Analysis of the impact of terrestrial habitats on the evolutionary dynamics in the phylum Ciliophora

Abstract Ciliates inhabit a wide range of habitats, including terrestrial environments. However, macroevolutionary studies on the evolution of habitat preferences within the phylum remain scarce. In this study, we inferred a dated phylogeny, which allowed us to map habitats over time, and assess the macroevolutionary dynamics of these ciliates. Our results show that the last common ancestor of Ciliophora exploited an environment similar to that currently classified as marine/brackish, with terrestrial habitats being occupied only later. Furthermore, we identified two possible evolutionary routes for the transition of ciliates to terrestrial environments: (i) via a marine/brackish ancestor and (ii) via a freshwater ancestor. We also estimated a robust phylogenetic signal, indicating that closely related lineages tend to share similar habitat. Macroevolutionary analyses based on BAMM revealed elevated diversification rates in lineages associated with terrestrial habitats. However, model comparison using HiSSE indicated that diversification dynamics are best explained by a character-independent model with multiple hidden rate regimes. This suggests that terrestrial habitat may not be the sole factor associated with the increased diversification rates, and that the evolutionary success of terrestrial ciliates could also be influenced by morphological, physiological, behavioral, or other unmeasured evolutionary factors.