Browsing by Author "Bishop, Jacqueline M"
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- ItemOpen AccessA genetic perspective on leopard (Panthera pardus) conservation units across southern Africa(2021) Thacker, Thomas M; Bishop, Jacqueline M; Naude, Vincent NConservation units are a tool to guide policy such that conservation goals can be achieved. These units should ideally synthesise a wide array of data – genetic, ecological, demographic – to identify the appropriate scales at which conservation actions can then be directed. Despite being the most widespread of all felids in Africa, and facing numerous threats across its range, it has been proposed that the entirety of southern Africa be considered one conservation unit for leopards (Panthera pardus pardus). This proposal does not take into consideration the likelihood of existing population genetic structure across an increasingly fragmented landscape. Further complicating regional leopard conservation is the variability in conservation policies among the geopolitical leopard-range states. Within this single proposed conservation unit, the patchwork of different legislation does not support a unified policy for leopard conservation. Using a population genetic perspective, this study explores and tests the values and shortcomings of southern Africa as a single conservation unit, and explores the importance of leopard range states within the context of conservation units. Parallel investigations of leopard microsatellite genotype data within the framework of a genetic population study spanning eight countries across southern Africa were carried out. This study presents consilient evidence supporting the finding that southern Africa contains six clusters of unique genetic lineages, and as such does not constitute a single genetic unit. Furthermore, it is shown here that the spatial genetic structure that exists does not correlate with the separate geopolitical range states. Leopard range states within southern Africa instead capture varying levels of unique genetic structure and thus are not of equal value with respect to the conservation of genetic lineages. These findings have several implications for leopard conservation across the region. While the data presented here specifically consider a genetic element of conservation units, they do suggest shortcomings in adopting either the entirety of southern Africa as a single unit or separate geopolitical range states as conservation units. The variability in leopard conservation policy across southern Africa is unlikely to sufficiently protect their existing regional genetic structure. If conservation units are indeed a tool to guide conservation policy, then the southern Africa unit for leopards is potentially less effective than a smaller unit whose spatial scale more accurately captures the discrete variation in population genetic structure. Genetic diversity and population structure is an important component of conservation units and should not be neglected. Currently, however, an appropriate framework allowing for conservation policy to be informed at the necessary scale does not exist; although the establishment of Transfrontier Conservation Areas speaks to the growing acknowledgement that conservation needs to evolve beyond the historical confines of geopolitical range states. The evidence presented here further supports the need for a rethinking of existing policy structures.
- ItemOpen AccessAssociations between MHC class I variation and blood pathogen prevalence in caracal(2017) Ly, Alicia; Bishop, Jacqueline MAdaptive genetic variability is vital to long-term species survival, as it presents the potential for evolutionary adaptive responses to environmental change. Genes of the Major Histocompatibility Complex (MHC) trigger the vertebrate adaptive immune response to pathogens through the recognition and presentation of foreign peptides, and thus provide an informative genetic marker for studying the adaptive potential of species with respect to disease. MHC class I loci mediate the immune system's recognition of intracellular pathogens, including protozoans, viruses and bacteria, and the high levels of genetic diversity reported at these loci is thought to be primarily the result of pathogen-mediated selection. Although variation within a number of MHC genes has been described in many felid species, the relationship between MHC diversity and pathogen prevalence within wild felid populations has rarely been examined previously. Because many wild felids are highly sensitive to the effects of anthropogenic-induced environmental changes, evolutionarily relevant adaptive genetic variation is particularly important for their conservation. This study explored the relationship between MHC class I exon 2 and exon 3 diversity and a number of tick-borne blood pathogens in a population of caracal (Caracal caracal) in the urban landscape of Cape Town, South Africa. The characterization of MHC class I diversity identified 38 and 45 unique, putatively functional alleles in the population, from exon 2 and exon 3 respectively. The influence of MHC allelic diversity and specific alleles, together with sex, age class, home range size and urban cover within home range, on individual pathogen prevalence was assessed using Generalized Linear Models. A positive relationship between Babesia infection and multiple measures of MHC diversity, including nucleotide diversity, average number of nucleotide differences and number of exon 3 alleles, was detected. Additionally, the presence of two specific alleles was significantly correlated with Babesia infection. High levels of infection by a number of tick-borne pathogens were observed in the population, suggesting environmental factors also have an important influence on pathogen prevalence. However, home range and urban cover within home range, as well as sex and age, were not significantly associated with Babesia infection. This study provides the first assessment of the relationship between MHC class I adaptive genetic variation and individual pathogen prevalence in caracal.
