Browsing by Author "Winker, Henning"

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    Open Access
    Environmental correlates of geographic divergence in a phenotypic trait: A case study using bat echolocation
    (Wiley, 2017-06-28) Maluleke, Tinyiko; Jacobs, David S; Winker, Henning
    Divergence in phenotypic traits may arise from the interaction of different evolutionary forces, including different kinds of selection (e.g., ecological), genetic drift, and phenotypic plasticity. Sensory systems play an important role in survival and reproduction, and divergent selection on such systems may result in lineage diversification. Such diversification could be largely influenced by selection in different environments as a result of isolation by environment (IbE). We investigated this process using geographic variation in the resting echolocation frequency of the horseshoe bat species, Rhinolophus damarensis, as a test case. Bats were sampled along a latitudinal gradient ranging from 16°S to 32°S in the arid western half of southern Africa. We measured body size and peak resting frequencies (RF) from handheld individual bats. Three hypotheses for the divergence in RF were tested: (1) James’ Rule, (2) IbE, and (3) genetic drift through isolation by distance (IbD) to isolate the effects of body size, local climatic conditions, and geographic distance, respectively, on the resting frequency of R. damarensis. Our results did not support genetic drift because there was no correlation between RF variation and geographic distance. Our results also did not support James’ Rule because there was no significant relationship between (1) geographic distances and RF, (2) body size and RF, or (3) body size and climatic variables. Instead, we found support for IbE in the form of a correlation between RF and both region and annual mean temperature, suggesting that RF variation may be the result of environmental discontinuities. The environmental discontinuities coincided with previously reported genetic divergence. Climatic gradients in conjunction with environmental discontinuities could lead to local adaptation in sensory signals and directed dispersal such that gene flow is restricted, allowing lineages to diverge. However, our study cannot exclude the role of processes like phenotypic plasticity in phenotypic variation.
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    Fishery, population dynamics and stock assessment of geelbek (Atractoscion aequidens), a commercially important migrant fish species off the coast of South Africa
    (2018) Boyd, Danielle Winona; Altwegg, Res; Winker, Henning; Kerwath, Sven E
    Geelbek (Atractoscion aequidens) is an important fish species in South Africa's linefishery, a fishing sector defined by its fishing gear of rod and reel or handline. Distributed from Cape Point (34°21'S, 18°29'E) on the south west coast to Kosi Bay (26°51'S, 32°53'E) on the east coast, they are targeted throughout their range by the commercial linefishery, recreational anglers and small-scale fishers. The majority of geelbek are caught on the Agulhas Bank during austral summer. Due to current minimum size limits of 600 mm (total length, TL), well below the 50% size-at-maturity (950 mm TL), the majority of the catches are comprised of immature fish, making the stock vulnerable to growth overfishing. Adults (>5 years) migrate seasonally to spawn off KwaZulu-Natal and congregate in offshore shoals at night. These spawning aggregations allow fishermen to catch large numbers of fish, making geelbek also vulnerable to recruitment overfishing. This study aims to improve understanding of the fishery and population dynamics of geelbek to help inform natural resource management of the geelbek linefishery. A stock assessment of South African geelbek was undertaken to fulfil this aim. For this purpose, spatially and seasonally explicit equilibrium per-recruit and dynamic age-structured operating models were developed for geelbek to account for the dynamic in stock structure as a result of the intra-annual coastal migration and differences in the vulnerability of life history stages to varying fishing pressure along South Africa's coastline. These models were developed using statistical programming environment R. The models were parameterised and calibrated using length and catch data from the National Marine Linefish System (NMLS) and life history parameters sourced from peer-reviewed literature. Per-recruit analyses were performed to estimate current stock-specific fisheries mortality rates and the spawner biomass depletion. These estimates were used as input into the stochastic age-structured simulation model and calibrated using available commercial catch data (1987 - 2011). The stochastic operating model was used to predict the probability of stock recovery and long-term sustainability under eleven alternative fisheries management strategies. The current stock