Observed genetic differentiation between Atlantic bluefin tuna spawning components cannot be attributed to local adaptation acting on few loci of large effect
To better understand the evolutionary processes behind genetic differentiation in ABFT, we separately studied genetic diversity at neutral (i.e. those that are mostly influenced by genetic drift and migration) and outlier SNPs markers (i.e. those that are potentially under selection or in tight linkage with selected loci). Removing the 123 identified outlier markers did not change the overall population structure pattern nor differentiation values (Figure S9), suggesting that observed genetic differentiation cannot be explained by local adaptation only. On the other hand, analyses based on the 123 markers identified as potentially under selection provided higher genetic differentiation values among spawning grounds (Figure S9) but revealed three groups of samples that do not correspond to the overall population structure (Figure 3A and S10) and that are neither related to laboratory nor phenotypic sex effects (Figure S11). The 20% of the SNP markers that contribute the most to this grouping are located within the same region of the genome (mapping on two scaffolds spanning 2.63 Mb region of the PBFT reference genome) (Table S7) and show strong pairwise linkage disequilibrium (LD) across the whole region (meaning that variant versions of SNP pairs are non-randomly associated and the same combination is often found among individuals haplotypes) (Figure 3B). The SNPs located within this high-LD region support a three-grouping pattern (Figure S12), with the intermediate group of individuals in the PCA presenting increased heterozygosity values (Figure 3C). This suggests the existence of two main haplotypes (unique allelic combinations across multiple SNPs) in this region combined into three possible genotypes (e.g. AA, AB, BB), which shows characteristics typical of a chromosomal inversion. These two haplotypes, presumably the inverted and collinear versions, are present at different frequencies among spawning grounds, the rarest found to be homozygous only in the Mediterranean Sea, where it is more frequent, and the alternative being more abundant in the Gulf of Mexico and Slope Sea (Figure 3D). A PCA based on genetic markers from this genomic region including otherThunnus species (Figure 4A) showed that homozygous individuals for the most abundant haplotype group associated with the PBFT, whereas those homozygous for the rarest variant were close to albacore. By contrast, the PCA based on the genome-wide SNP dataset showed the expected grouping pattern reflecting species membership, where PBFT and ABFT cluster together and were separated from albacore and Southern bluefin tunas (Figure S13). Test for deviation from a strict bifurcating evolutionary history (ABBA/BABA) showed a much more pronounced signal of introgression from albacore into the Mediterranean and Slope Sea spawning ground samples in the high-LD region (Figure 4B) than when considering the overall genome (Figure 2B). Yet, this pattern remained when removing all SNPs from the high-LD region (Figure S14), indicating that the signal of introgression is present genome-wide.
These results suggest that the genetic differentiation observed between ABFT from different spawning grounds is maintained despite gene flow between the Mediterranean Sea and the Slope Sea and cannot be explained by local adaptation acting on a few loci of large effect. Additionally, a large genomic region of albacore ancestry, introgressed into the ABFT genome in the Mediterranean Sea, has retained high LD while expanding towards the western Atlantic, following the previously detected genome-wide signal of albacore ancestry. Altogether, our results point towards a situation where the two ancestral genetic components of ABFT (Western Atlantic and Mediterranean) have initially diverged in isolation, independently experiencing genetic drift combined with introgression of genetic material from albacore in the Mediterranean Sea. More recently, homogenization between western Atlantic and Mediterranean components could have been initiated by the intensification of gene flow, without completely eroding existing genetic differentiation.