- ItemOpen AccessA conservation genetic study of threatened, endemic southern African seabirds(2014) Nupen, Lisa Jane; Bishop, Jacqueline M; Ryan, Peter GMolecular techniques have a broad, and growing, application in the field of wildlife conservation, ranging from the systematic identification and classification of taxa, through studying genetic connectivity between populations, to parentage and individual barcoding. While they are applied to a wide range of spatial- and temporal-scales, molecular approaches complement traditional methods used to classify, investigate and understand the natural world. This study uses multiple lines of evidence, at various scales, to investigate how seabird biology influences population-level responses to changing environments. The focal area is the Agulhas-Benguela Ecosystem (ABE) along the south-western coast of Africa. Globally, biodiversity loss due to environmental change in marine ecosystems is significantly affecting the phenology, distribution, dispersal patterns, and demographic rates of organisms across trophic-levels. Broad-scale changes are occurring that have consequences for both commercial fisheries and threatened marine top-predators. Seabirds are valuable indicators of the state of marine ecosystems, and changes in their distribution and dispersal patterns may reflect those of species in lower trophic-levels. This is the case in the ABE, where some endemic seabird species are better at responding to changes in their environment than others. Twentieth century shifts in the distribution of key pelagic prey species in the ABE have had serious consequences for endemic seabirds. The African Penguin Spheniscus demersus, Cape _ Gannet Moms capensis and Cape Cormorant Phalacrocorax capensis rely on these pelagic fish, and all three species are threatened and in decline. In this study population genetic and phylogeographic methods are used to: (i) quantify levels of genetic diversity, and determine regional-scale structure within all three focal species; (ii) explore fine-scale population structure in African Penguin; and (iii) compare wild and captive populations of African Penguins. The conservation of genetic diversity is essential for the long-term persistence of species. Population genetics can help us to understand the evolutionary processes that have shaped patterns of genetic diversity in the focal species, and predict how they might respond to further environmental changes. Comparative phylogeography, combined with capture-mark- recapture models based on ringing data and annual census counts, provide the most complete picture of the micro-evolutionary forces at play in this unique ecosystem, and highlight seabird life-history characteristics may facilitate adaptation and survival under novel conditions. This is the first conservation genetic study of endemic seabirds in the ABE. Although the three focal species differ in a number of aspects of their breeding and foraging ecology, and in some life-history characteristics, they have evolved under similar selective pressures across their shared range, and represent natural replicates that allow us to determine the dominant drivers of population genetic change. Flexibility in foraging behaviour and the degree of breeding site fidelity exhibited by each of the three focal species affect the rate and effectiveness of their demographic responses to changes in their environment. Understanding connectivity among seabird populations is crucial for their long-term conservation, and has been investigated in numerous studies of seabird species from around the world. Similar to many of these, this study found very low levels of genetic structure among populations of all three focal species based on DNA sequence data, suggesting long-term gene-flow among them, despite potential physical and non-physical barriers. Overall, the patterns observed suggest that high connectivity characterises their breeding regions, and most breeding colonies, buffering the respective populations against environmental variability. These results were supported by fine-scale analyses of the African Penguin using microsatellite markers that also suggested high levels of gene-flow, which may have masked genetic signatures of the regional- and colony-level bottlenecks experienced by this species. Microsatellite-based genetic diversity and fine-scale structure were also compared among wild and captive populations of African Penguins to assess the genetic consequences of a planned conservation breeding program. The genetic composition of birds in captivity largely reflects that found in wild populations. The success of reintroduction in terms of decreasing extinction risk in the wild is uncertain, and should be implemented as part of a broader management plan that addresses the primary threats to wild populations. Further research is required to improve our understanding of many aspects of endemic southern African marine avifauna and better inform our ability to ensure their continued persistence in this system.
