Figure legends
Figure 1 Map showing the location of Lakes Bunnersjöarna in the
mountainous area of central Sweden. The lakes are found in the uppermost
part of the water system (elevation indicated, m =meters). Our
samples were collected in the northern Bunnersjön (N. Bunnersjön;n = 68) and in the southern Bunnersjön (S. Bunnersjön;n =72). For comparison, we also used material from Lake Ånnsjön
(shown here) as well as from several other lakes in other areas (see
Figure S1a-d).
Figure 2 Membership coefficient (Q ) plots showing the
assignment probability of individual fish (total n =140) to
clusters using 96 SNPs. Membership coefficients (Q ) were obtained
from STRUCTURE and the most likely number of clusters (K ) for the
data was estimated using three different ad hoc methods: log
probability of data (lnPrX │K ), ΔK , and parsimony
index (PI ). Panel a) shows K =2, panel b) K =3, and
panel c) K =11 as the most likely numbers of K suggested by
ΔK , PI, and lnPrX │K , respectively. Each fish is
represented by a vertical bar and the order of individuals is the same
in all panels, starting with 68 individuals classified to Deme I,
followed by 72 individuals classified to Deme II based on genotype in
the allozyme locus LDH-1 .
Figure 3 Individual-based neighbor-joining tree illustrating
the genetic relationship among brown trout from Lakes Bunnersjöarna
using 70 SNP loci. Individuals marked I vs. II (purple vs. blue color)
are classified to belong to Deme I vs. Deme II based on their allozymeLDH-I genotype. The tree was constructed based on Nei’s
DA distance, and has been compressed to include branches
with bootstrap values of at least 70%. Numbers along the branches
indicate bootstrap values in percentages. The black dots mark the four
individuals that were randomly selected for individual whole-genome
sequencing.
Figure 4 Pairwise F ST values between
Deme I and II of Lakes Bunnersjöarna estimated from whole-genome
Pool-seq data using 5 kb windows across 40 brown trout chromosomes. NA=F ST values from scaffolds not possible to assign
to a chromosome. The horizontal black dashed line shows the genome-wide
mean F ST=0.13 while the red dashed line marks the
97.5% limiting F ST=0.35.
Figure 5: Distribution of observed (range: 0 to 1) and
simulated (“expected”; range: 0 to 0.864) F STvalues based on the POWSIM method (Ryman
& Palm, 2006). A total of 12,177,462 SNPs derived from Pool-seq data
were analyzed and the mean F ST for these was
0.083 (Table S2). The largest simulated F ST was
0.864 and we had 194 observed F ST values above
this value. The framed subfigure is a close-up to show the distribution
of the extreme values in the right-hand tail.
Figure 6 a) Estimates of total lengths of runs of homozygosity
(LnROH ) of three categories and b) F ROH(fraction of runs of homozygosity, ROH, expanded over the genome)
using individual whole-genome sequencing data from each of two
individuals per deme from Lakes Bunnersjöarna.
Figure 7 : The genetic relationships among brown trout
populations from the two demes of Lakes Bunnersjöarna and from other
lakes in the same geographic region and TreeMix analysis assuming
potential migration between lakes in the same geographic area where
creek waterways between lakes exist (cf. Figure 1, Figure S1, Appendix
S1). The scale indicates the proportion of genetic divergence per unit
length of the branch (indicated by the scale length).