Sophie von der Heyden

Stellenbosch University | SUN · Department of Botany and Zoology

Seagrasses are important marine ecosystem engineers but anthropogenic impacts and climate change have led to numerous population declines globally. In South Africa, Zostera capensis is endangered due to fragmented populations and heavy anthropogenic pressures on estuarine ecosystems that house the core of the populations. Addressing questions of ho...

Past climatic change as a driving force of marine diversification is still largely unclear, particularly for Southern Hemisphere species. Here, we present a case using the brown fur seal, Arctocephalus pusillus, assessing the geographical structure and demographic history using mitochondrial and nuclear data. Results show the two previously defined...

Shallow-water hake (Merluccius capensis) is a valuable demersal resource distributed throughout the Benguela Current region, from southern Angola to eastern South Africa. Previous molecular work revealed distinct populations confined to the northern and southern Benguela sub-systems, with asymmetrical migratory patterns. Here, we re-evaluated the g...

Figure S3. Graphs illustrating the mean and standard deviation for each locality with regards to shape PC3 and shape PC4. The fish outline drawings depict the variation in fish body shape for each PC axis, with the light blue line representing the average shape for all fish, while the dark blue line represents the upper and lower body shape extremi...

Figure S4. PCA analyses conducted on the combined microsatellite genotypes for the seven localities (A – D, H – J). Each dot represents a genotyped individual, with colours corresponding to sampled localities.

Figure S2. Variation in PCLINEAR1 among the age classes for each locality (A-J).

Figure S5. STRUCTURE HARVESTER (Earl and vonHoldt, 2012) output files, implementing the Evanno method. The most probably Delta K as well as LnP(D) values for all K values (1 < K > 10).

Figure S6. Mantel test indicating the significant (P =0.001) isolation-by-distance signal detected.

Figure S1. Photographs capturing the variation in habitat along the Olifants River system during the summer months (December – February). Left: Locality A situated along the upper reaches of the Jan Dissels tributary; Centre: two photographs representing the middle reaches of the Olifants River (top image taken from DWA, 2006); Right: the sampling...

Dispersal is an essential life-history trait crucial to species persistence and diversification. This is particularly important in spatiotemporal fluctuating environments such as freshwater habitats, where species movement is confined to the dendritic network and wetted boundaries. To persist in such fluctuating environments, a species can modify,...

Aim Intraspecific diversity is a significant component of adaptive potential, and thus, it is important to identify the evolutionary processes that have and will continue to shape the molecular diversity of natural populations. This study aims to untangle the possible drivers of intraspecific molecular diversity by testing whether patterns of histo...

Safeguarding marine ecosystems is essential for maintaining ecosystem function and biodiversity, but effective monitoring of marine habitats can be logistically challenging, costly, and difficult to regularly implement. Environmental DNA-based biomonitoring is a rapidly growing tool that is non-destructive, cost-effective, and reliable. However, di...

Although genomic diversity is increasingly recognised as a key component of biodiversity, it is seldom used to inform conservation planning. Estuaries and keystone species such as the seagrass, Zostera capensis, are under severe anthropogenic pressure and are often poorly protected. In this study we integrated Single Nucleotide Polymorphism data ge...

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 varia...

Seagrass ecosystems face many anthropogenic pressures, yet globally there is a lack of knowledge of their associated biodiversity. Molecular barcoding can aid in biomonitoring efforts, but few South African invertebrates are accounted for. We provide 48 new sequences for 15 invertebrate species across a range of taxonomic groups sampled from Zoster...

Uncertainty surrounding the number and identity of species of genus Limacia O.F. Müller, 1781, in southern African and European coastal waters presents an ongoing conundrum. Limacia clavigera (O.F. Müller, 1776) was previously thought to be the only species of its genus in the eastern Atlantic, with a distribution covering north- to south-eastern A...

The sponge Leucetta chagosensis Dendy (1913) has a wide distribution throughout the Indo-Pacific (IP) region, with previous studies focussing primarily on the western Pacific Ocean. To increase our knowledge of the spatial variation of genetic diversity throughout the IP, we constructed a phylogeny for L. chagosensis for the IP to assess the evolut...

Designing marine protected area (MPA) networks has relied primarily on species- or habitat-based measures that assess spatial distributions of biodiversity. Molecular and functional data have the potential to unlock information regarding the evolutionary uniqueness and resilience of natural communities, making phylogenetic diversity (PD) and functi...

Kingklip, Genypterus capensis, is a valuable fish resource in southern African waters, with a wide geographic distribution spanning South Africa and Namibia. Previous studies have provided evidence for multiple stocks in South Africa, but the extent of stock structuring across the southern Africa region remains unclear. In this study we genotyped o...

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 o...

Emerging global change stressors have underlined the importance of informing conservation decisions with molecular diversity, particularly including intraspecific adaptive or evolutionary potential across species and populations. Population-level evolutionary potential is best captured by genomic approaches, yet these data types mostly remain limit...

Although genomic diversity is increasingly recognised as a key component of biodiversity, it is seldom used to inform conservation planning. Estuaries and keystone species such as the southern African seagrass, Zostera capensis, are under severe anthropogenic pressure and are often poorly protected. In this study we integrated SNP data generated fr...

