Figures:
Figure 1: The sampling location for each species of fish.
Threespine locations are represented by green triangles, ninespines by
blue squares and tubesnouts by orange circles. Labels for each
population are used consistently throughout this paper; the first half
of the label denotes the species (Ts = thresspine stickleback, Tu =
tubesnout and Ns = ninespine stickleback). The second half of the label
denotes the state or province where the population was collected (AK =
Alaska, USA; BC = British Columbia, Canada; OR = Oregon, USA; AB =
Alberta, Canada; NU = Nunavut, Canada). The two Albertan ninespine
populations are combined into a single point (NsABm & NsABk) for visual
clarity. The base map is projected in Azimutahl equal distances (datum =
WGS84) orientated to centre on Canada (latitude = 90 & longitude =
-98.4). Ocean water is coloured by the annual range in sea surface
temperature (°C) taken from the Bio-ORACLE database
(https://www.bio-oracle.org/). Threespine and tubesnout photos were
taken by Hazel Cameron-Inglis and used with permission, the ninespine
photo was taken by Piet Spanns and used under an open license. The final
plot was compiled in R using the sf, ggplot, raster and grid packages.
Figure 2: Genome wide patterns of genetic diversity within the
threespine stickleback, ninespine stickleback and tubesnout. A )
FST per SNP and B )\({\overset{\overline{}}{H}}_{E}\) per 50Kb window for each species,
excluding windows in intergenic regions. Ninespine scores were mapped
onto their position on the threespine genome. Threespine and tubesnout
FST was downsized by sampling every
100th SNP along the genome, and approximately 70
windows were filtered out of the \({\overset{\overline{}}{H}}_{E}\)plots for visual clarity. The red-dashed lines show the
999th FST and 99th\({\overset{\overline{}}{H}}_{E}\) quantiles. This plot was generated in
R using the ggplot and gridExtra packages.
Figure 3: Comparison of genomic patterns among species.A) shows the relationship in average genetic diversity
(\({\overset{\overline{}}{H}}_{E}\)) among genes for each species pair.
Each point is a gene which is orthologous among the species. The dashed
lines represent the 95th and 5thquantile of \({\overset{\overline{}}{H}}_{E}\) in each species. Any
points on the bottom left or top right segments of a panel are genes
with extreme \({\overset{\overline{}}{H}}_{E}\) that are shared among
species. B) is a matrix of \({\overset{\overline{}}{H}}_{E}\)Spearman’s correlations among all population pairs, where the colour
represents Spearman’s ρ and the text shows the significance level of a
correlation test (* P < 0.05; ** P
< 0.01; *** P < 0.001). C) shows the
relationship and between the average FST per gene for
each species. Colored points are signatures of local adaptation for each
species; red for threespine sticklebacks and blue for tubesnouts. Gray
points are genes not associated with local adaptation; they are
partially transparant to show overlapping genes. No signatures of
selection overlaped among species.
Figure 4: Detecting genes with elevated divergence and testing
for signatures of convergent evolution. A-B) Show the
top-candidate approach where each point is a separate gene. The total
number of SNPs is compared to the number of SNP outliers in each gene,
with top candidates identified as those genes that exceed the number of
outliers expected under a binomial distribution, represented by the
jagged red line. C-D) Null-W test results between C)tubesnout orthologs of threespine top candidates and D)threespine orthologs of tubesnout top candidates. The grey curve is the
null-distribution of Z-scores from all orthologs of candidate genes in
the focal species (i.e. tubesnout orthologs in C and threespine
orthologs in D ). The blue points are top-candidate-orthologs,
whose values on the y-axis have been jittered for visual clarity. The
red dashed line is the 95th quantile of Z-scores. FDR corrections are
not shown.