- ItemOpen AccessDemographic and genetic variability in Cape Dwarf Chameleons, Bradypodion pumilum, withink a fragmented, urban habitat(2012) Katz, Eric Michael; Tolley, Krystal A; Bishop, Jacqueline M; Altwegg, ResHabitat fragmentation is recognized as a primary cause of biodiversity loss. To maximize biodiversity maintenance, researchers in the field of conservation biology often investigate population demography and genetic variability for species inhabiting fragmented landscapes. Findings from such work enable effective conservation management, maximizing viability for potentially imperiled populations. Previous research has relied predominately on spatial analysis when investigating population demography and genetic variability; however, temporal analysis is also important to species conservation. As of 2006, reptiles and amphibians had the highest threat status among small, terrestrial vertebrates, warranting continual investigation of herpetofaunal species inhabiting fragmented landscapes. Of the two, reptiles are the more poorly studied, though are suggested to be equally or more threatened than amphibians. The Cape Dwarf Chameleon, Bradypodion pumilum, exemplifies one potentially threatened reptile species which has suffered habitat loss, due to urbanization, inducing fragmentation and transformation among much of its habitat. As a result, many B. pumilum populations currently exist as a collection of isolated groups inhabiting critically endangered ecosystems.
- ItemOpen AccessExploring the maintenance of plumage polymorphism in the Black Sparrowhawk(2016) Tate, Gareth John; Amar, Arjun; Bishop, Jacqueline MAnimals often display striking variation with respect to their phenotype. Intraspecific and interspecific variation in body colour represents one of the most well studied forms of phenotypic variation. For decades evolutionary biologists have been fascinated by the mechanisms that maintain colour variation in species and traditional explanations for this diversity of colour in nature often invoke an interaction between selection for conspicuous signals and natural selection for crypsis. Colour polymorphic species have frequently been used to explore the evolutionary processes that lead to colour variation in species. Geographic variation in colour morph ratios also occurs frequently in polymorphic species and is often considered an ideal model system to examine the interplay of gene flow and local adaptation in populations. This thesis aims to explore the role and maintenance of plumage colour polymorphism in a raptor, the black sparrowhawk. The black sparrowhawk exhibits discrete colour polymorphism, with adults occurring as either white or dark morphs. Within South Africa, the species has undergone a recent range expansion, successfully colonising the Cape Peninsula in the Western Cape. As winter breeders, black sparrowhawks in South Africa now experience two contrasting climatic regimes; dry winters in their historical north-eastern range, and wet winters in the recently colonised Western Cape region. Within this newly colonised region, the dark morph occurs in greatest frequency. Across South Africa, the species displays clinal variation, with the frequency of dark morphs declining from > 75 % in the far south-west on the Cape Peninsula, to < 20 % in the north-east of the country. Two contrasting hypotheses have been proposed for the high frequency of dark morph birds in the Cape Peninsula population; (1) that colour variation is non-adaptive and is simply due to a chance founder effect and strong genetic drift and (2) this is reflective of local adaptation and that irrespective of the founding morph ratios, dark morphs have a selective advantage in this newly colonised environment with its novel winter rainfall regime. The main aims of this study were to determine the (i) ecological and evolutionary mechanisms that influence the maintenance of colour polymorphism in the species and (ii) to establish explanations for the unusually high proportion of dark morphs on the Cape Peninsula. In this thesis I have used a range of ecological and genetic approaches to explore both neutral and adaptationist explanations for the high frequency of dark morphs in my study population. Data from the mitochondrial control region was used to examine the distribution of genetic diversity in several geographic populations of black sparrowhawks across South Africa, allowing the exploration of trait divergence under neutrality. Using a phylogeographic framework, genetic variation was used to (i) quantify the extent to which population structure and gene flow may influence the observed pattern of colour morphs in the focal study population on the Cape Peninsula, and (ii) explore how selection and gene flow may interact to explain the patterns of morph frequencies in my study system. I found very low genetic differentiation between sample sites across South Africa suggesting that substantial gene flow occurs among populations, supporting the hypothesis that selection, and thus local adaptation, is the primary force maintaining colour variation on the Peninsula.
