Data and code from: Tracing the evolution of key traits in dorid nudibranchs

Reconstructing trait evolution is critically important for elucidating the processes generating biodiversity. However, this work is in its infancy in non-model clades for which we lack a basic understanding of their ecology and biology. Here, we compile information about prey preference, chemical acquisition, and colour pattern in dorid nudibranchs (Nudibranchia: Doridoidei) and reconstruct their ancestral states using a multi-gene phylogeny to investigate the evolution of these key traits. Our analyses show that the most recent common ancestor (MRCA) of Doridoidei preferred sponge prey from which they sequestered metabolites, and subsequent shifts to different prey types and de novo synthesis of defensive compounds occurred multiple times independently across the phylogeny. Additionally, the MRCA likely exhibited complex colour patterns, including spots or stripes, with uniform morphotypes evolving in all families except Chromodorididae. Despite the fact that many dorid nudibranchs der..., , , # Data and code from: Tracing the evolution of key traits in dorid nudibranchs

[https://doi.org/10.5061/dryad.8sf7m0d0m](https://doi.org/10.5061/dryad.8sf7m0d0m)

## Description of the data and file structure

### Files and variables

#### File: Dorid_IQtree.treefile

**Description:** The final maximum-likelihood tree file produced by IQtree with 1000 bootstrap replicates. This was also used as input for ancestral state reconstruction in R.

#### File: Dorid_alignment.fasta

**Description:** The sequence alignment used for phylogenetic analysis.

#### File: Dorid_R_input.csv

**Description:** The trait data used for ancestral state reconstruction in R. The first column 'Prey' corresponds to prey preference, the second column 'Chem' corresponds to chemical acquisition (sequestration or synthesis) and the third column 'Colour' corresponds to colour pattern (e.g. uniform, mottled). Multistate characters are represented with '&' (e.g. if taxa in a genus possess both uniform and mottled col...,