Browsing by Author "Lamb, Jennifer Margaret."

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Aspects of the molecular systematics, taxonomy and population genetics of Otomops (Chiroptera: Molossidae) in Africa and Madagascar.
(2015) Ralph, Taryn Marietta Cecilia.; Lamb, Jennifer Margaret.; Taylor, Peter John.; Goodman, Steven Michael.
Abstract available in the print copy.
Beyond DNA sequencing : integrative approaches to resolving selected higher and lower taxonomic problems in Afrotropical Chiroptera.
(2013) Richards, Leigh Rosanne.; Lamb, Jennifer Margaret.; Taylor, Peter John.; Schoeman, Marthinus Cornelius.; Goodman, Steven Michael.
Of the approximate 300 currently recognised bat species known from the Afrotropics, very few have been studied in sufficient detail to a) provide accurate species and distributional limits for extant taxa, b) identify possible cryptic species, and c) ascertain the closest sister lineage of numerous taxonomic groups. For those species where DNA-based phylogenies are available, the use of additional taxonomic markers and methods has provided further insights into the evolutionary history of certain extant chiropteran groups. This work comprises a series of systematic studies of African and Malagasy Chiroptera aimed at investigating sequence-based evolutionary hypotheses of higher and lower level taxa using comparative molecular cytogenetic and morphometric techniques. Efforts were directed at resolving taxonomic inconsistencies of chiropteran taxa from the African subregion and/or Madagascar, for which there is a general paucity of comprehensive and/or resolved phylogenies. Taxa belonging to the families Pteropodidae, Hipposideridae, Myzopodidae, and Molossidae were chosen for study because molecular-based have failed to provide consensus regarding evolutionary relationships amongst the above-mentioned taxonomic groups, or are in stark contrast to phylogenies based on morphological data. In addition, molecular cytogenetics and geometric morphometric approaches were used because they have had been applied in few evolutionary studies of Afrotropical bats. With the exception of a few karyotypic descriptions, scant data are available that details the chromosomal diversity and karyotypic evolution of bats from Madagascar in relation to their conspecifics or congenerics on other continents. To understand better the mechanisms that may have structured the karyotypes of extant Malagasy Chiroptera and the utility of chromosomal characters in retracing their evolutionary history, eight species from seven families were analysed using G- and C-banding and chromosome painting. Robertsonian (Rb) fusions and fissions were the dominant mode of genome restructuring amongst taxa and, for the most part, proved useful characters for investigations of phylogenomic relationships amongst families and genera. Chromosomal data generated from painting studies employing Myotis myotis (MMY) chromosomal probes, produced phylogenetically important characters that supported two conflicting hypotheses regarding the evolutionary affinities of the Myzopodidae, a family of bats endemic to Madagascar. The Rb fusion MMY 9+11 detected in Myzopodidae, also common to Phyllostomidae, could suggest a close association of Myzopoda aurita with the superfamily Noctilionoidea. However, the Rb fusion MMY 3+4 that is also present in vesper bats, suggests closer evolutionary ties between M. aurita and the Vespertilionoidea. A sex-autosome translocation, a cytogenetic character previously confined to phyllostomid and vespertilionid bats, was also detected in M. aurita casting further uncertainties on the evolutionary origins of this deep-branching species. This study highlighted the need for more refined cytogenetic investigations based on human-derived chromosomal paints and the application of highresolution bacterial artificial chromosomal (BACs) probes to map intrachromosomal breakpoints and/or subchromosomal rearrangements in the genome of Myzopoda. Heterochromatic polymorphisms and inversions appear to be important mechanisms of karyotypic evolution amongst pteropodid genera. Painting data revealed that at least five structural arrangements might be linked to the evolutionary divergence of pteropodine and rousettine fruit bats. A cryptic pericentric inversion was detected in the genome of Pteropus rufus corresponding to the homologue of MMY 4+19 (equivalent to HSA3+21); an ancestral syntenic character proposed for eutherian mammals. Proposed synapomorphies of the rousettine clade, as defined by molecular DNA studies, include the derived state of the MMY 4+19 homologue and the non-centric fusion of MMY 16/17+24 homologue. Integration of painting data