A general framework for branch length estimation in Ancestral Recombination Graphs

Abstract

Model misspecification is a common challenge in population genetic inference, as oversimplified mathematical models often fail to capture complex evolutionary processes. Here, we introduce a framework for branch length estimation in whole-genome genealogies, which enables accurate inference using noninformative priors and subsequent posterior calibration, rather than relying on heavily parameterized models. This flexible approach has been validated in various simulation settings. When applied to real genomic data, it enables robust inference of demography, mutation rates, and trans-species polymorphisms. Keywords: Ancestral Recombination Graph, branch length estimation, noninformative prior