Leveraging graphical model techniques to study evolution on phylogenetic networks

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 380(1919)

Published: Feb. 13, 2025

The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be tree, or network if it includes reticulations, representing events such as hybridization admixture. Computing the likelihood data observed at leaves costly size complexity grows. Efficient algorithms exist for trees, but cannot applied to networks. We show that vast array models trait phylogenetic networks reformulated graphical models, which efficient belief propagation exist. provide brief review on general then focus linear Gaussian continuous traits. how techniques exact approximate (but more scalable) gradient calculations, prove novel results parameter inference some models. highlight possible fruitful interactions between methods. For example, approaches have potential greatly reduce computational costs phylogenies with reticulations.

Language: Английский

Mathematically tractable models of random phylogenetic networks: an overview of some recent developments

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 380(1919)

Published: Feb. 13, 2025

Models of random phylogenetic networks have been used since the inception field, but introduction and rigorous study mathematically tractable models is a much more recent topic that has gained momentum in last 5 years. This manuscript discusses some developments field through selection examples. The emphasis on techniques rather than results themselves, probabilistic tools combinatorial ones. article part theme issue ‘“A mathematical theory evolution”: dating back 100 years’.

Language: Английский

Identifying circular orders for blobs in phylogenetic networks

Advances in Applied Mathematics, Journal Year: 2024, Volume and Issue: 163, P. 102804 - 102804

Published: Nov. 20, 2024

Language: Английский