SUNScholar - Browsing by Author "Von der Heyden, Sophie"

Browsing by Author "Von der Heyden, Sophie"

Now showing 1 - 13 of 13

Complex signatures of genomic variation of two non-model marine species in a homogeneous environment
(BioMed Central, 2018-05-09) Nielsen, Erica Spotswood; Henriques, Romina; Toonen, Robert J.; Knapp, Ingrid S. S.; Guo, Baocheng; Von der Heyden, Sophie
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.
The cushion–star Parvulastra exigua in South Africa : one species or more?
(Pensoft, 2015-09) Payne, Robyn P.; Griffiths, Charles L.; Von der Heyden, Sophie; Koch, Erich
The cushion–star Parvulastra exigua (Lamarck, 1816) is a widely distributed member of the temperate intertidal fauna in the southern hemisphere. In South Africa, it occurs in sympatry with the endemic Parvulastra dyscrita (Clark, 1923), the two species being differentiated predominantly by gonopore placement. Several recent studies have suggested that there may be additional cryptic species within the P. exigua complex in South Africa, based variously on color morphology, genetic evidence and the differential placement of the gonopores. This paper attempts to resolve whether one or more species are represented within P. exigua. A total of 346 P. exigua and 8 P. dyscrita were collected from sites on the west and south– west coasts of South Africa; morphological, anatomical and genetic analyses were performed to determine whether cryptic species and/or P. exigua specimens with aboral gonopores were present. Results show that neither cryptic species nor P. exigua specimens with aboral gonopores occur at these sites. This study thus refutes previous claims of the existence of aboral gonopores in South African P. exigua, and suggests that a single species is represented. The distinction between P. exigua and P. dyscrita is also confirmed, and features separating these two species are clarified and documented.
Evidence for panmixia despite barriers to gene flow in the southern African endemic, Caffrogobius caffer (Teleostei: Gobiidae)
(BioMed Central, 2008-12) Neethling, Marlene; Matthee, Conrad A.; Bowie, Rauri C. K.; Von der Heyden, Sophie
Background: Oceanography and life-history characteristics are known to influence the genetic structure of marine species, however the relative role that these factors play in shaping phylogeographic patterns remains unresolved. The population genetic structure of the endemic, rocky shore dwelling Caffrogobius caffer was investigated across a known major oceanographic barrier, Cape Agulhas, which has previously been shown to strongly influence genetic structuring of South African rocky shore and intertidal marine organisms. Given the variable and dynamic oceanographical features of the region, we further sought to test how the pattern of gene flow between C. caffer populations is affected by the dominant Agulhas and Benguela current systems of the southern oceans. Results: The variable 5' region of the mtDNA control region was amplified for 242 individuals from ten localities spanning the distributional range of C. caffer. Fifty-five haplotypes were recovered and in stark contrast to previous phylogeographic studies of South African marine species, C. caffer showed no significant population genetic structuring along 1300 km of coastline. The parsimony haplotype network, AMOVA and SAMOVA analyses revealed panmixia. Coalescent analyses reveal that gene flow in C. caffer is strongly asymmetrical and predominantly affected by the Agulhas Current. Notably, there was no gene flow between the east coast and all other populations, although all other analyses detect no significant population structure, suggesting a recent divergence. The mismatch distribution suggests that C. caffer underwent a population expansion at least 14 500 years ago. Conclusion: We propose several possible life-history adaptations that could have enabled C. caffer to maintain gene flow across its distributional range, including a long pelagic larval stage. We have shown that life-history characteristics can be an important contributing factor to the phylogeography of marine species and that the effects of oceanography do not necessarily suppress its influence on effective dispersal.
Fine-scale biogeography : tidal elevation strongly affects population genetic structure and demographic history in intertidal fishes
(University of California, eScholarship, 2013) Von der Heyden, Sophie; Gildenhuys, Enelge; Bernardi, Giacomo; Bowie, Rauri C. K.
Numerous studies have demonstrated population genetic structuring in marine species, yet few have investigated the effect of vertical zonation on gene flow and population structure. Here we use three sympatric, closely related clinid species, Clinus cottoides, C. superciliosus and Muraenoclinus dor‐ salis, to test whether zonation on South African intertidal rocky shores affects phylogeographic patterns. We show that the high‐shore restricted species has reduced gene flow and considerably higher FST val‐ ues (FST = 0.9) than the mid‐ and low‐shore species (FST < 0.14). Additionally, we provide evidence for remarkably different demographic and evolutionary histories, ranging from extreme population bottle‐ necks to population persistence, which are probably linked to effective population size and habitat spe‐ cialisation. This study further highlights the need for a multispecies approach to unravel the biological and evolutionary processes that drive extant population genetic patterns in marine species, as even closely related species with similar life histories show highly variable results.
Genetic and biophysical models help define marine conservation focus areas
(Frontiers Media, 2018-08-06) Mertens, Lisa E. A.; Treml, Eric A.; Von der Heyden, Sophie; Lipcius, Romuald
