Title:	Phylogenetic inference under time-decaying migration
DNr:	NAISS 2025/22-1079
Project Type:	NAISS Small Compute
Principal Investigator:	Bengt Oxelman <bengt.oxelman@bioenv.gu.se>
Affiliation:	Göteborgs universitet
Duration:	2025-08-15 – 2026-09-01
Classification:	10610
Keywords:

Abstract

This research is concerned with optimizing phylogenetic accuracy in the presence of post-speciation gene flow. While several methods exist for phylogenetic estimation while accounting for migration, no study to date has systematically evaluated the influence of defining standard MultiSpecies Coalescent with migration (MSC-M) priors on migration when the rate of migration between branches declines with evolutionary divergence. This project uses the MSC-M model DENIM (Jones 2019) to evaluate the impact of misspecified priors on migration during phylogenetic estimation using replicate datasets simulated under time-decaying migration. We analyse these data with standard migration priors and priors assuming time-decaying migration, and evaluate phylogenetic accuracy under either approach. As an empirical evaluation, we also analyse a dataset comprising 19 multiple sequence alignments for 12 species in Silene (Caryophyllaceae), which shows evidence of reproductive isolation being positively correlated with genetic distance (Moyle et al. 2004). The proposed work is a rapidly developing area of research in biological systematics. Insights provided by our work will inform project design in molecular phylogenetics and will also help inform best practices for tree estimation using fully-parameterised Bayesian tree inference with migration.