Longevity in plants impacts phylogenetic and population dynamics

Many long-lived plant species exhibit notable patterns in phylogenies, such as short molecular branch lengths and high gene-tree conflict. However, it is not clear what biological properties of long-lived plant species or concomitant processes acting within these lineages generate these patterns. To explore this mystery, we implemented an agent-based model and conducted simulations to investigate how longevity affects molecular evolution and population dynamics. Through these simulations, we demonstrated that the patterns exhibited in empirical datasets for long-lived species can be explained by their lifespan and overlapping generations. We also show that somatic mutations can exacerbate these patterns, although evidence for substantive rates in empirical systems high enough to impact phylogenetic patterns is scarce. We discuss several empirical datasets containing life history shifts that exhibit diverse phylogenomic patterns. The variation produced through different parameterizations of our simulations reflects the diversity of patterns found in empirical datasets. Our results have broad implications for phylogenomic patterns and population genetics in general, as well as for specifically explaining patterns of evolution in long-lived lineages.