- ItemOpen AccessGenetic signatures for enhanced olfaction in the African mole-rats(Public Library of Science, 2014) Stathopoulos, Sofia; Bishop, Jacqueline M; O'Ryan, ColleenThe Olfactory Receptor (OR) superfamily, the largest in the vertebrate genome, is responsible for vertebrate olfaction and is traditionally subdivided into 17 OR families. Recent studies characterising whole-OR subgenomes revealed a ‘birth and death’ model of evolution for a range of species, however little is known about fine-scale evolutionary dynamics within single-OR families. This study reports the first assessment of fine-scale OR evolution and variation in African mole-rats (Bathyergidae), a family of subterranean rodents endemic to sub-Saharan Africa. Because of the selective pressures of life underground, enhanced olfaction is proposed to be fundamental to the evolutionary success of the Bathyergidae, resulting in a highly diversified OR gene-repertoire. Using a PCR-sequencing approach, we analysed variation in the OR7 family across 14 extant bathyergid species, which revealed enhanced levels of functional polymorphisms concentrated across the receptors’ ligand-binding region. We propose that mole-rats are able to recognise a broad range of odorants and that this diversity is reflected throughout their OR7 gene repertoire. Using both classic tests and tree-based methods to test for signals of selection, we investigate evolutionary forces across the mole-rat OR7 gene tree. Four well-supported clades emerged in the OR phylogeny, with varying signals of selection; from neutrality to positive and purifying selection. Bathyergid life-history traits and environmental niche-specialisation are explored as possible drivers of adaptive OR evolution, emerging as non-exclusive contributors to the positive selection observed at OR7 genes. Our results reveal unexpected complexity of evolutionary mechanisms acting within a single OR family, providing insightful perspectives into OR evolutionary dynamics.
- ItemOpen AccessMajor histocompatibility complex diversity in an urban Chacma baboon (Papio ursinus) population: Implications for conservation(2012) McCarter, Jenneca M; Bishop, Jacqueline MSince the 15th century, human activity has altered and degraded nearly half of the available land of the Cape Peninsula, South Africa; this has resulted in significant restriction and fragmentation of the historic geographic range of the peninsula's Chacma baboon (Papio ursinus) population.
- ItemOpen AccessMHC Class I diversity influences haematozoon infection intensity in the polymorphic black sparrowhawk (Accipiter melanoleucus)(2015) Le Roux, Liezl; Bishop, Jacqueline M; Amar, ArjunThe major histocompatibility complex (MHC) is a multigene family known to be the most variable gene group in vertebrates in terms of allelic diversity and gene number. Pathogen mediated selection is thought to be the major driving force behind the unusually high levels of MHC polymorphism in natural populations. In this study the relationship between MHC class I diversity and blood parasite infection intensity is explored in a population of black sparrowhawks (Accipiter melanoleucus). The species is of particular ecological and evolutionary interest as black sparrowhawks display a discrete polymorphism in plumage pattern across its range, occurring as a light and dark morph. It is well established in birds that carotenoïd and melanin-based pigmentation patterns are often associated with parasite resistance. In this study, functional variation at the peptide binding region (PBR) of MHC class I loci is investigated to explain individual variation in blood parasite infection in black sparrowhawks. Using DNA sequence data together with individual estimates of blood parasite load (for Haemoproteus nisi and Leucocytozoon toddi); the study tested the relationship between (i) allelic diversity and individual parasite load and (ii) specific alleles and individual parasite load using a Generalized Linear Model framework. Seven different, putatively functional, MHC class I alleles were identified. Number of alleles per individual ranged from one to three in individuals infected with H. nisi, whereas individuals infected with L. toddi had either two or three different alleles. A significant positive association was found between H. nisi infection intensity and MHC allele Acme_BF2*03. No significant association was found between L. toddi infection intensity and a specific allele. The results reported support the role of pathogen mediated selection of genetic variation at evolutionary relevant MHC genes through rare allele advantage. By characterizing the variation at MHC class I loci and testing for a relationship with parasitemia, it is now possible to elucidate the mechanisms and significance of MHC molecular adaptation in the black sparrowhawk.
