The book "Analysis of Phylogenetics and Evolution with R" offers a comprehensive introduction to the application of R for the analysis of phylogenetic data and evolution. In its second edition, it continues to integrate a variety of data analysis methods within a flexible interface, enabling biologists to address new questions regarding molecular evolution and to reassess existing concepts, such as the role of adaptation in biodiversity. The use of R as the primary tool for phylogenetic analyses enhances the workflow in data analysis and promotes scientific reproducibility as well as the exchange of ideas and methodological developments. This updated edition includes all new R packages that have been released since the previous publication and features a new chapter on simulating evolutionary data. The book is aimed at students and researchers in evolutionary biology, as well as bioinformaticians interested in implementing these methods in R.