MorphSim : An R package for simulating discrete morphological data

Abstract Morphological data are essential for reconstructing evolutionary histories, particularly for fossil taxa, as they represent the primary source of information for integrating extinct lineages into phylogenetic analyses. Despite this, tools for simulating realistic morphological datasets for fossil‐inclusive phylogenetic workflows remain limited. We introduce MorphSim, an R package for simulating discrete morphological characters specifically designed for total‐evidence and tip‐dated phylogenetic analyses, focusing on the morphological component. It generates synthetic datasets that closely match the structure of empirical morphological matrices, accommodating diverse character coding designs and biologically structured missing data reflecting taphonomic preservation biases. MorphSim integrates directly with TreeSim, FossilSim and SimClock, providing a complete end‐to‐end pipeline for generating datasets compatible with Bayesian total‐evidence dating software such as RevBayes and BEAST2. This enables simulation of complex, biologically informed datasets spanning deep timescales, incorporating both extinct and extant lineages. It implements the Mk model and its extensions, including among‐character rate variation and user‐defined rate matrices, across single and multi‐partition schemes. Additionally, we developed MorphSimShiny, an interactive Shiny application providing a beginner‐friendly interface for exploring model assumptions and simulating morphological datasets without requiring familiarity with R.