status was estimated at 9.9% (approximately 10%) of the pristine spawner biomass (SB₀) using per-recruit analysis. This was compared to the stock depletion estimates of ~5 and 7% SB₀ from prior assessments conducted in the late 1990s and 1980s. This study indicated that there was a ~50 to 100% increase in spawner biomass over the past twenty years. However, this level of stock depletion is still considered critically low with respect to the previous limit management goal of increasing spawner biomass depletion rates above 25% SB₀, the collapsed limit reference level, advised by Griffiths in 1997. Eleven management strategies were simulated, examining the effects of decreases in harvest rates, closed seasons and areas and changes in minimum size limits, initiated in 2020, and tested over the medium (ten years) to long (twenty years) term. The least efficient management strategy was continuing at the status quo, with a minimum size limit of 600 mm (TL), which predicted only 1% and 2% increase in SB by 2030 and 2040, respectively. The most efficient in terms of a rapid recovery was a full fishery closure 'control scenario' (moratorium), which predicted a recovery to the threshold reference level for sustainable fishing at 40% SB₀ by 2025, and approaching pristine levels by 2040. Increasing the minimum size limit to the size-at-50%-maturity, 950 mm TL, had the second highest recovery rate, reaching 25% SB₀ by 2027, and nearing 40% SB₀ by 2035, at which point its trajectory is asymptotic to 40% SB₀. Decreasing the harvest rate by 50% across all regions and seasons had the third highest recovery rate, reaching 25% SB₀ by 2035, but levelling off thereafter. All the other management strategies resulted in slight stock recoveries, but with all stock trajectories remaining below 14% SB₀ in the long term. Additionally, the impact of various strategies, such as increasing the minimum size limit to the size-at-50%-maturity, 950 mm TL, were unequal, with the east coast experiencing increasingly higher catches over time, whereas the catches for the south south west coast declined drastically throughout the year, and did not improve with time. Such unequal distribution of the impact of management intervention is a consequence of the migratory life history of the geelbek stock. These results provide comprehensive insights into the population dynamics and current impacts on the geelbek stock, suggesting that this species remain severely depleted at ~10% SB₀. Rebuilding the stock to sustainable levels would require serious management intervention.
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    Geographic variation in the phenotype of an African horseshoe bat species, Rhinolophus damarensis, (Chiroptera: Rhinolophidae)
    (2018) Maluleke, Tinyiko; Jacobs, David; Winker, Henning
    Studies involving geographic variation in the phenotypes of bats help scientists to explain why these mammals are the most species rich mammalian order second only to rodents, with well more than 1 300 species occurring worldwide. Such species richness or high diversity is the manifestation of the generation of biodiversity through the splitting of lineages within bat species. A lineage of bat species can diversify into several lineages which then differentiate from each other in allopatry. Thus, the spatial separation of a lineage into several lineages could be attributed to geographical, ecological and environmental factors across the distributional range of the species. Similarly, vicariant events may also play a role in separating lineages within species. The Damara horseshoe bat species, Rhinolophus damarensis, is widely distributed but restricted to the western half of southern Africa, where it occurs across several major biomes. Formerly regarded as the subspecies, R. darlingi damarensis, it was elevated to full species status on the basis of genetic and phenotypic differences between it and R. darlingi darlingi. Rhinolophus damarensis is itself made up of two ecologically separated genetic lineages. A total of 106 individuals of R. damarensis were sampled from seven localities across its distributional range, with a view to determining and documenting the extent of geographic variation in body size, echolocation parameters, wing parameters, cranial shape and postcranial morphology of individuals from populations of R. damarensis across the distributional range of the species. Firstly, an investigation into geographic variation in resting echolocation frequency (RF) of the horseshoe bat species, R. damarensis was carried out in the western half of southern Africa (Chapter 2). Three hypotheses were tested. The first one, James’Rule (JR), states that individuals occurring in hot humid environments generally have smaller body sizes than conspecifics that occur in cooler, dryer environments, and the largest are expected to occur in cool, dry areas. On this basis and because of the known