Responses of population structure and genomic diversity to climate change and fishing pressure in a pelagic fish.

The responses of marine species to environmental changes and anthropogenic pressures (e.g., fishing) interact with ecological and evolutionary processes that are not well understood. Knowledge of changes in the distribution range and genetic diversity of species and their populations into the future is essential for the conservation and sustainable management of resources. Almaco jack (Seriola rivoliana) is a pelagic fish with high importance to fisheries and aquaculture in the Pacific Ocean. In this study, we assessed contemporary genomic diversity and structure in loci that are putatively under selection (outlier loci) and determined their potential functions. Using a combination of genotype-environment association, spatial distribution models, and demogenetic simulations, we modeled the effects of climate change (under three different RCP scenarios) and fishing pressure on the species' geographic distribution and genomic diversity and structure to 2050 and 2100. Our results show that most of the outlier loci identified were related to biological and metabolic processes that may be associated with temperature and salinity. The contemporary genomic structure showed three populations-two in the Eastern Pacific (Cabo San Lucas and Eastern Pacific) and one in the Central Pacific (Hawaii). Future projections suggest a loss of suitable habitat and potential range contractions for most scenarios, while fishing pressure decreased population connectivity. Our results suggest that future climate change scenarios and fishing pressure will affect the genomic structure and genotypic composition of S. rivoliana and lead to loss of genomic diversity in populations distributed in the eastern-central Pacific Ocean, which could have profound effects on fisheries that depend on this resource.

Las respuestas de las especies marinas ante los cambios ambientales y presiones antropogénicas (por ejemplo, la sobrepesca) interactúan con procesos ecológicos y evolutivos que no se comprenden bien. El conocimiento del cambio en el rango de distribución y la diversidad genética de las especies y sus poblaciones en el futuro es fundamental para la conservación y gestión sostenible de los recursos. El jurel (Seriola rivoliana) es un pez pelágico de gran importancia para la pesca y la acuicultura en el Océano Pacífico. En este estudio, evaluamos la diversidad y estructura genómica contemporánea en loci que supuestamente están bajo selección (loci atípicos) y determinamos sus funciones potenciales. Se utilizó la combinación de métodos de asociación genotipo-ambiente, modelos de distribución espacial y simulaciones demogenéticas, para modelar los efectos del cambio climático (bajo tres escenarios RCP diferentes) y presión de pesca sobre la distribución geográfica de la especie, la diversidad y estructura genómica para los años 2050 y 2100. Nuestros resultados mostraron que la mayoría de los loci atípicos están relacionados con procesos biológicos y metabólicos que pueden estar asociados con la temperatura y la salinidad. La estructura genómica contemporánea mostró tres poblaciones: dos en el Pacífico oriental (Cabo San Lucas y el Pacífico oriental) y una en el Pacífico central (Hawai). Las proyecciones futuras sugieren una pérdida de hábitat idóneo y posibles contracciones del área de distribución para la mayoría de los escenarios, mientras que la presión de la pesca redujo la conectividad de las poblaciones. Nuestros resultados sugieren que los escenarios de cambio climático y la presión pesquera afectarán la estructura genómica y la composición genotípica de S. rivoliana y conducirán a la pérdida de diversidad genómica en las poblaciones distribuidas en el Océano Pacífico centro-oriental, lo que podría tener efectos en las pesquerías que dependen de este recurso.

Evolutionary Genomics at the Human-Environment Interface in Africa.

We report on the first meeting of SMBE in Africa. SMBE Malawi was initiated to bring together African and international researchers who use genetics or genomics to study natural systems impacted by human activities. The goals of this conference were 1) to reach a world-class standard of science with a large number of contributions from Africa, 2) to initiate exchange between African and international researchers, and 3) to identify challenges and opportunities for evolutionary genomics research in Africa. As repored, we think that we have achieved these goals and make suggestions on the way forward for African evolutionary genomics research.

Distinct interspecific and intraspecific vulnerability of coastal species to global change.

