DOI: 10.5061/dryad.75427
title: Data from: Molecular evolution of the neural crest regulatory network in ray-finned fish

description: Gene regulatory networks (GRN) are central to developmental processes.
 They are composed of transcription factors and signaling molecules
 orchestrating gene expression modules that tightly regulate the
 development of organisms. The neural crest (NC) is a multipotent cell
 population that is considered a key innovation of vertebrates. Its
 derivatives contribute to shaping the astounding morphological diversity
 of jaws, teeth, head skeleton or pigmentation. Here, we study the
 molecular evolution of the NC GRN by analyzing patterns of molecular
 divergence for a total of 36 genes in 16 species of bony fishes. Analyses
 of non-synonymous to synonymous substitution rate ratios (dN/dS) support
 patterns of variable selective pressures among genes deployed at different
 stages of NC development, consistent with the developmental hourglass
 model. Model-based clustering techniques of sequence features support the
 notion of extreme conservation of NC-genes across the entire network. Our
 data show that most genes are under strong purifying selection that is
 maintained throughout ray-finned fish evolution. Late NC development genes
 reveal a pattern of increased constraints in more recent lineages.
 Additionally, seven of the NC-genes showed signs of relaxation of
 purifying selection in the famously species-rich lineage of cichlid
 fishes. This suggests that NC genes might have played a role in the
 adaptive radiation of cichlids by granting flexibility in the development
 of NC-derived traits – suggesting an important role for NC network
 architecture during the diversification in vertebrates.
description: AlignmentsWe downloaded gene sequences of 11 of the 16 species from Ensembl release 75 (Flicek et al. 2014). After identifying orthologous loci using the EnsemblCompara pipeline (Vilella et al. 2009), we extracted the longest transcript coding sequence (CDS) of each gene. Sequences for cichlid species other than the Nile Tilapia, Oreochromis niloticus, were obtained from the deposited genome assemblies (Brawand et al. 2014; Elmer et al. 2014). Orthologous loci in cichlid genomes were identified by BLASTN searches using Nile Tilapia sequences as queries and an e-value threshold of 10 -4.The integrity of obtained sequences was double-checked by BLASTN searches against available transcriptomes to ensure correct reading frames. Multiple sequence alignments of individual genes were constructed with translatorX (Abascal et al. 2010): After translation, sequences are aligned at the amino acid level using MUSCLE (Edgar 2004), unreliable amino acid positions are removed with Gblocks (Castresana 2000) under the least stringent parameters, and the corresponding nucleotide alignments are created guided by trimmed amino acid alignments. Maximum-likelihood phylogenetic reconstruction was performed with PhyML version 3.1 (Guindon et al. 2010) after best-fit models of evolution were chosen based on AICc (Akaike information criterion with correction) scores (Hurvich and Tsai 1989) calculated in jModeltest version 2.1.5 (Posada 2008).