- ItemOpen AccessMolecular detection of tick-borne pathogens in caracals (Caracal caracal) living in human-modified landscapes of South Africa(2020-04-30) Viljoen, Storme; O’Riain, M J; Penzhorn, Barend L; Drouilly, Marine; Serieys, Laurel E K; Cristescu, Bogdan; Teichman, Kristine J; Bishop, Jacqueline MBackground Wild carnivores living alongside humans and domestic animals are vulnerable to changes in the infectious disease dynamics in their populations. The aims of this study were to determine the prevalence and diversity of selected tick-borne pathogens (TBPs) of veterinary and/or zoonotic concern in wild populations of caracals (Caracal caracal) occurring in human-modified landscapes in South Africa. Using molecular techniques, we screened 57 caracal blood samples for infection by rickettsial bacteria and piroplasms in three regions of South Africa: rangeland in the Central Karoo (n = 27) and Namaqualand (n = 14) as well as the urban edge of the Cape Peninsula (n = 16) of South Africa. To characterise pathogen identity, we sequenced the 18S rRNA and 16S rRNA genes from positive samples and analysed sequences within a phylogenetic framework. We also examine the diversity of potential tick vectors. Results All individuals tested were infected with at least one tick-borne pathogen. Pathogens included Hepatozoon felis, Babesia felis, Babesia leo and a potentially novel Babesia species. An Anaplasma species previously described in South African domestic dogs was also found in 88% of urban edge caracals. Higher rates of co-infection characterised urban edge caracals (81% vs 15% and 0% in the two rangeland populations), as well as a greater incidence of mixed infections. Host attached tick species include Haemaphysalis elliptica, an important pathogen vector among carnivore hosts. Conclusions This study confirms the occurrence of previously undocumented tick-borne pathogens infecting free-ranging caracals in human-modified landscapes. We identify clear differences in the pathogen profiles among our study populations and discuss the likely health costs to caracals living adjacent to urban areas.
- ItemOpen AccessPhenotypic convergence in genetically distinct lineages of a Rhinolophus species complex (Mammalia, Chiroptera)(Public Library of Science, 2013) Jacobs, David S; Babiker, Hassan; Bastian, Anna; Kearney, Teresa; Eeden, Rowen van; Bishop, Jacqueline MPhenotypes of distantly related species may converge through adaptation to similar habitats and/or because they share biological constraints that limit the phenotypic variants produced. A common theme in bats is the sympatric occurrence of cryptic species that are convergent in morphology but divergent in echolocation frequency, suggesting that echolocation may facilitate niche partitioning, reducing competition. If so, allopatric populations freed from competition, could converge in both morphology and echolocation provided they occupy similar niches or share biological constraints. We investigated the evolutionary history of a widely distributed African horseshoe bat, Rhinolophus darlingi , in the context of phenotypic convergence. We used phylogenetic inference to identify and date lineage divergence together with phenotypic comparisons and ecological niche modelling to identify morphological and geographical correlates of those lineages. Our results indicate that R. darlingi is paraphyletic, the eastern and western parts of its distribution forming two distinct non-sister lineages that diverged ~9.7 Mya. We retain R. darlingi for the eastern lineage and argue that the western lineage, currently the sub-species R . d. damarensis , should be elevated to full species status. R. damarensis comprises two lineages that diverged ~5 Mya. Our findings concur with patterns of divergence of other co-distributed taxa which are associated with increased regional aridification between 7-5 Mya suggesting possible vicariant evolution. The morphology and echolocation calls of R. darlingi and R. damarensis are convergent despite occupying different biomes. This suggests that adaptation to similar habitats is not responsible for the convergence. Furthermore, R. darlingi forms part of a clade comprising species that are bigger and echolocate at lower frequencies than R. darlingi , suggesting that biological constraints are unlikely to have influenced the convergence. Instead, the striking similarity in morphology and sensory biology are probably the result of neutral evolutionary processes, resulting in the independent evolution of similar phenotypes.
- ItemOpen AccessPleistocene aridification cycles shaped the contemporary genetic architecture of southern african baboons(Public Library of Science, 2015) Sithaldeen, Riashna; Ackermann, Rebecca Rogers; Bishop, Jacqueline MPlio-Pleistocene environmental change influenced the evolutionary history of many animal lineages in Africa, highlighting key roles for both climate and tectonics in the evolution of Africa’s faunal diversity. Here, we explore diversification in the southern African chacma baboon Papio ursinus sensu lato and reveal a dominant role for increasingly arid landscapes during past glacial cycles in shaping contemporary genetic structure. Recent work on baboons ( Papio spp.) supports complex lineage structuring with a dominant pulse of diversification occurring 1-2Ma, and yet the link to palaeoenvironmental change remains largely untested. Phylogeographic reconstruction based on mitochondrial DNA sequence data supports a scenario where chacma baboon populations were likely restricted to refugia during periods of regional cooling and drying through the Late Pleistocene. The two lineages of chacma baboon, ursinus and griseipes , are strongly geographically structured, and demographic reconstruction together with spatial analysis of genetic variation point to possible climate-driven isolating events where baboons may have retreated to more optimum conditions during cooler, drier periods. Our analysis highlights a period of continuous population growth beginning in the Middle to Late Pleistocene in both the ursinus and the PG2 griseipes lineages. All three clades identified in the study then enter a state of declining population size (Ne f ) through to the Holocene; this is particularly marked in the last 20,000 years, most likely coincident with the Last Glacial Maximum. The pattern recovered here conforms to expectations based on the dynamic regional climate trends in southern Africa through the Pleistocene and provides further support for complex patterns of diversification in the region’s biodiversity.