Characterising and predicting species responses to anthropogenic global change is one of the key challenges in contemporary ecology and conservation. The sensitivity of marine species to climate change is increasingly being described with forecasted species distributions, yet these rarely account for population level processes such as genomic variation and local adaptation. This study compares inter- and intraspecific patterns of biological composition to determine how vulnerability to climate change, and its environmental drivers, vary across species and populations. We compare species trajectories for three ecologically important southern African marine invertebrates at two time points in the future, both at the species level, with correlative species distribution models, and at the population level, with gradient forest models. Reported range shifts are species-specific and include both predicted range gains and losses. Forecasted species responses to climate change are strongly influenced by changes in a suite of environmental variables, from sea surface salinity and sea surface temperature, to minimum air temperature. Our results further suggest a mismatch between future habitat suitability (where species can remain in their ecological niche) and genomic vulnerability (where populations retain their genomic composition), highlighting the inter- and intraspecific variability in species' sensitivity to global change. Overall, this study demonstrates the importance of considering species and population level climatic vulnerability when proactively managing coastal marine ecosystems in the Anthropocene.

Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species.

BACKGROUND: As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species' potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis). RESULTS: Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus, but not for C. punctatus. CONCLUSION: The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.

Anthropogenic pressures negatively impact genomic diversity of the vulnerable seagrass Zostera capensis.

Zostera capensis is a keystone species providing essential ecosystem services to southern African coastal systems. Like most seagrasses globally, Z. capensis is declining and under threat from anthropogenic pressures, and indicators of seagrass health and resilience may be of interest in preventing further declines. As intraspecific diversity is an important component of resilience, we used a pooled RADseq approach to generate genome-wide measures of variation across the entire South African distribution of Z. capensis. Using nucleotide diversity, heterozygosity and allelic richness we tested for associations with fine-scale anthropogenic pressure data compiled by the South African National Biodiversity Assessment using generalised linear models. Increased fishing effort, habitat loss, sand mining and a change in estuary flow dynamics were found to play an important role in decreasing nucleotide diversity and expected heterozygosity, most likely due to the loss of less resilient genotypes as a result of direct physical damage or indirect consequences. As the building block for adaptation, nucleotide diversity is particularly important for resilience. Because of this, as well as the fact that nucleotide diversity displayed the most distinct difference between the west and east coast, and responded most strongly to anthropogenic pressures, we suggest that this may be a useful measure for monitoring genetic or genomic variation. As genomic diversity influences resilience and resistance to disturbances, the remaining diversity in South African seagrass beds urgently needs to be conserved through restoration efforts and careful management of pressures.

Thermal selection as a driver of marine ecological speciation.

Intraspecific genetic structure in widely distributed marine species often mirrors the boundaries between temperature-defined bioregions. This suggests that the same thermal gradients that maintain distinct species assemblages also drive the evolution of new biodiversity. Ecological speciation scenarios are often invoked to explain such patterns, but the fact that adaptation is usually only identified when phylogenetic splits are already evident makes it impossible to rule out the alternative scenario of allopatric speciation with subsequent adaptation. We integrated large-scale genomic and environmental datasets along one of the world's best-defined marine thermal gradients (the South African coastline) to test the hypothesis that incipient ecological speciation is a result of divergence linked to the thermal environment. We identified temperature-associated gene regions in a coastal fish species that is spatially homogeneous throughout several temperature-defined biogeographic regions based on selectively neutral markers. Based on these gene regions, the species is divided into geographically distinct regional populations. Importantly, the ranges of these populations are delimited by the same ecological boundaries that define distinct infraspecific genetic lineages in co-distributed marine species, and biogeographic disjunctions in species assemblages. Our results indicate that temperature-mediated selection represents an early stage of marine ecological speciation in coastal regions that lack physical dispersal barriers.

Complex signatures of genomic variation of two non-model marine species in a homogeneous environment.

