Gene_Trees_30_genes_dataset

To examine the evolutionary association between agrp2 expression and the presence of stripes, phylogenetic relationships among 24 focal cichlid species that either possess or do not possess stripes from Lakes Victoria, Malawi and Tanganyika were reconstructed. Oreochromis niloticus was also included as an outgroup to these species. To obtain an independent phylogenetic hypothesis for testing associations between agrp2 expression and the presence of stripes, we constructed a phylogenetic matrix for 22 of the 25 species used in the Gene_Trees_6_genes_dataset using genomic sequences of 30 additional genes (arnt, azin1a, bcanb, bmp4, cspg5a, ctnnb1, dlx1a, dlx2a, dlx3b, dlx4a, dlx4b, edn2, fzd6, irx1a, irx2a, irx4a, isl1, myg1, ndrg1b, nrp2b, ntrk1, osr2, pitx1, pitx2, pitx3, shh, smo, sostdc1a, tuft1a and wnt4b) from published genomes as well as from target enrichment data. Also here, the analysis was run five times for 20 million generations each and we discarded the first 10 million trees for each run as burn-in. The zip file contains the alignment of the 22 species and 30 loci (Gene_Sequences_*.nex), a table with phenotype and relative agrp2 gene expression (Matrix_expression_stripes_30_genes.csv) and the gene trees of the 5 runs (Gene_Trees_30_genes_*run.trees).