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Abstract

Population genetics is undergoing a transformative shift, replacing summary statistics with methods that leverage ancestral recombination graphs (ARGs) to synthesize genetic data inferences about molecular evolution. We propose defining “haplotype block” as fundamental unit for such analysis: based on ARG structure and containing complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relation between haplotype blocks and ancestral structure, emphasising the stochasticity of the processes that generate them. In Heliconius butterflies and Littorina snails, we demonstrate using haplotype blocks for adaptive introgression and selective sweeps. Understanding and applying the concept of the haplotype block will be essential to fully exploit frontier methods in modern data driven life science such as long and linked-read sequencing technologies.