BACKGROUND: Genomic tools are increasingly being used on non-model organisms to provide insights into population structure and variability, including signals of selection. However, most studies are carried out in regions with distinct environmental gradients or across large geographical areas, in which local adaptation is expected to occur. Therefore, the focus of this study is to characterize genomic variation and selective signals over short geographic areas within a largely homogeneous region. To assess adaptive signals between microhabitats within the rocky shore, we compared genomic variation between the Cape urchin (Parechinus angulosus), which is a low to mid-shore species, and the Granular limpet (Scutellastra granularis), a high shore specialist. RESULTS: Using pooled restriction site associated DNA (RAD) sequencing, we described patterns of genomic variation and identified outlier loci in both species. We found relatively low numbers of outlier SNPs within each species, and identified outlier genes associated with different selective pressures than those previously identified in studies conducted over larger environmental gradients. The number of population-specific outlier loci differed between species, likely owing to differential selective pressures within the intertidal environment. Interestingly, the outlier loci were highly differentiated within the two northernmost populations for both species, suggesting that unique evolutionary forces are acting on marine invertebrates within this region. CONCLUSIONS: Our study provides a background for comparative genomic studies focused on non-model species, as well as a baseline for the adaptive potential of marine invertebrates along the South African west coast. We also discuss the caveats associated with Pool-seq and potential biases of sequencing coverage on downstream genomic metrics. The findings provide evidence of species-specific selective pressures within a homogeneous environment, and suggest that selective forces acting on small scales are just as crucial to acknowledge as those acting on larger scales. As a whole, our findings imply that future population genomic studies should expand from focusing on model organisms and/or studying heterogeneous regions to better understand the evolutionary processes shaping current and future biodiversity patterns, particularly when used in a comparative phylogeographic context.

Sleeping with the enemy: introgressive hybridization in two invasive centrarchids.

Introgressive hybridization between Micropterus dolomieu and Micropterus salmoides was assessed in their invaded South African range using nine microsatellite markers and two mtDNA gene regions. Although M. dolomieu and M. salmoides are distantly related, indicated by the large uncorrected pairwise distances observed between the two species, mitochondrial introgression and unidirectional admixture was detected.

Multispecies genetic objectives in spatial conservation planning.

Growing threats to biodiversity and global alteration of habitats and species distributions make it increasingly necessary to consider evolutionary patterns in conservation decision making. Yet, there is no clear-cut guidance on how genetic features can be incorporated into conservation-planning processes, despite multiple molecular markers and several genetic metrics for each marker type to choose from. Genetic patterns differ between species, but the potential tradeoffs among genetic objectives for multiple species in conservation planning are currently understudied. We compared spatial conservation prioritizations derived from 2 metrics of genetic diversity (nucleotide and haplotype diversity) and 2 metrics of genetic isolation (private haplotypes and local genetic differentiation) in mitochondrial DNA of 5 marine species. We compared outcomes of conservation plans based only on habitat representation with plans based on genetic data and habitat representation. Fewer priority areas were selected for conservation plans based solely on habitat representation than on plans that included habitat and genetic data. All 4 genetic metrics selected approximately similar conservation-priority areas, which is likely a result of prioritizing genetic patterns across a genetically diverse array of species. Largely, our results suggest that multispecies genetic conservation objectives are vital to creating protected-area networks that appropriately preserve community-level evolutionary patterns.

A synthesis of genetic connectivity in deep-sea fauna and implications for marine reserve design.

