Figure legends
Figure 1. A. Distribution map of the black-faced (red: breeding range;
gold: wintering range) and royal spoonbills (blue; modified from Hancock
et al. 1992). The arrows indicate the two sampling sites, Tainan, Taiwan
(blue) and Hong Kong (orange), of the black-faced spoonbill used in
current study. B. The cross-validation (CV) error of theADMIXTURE analysis (K : 1- 5) of the black-faced spoonbill
from Taiwan and Hong Kong was smallest when K was equal to 1. The
origin of samples is labeled at the bottom: T: Tainan, Taiwan; HK: Hong
Kong. C. Samples of the black-faced spoonbill from Tainan, Taiwan and
Hong Kong did not form distinct clusters in the plot of scores of PC1
(1.33% of genetic variance) versus PC2 (1.28% of genetic variance).
The origin of the samples is indicated by colors: blue: Tainan, Taiwan;
orange: Hong Kong.
Figure 2. A. The historical effective population size
(N e) trajectories estimated by SMC ++ for
both the black-faced and the royal spoonbill since the last glacial
maximum (c.a. 22,000 years before the present); the fullN e trajectories of the two spoonbill species
estimated by SMC ++ are shown within the inset. The black-faced
spoonbill in magenta and the royal spoonbill in apricot. B. Demographic
parameters of the recent bottleneck model for the black-faced spoonbill
estimated from simulations of Fastsimcoal2 based on the folded
site frequency spectrum of the 215,722 unlinked autosomal SNPs. The
solid line is the maximum likelihood estimate of variousN e; The dashed line is the 95% CI ofN anc and N cur.T bot: initiation time of the bottleneck;T endbot: termination time of the bottleneck;N anc: long term N e before
the bottleneck; N bot: N eduring the bottleneck; and N cur: the
post-bottleneck N e.
Figure 3. A. The black-faced spoonbills sequenced had more runs of
homozygosity (> 100 Kb; NROH) and longer total runs of
homozygosity (SROH) than the royal spoonbills sequenced. The black-faced
spoonbills are shown in circles, and the royal spoonbills in triangles.
B. The linkage (r 2) between SNPs on the same
scaffold decayed more slowly in the black-faced spoonbill genome than in
the royal spoonbill genome. C. The proportion of singletons in the
folded site frequency spectrum for unlinked
(r 2< 0.2) autosomal SNPs was
significantly lower in the black-faced spoonbill genomes (21.9%) than
in the royal spoonbill genome (31.7%; χ 2=
24.82, p = 0.000). D. The Tajima’s D value for all
autosomal SNPs of the black-faced spoonbill (0.24± 0.98, n =
4,522,032) is higher than that of the royal spoonbill (0.05± 0.99,n = 4,437,044; t = 296.51, p < 0.001). The
black-faced spoonbill is shown in magenta and the royal spoonbill in
apricot.
Figure 4. A. Significantly
more genes in the black-faced spoonbill (2,094, 37.0%) are under
relaxed selection (relaxation parameter k <1,p < 0.05) than in the royal spoonbill (1,542, 27.2%;χ 2= 123.04, p = 2.2e-16; Figure 4A); but
not for genes under intensified selection χ 2=
3.17, p = 0.075). B. The mean number of nonsynonymous
substitutions found in each individual of the black-faced spoonbill
genome (8294.00± 332.66 substitutions) is higher than that found in the
royal spoonbill genome (8025.78± 211.77 substitutions; t = -1.91,p < 0.035). C. The average Grantham’s score for each
deleterious nonsynonymous substitution (Grantham’s score >
50) is significantly higher for the black-faced spoonbill (56.98± 0.69)
than for the royal spoonbill (53.25± 1.83; two-sample t test=
6.5154, p = 3.6e-6). D. The ratio of homozygous to heterozygous
nonsynonymous substitutions in the genome of the black-faced spoonbill
(0.13± 0.04) is higher than that in the royal spoonbill genome (0.11±
0.007; t = -1.86, p < 0.04). The black-faced
spoonbill is shown in magenta and the royal spoonbill in apricot.