Figure
legends
Figure
1: Map showing sample distribution. The blue contour line shows 50m line
where snapper primary occur, and red shows 200m indicating the maximum
depth where snapper is found. Left panel shows the five different
management areas in which snapper are currently managed. Top right shows
an illustration of snapper (Courtesy of Plant and Food Research).
Figure 2: Genetic structure of
snapper in New Zealand. A) PCA showing the genetic structure based on
neutral loci. Individuals were grouped by sample location. similar PCAs
based using high-quality and outlier loci are shown in Figure S3)
Admixture plot for K=2. Admixture proportions correspond with PCA
results, with evidence of populations mixing on either side of the
proposed genetic disjunctions at Cape Reinga and Mahia peninsula. Blue
shows ancestry to the West cluster, red shows ancestry to the East
cluster. C) Analyses of ancestry proportions to the East cluster shows
the presence of directional gene flow from the East to the West cluster.
D) Heatmap showing pairwise weighted FST estimates for sampling
locations.
Figure 3: Manhattan plot showing
summary statistics for 5,000 base pair non-overlapping windows.
Nucleotide diversity (π), FST ,dxy, and delta Tajima’s D(ΔDT). Dashed black line shows theFST = 0.15 boundary, andFST > 0.15 are indicated in red.
Regions of interest on Linkage groups 1, 7, 8 and 10 are indicated with
vertical black lines and shown in Figure 4.
Figure 4: Manhattan plots showing
the four genomics regions showing high levels of genetic differentiation
between the East and West genetic cluster. Nucleotide diversity (π),FST , dxy and deltaTajima’s D (ΔDT). Grey areas indicate regions of
high relative genetic divergence (FST> 0.15). Solid black horizontal lines indicated the median.
Dashed black horizontal lines indicate the 0.95 quantile (π,FST , and dxy ) or 0.025 and
0.975 quantiles (DT and ΔDT). Locations
of genes within regions of interest are shown at the top of each plot in
black and grey. Relevant genes are indicted by name. X-axis shows
position on linkage group in Mbp.
Figure 5: Box plots showing
levels of heterozygosity among individuals between the East and West
genetic clusters for all high-quality loci, neutral loci, and outlier
loci. Mean levels of heterozygosity are depicted in the middle of each
boxplot. Levels of significant between genetic clusters for each SNP
dataset are shown at the top of each panel.
Figure 6: Spatial distribution of
the East and West genetic cluster. Arrows show the direction of gene
flow from the East to the West genetic cluster. Blue and red show the
50m bathymetry line for each of the genetic clusters, and light blue and
light red indicate the 200m bathymetry line for each of the genetic
lusters. Dashed lines show boundaries between fisheries management areas
(SNA1, SNA2, SNA7, and SNA8). Solid arrows show the direction of gene
flow, dashed lined with triple arrowheads indicate relevant ocean
currents, WAUC = West Auckland Current, EAUC = East Auckland Current,
ECC = East Coast Current.
Supplementary table –
legends
Table
S1 Information Samples sites
Supplementary figure –
legends
Figure S1: Scree plot used to
determine the number of informative principal components (K=1) for the
identification of outliers using pcadapt.
Figure S2: Coverage of each
individual A) before and B) after normalisation of bam files. Each point
is an individual, and colours indicate sample locations.
Figure S3: PCA generated using
three different SNP datasets. High-Quality, Neutral, and Outlier loci.
PCAs show a consistent grouping of sample location which cluster into
two genetic clusters, East and West.
Figure S4: Cross validation
scores for ADMIXTURE suggesting K=2 is the most appropriate number of
clusters. Lowest cross validation error indicating most appropriate
number of K is shown in red (K=2).
Figure S5: Genetic distance
(weighted FST) between populations plotted against geographic distance.
show the linear regression between points. Colours indicate if
comparisons were made between sample locations from the same cluster, or
between different clusters. The black line shows the regression line
between all points.
Figure S6: Boxplots showing
levels of heterozygosity for A) neutral and B) outlier loci per sample
location.
Figure S7: plots showing
environmental gradient for mean ocean temperature at max depth, pH, and
Dissolved oxygen concentration at max depth. Figures show heterogeneous
environmental gradients that pose selective pressures on snapper
populations. Data has been obtained from the Bio-Oracle database and
plotted in R.
Figure S8: Boxplots showing
levels of heterozygosity among neutral loci before normalisation of bam
files.