With anthropogenic impacts rapidly advancing into deeper waters, there is growing interest in establishing deep-sea marine protected areas (MPAs) or reserves. Reserve design depends on estimates of connectivity and scales of dispersal for the taxa of interest. Deep-sea taxa are hypothesized to disperse greater distances than shallow-water taxa, which implies that reserves would need to be larger in size and networks could be more widely spaced; however, this paradigm has not been tested. We compiled population genetic studies of deep-sea fauna and estimated dispersal distances for 51 studies using a method based on isolation-by-distance slopes. Estimates of dispersal distance ranged from 0.24 km to 2028 km with a geometric mean of 33.2 km and differed in relation to taxonomic and life-history factors as well as several study parameters. Dispersal distances were generally greater for fishes than invertebrates with the Mollusca being the least dispersive sampled phylum. Species that are pelagic as adults were more dispersive than those with sessile or sedentary lifestyles. Benthic species from soft-substrate habitats were generally less dispersive than species from hard substrate, demersal or pelagic habitats. As expected, species with pelagic and/or feeding (planktotrophic) larvae were more dispersive than other larval types. Many of these comparisons were confounded by taxonomic or other life-history differences (e.g. fishes being more dispersive than invertebrates) making any simple interpretation difficult. Our results provide the first rough estimate of the range of dispersal distances in the deep sea and allow comparisons to shallow-water assemblages. Overall, dispersal distances were greater for deeper taxa, although the differences were not large (0.3-0.6 orders of magnitude between means), and imbalanced sampling of shallow and deep taxa complicates any simple interpretation. Our analyses suggest the scales of dispersal and connectivity for reserve design in the deep sea might be comparable to or slightly larger than those in shallow water. Deep-sea reserve design will need to consider the enormous variety of taxa, life histories, hydrodynamics, spatial configuration of habitats and patterns of species distributions. The many caveats of our analyses provide a strong impetus for substantial future efforts to assess connectivity of deep-sea species from a variety of habitats, taxonomic groups and depth zones.

Spatio-temporal genetic structure and the effects of long-term fishing in two partially sympatric offshore demersal fishes.

Environmental gradients have been shown to disrupt gene flow in marine species, yet their influence in structuring populations at depth remains poorly understood. The Cape hakes (Merluccius paradoxus and M. capensis) are demersal species co-occurring in the Benguela Current system, where decades of intense fishing resulted in severely depleted stocks in the past. Previous studies identified conflicting mtDNA genetic substructuring patterns and thus contrasting evolutionary trajectories for both species. Using 10 microsatellite loci, the control region of mtDNA and employing a seascape genetics approach, we investigated genetic connectivity and the impact of prolonged exploitation in the two species, which are characterized by different patterns of fishing pressure. Three consecutive years were sampled covering the entire distribution (N = 2100 fishes). Despite large estimated population sizes, both species exhibited low levels of contemporary genetic diversity (0.581 < HE  < 0.692), implying that fishing has had a significant impact on their genetic composition and evolutionary trajectories. Further, for M. paradoxus, significant temporal, but not spatial, divergence points to the presence of genetic chaotic patchiness. In contrast, M. capensis exhibited a clear latitudinal cline in genetic differentiation between Namibia and South Africa (FST  = 0.063, P < 0.05), with low (0.2% per generation) estimates of contemporary gene flow. Seascape analyses reveal an association with bathymetry and upwelling events, suggesting that adaptation to local environmental conditions may drive genetic differentiation in M. capensis. Importantly, our results highlight the need for temporal sampling in disentangling the complex factors that impact population divergence in marine fishes.

Molecular systematics and biogeography of the circumglobally distributed genus Seriola (Pisces: Carangidae).

The genus Seriola includes several important commercially exploited species and has a disjunct distribution globally; yet phylogenetic relationships within this genus have not been thoroughly investigated. This study reports the first comprehensive molecular phylogeny for this genus based on mitochondrial (Cytb) and nuclear gene (RAG1 and Rhod) DNA sequence data for all extant Seriola species (nine species, n=27). All species were found to be monophyletic based on Maximum parsimony, Maximum likelihood and Bayesian inference. The closure of the Tethys Sea (12-20 MYA) coincides with the divergence of a clade containing ((S. fasciata and S. peruana), S. carpenteri) from the rest of the Seriola species, while the formation of the Isthmus of Panama (±3 MYA) played an important role in the divergence of S. fasciata and S. peruana. Furthermore, factors such as climate and water temperature fluctuations during the Pliocene played important roles during the divergence of the remaining Seriola species.