- ItemOpen AccessPopulation genetic structuring in the common mole-rat, Cryptomys hottentotus hottentotus(2002) Bishop, Jacqueline M; Jarvis, J U M; O'Ryan, CThis thesis addresses the population genetic consequences of divergent social structure and dispersal regimes in two study populations of the common mole-rat Cryptomys hottentotus hottentotus. Aspects relating to the relationship between, gene flow and genetic variation, the roles of mutation and drift in promoting genetic structuring, and the role of genetic parentage in the species' mating system were investigated using a suite of cryptomys-specific microsatellite markers. C. h. hottentotus is a social species living in colonies of 2-14 individuals, permanently inhabiting a network of burrows. The species is a co-operative whose colonies are composed of a breeding pair, their offspring and a number of potentially unrelated individuals. C. h. hottentotus is an obligate outbreeder whose offspring delay dispersal and the opportunities for independent reproduction until both social and ecological conditions are favourable. The species is widely distributed across South Africa from extreme arid regions where low rainfall restricts dispersal for much of the year, to highly mesic areas where dispersal is facilitated all year round. In response to varying ecological constraints on dispersal, the species displays differential degrees of social elaboration across its range. This appears to be in response to the high energetic costs of burrowing and the low probability of locating geophyte clumps in increasingly arid environments.
- ItemOpen AccessPrevalence and drivers of blood parasitism in African penguins (Spheniscus demersus)(2014) Naude, Vincent Norman; Bishop, Jacqueline MIn the past decade African penguin (Spheniscus demersus) populations have experienced declining population sizes of > 60% in some instances. This has primarily been attributed to shifting prey availability and competition with regional purse-seine fisheries; however, possible novel threats exacerbated by diminishing population sizes and increased stress, may also be important contributors to the regional persistence of the species. These threats include the impacts of arthropod-borne blood parasites on the health of penguin populations. While parasitism of wild penguins has been poorly studied, susceptibility to infection with blood protozoa is well established in a wide range of penguin species held in captivity. This thesis assesses the prevalence of blood parasites in wild African penguins throughout the greater Agulhas-Benguela ecosystem. Using PCR-based techniques, 317 individuals were screened for the presence of known haemoparasite species of Plasmodium, Haemoproteus and Babesia across 12 breeding colonies. Babesia infection was confirmed for 60% of wild birds sampled, but methods used did not indicate infection with either Haemoproteus or Plasmodium species. Generalised linear modelling of ecological and life history parameters suggests that Babesia prevalence is primarily driven by a colony’s distance from the mainland, decreasing significantly as distance from the mainland increases. Captive birds held at the SANCOBB rehabilitation facility in Cape Town present with both Plasmodium and Babesia species, providing the positive controls for the study. The relative scarcity of Plasmodium and Haemoproteus infection in the wild may be the result of an absence of suitable vectors and/or high post mortality in the host. Alternatively, the sensitivity of the method used requires further investigation as Plasmodium infection has been confirmed previously in penguin populations using PCR-based approaches. This study provides the first baseline estimate of blood parasitism in African penguins across their breeding range, and raises the need for further research and monitoring. The results suggest that high Babesia prevalence in African penguins may be related to (1) an ecological system of chronicexposure to infection reservoirs, such as the co-occurring cormorant and gannet populations and (2) increasing anthropogenic impacts, especially in mainland colonies. Data on blood parasitism in co-occurring seabird species is required to fully elucidate their role in Babesia infection dynamics in the region. To improve understanding and facilitate timely detection of changes in blood parasite exposure, standardised methodologies are advocated to better inform the conservation management of this iconic species.
