ArticleGenetics2026
PhaseGen: exact solutions for time-inhomogeneous multivariate coalescent distributions under diverse demographies.
Article in Genetics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Not yet cited in PubMed.
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Corrections and comments
- Erratum issued
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2 authors.
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Abstract
Phase-type theory is emerging as a powerful framework for modeling coalescent processes, allowing for the exact computation of quantities of interest. This includes moments of tree height, total branch length, the site-frequency spectrum, and the full distribution of the time to the most recent common ancestor. However, prior applications have largely been limited to time-homogeneous settings, with constant population sizes and migration rates, restricting the range of demographic scenarios that can be modeled. In this study, we apply time-inhomogeneous phase-type theory to enable the exact computation of (cross-)moments of arbitrary order and reward structure under piecewise-constant demographies. This extension enables the modeling of significantly more complex demographic scenarios, including population expansions, contractions, bottlenecks, and splits. It furthermore supports fitting demographic models to data through gradient-based optimization. To support these advancements, we introduce PhaseGen-a software package designed for the numerically stable computation of exact moments under diverse demographic scenarios, with support for gradient-based parameter estimation.
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