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

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

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

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

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

Shorebird_Count_Data_DESeq.txt

This file holds the count data for all the transcripts with putative "avian origins" i.e., those contigs that have a 1:1 ortholog within the genomes of chicken and/or zebra finch. Differential gene expression was conducted using the R Bioconductor package, DESeq (version 10.1.1) (Anders & Huber 2010)

Changes in SAA frequency in the light and dark populations.

<p>SAA frequency was affected by the manipulation of light/dark regimes (χ²₁ = 18.82, p<0.0001) across (a) P1 light and dark populations and (b) P2 light and dark populations. There was a significant interaction between light treatment and generation (χ²₁ = 4.54, p = 0.033) showing that SAA frequency significantly diverged between the continuous light and continuous dark populations. SAA frequency did not significantly change in light populations (χ²₁ = 2.97, p = 0.085) but significantly declined in dark populations (χ²₁ = 4.81, p = 0.028).</p

README

READM

Putative_Z_SSR

Contains the SSR information for all the putative Z-linked transcripts