Data for: A morphological basis for path-dependent evolution of visual systems

Path dependence influences macroevolutionary predictability by constraining potential outcomes after stochastic evolutionary events. Although demonstrated in laboratory experiments, the basis of path dependence is difficult to demonstrate in natural systems because of a lack of independent replicates. Here we show two types of complex distributed visual systems, each recently evolved twice within chiton mollusks, demonstrating rapid and path-dependent evolution. The type of visual system a chiton lineage evolves is constrained by the number of openings for sensory nerves in its shell plates: lineages with more openings evolve visual systems with thousands of eyespots, whereas those with fewer evolve visual systems with hundreds of shell eyes. These macroevolutionary outcomes shaped by path dependence are both deterministic and stochastic because possibilities are restricted yet not entirely predictable., 1.1 Taxon sampling and sequencing
To generate sequencing data from specimens that were not preserved in ideal conditions and/or are more than five years post-collection (including a large library of previously sequenced chiton specimens from the personal collections of D. J. Eernisse as part of ongoing systematic revisions), we generated a suite of target capture loci. We designed target capture baits to predict exon regions following a similar approach to Hugall et al., 2016. We identified a set of 891 orthologs from 19 chiton transcriptomes and three reference molluscan genomes (Octopus bimaculoides, Lottia gigantea, and Crassostrea gigas) using the phylogenomics pipeline from Kocot et al., 2017. We identified conserved exons from the three mollusc genomes using EnsemblMetazoa and predicted intron-exon boundaries in the chiton sequences with a custom script using tBLASTx. From this, we compiled a set of predicted chiton exons from 355 genes that had at least four representative chiton..., , # Data for: A morphological basis for path-dependent evolution of visual systems

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This supplementary data contains the raw input/output files for all phylogenies described in the manuscript, as well as the raw image files for the morphological measurements taken.

## Description of the data and file structure

This supplementary data is divided into the following directories:

* `SEMimages`: Raw scanning electron micrographs of all taxa included in the phylomorphospace. We took multiple images for each taxon. Within this folder, examples of the counted macraesthetes can be viewed in the subfolder `CountedExamples`. Numbers in image titles correspond to the museum catalog of the Santa Barbara Museum of Natural History.
* `MLtree`: The input and output files that resulted in our maximum likelihood phylogeny of chitons via iqtree2, using Model Finder on a partitioned dataset.
* `TimeTree`: The input and output files that resulted in our time-calibrated phylogeny of chitons via MrBayes...,