Genes shared between morphs.

<p>Venn diagrams for the number of autosomal (panel A) and Z-linked (panel B) genes expressed in females (red), subordinate males (light blue) and dominant males (dark blue).</p

Rates of non-synonymous (d_N) and synonymous (d_S) substitution for autosomal sex-biased and unbiased genes.

<p>Rates of non-synonymous (d_N) and synonymous (d_S) substitution for autosomal sex-biased and unbiased genes.</p

Sex-bias in the spleen of females (red), subordinate males (light blue) and dominant males (dark blue).

<p>Sex-bias was defined in panel A based on a 1.5-fold change threshold between females and dominant males, with a p-value<0.05. Sex-bias in panel B is defined solely on statistical difference (<i>p</i><0.05) between females and dominant males. Significant difference between dominant and subordinate males is indicated (Wilcoxon test, * <i>p</i><0.05, ** <i>p</i><0.01, *** <i>p</i><0.001, **** <i>p</i><0.0001).</p

Heat maps and hierarchical clustering of gene expression for females, subordinate males and dominant males.

<p>Shown is the relative expression for autosomal male-biased (n = 2,217, panel A), female-biased (n = 2,908, panel B) and Z-linked (n = 364, panel C) genes. Hierarchical gene clustering is based on Euclidean distance for average log₂ expression for each gene for the three sexual morphs. The number at each node is the percentage bootstrap result from 1000 replicates.</p

Average log₂ expression for all sex-biased genes.

<p>Panel A, autosomal male-biased and female-biased genes in females (red), subordinate males (light blue) and dominant males (dark blue). Panel B, autosomal male-biased genes ranked by male-bias. Panel C, autosomal female-biased genes ranked by female bias, and Panel D, Z-linked male-biased genes ranked by male-bias. Whiskers extend to the most extreme data point, excluding outliers that exceeded 1.5× the interquartile range. Significant <i>p</i>-values as calculated by Wilcoxon tests are indicated by asterisks above each comparison between dominant and subordinate males (* <i>p</i><0.05, ** <i>p</i><0.01, *** <i>p</i><0.001, **** <i>p</i><0.0001).</p

Expression similarity across sexual forms.

<p>Spearman rank order (ρ) correlations for average expression for females, subordinate males and dominant males for autosomal unbiased (panel A), autosomal male-biased (panel B), autosomal female-biased (panel C), and Z-linked (panel D) genes. Correlation values are colour coded with lighter colours indicating greater correlation.</p

Sequence alignments used for divergence analysis

Contains 2649 phylip alignment files used to calculate divergence in PAML. Each phylip file contains cDNA sequence of the six species plus zebra finch outgroup. Orthogroups were aligned with PRANK v121218 using the orthologous Taeniopygia guttata cDNA (taeGut3.2.4.75) as an outgroup and specifying the following guidetree; (((A. cygnoides, A. platyrhynchos), (N. meleagris, (P. cristatus, (M. gallopavo, P. colchicus)))), T. guttata). APL = Anas platyrhynchos, ACY = Anser cygnoides, MGA = Meleagris gallopavo, NME = Numida meleagris, PCO = Phasianus colchicus, PCR = Pavo cristatus, TGU= Taeniopygia guttata

Sequences of Trinity contigs for each of the six Galloanserae species

Contains a fasta file of Trinity assembly contig sequences for each of the six species. APL = Anas platyrhynchos, ACY = Anser cygnoides, MGA = Meleagris gallopavo, NME = Numida meleagris, PCO = Phasianus colchicus, PCR = Pavo cristatus.The left gonad and spleen were dissected separately from five males and five females of each species. The exceptions were P. colchicus, where six male gonad and spleen samples were collected, and M. gallopavo, where four male and two female spleens were collected. Samples were homogenzied and stored in RNAlater until preparation. We used the Animal Tissue RNA Kit (Qiagen) to extract RNA, and the samples were prepared and barcoded at The Wellcome Trust Centre for Human Genetics, University of Oxford using Illumina’s Multiplexing Sample Preparation Oligonucleotide Kit with an insert size of 280bp. RNA was sequenced on an Illumina HiSeq 2000. The data was quality assessed using FastQC v0.10.1 (www.bioinformatics.babraham.ac.uk/projects/fastqc) and filtered using Trimmomatic v0.22 (Lohse et al. 2012). Specifically, we removed reads containing adaptor sequences and trimmed reads if the sliding window average Phred score over four bases was <15 or if the leading/trailing bases had a Phred score <4. Reads were removed post filtering if either read pair was <25 bases in length. We constructed de novo transcriptome assemblies for each species using Trinity with default parameters (Grabherr et al. 2011)

RPKM data for each of the six Galloanserae species

Contains a file of RPKM expression data for each of the six species. APL = Anas platyrhynchos, ACY = Anser cygnoides, MGA = Meleagris gallopavo, NME = Numida meleagris, PCO = Phasianus colchicus, PCR = Pavo cristatus. Gene expression was quantified using only adult gonad samples and estimated as reads per kilobase per million mappable reads (RPKM) using RSEM v1.1.21 with default parameters (Li and Dewey 2011)

RPKM data for each of the six Galloanserae species

Contains a file of RPKM expression data for each of the six species. APL = Anas platyrhynchos, ACY = Anser cygnoides, MGA = Meleagris gallopavo, NME = Numida meleagris, PCO = Phasianus colchicus, PCR = Pavo cristatus. Gene expression was quantified using only adult gonad samples and estimated as reads per kilobase per million mappable reads (RPKM) using RSEM v1.1.21 with default parameters (Li and Dewey 2011)