- ItemOpen AccessSensory divergence among populations of a southern African endemic horseshoe bat (Chiroptera: Rhinolophidae ): a multidisciplinary approach(2015) Odendaal, Lizelle Janine; Jacobs, David S; Bishop, Jacqueline MA fundamental goal of evolutionary biology is to understand how natural selection, random genetic drift and gene flow interact to promote adaptive trait divergence within species. Environmental gradients are ideal opportunities for disentangling the relative effects of selection and gene flow in promoting local adaptation among populations experiencing different selective regimes. In this study a multidisciplinary approach combining the methods of sensory ecology, functional morphology, population genetics and functional genetics was used to explore the relative roles of neutral and adaptive processes in the evolution of sensory divergence in Cape horseshoe bats, Rhinolophus capensis. Geographic variation in echolocation resting frequencies (RFs) in this species is characterised by increasing frequency from west (75.7 kHz: xeric habitats) to east (86 kHz: mesic habitats) across their distribution in South Africa. Here the species is found across a wide range of habitats characterised by a gradient of increasing vegetation clutter from xeric habitats in the west, to mesic habitats in the east. To better understand how selection contributes to the evolution of RF variation in R. capensis, the relationships between RF and different ecological and morphological correlates of echolocation frequency were explored.
- ItemOpen AccessSensory trait variation in an echolocating bat suggests roles for both selection and plasticity(BioMed Central, 2014-03-27) Odendaal, Lizelle J; Jacobs, David S; Bishop, Jacqueline MBackground: Across heterogeneous environments selection and gene flow interact to influence the rate and extent of adaptive trait evolution. This complex relationship is further influenced by the rarely considered role of phenotypic plasticity in the evolution of adaptive population variation. Plasticity can be adaptive if it promotes colonization and survival in novel environments and in doing so may increase the potential for future population differentiation via selection. Gene flow between selectively divergent environments may favour the evolution of phenotypic plasticity or conversely, plasticity itself may promote gene flow, leading to a pattern of trait differentiation in the presence of gene flow. Variation in sensory traits is particularly informative in testing the role of environment in trait and population differentiation. Here we test the hypothesis of ‘adaptive differentiation with minimal gene flow’ in resting echolocation frequencies (RF) of Cape horseshoe bats (Rhinolophus capensis) across a gradient of increasingly cluttered habitats. Results: Our analysis reveals a geographically structured pattern of increasing RF from open to highly cluttered habitats in R. capensis; however genetic drift appears to be a minor player in the processes influencing this pattern. Although Bayesian analysis of population structure uncovered a number of spatially defined mitochondrial groups and coalescent methods revealed regional-scale gene flow, phylogenetic analysis of mitochondrial sequences did not correlate with RF differentiation. Instead, habitat discontinuities between biomes, and not genetic and geographic distances, best explained echolocation variation in this species. We argue that both selection for increased detection distance in relatively less cluttered habitats and adaptive phenotypic plasticity may have influenced the evolution of matched echolocation frequencies and habitats across different populations. Conclusions: Our study reveals significant sensory trait differentiation in the presence of historical gene flow and suggests roles for both selection and plasticity in the evolution of echolocation variation in R. capensis. These results highlight the importance of population level analyses to i) illuminate the subtle interplay between selection, plasticity and gene flow in the evolution of adaptive traits and ii) demonstrate that evolutionary processes may act simultaneously and that their relative influence may vary across different environments.
- ItemOpen AccessSignificant Population Structure and Little Connectivity in South African Rocky Shore Species: Implications for the Conservation of Regional Marine Biodiversity(2012) Wright, Daniel B; Bishop, Jacqueline M; Von der Heyden, SophieSouth Africa has 3650 km of coastline that spans the boundary between the Atlantic and Indo-Pacific biomes. The coastal waters boast a remarkable array of biological diversity and high levels of species abundance and endemism. Currently around 23% of the coastline is formally protected via marine protected areas (MPA) with 9% enforced as no-take zones. Even with this relatively high level of protection (as compared to other nations globally) the MPA network is still relatively sparse with protected areas that are on average ~110 km apart and unevenly distributed with the majority of MPAs situated along the species-rich east coast. This has led to concerns that the current MPA network is not protecting a representative sample of the genetic diversity among marine species nor is it sufficiently genetically connected via dispersal and gene flow to ensure their long-term persistence. To test a number of questions regarding the distribution of genetic diversity and degree of population genetic structuring along the South African coast we analyzed mitochondrial DNA sequence data for 10 sessile rocky-shore species and one reef-fish that represent three distinct life history strategies. We find that the distribution of genetic diversity across the South African coastline closely mirrors the distribution of species richness, increasing from west to east. We also find similar levels of population genetic structure among brooders, broadcast spawners and live-bearers, demonstrating that life histories are a poor predictor of genetic connectivity for South African marine species. Finally, we find that estimates of effective dispersal distance for taxa from each of the life history categories are low (~0.5-1.5 km per generation) suggesting that populations within MPAs are reliant on populations in unprotected areas via a steppingstone model of genetic connectivity. In light of these findings, we discuss a number of recommendations to enhance the role of the existing South African MPA network and echo previous calls for the establishment of protected areas along the west coast.