Variation in palaeo-shorelines explains contemporary population genetic patterns of rocky shore species.

Processes driving and maintaining disjunct genetic populations in marine systems are poorly understood, owing to a lack of evidence of hard barriers that could have shaped patterns of extant population structure. Here, we map two genetically divergent lineages of an obligate rocky shore fish, Clinus cottoides, and model sea-level change during the last 110 000 years to provide the first evidence of a vicariant event along the southern coastline of Africa. Results reveal that lowered sea levels during glacial periods drastically reduced rocky intertidal habitat, which may have isolated populations in two refugia for at least 40 000 years. Contemporary coastal dynamics and oceanography explain secondary contact between lineages. This scenario provides an explanation for the origin of population genetic breaks despite a lack of obvious present-day geographical barriers and highlights the need for including palaeo-oceanography in unravelling extant population patterns.

Large-scale environmental signals in seagrass blue carbon stocks are hidden by high variability at local scales.

Increasing focus on nature-based climate change mitigation and adaptation strategies has led to the recognition of seagrasses as globally significant organic carbon (Corg) stocks. However, estimates of carbon stocks have been generally confined to a few regions, with few African studies represented in global datasets. In addition, the extent to which biogeographical and environmental variation shape carbon stocks in marine vegetated environments remains uncertain. For South Africa, Zostera capensis is the dominant seagrass species with limited mapping and quantification of its Corg stocks. Here, we measured Z. capensis Corg stocks at six South African estuaries spanning ∼1800 km of the cool-temperate to subtropical marine environmental gradient. Targeting the intertidal zone of the upper and lower estuary reaches, we collected Z. capensis sediments to a depth of 50 cm and measured the Corg, with the median Corg stock estimated at 24.11 Mg C ha-1 (40.4 ± 53.02; mean ± SD). While this is lower than the global average, these data demonstrate that Z. capensis ecosystems are important contributors to blue carbon stocks in the region. Measured Corg stocks showed significant differences between sampling sites for estuaries; however, we did not detect significant differences between estuaries due to high intra-estuarine Corg variability. Examination of biogeographical regions, terrestrial and marine environmental variables as drivers of Corg variability revealed that annual mean sea surface temperature may explain variation in Corg stocks. Furthermore, we found evidence of signals of biogeographical regions and precipitation driving some of the variability in Corg stocks; however, this requires further investigation. Overall, our estimates for Z. capensis add to ongoing national and global efforts to quantify seagrass Corg stocks across environmental and biogeographic gradients to better determine their contributions as nature-based solutions to climate change.

Detecting kelp-forest associated metazoan biodiversity with eDNA metabarcoding.

Environmental DNA (eDNA) metabarcoding is a promising tool for monitoring marine biodiversity, but remains underutilised in Africa. In this study, we evaluated the ability of aquatic eDNA metabarcoding as a tool for detecting biodiversity associated with a South African kelp forest, an ecosystem that harbours high diversity of species, many of which are endemic, but are also sensitive to changing environmental conditions and anthropogenic pressures. Using fine-scale spatial (1 m and 8 m) and temporal (every four hours for 24 h) sampling of aquatic environmental DNA and targeting two gene regions (mtDNA COI and 12S rRNA), metabarcoding detected 880 OTUs representing 75 families in the broader metazoan community with 44 OTUs representing 24 fish families. We show extensive variability in the eDNA signal across space and time and did not recover significant spatio-temporal structure in OTU richness and community assemblages. Metabarcoding detected a broad range of taxonomic groups, including arthropods, ascidians, cnidarians, echinoderms, ctenophores, molluscs, polychaetes, ichthyofauna and sponges, as well as Placozoa, previously not reported from South Africa. Fewer than 3% of OTUs could be identified to species level using available databases (COI = 19 OTUs, 12S = 11 OTUs). Our study emphasizes that kelp-forest associated biodiversity in South Africa is understudied, but that with careful consideration for sampling design in combination with increased barcoding efforts and the construction of regional databases, eDNA metabarcoding will become a powerful biomonitoring tool of kelp-forest associated biodiversity.

