DOI: 10.5061/dryad.7kh2n
title: Data from: Prey preference follows phylogeny: evolutionary dietary patterns within the marine gastropod group Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia)

description: Background: The impact of predator-prey interactions on the evolution of
 many marine invertebrates is poorly understood. Since barriers to genetic
 exchange are less obvious in the marine realm than in terrestrial or
 freshwater systems, non-allopatric divergence may play a fundamental role
 in the generation of biodiversity. In this context, shifts between major
 prey types could constitute important factors explaining the biodiversity
 of marine taxa, particularly in groups with highly specialized diets.
 However, the scarcity of marine specialized consumers for which reliable
 phylogenies exist hampers attempts to test the role of trophic
 specialization in evolution. In this study, RNA-Seq data is used to
 produce a phylogeny of Cladobranchia, a group of marine invertebrates that
 feed on a diverse array of prey taxa but mostly specialize on cnidarians.
 The broad range of prey type preferences allegedly present in two major
 groups within Cladobranchia suggest that prey type shifts are relatively
 common over evolutionary timescales. Results: In the present study, we
 generated a well-supported phylogeny of the major lineages within
 Cladobranchia using RNA-Seq data, and used ancestral state reconstruction
 analyses to better understand the evolution of prey preference. These
 analyses answered several fundamental questions regarding the evolutionary
 relationships within Cladobranchia, including support for a clade of
 species from Arminidae as sister to Tritoniidae (which both preferentially
 prey on Octocorallia). Ancestral state reconstruction analyses supported a
 cladobranchian ancestor with a preference for Hydrozoa and show that the
 few transitions identified only occur from lineages that prey on Hydrozoa
 to those that feed on other types of prey. Conclusions: There is strong
 phylogenetic correlation with prey preference within Cladobranchia,
 suggesting that prey type specialization within this group has inertia.
 Shifts between different types of prey have occurred rarely throughout the
 evolution of Cladobranchia, indicating that this may not have been an
 important driver of the diversity within this group.
description: nt123 data matrix -
 FASTAFASTA file with the
 concatenated individual orthologous group alignments (406 total), with 40
 taxa. This is the unaltered, original matrix. This matrix is 33.1%
 complete with 966,888 sites.nt123.fant123_sitesremoved data matrix - FASTAFASTA file with the concatenated individual orthologous group alignments (406 total), with 40 taxa. This is the nt123 data matrix with sites removed that are represented in fewer than four taxa. This resulted in a matrix that is 50.7% complete with 605,934 sites.nt123_sitesremoved.fant123 data matrix partitioned by codon position - NEXUSNEXUS file with the concatenated individual orthologous group alignments (406 total), with 40 taxa. This is the nt123 data matrix converted to nexus format with a block partitioning the data by codon position.nt123_allsitespartitioned.nexnt123 data matrix partitioned by 1st and 2nd positions - NEXUSNEXUS file with the concatenated individual orthologous group alignments (406 total), with 40 taxa. This is the nt123 data matrix converted to nexus format, with a block added partitioning by codon position but excluding 3rd positions. Only positions 1 and 2 for each codon were included.nt123_partitionednt12.nexnt123 data matrix with sites removed partitioned by codon position - NEXUSNEXUS file with the concatenated individual orthologous group alignments (406 total), with 40 taxa. This is the nt123 data matrix with sites removed converted to a nexus file, with a block added that partitions the data by codon position.nt123_sitesremoved_allsitespartitioned.nexnt123partitioned treeBest tree with bootstrap values from the Garli 2.1 run using the nt123_allsitespartitioned.nex data matrix.nt123partitioned_best_with_BS.trent123partitioned with sites removed treeBest tree with bootstrap values from the Garli 2.1 run using the nt123_sitesremoved_allsitespartitioned.nex data matrix.nt123partitioned_sitesremoved_best_tree_with_BS.trent123unpartitioned with sites removed treeBest tree with bootstrap values from the Garli 2.1 run using the nt123_sitesremoved.fa data matrix.nt123unpartitioned_sitesremoved_best_with_BS.trent12partitioned treeBest tree with bootstrap values from the Garli 2.1 run using the nt123_partitionednt12.nex data matrix.nt12partitioned_with_BS.tre