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.