Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate definitive taxonomic conclusions. Salvia L., with ∼1,000 species, makes up nearly 15% of the species diversity in the mint family and has attracted great interest from biologists across subdisciplines. Despite the great progress that has been achieved in discerning the placement of Salvia within Lamiaceae and in clarifying its infrageneric relationships through plastid, nuclear ribosomal, and nuclear single-copy genes, the incomplete resolution has left open major questions regarding the phylogenetic relationships among and within the subgenera, as well as to what extent the infrageneric relationships differ across genomes. We expanded a previously published anchored hybrid enrichment dataset of 35 exemplars of Salvia to 179 terminals. We also reconstructed nearly complete plastomes for these samples from off-target reads. We used these data to examine the concordance and discordance among the nuclear loci and between the nuclear and plastid genomes in detail, elucidating both broad-scale and species-level relationships within Salvia. We found that despite the widespread gene tree discordance, nuclear phylogenies reconstructed using concatenated, coalescent, and network-based approaches recover a common backbone topology. Moreover, all subgenera, except for Audibertia, are strongly supported as monophyletic in all analyses. The plastome genealogy is largely resolved and is congruent with the nuclear backbone. However, multiple analyses suggest that incomplete lineage sorting does not fully explain the gene tree discordance. Instead, horizontal gene flow has been important in both the deep and more recent history of Salvia. Our results provide a robust species tree of Salvia across phylogenetic scales and genomes. Future comparative analyses in the genus will need to account for the impacts of hybridization/introgression and incomplete lineage sorting in topology and divergence time estimation.

Disturbance and environmental change may cause communities to converge on a steady state, diverge towards multiple alternative states, or remain in long-term transience. Yet, empirical investigations of successional trajectories are rare, especially in systems experiencing multiple concurrent anthropogenic drivers of change. We examined succession in old field grassland communities subjected to disturbance and nitrogen fertilization using data from a long-term (22-year) experiment. Regardless of initial disturbance, after a decade communities converged on steady states largely determined by resource availability, where species turnover declined as communities approached dynamic equilibria. Species favored by the disturbance were those that eventually came to dominate the highly fertilized plots. Furthermore, disturbance made successional pathways more direct under low nutrients, revealing an important interaction effect between nutrients and disturbance as drivers of community change. Our results underscore the dynamical nature of grassland and old field succession, demonstrating how community properties such as beta-diversity change through transient and equilibrium states.

Disturbance and environmental change may cause communities to converge to a steady state, diverge towards multiple alternative states, or remain in long-term transience. Yet, empirical tests of these successional trajectories are rare, especially in systems experiencing multiple concurrent anthropogenic drivers of change. We compared competing models of succession in grassland communities subjected to disturbance and nitrogen fertilization using data from a long-term (22-year) experiment. Regardless of disturbance, after a decade communities settled on equilibrium states largely determined by resource availability, with species turnover declining as communities approached dynamic equilibria. Species favored by the disturbance were those that eventually came to dominate the highly fertilized plots. Furthermore, disturbance made successional pathways more direct, revealing an important interaction effect between nutrients and disturbance as drivers of community change. Our results underscore the dynamical nature of grassland succession, demonstrating how community properties such as beta-diversity change through transient and equilibrium states.