Atlantic mackerel population structure does not support genetically distinct spawning components

Abstract

Background: The Atlantic mackerel, Scomber scombrus (Linnaeus, 1758) is a commercially valuable migratory pelagic fish inhabiting the northern Atlantic Ocean and the Mediterranean Sea. Given its highly migratory behaviour for feeding and spawning, several studies have been conducted to assess differentiation among spawning components to better define management units, as well as to investigate possible adaptations to comprehend and predict recent range expansion northwards.

Methods: Here, the genome of S. scombrus was sequenced and annotated, as an increasing number of population genetic studies have proven the relevance of reference genomes to investigate genomic markers/regions potentially linked to differences at finer scale. Such reference genome was used to map Restriction-site-associated sequencing (RAD-seq) reads for SNP discovery and genotyping in more than 500 samples distributed along the species range. The resulting genotyping tables have been used to perform connectivity and adaptation analyses.

Results: The assembly of the reference genome for S. scombrus resulted in a genome of 741 Mb. Our population genetic results show that the Atlantic mackerel consist of three previously known genetically isolated units (Northwest Atlantic, Northeast Atlantic, Mediterranean), and provide no evidence for genetically distinct spawning components within the Northwest or Northeast Atlantic.

Conclusions: Therefore, our findings resolved previous uncertainties by confirming the absence of genetically isolated spawning components in each side of the northern Atlantic, thus rejecting homing behaviour and the need to redefine management boundaries in this species. In addition, no further genetic signs of ongoing adaptation were detected in this species.

Keywords: Atlantic mackerel; RAD-seq; complete genome; fisheries management; genome-wide SNPs; population structure.

Figure 1.. Snailplot summary of the assembly metrics for the Scomber scombrus genome.

The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 741,290,950 bp assembly. The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (10,208,092 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (1,748,220 and 152,403 bp), respectively. The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude. The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot. A summary of complete, fragmented, duplicated and missing BUSCO genes in the actinopterygii_odb10 set is shown in the top right.

Figure 2.. Population structure analyses.

( A) Map of sampling collections included in the study. Each colour represents a sampling area. Names and sample sizes of each group are reported in the map. Different shapes are used to identify different life stages (larvae, juvenile, adult, and spawning adult). ( B) Admixture results for best K=3. Levels of admixture are shown on the y-axis and are ordered by Q-values within each group and for each life stage. Life stages are coded on top of the admixture plot as: L=larvae, J=juvenile, N=adult not-spawning, S=spawning adult. In green, the western Atlantic ancestry component, in sky-blue, the eastern Atlantic, and in red the Mediterranean one as estimated by ADMIXTURE. ( C) Principal component analyses (PCA) performed on individuals of the Atlantic mackerel based on the genomic dataset of 24,271 SNPs and 515 individuals in the overall dataset and for the different age classes within the NWA ( D; 150 individuals, 39,541 SNPs) and NEA ( E; 273 individuals, 39,528 SNPs).