| Title: |
PhaseGen:exact solutions for time-inhomogeneous multivariate coalescent distributions under diverse demographies |
| Authors: |
Sendrowski, Janek; Hobolth, Asger |
| Source: |
Sendrowski, J & Hobolth, A 2026, 'PhaseGen : exact solutions for time-inhomogeneous multivariate coalescent distributions under diverse demographies', Genetics, vol. 232, no. 1, iyaf135. https://doi.org/10.1093/genetics/iyaf135 |
| Publication Year: |
2026 |
| Collection: |
Aarhus University: Research |
| Subject Terms: |
coalescent theory; demographic inference; multiple-merger coalescents; numerical optimization; phase-type theory; population genetics; SFS; software; statistical inference; time-inhomogeneous processes |
| Description: |
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. |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| ISSN: |
0016-6731 |
| Relation: |
info:eu-repo/semantics/altIdentifier/pmid/40694609; info:eu-repo/semantics/altIdentifier/pissn/0016-6731; info:eu-repo/semantics/altIdentifier/eissn/0016-6731 |
| DOI: |
10.1093/genetics/iyaf135 |
| Availability: |
https://pure.au.dk/portal/en/publications/34ac8c7f-1fb5-4590-9ebb-aae054c1b409; https://doi.org/10.1093/genetics/iyaf135; https://www.scopus.com/pages/publications/105027101752 |
| Rights: |
info:eu-repo/semantics/openAccess |
| Accession Number: |
edsbas.78FE86BB |
| Database: |
BASE |