Figure legends
Figure 1. Population structure and connectivity of Atlantic bluefin tuna. (a) Map showing capture location and life stage of Atlantic bluefin tuna samples included in this study. Capture location of adults from the Gulf of Mexico are enclosed within the purple rounded polygon to fulfil confidentiality requirements. (b) Estimated individual ancestry proportions assuming two ancestral populations. (c) Principal Component Analysis (PCA) of genetic variability among Atlantic bluefin tuna samples, following colour codes identical to (b). (d) Density distribution of individual MED-like ancestry proportions per spawning ground. (e) F3-statistics for each combination of sources and target populations, where the Slope Sea and Mediterranean Sea contain larvae and young of the year and larvae, young of the year and adults, respectively (see detailed results in Table S4 and Figure S5). (f) Visual representation of the best-fit demographic model, where arrow and branch widths are proportional to directional migration rates (m) and effective population sizes (n) respectively, and where T represents the duration of population splits. Estimated parameter values are given in units of 2nA, where nA is the effective size of the ancestral population, related to the population-scaled mutation rate parameter of the ancestral populations by θ=4nAµ.
Figure 2. Interspecific introgression between albacore and Atlantic bluefin tuna. (a) Phylogenetic tree estimated by TreeMix based on nuclear data allowing one migration event (the arrow indicates migration direction and rate). Numbers indicate the percentage of individuals (from those included in the tree) showing the introgressed mitochondrial haplotype for each location and age class (abbreviations as in Figure 1). On the upper right, zoom on the phylogenetic relationships among Atlantic bluefin tuna groups. (b) D statistical values estimated from the ABBA/BABA test used to detect introgression from albacore to different targets (rows) using different references (colours). The higher the value, the more introgressed is the target group respect to the reference.
Figure 3. Outlier markers in Atlantic bluefin tuna cluster within one 2.63Mb genomic regions showing high long-distance linkage disequilibrium. (a) PCA performed using the 123 outlier SNPs showing the three-cluster grouping (shades of blue) where shapes and colours of samples are those indicated in Figure 1. (b) SNP pairwise linkage disequilibrium plot among the 110 SNPs found within a high linkage region covering scaffolds BKCK01000075 (partially) and BKCK01000111 of the reference genome where most of the SNPs contributing to PC1 from (a) are located. (c) Boxplot showing heterozygosity values (y axis) at the three sample groups show in (a), represented by the same blue colour , and based on the 110 SNPs within the genomic region shown in (b). (d) Proportion of samples from each location and age class assigned to each of the three groups shown in (c).
Figure 4. Evolutionary origin of Atlantic bluefin tuna within the region of high-linkage disequilibrium. () Principal component analysis (PCA) including other Thunnus species (albacore in blue, Southern bluefin tuna in green and Pacific bluefin tuna in yellow) performed using 156 genetic variants located within the genomic region under high linkage disequilibrium hosting a candidate structural variant (b) Estimated D values from an ABBA/BABA test based on variants located within the genomic region of high-linkage disequilibrium, using Southern bluefin tuna as an outgroup, albacore as a donor species and all different groups of Atlantic bluefin tuna as alternative targets ordered along the y-axis.