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).