B cells are an evolutionary system, undergoing rapid somatic hypermutation and antigen-driven selection as part of the adaptive immune response. B cell lineage trees inferred from B cell receptor sequencing data represent the history of mutations in a lineage, and can also link multiple forms of B cell diversity. For example, B cell lineage trees sampled from multiple tissues from the same subject could represent B cell migration between tissues. Trees sampled at different timepoints in the same subject represent clonal persistence over time. Here, we introduce new phylogenetic methods that use lineage trees to understand patterns of B cell migration, differentiation, and evolution over time. We demonstrate how this framework has been used to understand the role of B cell migration and differentiation in multiple immune conditions. Further, we show how longitudinally sampled data can be used to test for ongoing evolution in B cell lineages. Using large, publicly available AIRR-seq datasets, we demonstrate how different infections, vaccinations, and other conditions differ significantly in their ability to stimulate evolution over time in B cells. Some conditions, such as HIV infection, stimulate high strong signatures of B cell evolution, while others such as influenza vaccination produce a more compartmentalized response detectable only with direct germinal center sequencing. These methods are widely applicable and implemented in the R package dowser, available at https://bitbucket.org/kleinstein/dowser.