DOI: 10.5061/dryad.66942
title: Data from: The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach

description: The most striking feature of peafowl (Pavo) is the males' elaborate
 train, which exhibits ocelli (ornamental eyespots) that are under sexual
 selection. Two additional genera within the Phasianidae (Polyplectron and
 Argusianus) exhibit ocelli, but the appearance and location of these
 ornamental eyespots exhibit substantial variation among these genera,
 raising the question of whether ocelli are homologous. Within
 Polyplectron, ocelli are ancestral, suggesting ocelli may have evolved
 even earlier, prior to the divergence among genera. However, it remains
 unclear whether Pavo, Polyplectron and Argusianus form a monophyletic
 clade in which ocelli evolved once. We estimated the phylogeny of the
 ocellated species using sequences from 1966 ultraconserved elements (UCEs)
 and three mitochondrial regions. The three ocellated genera did form a
 strongly supported clade, but each ocellated genus was sister to at least
 one genus without ocelli. Indeed, Polyplectron and Galloperdix, a genus
 not previously suggested to be related to any ocellated taxon, were sister
 genera. The close relationship between taxa with and without ocelli
 suggests multiple gains or losses. Independent gains, possibly reflecting
 a pre-existing bias for eye-like structures among females and/or the
 existence of a simple mutational pathway for the origin of ocelli, appears
 to be the most likely explanation.
description: Trees_UCE_15sp_RAxMLTrees estimated from UCEs for all 15 species using RAxML. Results from both unpartitioned and partitioned by GC analyses are included.UCE_15sp_RAxML.treTrees_UCE_13sp_RAxMLTrees estimated from UCEs of 13 species using RAxML. Results of both unpartitioned and partitioned by GC analyses are included.UCE_13sp_RAxML.treTrees_MT_MrBayes_pavonineTrees estimated in MrBayes using the mitochondrial matrix (ND2, CYB, and 12S) from 233 galliforms.MT_MrBayes_pavonine.treTrees_MT_RAxML_pavonineTrees estimated in RAxML from the mitochondrial matrix (ND2, CYB, and 12S) for 233 galliforms.MT_RAxML_pavonine.treTrees_MTandUCE_pavonineMost likely tree estimated tree using the combined mitochondrial plus UCE data. There are two trees. First is the one with original estimated branch lengths. Second is the same tree with branch lengths re-estimated using mitochondrial data.MTandUCE_pavonine.treTree_UCE_SMRT-ML.bootconsTree estimated using the SMRT-ML method.UCE_SMRT-ML.bootcons.treTrees_UCE_MrBayes_pavonineTrees estimated using MrBayes from the UCE data (all 15 species).UCE_MrBayes_pavonine.treAlignment_Sun_MtUCE_alignmentAlignment of the combined mitochondrial (CYB, ND2, 12S) and UCE data for 233 species of galliforms.Sun_MtUCE_alignment.nexAlignment_Sun_1966_UCEsAlignments of all of the 1966 UCEs included in the study.Sun_1966_UCEs.zipAlignment_Sun_MtAlignment of the mitochondrial data (CYB, ND2, 12S) from 233 galliform species.Sun_Mt_alignment.nexTraitMatrix_OcelliPresence/Absence of ocelli for the 233 taxa included in the mitochondrial matrix (all of the 15 species sampled for UCEs are included in that 233).Script_SMRTraxPerl script for the SMRT-ML analysis.SMRTrax.pl