DOI: 10.5061/dryad.sn02v6x8n
title: Cryptic population substructure in Cape Hakes

description: 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.
description: 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 <em>M.
 capensis</em>, 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 <em>M.
 paradoxus</em>, 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 <em>M. capensis</em>
 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
 <em>M. capensis</em> pools were obtained: northern Namibia
 (CNN), central Namibia (CCN), northern South African west coast (CWC) and
 southern South African west coast (CWC2). The five <em>M.
 paradoxus</em> 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.