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.