- ItemOpen AccessThe tangled history of olfaction in African mole-rats, Bathyergidae: insights from Olfactory Receptor genes(2012) Stathopoulos, Sofia; Bishop, Jacqueline M; O'Ryan, ColleenThis thesis reports the first assessment of OR variation in Bathyergidae, and therefore, the first for a family of subterranean mammals. Using a PCR-sequencing approach, 178 unique OR sequences, corresponding to 119 unique OR genes are characterised from 14 mole-rat species. Bathyergidae OR genes are classified using sequence similarity and phylogenetic comparison with more than 50 mammalian OR subgenomes.
- ItemOpen AccessWildlife health in human-modified landscapes: epidemiology of tick-borne pathogens affecting black-backed jackals and caracals(2017) Viljoen, Storme; Bishop, Jacqueline M; O'Riain, M JustinDespite the importance of disease as a wildlife management challenge, baseline research on the epidemiology of pathogens occurring in wildlife populations within both rural and urban landscapes has received little attention to date. The aim of this study was to improve our understanding of wildlife health in human-modified landscapes in South Africa, by providing comparisons of body condition, host-attached tick diversity and tick-borne pathogen (TBP) epidemiology of two common mesocarnivore species, the black-backed jackal (Canis mesomelas) and caracal (Caracal caracal). Jackals (n=46) and caracals (n=27) were sampled from small livestock farmlands in the Central Karoo region, in addition to caracals from farmlands in Namaqualand (n=14), and the urban matrix of the Cape Peninsula (n=16). Body condition was evaluated using both ratio (Body Mass Index) and residual (Ordinary Least Squares) methods, and morphometry was compared with historical datasets for each species. There was no apparent effect of sex, age class or location on body condition of jackals or caracals. Host-attached tick diversity was highest in urban caracals compared with the two other caracal populations, possibly indicating that they are exposed to a greater diversity of potential tick vectors. Molecular methods (mPCR/RLB; conventional PCR screening and phylogenetic analysis) used to screen for selected pathogens of veterinary and/or zoonotic concern, including Ehrlichia, Anaplasma, Babesia and Theileria species, revealed that Central Karoo jackals exhibited a lower prevalence of TBPs, compared with sympatric caracals. Hepatozoon canis, a ubiquitous pathogen of domestic and wild canids globally, was observed in 46.5% of jackals. Theileria ovis, a piroplasm of small livestock, was found in 4.7% of jackals. Jackals and caracals appear to be distinct in their TBP epidemiological roles, despite sharing similar tick communities. Pathogens found in caracals include Hepatozoon felis, Babesia felis, Babesia leo and a potentially undescribed Babesia species, genetically similar to B. venatorum, an emerging zoonosis. An Anaplasma species previously described in South African domestic dogs was also found in the urban caracals. All caracals were infected with at least one TBP. Together, these findings suggest that land use does not significantly influence the body condition of these adaptable predators, but that there is a health cost associated with living in the urban space. Cape Peninsula caracals show substantially higher rates of TBP co-infection (81% versus 14.8% and 0% in farmlands) and greater pathogen diversity compared to farmland caracals. The findings of this study include numerous examples of previously undescribed genetic diversity of tick-borne pathogens infecting South African mesocarnivores living in transformed landscapes. This work adds to our understanding of wildlife health within the 'One Health' framework and represents the first detailed examination of TBPs in jackals on farmlands and is also the first work that focuses specifically on TPBs in caracals anywhere in the world.