Message in a bottleneck: Nested founder effects from French Polynesia to Rapa Nui and Hawaiʻi

Founder effects can lead to strong, population-specific allele frequency differentiation, including autosomal recessive conditions. Their characterization in European-descent groups, such as the Finnish and Amish, has resulted in actionable genetic tests for each. We show that Polynesians experienced order-of-magnitude stronger cumulative founder effects during their settlement of Eastern Polynesia. Using whole-genome sequences spanning Polynesia, we show that two of the most bottlenecked populations are Hawaiʻi and Easter Island (Rapa Nui) and that these two most closely genetically related yet geographically distant islands were likely settled by the same ultravoyagers with earlier ancestral roots in Mangareva. We identify clinical genetic variation generated by this sequence of successive oceanic founder events, including a loss-of-function FAN1 mutation common in Eastern Polynesia (>1%) but entirely absent from gnomAD.