic and Bronze Age — then plateaued.
Strong positive selection from 8,000-2,000 years BP, particular Eastern and Caucasus Hunter Gatherers
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In summary:
✅ CCR5delta32 arose once, >6,700 years ago
✅ It spread via Bronze Age demographic expansions
✅ Underwent strong positive selection
✅ Is now a globally relevant variant in medicine
All from an ancient immunogenetic adaptation.
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And much more, have a look at the paper and thanks to all contributors and co-authors!
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We used this information to develop HAPI: Haplotype Aware Probabilistic modeling of Indels
Use entire haplotype information to call deletion in ancient samples