Worldwide, the spread of alien species in marine ecosystems has increased, with mussels frequently being involved. In South Africa, 91 alien and 39 cryptic marine and estuarine species, from 17 taxonomic groups, are known. Of these, three are associated with major invasions, including the Pacific mussel, Semimytilus algosus, which has rapidly sprea...

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...

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...

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...

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 within Afri...

Sandy beach ecosystems are ecologically and culturally important, yet they face a wide range of anthropogenic stressors. Their constituent biodiversity is usually poorly resolved, with numerous instances of cryptic species described. In addition, there are few studies on the spatio-temporal patterns of evolutionary diversity, although these are vit...

Marine management areas provide a key tool for efforts towards sustainable development, reconciling socio-economic goals with those for biodiversity conservation. Decisions about where and when to establish spatial management areas in the oceans are currently hampered by the uncertainties of incomplete, or overly general, information about biodiver...

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...

South African coastline surveys conducted since 1972 reveal fluctuations and a recent reversal in a long-running increasing trend in regional abundance of southern right whales (Eubalaena australis, hereafter SRWs), whose populations have been recovering from historic whaling. Furthermore, the surveys reveal that the typical three-year calving cycl...

The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled g...

Biogeographic and phylogeographic patterns of sandy beach species are poorly understood, although these ecosystems are heavily impacted by anthropogenic pressures and are of elevated conservation concern. To contribute towards filling the knowledge gap on sandy beaches, we made use of phylogeographic approaches to determine levels of genetic struct...

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, b...

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, b...

Many marine species do not display genetic structure across the barriers between marine bioregions that in other species with similar life histories define distinct cryptic species. This paradox is often explained by unexpectedly high dispersal potential in the former. Using genomic data from a coastal fish that exists as a single population across...

The seagrass, Zostera capensis , occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled...

The seagrass, Zostera capensis , occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled...

Understanding the demographic history of introduced populations is essential for unravelling their invasive potential and adaptability to a novel environment. To this end, levels of genetic diversity within the native and invasive range of a species are often compared. Most studies, however, focus solely on contemporary samples, relying heavily on...

Ecological and environmental variables play a major role in the genetic structure of marine populations, but how oceanography affects their dispersal and associated connectivity remains far from being understood. To account for the effect of different dispersal strategies in terms of pelagic larvae and non-pelagic reproduction, we utilize the power...

Tests for isolation by distance (IBD) are the most commonly used method of assessing spatial genetic structure. Many studies have exclusively used mitochondrial DNA (mtDNA) sequences to test for IBD, but this marker is often in conflict with multilocus markers. Here, we report a review of the literature on IBD, with the aims of determining (a) whet...

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, mitoch...

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. Theref...

Tests for isolation by distance (IBD) are the most commonly used method of assessing spatial genetic structure. Many studies have exclusively used mitochondrial DNA (mtDNA) sequences to test for IBD, but this marker is often in conflict with multilocus markers. Here, we report a review of the literature on IBD, with the aims of determining (a) whet...

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 th...

Understanding the demographic history of introduced populations is essential for unravelling their invasive potential and adaptability to a novel environment. To this end, levels of genetic diversity within the native and invasive range of a species are often compared. Most studies, however, focus solely on contemporary samples, relying heavily on...

Landscape genomics is a rapidly advancing research field that combines population genomics, landscape ecology, and spatial analytical techniques to explicitly quantify the effects of environmental heterogeneity on neutral and adaptive genetic variation and underlying processes. Landscape genomics has tremendous potential for addressing fundamental...

Irion et al. (2017; Mar Ecol Prog Ser 577:251-255) disputed the population estimates of white sharks Carcharodon carcharias along the South African coastline as presented in Andreotti et al. (2016; Mar Ecol Prog Ser 552:241-253), claiming that both the genetic and the capture-markrecapture results are poorly supported by the methods and data provid...

Anthropogenic activities are having devastating impacts on marine systems with numerous knock-on effects on trophic functioning, species interactions and an accelerated loss of biodiversity. Establishing conservation areas can not only protect biodiversity, but also confer resilience against changes to coral reefs and their inhabitants. Planning fo...

The 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, with multiple molecular markers and sev...

Research is a key resource in a knowledge economy and governance system. In order to enable research to benefit the nation and to contribute to growing the knowledge-based economy (the aims of the Global Change Grand Challenge, and specifically the Society and Sustainability Research Programme), the gap between research, knowledge production and po...

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 stoc...

Seascape genetics, a term coined in 2006, is a fast growing area of population genetics that draws on ecology, oceanography and geography to address challenges in basic understanding of marine connectivity and applications to management. We provide an accessible overview of the latest developments in seascape genetics that merge exciting new ideas...

The loss of apex marine predators has been reported to have a cascade of detrimental effects on marine ecosystems; however, the general lack of empirical data can severely limit our understanding of the ecological interactions among marine species. In this study we propose an integrated approach using mark-recapture and genetic techniques to assess...

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, whi...