relationship between body size and RF, it was predicted that there should be a correlation between body size and climatic factors and between body size and RF. The second hypothesis was Isolation by Environment (IbE) mediated through sensory drive, which proposes that diversification of lineage may be driven by environmentally-mediated differences in sensory systems. Under this hypothesis, it was predicted that call frequency variation should be correlated with climatic variables. The third hypothesis was that Isolation by Distance (IbD) can influence phenotypic trait variation by restricting gene flow between populations. Under the Isolation by Distance (IbD) Hypothesis, it was predicted that call frequency variation should be partitioned in accordance with geographic distance between populations. To investigate the probability of the JR, IbE and IbD, the Akaike’s information criterion AICc candidate models were evaluated with different combinations of environmental (annual mean temperature and relative humidity), spatial (latitude and region) and biological (forearm as a proxy for body size) predictor variables to determine their influence on resting frequency (RF) across the distributional range of R. damarensis. Linear mixed effects models (LMEs) were employed to analyse the relationship between the response variable (RF) and the environmental, spatial and biological predictor variables. The influence of prey detection range and atmospheric attenuation was also investigated. The results showed no evidence for JR or for random genetic drift. Body size was neither correlated with RF nor environmental variables, suggesting that variation in RF was not the result of concomitant variation in body size as proposed by JR. Similarly, the Mantel test showed no IbD effect and there was therefore no evidence that genetic drift was responsible for the variation in RFs. In contrast, the LMEs showed that there was support for IbE in the form of an association between RF and region (in the form of the variable “Reg”) which was based on the two geographically separated genetic lineages. Furthermore, RF variation was also associated with the climatic variable AMT. The taxonomic status of R. damarensis was investigated using ecological traits and phenotypic characters including skulls, wings and echolocation (Chapter 3) and three dimensional (3D) scanned skulls and mandibles (Chapter 4). The main objective (Chapter 3 and Chapter 4) was to test whether previously reported genetic divergence between the two R. damarensis lineages was associated with phenotypic divergence. Morphometric and echolocation measurements were taken from hand held individual bats in the field, and skull measurements were taken from field collected voucher specimens as well as museum specimens. Discriminant Function Analyses (DFA) revealed that there was geographic variation among populations and lineages of R. damarensis. Multivariate Linear Regressions (MLV) and Linear models (LM) on the basal parts of bacula revealed significant differences between the southern and northern lineages of R. damarenis. The bacula of the two lineages of R. damarensis appear to have different shapes. Diversification through shape analyses (Chapter 4) was investigated using three dimensional (3D) geometric morphometric analyses based on X-ray microcomputed tomography (µCT) scanning of dried skulls and mandibles of R. damarensis. Procrustes Anova results of both mandibles and skulls indicated that there were no significant differences between sexes but that the shape of skulls and mandibles varied across different localities (Chapter 4). Canonical Variate Analysis (CVA) suggested that geographic variation in R. damarensis mandibles was based on the shape and thickness of the alveolar bone. Geographic variation in the skulls was based on changes in the rostrum, anterior medial swelling and brain case. Some populations had slightly deeper rostra, slightly larger anterior medial swellings and smaller braincases, whilst others had slightly shallower rostra, slightly smaller anterior medial swellings and larger braincases. The northern lineage was found to be separated from the southern lineage based on the changes in skull and mandible shape. Therefore, separation of lineages within R. damarensis (Chapter 4) could be associated with the foraging and feeding behaviour of the species under different ecological conditions due to ecological opportunity. Overall, differences in the RF were found to be associated with Isolation by Environment mediated through sensory drive and this has led to the formation of two regional (northern and southern) groupings in RF (Chapter 2). The two lineages were supported by both the phenotypic divergence (Chapter 3) and shape variation within R. damarensis skulls and mandibles (Chapter 4). Thus, phenotypic differences corresponded to genetic differences between the two lineages and provide support for IbE.