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 of comparative phylogeographic analyses of five phylogenetically and functionally diverse intertidal species along the west coast of South Africa using population genetics and biophysical models within the Benguela Current system. Some broadcast spawners exhibit genetic panmixia, others show genetic structure similar to direct-developing species, suggesting complex recruitment patterns in rocky shore environments. Patterns of genetic structure do not correspond with pelagic larval competency period, with a broadcast spawning urchin displaying the highest levels of population structure. Biophysical models of larval dispersal reveal mixed dispersal patterns, with the strongest connections in a northward direction following the Benguela Current, yet most modeled species also show the capacity for southward (albeit weaker) migration among some sample localities. Some sites, particularly the most northern areas, show very low levels of potential connectivity. Lastly, we synthesized our results to highlight key areas for the development of Marine Protected Areas (MPAs) that capture the evolutionary patterns of marine species of the west coast and find that the results from our molecular and biophysical analyses are coherent with previous suggestions for a network of protected areas.
The ghost of introduction past : spatial and temporal variability in the genetic diversity of invasive smallmouth bass
(Wiley Open Access, 2018) Diedericks, Genevieve; Henriques, Romina; Von der Heyden, Sophie; Weyl, Olaf L. F.; Hui, Cang
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 the premise that the historic population structure within the native range has been maintained over time. Here, we assess this assumption by conducting a three-way comparison of the genetic diversity of native (historic and contemporary) and invasive (contemporary) smallmouth bass (Micropterus dolomieu) populations. Analyses of a total of 572 M. dolomieu samples, representing the contemporary invasive South African range, contemporary and historical native USA range (dating back to the 1930s when these fish were first introduced into South Africa), revealed that the historical native range had higher genetic diversity levels when compared to both contemporary native and invasive ranges. These results suggest that both contemporary populations experienced a recent genetic bottleneck. Furthermore, the invasive range displayed significant population structure, whereas both historical and contemporary native US populations revealed higher levels of admixture. Comparison of contemporary and historical samples showed both a historic introduction of M. dolomieu and a more recent introduction, thereby demonstrating that undocumented introductions of this species have occurred. Although multiple introductions might have contributed to the high levels of genetic diversity in the invaded range, we discuss alternative factors that may have been responsible for the elevated levels of genetic diversity and highlight the importance of incorporating historic specimens into demographic analyses.
Indo-Pacific phylogeography of the lemon sponge Leucetta chagosensis
(MDPI, 2020-12-07) Pasnin, Olivier; Voigt, Oliver; Worheide, Gert; Murillo Rincon, Andrea P.; Von der Heyden, Sophie
The sponge Leucetta chagosensisDendy (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 evolutionary patterns for this species. We generated 188 sequences of L. chagosensis and constructed maximum likelihood and Bayesian inference trees, using concatenated mitochondrial cytochrome oxidase subunit 3 gene (cox3) and nuclear ribosomal RNA gene (28S) markers for the first time. The spatial variation of genetic diversity of L. chagosensis was assessed using a phylogeographic approach. Leucetta chagosensis is composed of five cryptic lineages confined to different biogeographic regions with the specimens found in the Indian Ocean differing significantly from those found in the rest of the IP region. Genetic divergence was particularly high for the cox3 marker, with a low nucleotide diversity but high haplotype diversity for most lineages. This study highlights the need for a sustained effort in studying sponge diversity, boosted by the ongoing discovery of hidden biodiversity among this ecologically important taxon.
The influence of pleistocene climatic changes and ocean currents on the phylogeography of the Southern African Barnacle, Tetraclita serrata (Thoracica; Cirripedia)
(Public Library of Science, 2014-07) Reynolds, Terry V.; Matthee, Conrad A.; Von der Heyden, Sophie
Abstract The evolutionary effects of glacial periods are poorly understood for Southern Hemisphere marine intertidal species, particularly obligatory sessile organisms. We examined this by assessing the phylogeographic patterns of the southern African volcano barnacle, Tetraclita serrata, a dominant species on rocky intertidal shores. Restricted gene flow in some geographical areas was hypothesized based on oceanic circulation patterns and known biogeographic regions. Barnacle population genetic structure was investigated using the mitochondrial cytochrome oxidase subunit 1 (COI) region for 410 individuals sampled from 20 localities spanning the South African coast. The mtDNA data were augmented by generating nuclear internal transcribed spacer 1 (ITS1) sequences from a subset of samples. Phylogenetic and population genetic analyses of mitochondrial DNA data reveal two distinct clades with mostly sympatric distributions, whereas nuclear analyses reveal only a single lineage. Shallow, but significant structure (0.0041–0.0065, P,0.01) was detected for the mtDNA data set, with the south-west African region identified as harbouring the highest levels of genetic diversity. Gene flow analyses on the mtDNA data show that individuals sampled in south-western localities experience gene flow primarily in the direction of the Benguela Current, while south and eastern localities experience bi-directional gene flow, suggesting an influence of both the inshore currents and the offshore Agulhas Current in the larval distribution of T. serrata. The mtDNA haplotype network, Bayesian Skyline Plots, mismatch distributions and time since expansion indicate that T. serrata population numbers were not severely affected by the Last Glacial Maximum (LGM), unlike other southern African marine species. The processes resulting in the two morphologically cryptic mtDNA lineages may be the result of a recent historical allopatric event followed by secondary contact or could reflect selective pressures due to differing environmental conditions.
