Extensions of the Multispecies Coalescent in Bayesian Phylogenetics: A Study of the Southern African-centred Stoebe Clade (Gnaphalieae: Asteraceae)

Abstract

The Tree of Life represents the complex relationships between all species, and recent advances in phylogenetic methods have dramatically expanded our ability to study these connections. However, there is still no universal solution to the species problem, and methodology to account for migration is in its infancy. This thesis evaluates extensions of the multispecies coalescent for species delimitation, and phylogenetic inference while accounting for post-divergence gene flow. We focus on the Stoebe clade of paper daisies (Gnaphalieae: Asteraceae), centred in the diverse Cape Floristic Region of South Africa. Analytical species delimitation and complementary taxonomic evidence are employed to resolve the Seriphium plumosum complex, revealing four species new to science, which we formally describe. Our phylogenetic analysis provides a refined resolution of the internal relationships within the Stoebe clade, supporting an updated classification that merges most genera under Stoebe L. Further analysis using target-capture sequencing largely corroborates previously inferred relationships and shows that probes designed with ingroup taxon sequences spanning intronic regions markedly enhance both sequence retrieval and length relative to the Asteraceae-wide Conserved Orthologous Probe Set II. We also introduce a robust method for rectifying sample misidentification by cross-referencing with existing molecular datasets. Further, we explore phylogenetic inference approaches that account for time-decaying migration after lineage divergence and demonstrate that models incorporating migration improve phylogenetic accuracy with relatively few loci while reducing computational demands relative to the standard multispecies coalescent. Collectively, this work refines the classification of species as monophyletic entities and advances our understanding of methods for reconstructing phylogenetic relationships while capturing the complex evolutionary processes that shape allele distributions through time.