Genomic information has the potential to aid in the establishment of sustainable management plans for commercially exploited marine fishes, aiding in the long-term conservation of these resources. The southern African hakes (Merluccius capensis and M. paradoxus) are commercially valuable demersal fishes with similar distribution ranges but exhibiting contrasting life histories. Using a comparative framework based on Pool-Seq genome-wide SNP data, we investigated whether the evolutionary processes that shaped extant patterns of diversity and divergence are shared among these two congeneric fishes, or unique to each one. Our findings revealed that M. capensis and M. paradoxus show similar levels of genome-wide diversity, despite different census sizes and life-history features. In addition, M. capensis shows three highly structured geographic populations across the Benguela Current region (one in the northern Benguela and two in the southern Benguela), with no consistent genome-environment associations detected. In contrast, although population structure and outlier analyses suggested panmixia for M. paradoxus, reconstruction of its demographic history suggested the presence of an Atlantic-Indian Ocean subtle sub-structuring pattern. Therefore, it appears that M. paradoxus might be composed of two highly connected populations, one in the Atlantic and one in the southwest Indian Ocean. The reported similarly low levels of genomic diversity, as well as newly discovered genetically distinct populations in both hake species can thus assist in informing and improving conservation and management plans for the commercially important southern African Merluccius.

Samples used in this study were collected in 2012 for the study of Henriques et al. (2016), from fisheries surveys by the Department of Forestry, Fisheries and Environment (DFFE – South Africa) and the Ministry of Fisheries (Namibia), and ethical clearance for data usage was obtained from the University of Pretoria (NAS217/2021). The sampling design mimicked the main oceanographic features of the Benguela Current system, with samples collected from north and south of the perennial upwelling cell, as well as past Cape Point towards the east in South Africa (Figure 1A). For M. capensis, samples were obtained from northern Namibia to the southern West Coast of South Africa, as previous findings reported a single population break across the Orange River. For M. paradoxus, sampling took place from northern Namibia to southwestern South Africa, as von der Heyden et al. (2007) reported a putative genetic break across Cape Point in South Africa, which was not detected by Henriques et al. (2016). A reduced representation, pooled sequencing approach was employed (ezRAD Pool-Seq – Toonen et al., 2013) to generate SNPs, as this methodology is a cost-effective way to accurately obtain population-based allele frequencies (Dorant et al., 2019).

Muscle tissue was sampled from 20–40 individuals for each pool per species, and their DNA was pooled based on average latitude and depth of the sampling sites, as well as the genotypes of M. capensis individuals obtained from microsatellite data (Henriques et al., 2016), meaning that for this species, northern and southern Benguela pools contained individuals with either a northern or southern genotype. Four M. capensis pools were obtained: northern Namibia (CNN), central Namibia (CCN), northern South African west coast (CWC) and southern South African west coast (CWC2). The five M. paradoxus pools included northern Namibia (PNN), central Namibia (PCN), northern South Africa west coast (PWC), southern South African west coast (PWC2) and South African southwest coast (PSW). DNA was extracted using the chlorophorm:isoamyl alcohol method of Winnepenninckx et al. (1993), and quantified using a broad-range QUBIT assay (Invitrogen) at the Central Analytical Facilities of Stellenbosch University. DNA samples were pooled in equal concentrations and sent for paired-end sequencing using at the Hawai’i Institute of Marine Biology (HIIMB), following the protocol of Knapp et al. (2016). This method employs a high-frequency restriction enzyme (DpnII – 5’ GATC 3’) to shear DNA and uses the Kapa Hyper Prep kit for library preparation. Sequencing was conducted on the Illumina MiSeq platform for 600 cycles, generating paired-end reads of 300bp.