Romina Henriques

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.

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.

When homoplasy mimics hybridization : a case study of Cape hakes (Merluccius capensis and M. paradoxus)

In the marine environment, an increasing number of studies have documented introgression and hybridization using genetic markers. Hybridization appears to occur preferentially between sister-species, with the probability of introgression decreasing with an increase in evolutionary divergence. Exceptions to this pattern were reported for the Cape hakes (Merluccius capensis and M. paradoxus), two distantly related Merluciidae species that diverged 3–4.2 million years ago. Yet, it is expected that contemporary hybridization between such divergent species would result in reduced hybrid fitness. We analysed 1,137 hake individuals using nine microsatellite markers and control region mtDNA data to assess the validity of the described hybridization event. To distinguish between interbreeding, ancestral polymorphism and homplasy we sequenced the flanking region of the most divergent microsatellite marker. Simulation and empirical analyses showed that hybrid identification significantly varied with the number of markers, model and approach used. Phylogenetic analyses based on the sequences of the flanking region of Mmerhk-3b, combined with the absence of mito-nuclear discordance, suggest that previously reported hybridization between M. paradoxus and M. capensis cannot be substantiated. Our findings highlight the need to conduct a priori simulation studies to establish the suitability of a particular set of microsatellite loci for detecting multiple hybridization events. In our example, the identification of hybrids was severely influenced by the number of loci and their variability, as well as the different models employed. More importantly, we provide quantifiable evidence showing that homoplasy mimics the effects of heterospecific crossings which can lead to the incorrect identification of hybridization.

How many daddies: microsatellite genotyping reveals polyandry in a live-bearing clinid fish Muraenoclinus dorsalis : POLYANDRY IN VIVIPAROUS M. dorsalis

Fishes belonging to the family Clinidae in South Africa display super-embryonation, a rare reproductive mode were females gestate broods at different gestational stages, but little is known regarding the mating systems of this family. Here we tested the hypothesis that multiple males would contribute not only to the offspring of each female, but that several males would contribute to each brood, by sampling Muraenoclinus dorsalis from three sampling locations along the west and south-west coast of South Africa. Larval (n = 97) and maternal (n = 14) genotpyes, generated with newly developed microsatellites, were used to estimate the number of potential mates per female. Our results show that up to 78% of females displayed multiple mating with an average of 2·1-2·2 males. In addition, 39-42% of females displayed polyandry with an average of 1·5-1·6 sires per brood. This study provides the evidence for multiple mating and polyandry within a clinid fish characterized by super-embryonation that offers important baseline information regarding rare reproductive strategies, highlighting several gaps in our knowledge concerning clinid reproduction and mating systems.

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

BackgroundGenomic 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.ResultsUsing 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.ConclusionsOur 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.

Population connectivity of an overexploited coastal fish, Argyrosomus coronus (Sciaenidae), in an ocean-warming hotspot

The West Coast dusky kob Argyrosomus coronus is a commercially exploited fish with a distribution confined to the Angola–Benguela Frontal Zone (ABFZ) of the southeastern Atlantic Ocean. A previous study revealed that during a recent period of local warming the species extended its distribution into Namibian waters, where it hybridised with the resident and congeneric Argyrosomus inodorus. Environmental changes are a major threat to marine biodiversity and when combined with overfishing have the potential to accelerate the decline of species. However, little is known regarding the evolutionary history and population structure of A. coronus across the ABFZ. We investigated genetic diversity, population structure and historical demographic changes using mtDNA control region sequences and genotypes at six nuclear microsatellite loci, from 180 individuals. A single, genetically homogeneous population was indicated across the distributional range of A. coronus (φST = 0.041, FST = 0.000, D = 0.000; p > 0.05). These findings imply that the oceanographic features within the ABFZ do not appear to significantly influence population connectivity in A. coronus, which simplifies management of the species. However, reconstruction of the demographic history points to a close link between the evolutionary history of A. coronus and the environmental characteristics of the ABFZ. This outcome suggests the species’ vulnerability to the rapid environmental changes being observed across this region, and highlights a pressing need for transboundary management to mitigate the impacts of climate change in this global hotspot of seawater temperature changes.