Mitochondrial DNA is unsuitable to test for isolation by distance
(Nature Research, 2018-05-31) Teske, Peter R.; Golla, Tirupathi Rao; Sandoval-Castillo, Jonathan; Emami-Khoyi, Arsalan; Van der Lingen, Carl D.; Von der Heyden, Sophie; Chiazzari, Brent; Van Vuuren, Bettine Jansen; Beheregaray, Luciano B.
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) whether significant IBD is primarily a result of lumping spatially discrete populations, and (b) whether microsatellite datasets are more likely to detect IBD when mtDNA does not. We also provide empirical data from four species in which mtDNA failed to detect IBD by comparing these with microsatellite and SNP data. Our results confirm that IBD is mostly found when distinct regional populations are pooled, and this trend disappears when each is analysed separately. Discrepancies between markers were found in almost half of the studies reviewed, and microsatellites were more likely to detect IBD when mtDNA did not. Our empirical data rejected the lack of IBD in the four species studied, and support for IBD was particularly strong for the SNP data. We conclude that mtDNA sequence data are often not suitable to test for IBD, and can be misleading about species’ true dispersal potential. The observed failure of mtDNA to reliably detect IBD, in addition to being a single-locus marker, is likely a result of a selection-driven reduction in genetic diversity obscuring spatial genetic differentiation.
Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species
(BMC (part of Springer Nature), 2020-09-16) Nielsen, Erica S.; Henriques, Romina; Beger, Maria; Toonen, Robert J.; Von der Heyden, Sophie
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.
A review of marine phylogeography in southern Africa
(Academy of Science of South Africa, 2011) Teske, Peter R.; Von der Heyden, Sophie; McQuaid, Christopher D.; Barker, Nigel P.
The southern African marine realm is located at the transition zone between the Atlantic and Indo-Pacific biomes. Its biodiversity is particularly rich and comprises faunal and floral elements from the two major oceanic regions, as well as a large number of endemics. Within this realm, strikingly different biota occur in close geographic proximity to each other, and many of the species with distributions spanning two or more of the region’s marine biogeographic provinces are divided into evolutionary units that can often only be distinguished on the basis of genetic data. In this review, we describe the state of marine phylogeography in southern Africa, that is, the study of evolutionary relationships at the species level, or amongst closely related species, in relation to the region’s marine environment. We focus particularly on coastal phylogeography, where much progress has recently been made in identifying phylogeographic breaks and explaining how they originated and are maintained. We also highlight numerous shortcomings that should be addressed in the near future. These include: the limited data available for commercially important organisms, particularly offshore species; the paucity of oceanographic data for nearshore areas; a dearth of studies based on multilocus data; and the fact that studying the role of diversifying selection in speciation has been limited to physiological approaches to the exclusion of genetics. It is becoming apparent that the southern African marine realm is one of the world’s most interesting environments in which to study the evolutionary processes that shape not only regional, but also global patterns of marine biodiversity.
Science to policy – reflections on the South African reality
(Academy of Science of South Africa, 2016) Von der Heyden, Sophie; Lukey, Peter; Celliers, Louis; Prochazka, Kim; Lombard, Amanda T.
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 policy and management (i.e. the knowing-doing gap1) needs to be closed, yet closing this gap remains a complex challenge2. This year’s annual SANCOR (South African Network for Coastal and Oceanic Research) Forum meeting addressed this gap through consultation with a variety of stakeholders from the coastal and marine science community. Our brief was to provide for reflection and discussion on aspects of the science–policy–management interface within South Africa and this commentary provides a summary of the Forum discussions. We detail some current challenges of integrating coastal and marine science into policy and decision- making in South Africa, highlight ‘success stories’ and provide some thoughts on maximising overlap and building a sound science–policy interface. Although couched in the context of marine and coastal sciences, our findings will resonate with other scientific disciplines. Similarly, the challenges in and opportunities for creating constructive dialogue for evidence-based decision-making are not specific to South Africa, so we draw on national, international and collective experience to provide an avenue for doing so. In this commentary we highlight current examples of mismatch between science and policy by focusing on barriers resulting from legislation, politics and a general lack of process for better integration. In particular, we focus on the complexities of evidence-based decision-making at different scales, and how international scientific engagement has helped shape policy in South Africa. We finish by providing some perspectives, directions and examples to help narrow the gap and foster better science–policy integration into the future.
When homoplasy mimics hybridization : a case study of Cape hakes (Merluccius capensis and M. paradoxus)
(PeerJ, 2016) Henriques, Romina; Von der Heyden, Sophie; Matthee, Conrad A.
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.

Browsing by Author "Von der Heyden, Sophie"

Results Per Page

Sort Options