FIGURE LEGENDS
Figure 1. Schematic of the distribution patterns of three types of sex-linked loci in the ZW sex-determination system: W-linked loci are found only in the W chromosome (yellow); Z-linked loci are found only in the Z chromosome (orange); gametolog loci are present in both chromosomes (green). The same principles apply to the XY sex-determination system but males are heterogametic (XY) and females homogametic (XX).
Figure 2. Distribution of some diagnostic parameters for autosomal and sex-linked loci. a) Autosomal loci (grey) are expected to present roughly the same call rate for males and females. W-linked loci (yellow) are expected to be called in females but absent in males because males lack a W chromosome. We refer to other loci whose call rate is biased by sex as ‘sex-biased’ (blue, drawn here for male-bias in call rate). b) Autosomal loci (grey) are expected to present roughly the same proportion of heterozygous males and females. For Z-linked loci (orange), females are expected to be homozygous because they have only one Z chromosome. For gametologous loci (green), males are expected to be homozygous because they have two Z chromosomes each with the same Z-associated allele.
Figure 3. Plots produced by function filter.sex.linkedafter being used to identify and remove sex-linked loci from eastern yellow robin (EYR) genetic data. Top panels: plots of female call rate against male call rate in which each point represents a locus, before (a ) and after (b ) removing 2,639 sex-linked loci with differential call rate between the sexes. Bottom panels: plots of the proportion of heterozygous females against the proportion of heterozygous males with each point representing a locus, before (c ) and after (d ) removing 1,168 sex-linked loci with differential heterozygosity between the sexes.
Figure 4. Progression of four types of sex-linked loci after different SNP filtering steps were applied to eastern yellow robin (EYR) and yellow-tufted honeyeater (YTH) datasets. Arrows to the right indicate the percentage of sex-linked loci (out of the initial 100%) that were removed. Down arrows indicate the percentage of sex-linked loci (out of the initial 100%) that remain in the dataset.
Figure 5. Percentage change of six measures of population genetic diversity after removing sex-linked loci (Ho: observed heterozygosity, He: expected heterozygosity, FIS: Wright’sF IS, P: polymorphism, PA: private alleles, and AR: allelic richness). Estimates are given per population of eastern yellow robin (EYR) and yellow-tufted honeyeater (YTH).
Figure 6. Principal Component Analyses (PCA) of the genomic dataset of eastern yellow robin, EYR, before (top panels) and after (bottom panels) removing sex-linked loci. On (a ) and (c ), individuals are coloured according to their population. On (b ) and (d ), individuals are coloured by sex.
Figure 7. Proportion of sex-linked loci that functionfilter.sex.linked was able to identify with variable number of known-sex individuals for EYR (a ) and YTH (b ) datasets. The sex ratio of known sex-individuals was 1:1, except for ‘all’ which included the whole set of known-sex individuals (EYR: 352 females and 429 males, YTH: 289 females and 347 males).