Gene flow from Mediterranean Sea towards the Slope Sea revealed by interspecific introgression
To understand why genetic differentiation is maintained despite presumable ongoing gene flow, we studied the effect of interspecific introgression. Mitochondrial introgression from albacore (Thunnus alalunga ) into ABFT has been previously reported, with all introgressed individuals detected so far found in the Mediterranean Sea and the Slope Sea (Alvarado Bremer et al. 2005, ViƱas et al. 2011), but not in the Gulf of Mexico. According to three diagnostic positions for mitochondrial ancestry (Table S2), we found albacore origin introgressed mitochondria in individuals of all age classes in both the Mediterranean Sea (4%) and the Slope Sea (6%), but also to a lower extent in Gulf of Mexico adults (1%) (Figure 2A and Table S1). These results were confirmed at the nuclear level by a tree-based analysis of population splits and admixture using allele frequency data (TreeMix), which supported an introgression event from albacore into the Mediterranean Sea ABFT (Figure 2A and S7). In accordance with this deviation from a strict bifurcating evolutionary history, we also found an excess of derived allele sharing between albacore and both the Slope Sea and the Mediterranean Sea with respect to the Gulf of Mexico (ABBA/BABA test, Figure 2B). However, the contribution of albacore introgression to genetic differentiation between Mediterranean Sea and Gulf of Mexico ABFT populations appears to be limited at best (Figure S8) and therefore it could contribute but not explain the maintenance of genetic differentiation between MED-like and GOM-like individuals.
Our results confirm the introgression of mitochondrial DNA and show for the first-time traces of introgression at the nuclear level from albacore to the ABFT. The gradient of albacore ancestry further suggests that this introgression occurred (or has been more intense) in the Mediterranean Sea where the signal is strongest, and then diffused towards the Slope Sea and, to a lesser extent the Gulf of Mexico through multigenerational gene flow. These different introgression signal intensities from east to west support gene flow between the Mediterranean Sea and Slope Sea spawning components, which is in accordance with the admixed nature of Slope Sea individuals. On the other hand, the differences in the introgression signal intensities also imply reduced gene flow from the Mediterranean Sea to the Gulf of Mexico, which contrasts with the frequency of MED-like spawners observed in the Gulf of Mexico. This, together with the fact that introgression is not the main contributor to genetic differentiation between spawning components, strongly suggests that other mechanisms, such as local adaptation, maintain genetic differentiation in the presence of gene flow, or that migration towards the Gulf of Mexico has increased recently.