Using transplantation to restore seagrass meadows in a protected South African lagoon.

Background: Seagrass meadows provide valuable ecosystem services but are threatened by global change pressures, and there is growing concern that the functions seagrasses perform within an ecosystem will be reduced or lost without intervention. Restoration has become an integral part of coastal management in response to major seagrass declines, but is often context dependent, requiring an assessment of methods to maximise restoration success. Here we investigate the use of different restoration strategies for the endangered Zostera capensis in South Africa. Methods: We assessed restoration feasibility by establishing seagrass transplant plots based on different transplant source materials (diameter (ø) 10 cm cores and anchored individual shoots), planting patterns (line, dense, bullseye) and planting site (upper, upper-mid and mid-intertidal zones). Monitoring of area cover, shoot length, and macrofaunal diversity was conducted over 18 months. Results: Mixed model analysis showed distinct effects of transplant material used, planting pattern and site on transplant survival and area cover. Significant declines in seagrass cover across all treatments was recorded post-transplantation (2 months), followed by a period of recovery. Of the transplants that persisted after 18 months of monitoring (~58% plots survived across all treatments), seagrass area cover increased (~112%) and in some cases expanded by over >400% cover, depending on type of transplant material, planting arrangement and site. Higher bioturbator pressure from sandprawns (Kraussillichirus kraussi) significantly reduced transplant survival and area cover. Transplant plots were colonised by invertebrates, including seagrass specialists, such as South Africa's most endangered marine invertebrate, the false-eelgrass limpet (Siphonaria compressa). For future seagrass restoration projects, transplanting cores was deemed the best method, showing higher long-term persistence and cover, however this approach is also resource intensive with potentially negative impacts on donor meadows at larger scales. There is a clear need for further research to address Z. capensis restoration scalability and improve long-term transplant persistence.

The role of seagrass meadows in the accumulation of microplastics: Insights from a South African estuary.

Microplastics are widespread in marine ecosystems, where they threaten biota and human wellbeing. Seagrasses may act as natural filters of microplastics due to their particle trapping abilities, yet little is known about the extent of microplastics in the sediment of seagrass beds. The aim of this study was to compare microplastic accumulation in the sediments of Zostera capensis meadows with adjacent bare sediments at a small spatial scale (~5 km) in the Knysna estuary in South Africa. No significant difference in total microplastic counts were found between seagrass and unvegetated sediments. However, fibre microplastic counts differed significantly between the two locations at which samples were collected. This may be due to pollution levels and proximity to larger human population densities. Importantly, our study reveals variability in microplastic abundance and type even at small spatial scales, an important consideration for the design of future studies aiming to monitor for microplastics.

Molecular ecology meets systematic conservation planning.

Integrative and proactive conservation approaches are critical to the long-term persistence of biodiversity. Molecular data can provide important information on evolutionary processes necessary for conserving multiple levels of biodiversity (genes, populations, species, and ecosystems). However, molecular data are rarely used to guide spatial conservation decision-making. Here, we bridge the fields of molecular ecology (ME) and systematic conservation planning (SCP) (the 'why') to build a foundation for the inclusion of molecular data into spatial conservation planning tools (the 'how'), and provide a practical guide for implementing this integrative approach for both conservation planners and molecular ecologists. The proposed framework enhances interdisciplinary capacity, which is crucial to achieving the ambitious global conservation goals envisioned for the next decade.

Management and conservation implications of cryptic population substructure for two commercially exploited fishes (Merluccius spp.) in southern Africa.

Genomic information can 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 substructuring pattern. Therefore, it appears that M. paradoxus might be composed by two highly connected populations, one in the Atlantic and one in the southwest Indian Ocean. The reported similar 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.