Estimating ancestral states of complex characters: A case study on the evolution of feathers

Feathers are a key novelty underpinning the evolutionary success of birds, yet the origin of feathers remains poorly understood. Debates about feather evolution hinge upon whether filamentous integument has evolved once or multiple times independently in the lineage leading to modern birds. These contradictory results stem from methodological differences in statistical ancestral state estimates. Here, we conduct a comprehensive comparison of ancestral state estimation methodologies applied to stem-group birds, testing the role of outgroup inclusion, tree time scaling method, model choice, and character coding strategy. Models are compared based on their Akaike Information Criteria (AIC), mutual information, as well as the uncertainty of marginal ancestral state estimates. Our results demonstrate that ancestral state estimates of stem-bird integument are strongly influenced by tree time scaling method, outgroup selection, and model choice, while character coding strategy seems to have le..., , # Estimating ancestral states of complex characters: A case study on the evolution of feathers

NB: Please note that, due to the sudden and tragic passing of Pierre Cockx, the first author of this study, we have been unable to update the Dryad submission with the full level of detail that would normally be provided.

The scripts and data required to run the analyses described and produce the plots are provided here.

## **Data**

The folder **Data** contains the following files:

* coding3: plumage data using coding strategy 3
* coding3_croco: same but with *Crocodylus* instead of *Aetosaurus* in the outgroups
* codingstrategies_plumage: file with plumage data coded using the different strategies described in the paper
* nodes: file with the age of the Avemetatarsalian node, used for time scaling of the tree
* ranges; ranges_croc: FAD and LAD of the taxa
* tree_raw; tree_raw_croco: raw trees
* treetime_croc: time-scaled tree with outgroup 4 for Experiment #1
* treetime_equal_tpp: time-s...,