#10 · Systems biology

Phylogenetic inference under violated assumptions: diagnostics and corrections

The dominant thread is the behaviour of tree-based phylogenetic inference when a modelling assumption is violated. A simulation study of phylogenetic comparative methods under reticulate evolution reports errors in ancestral state, rate and model estimates under hybridization, most severe for fast-evolving traits. A preprint proposes two maximum likelihood approaches that account for lineage abundance, reporting improved inference accuracy on SARS-CoV-2 data. DiagnoDating offers outlier detection, posterior predictive checks and residual analysis for dated phylogenies in microbial population genetics, and a Bayesian study of mixed Gaussian trait-evolution models adds posterior predictive evaluation with the bgphy R package. What is new is the shift from evaluation alone toward diagnostics and corrections that target identified violations.