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    Geographic variation in the phenotypes of two sibling horseshoe bats Rhinolophus simulator and R.swinnyi
    (2016) Mutumi, Gregory L; Jacobs, David S; Winker, Henning
    The study of geographic variation and its causes in the phenotypes of animals elucidates how evolutionary processes generate biodiversity. This thesis attempts to uncouple the relative contributions of adaptive and neutral mechanisms to population divergence in African horseshoe bats (genus Rhinolophus). The two species were sampled from their distributional ranges within southern Africa and several morphometric and echolocation parameters were taken. The relative contributions of adaptation and drift were first tested (Chapter 2) using the Lande's model. It was hypothesised that adaptation would predominate in the diversification of the two horseshoe bats owing to the flight-echolocation and diet-echolocation adaptive complexes that intricately tie these two species to environmental conditions. Selection was also hypothesised to be stronger in Rhinolophus swinnyi because it uses higher frequency sound which is more sensitive to atmospheric conditions. The hypotheses were tested using a combination of soft tissue parameters (Chapter 2) and hard tissue parameters (Chapter 3), i.e., 3D scanned skulls analysed using 3D geometric morphometrics. To reconstruct the selective forces, linear mixed-effects models were used to regress climatic variables against echolocation call signals (Chapter 4) based on two hypotheses, the Sensory Drive and the James' Rule as a guide. The Lande's model (Chapter 2 and 3) showed that drift had a minimal effect to the variation of body parameters and echolocation and that selection was stronger on echolocation than on morphometric parameters. Additionally selection was differentially exerted across different localities and between the two species, making the relative roles of selection and drift context specific. Climatic variables (mean annual temperature and relative humidity) were inversely related to the variation in echolocation signals (Chapter 4) within each species. Body size was unrelated to the observed variation, which provided evidence that echolocation signals did not vary as a result of the body size/climate relationship proposed by James' Rule. Bats rely on both flight and echolocation to survive and reproduce, systems that have to track local habitats closely to perform optimally. Hence selection plays a pivotal role in their diversification.
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    The influence of environmental variables on the presence of white sharks, Carcharodon carcharias at two popular Cape Town bathing beaches: A generalized additive mixed model
    (Public Library of Science, 2013) Weltz, Kay; Kock, Alison A; Winker, Henning; Attwood, Colin; Sikweyiya, Monwabisi
    Shark attacks on humans are high profile events which can significantly influence policies related to the coastal zone. A shark warning system in South Africa, Shark Spotters , recorded 378 white shark ( Carcharodon carcharias ) sightings at two popular beaches, Fish Hoek and Muizenberg, during 3690 six-hour long spotting shifts, during the months September to May 2006 to 2011. The probabilities of shark sightings were related to environmental variables using Binomial Generalized Additive Mixed Models (GAMMs). Sea surface temperature was significant, with the probability of shark sightings increasing rapidly as SST exceeded 14°C and approached a maximum at 18°C, whereafter it remains high. An 8 times (Muizenberg) and 5 times (Fish Hoek) greater likelihood of sighting a shark was predicted at 18°C than at 14°C. Lunar phase was also significant with a prediction of 1.5 times (Muizenberg) and 4 times (Fish Hoek) greater likelihood of a shark sighting at new moon than at full moon. At Fish Hoek, the probability of sighting a shark was 1.6 times higher during the afternoon shift compared to the morning shift, but no diel effect was found at Muizenberg. A significant increase in the number of shark sightings was identified over the last three years, highlighting the need for ongoing research into shark attack mitigation. These patterns will be incorporated into shark awareness and bather safety campaigns in Cape Town.
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    Life history traits that predispose South African linefishes to overexploitation
    (2018) Haupt, Meghan; Kerwath, Sven; Parker, Denham; Winker, Henning
    Globally, the status of many fish stocks remains unknown, of which the majority fall under data-limited small-scale fisheries. Management decisions in most of these fisheries are difficult due conflicting objectives and views from fisheries managers and scientists. In South Africa, the traditional boat-based ‘linefishery’ provides such an example of a small-scale, multi-species fishery with a long history. The historical de facto open access nature of this fishery resulted in continuous declines in catches of many linefish species, and in 2000 the fishery was declared to be in a state of emergency. This led to a reduction of up to 70% within the fishery, among other measures, such as introductions of size and bag limits. Assessing the status of linefish species is difficult due to a lack of reliable long-term data for the majority of species. The aims of this study were therefore: (1) to quantify the stock status for all linefish species with available life history and size composition information, (2) compare current and historical stock levels to ascertain if the reduction in effort facilitated any recovery in linefish species and (3) correlate the current stock status estimates to life history traits to identify simple indicators of resilience to exploitation. For this purpose, length frequency data from 1988-1990 and 2008-2010 and biological parameters sourced from literature were used to conduct per-recruit analysis to estimate spawner biomass depletion (SBD) for both time periods. The majority of the 26 species analyzed, (68%) showed improvements in spawner biomass between the two time periods, with 12 species undergoing a change in stock status (i.e. improving from collapsed or overexploited). Specifically, increases in length-at-capture (Lc) as well decreases in fishing mortality (F) facilitated recovery for many species. Asymptotic length (L∞), as well as the ratio between Lc / L∞ and Lc / Lopt (where Lopt is the optimum length) were found to be significantly correlated to spawner biomass depletion. Kruskal Wallis analyses revealed that only movement pattern had a significant relationship to SBD, more specifically, migratory species were significantly more depleted than resident ones. This study identifies simple indicators that, in the absence of conventional stock assessments, provide fisheries managers with a fundamental understanding of a species’ susceptibility to overexploitation – offering another decision making tool for use in data poor fisheries such as the South African linefishery.
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    Predictors of white shark Carcharodon carcharias presence at two recreational beaches in a major metropole
    (2017) Loosen, Kristina; O'Riain, M Justin; Kock, Alison A; Winker, Henning
    The presence of white sharks Carcharodon carcharias in False Bay, South Africa follows a clear seasonal cycle. In the austral winter months, white sharks aggregate around Seal Island with female sharks in particular moving to the inshore areas in summer. What triggers these fine scale migrations at one of the largest white shark aggregation sites in the world remains a subject of debate. Previous research identified the environmental variables, water temperature and lunar phase, as significant influences on white shark presence inshore. In this study, I attempt to investigate the influence of prey fish availability on the presence of white sharks at two inshore areas of False Bay, namely Muizenberg and Fish Hoek. In addition, I explored the influence of sea surface temperature (SST), El Niño/Southern Oscillation (ENSO), dolphin presence, diatom patch presence and the occurrence of purse-seine fishing (treknetting) on shark presence. A total of 1209 shark sightings were recorded from 1 January 2006 - 31 December 2015 with 742 sightings at Muizenberg and 467 at Fish Hoek. I used randomization tests to determine whether the occurrence of shark sightings was randomly distributed across the environmental and biological variables and determined the dependencies between the predictor variables. I confirmed that shark sightings were clearly seasonal and sightings peaked between 17.49 - 18.57°C. Fish presence revealed a similar peak at 17.94°C. Randomization tests indicate that a spotter is 66% more likely to detect a shark when fish are present, which supports my prediction of a prey mediated cue. The occurrence of treknetting was also found to be non-randomly linked to white shark presence, increasing the probability to spot a shark to 38% instead of 20% at random. The presence of diatom patches was found to be negatively correlated with SST; with numbers increasing in colder waters. The presence of dolphins, as other predators in False Bay, didn't show a significant pattern with any of the analysed variables. The influence of ENSO on the presence of white sharks was also hypothesized and the data revealed that there was a significant influence of weak negative ENSO values on their inshore occurrence. In addition to providing a better understanding of the ecology of white sharks in False Bay, my results can also be used in shark safety and education programs to reduce the risk of shark human conflict.
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    Sensory drive mediated by climatic gradients partially explains divergence in acoustic signals in two horseshoe bat species, Rhinolophus swinnyi and Rhinolophus simulator
    (Public Library of Science, 2016) Mutumi, Gregory L; Jacobs, David S; Winker, Henning
    Geographic variation can be an indicator of still poorly understood evolutionary processes such as adaptation and drift. Sensory systems used in communication play a key role in mate choice and species recognition. Habitat-mediated (i.e. adaptive) differences in communication signals may therefore lead to diversification. We investigated geographic variation in echolocation calls of African horseshoe bats, Rhinolophus simulator and R . swinnyi in the context of two adaptive hypotheses: 1) James' Rule and 2) the Sensory Drive Hypothesis. According to James' Rule body-size should vary in response to relative humidity and temperature so that divergence in call frequency may therefore be the result of climate-mediated variation in body size because of the correlation between body size and call frequency. The Sensory Drive Hypothesis proposes that call frequency is a response to climate-induced differences in atmospheric attenuation and predicts that increases in atmospheric attenuation selects for calls of lower frequency. We measured the morphology and resting call frequency (RF) of 111 R . simulator and 126 R . swinnyi individuals across their distributional range to test the above hypotheses. Contrary to the prediction of James' Rule, divergence in body size could not explain the variation in RF. Instead, acoustic divergence in RF was best predicted by latitude, geography and climate-induced differences in atmospheric attenuation, as predicted by the Sensory Drive Hypothesis. Although variation in RF was strongly influenced by temperature and humidity, other climatic variables (associated with latitude and altitude) as well as drift (as suggested by a positive correlation between call variation and geographic distance, especially in R . simulator ) may also play an important role.