on Hipposideros commersoni with published comparative maps of other hipposiderids enabled a brief revision of the postulated ancestral hipposiderid chromosomal complement. These data disputed previously proposed chromosomal synapomorphies of Hipposideridae and supported the basal position of H. commersoni within the genus. The inclusion of other hipposiderid genera, in particular Malagasy Paratriaenops and southern African Cloeotis, in chromosome painting studies may allow for further inferences regarding the evolutionary history of this diverse family. Morphometric approaches were employed to resolve uncertainties concerning species-level relationships within Afrotropical Otomops. Multivariate analyses delineated three well-supported morphological groups that corresponded to recently described genetic lineages and revealed several species-specific morphological traits for taxonomic diagnoses. Otomops from Djibouti, Ethiopia, Kenya, and Yemen constitute an undescribed morphologically and genetically cohesive group that requires a formal taxonomic description. Understanding the ecological and possible physiological adaptive value of morphological variation can provide valuable insights into the evolutionary history of this Afrotropical species complex. This work has provided further insights into the systematics of certain Afrotropical Chiroptera through the use of molecular cytogenetic and geometric morphometric techniques. Specifically, it has facilitated the interpretation of ancestral, independent and convergent chromosomal characters in the evolution of Afrotropical taxa belonging to the families Pteropodidae, Hipposideridae, and Myzopodidae, and has also elucidated lineage-specific morphological attributes in members of the genus Otomops thereby advancing our understanding of chiropteran diversity within the region.
Biosystematic studies in Southern African species of Strychnos L. (Loganiaceae)
(2014) Adebowale, Adekunle.; Nicholas, Ashley.; Lamb, Jennifer Margaret.; Naidoo, Yougasphree.
Strychnos L. is the largest genus of the pantropical or subtropical family Loganiaceae with about 200 species. Their habits range from trees and shrubs in open areas to lianas in rain forests. The genus is well-known as a source of alkaloids such as strychnine and brucine and other allied compounds, all of which have been used medicinally and in curare formulation for centuries. While taxonomic circumscription of the genus has never been contentious, there is no consensus about infrageneric affiliations, the latest of which recognises 12 sections based on morphological characters. Recent molecular evaluation of the genus on a global scale with the internal transcribed spacer (ITS) marker suggests that many of the currently recognised sections are not monophyletic. An understanding of regional patterns of evolution, which is relevant for biodiversity conservation, requires an in-depth study of the focus group on a regional scale. Using a multiplicity of approaches from morphological and molecular to biogeographical, this study is an attempt at elucidating diversity patterns at different levels among the southern African species of Strychnos. Various combinations of morphological attributes from branches, leaves, flowers and fruits distinguish seemingly homologous clusters of species, sometimes supported by molecular data. A lack of molecular support for a hypothetical relationship may viii indicate case(s) of convergent evolution in these features across the taxa involved. Molecular phylogenies based on the ITS and chloroplast markers confirm the nonmonophyletic nature of all but section Spinosae. Proposals for sectional recircumscriptions of the genus are provided. Patterns of speciation within Strychnos suggest a Miocene origin in the rain forests along the South America/Guinea-Congolian axis. Within the southern African subcontinent, the evolution of the genus carries a strong ecological signature along either the forest or savanna biome, with many accompanying morphological adaptations for the respective habitats. The non-synonymy of S. gerrardii with S. madagascariensis is demonstrated with multiple sources of data, as a case of integrative taxonomy succeeding where single-source data approaches might have failed. Routes to current distribution of the genus in southern Africa are hypothesised to involve a combination of palaeo-climatic oscillations and allopatric speciation, consistent with the process indicated in many other plant groups for the region. The findings are discussed in the wider context of their implications for taxonomy and biodiversity conservation in the face of climate change, food security and other relevant issues in systematics.
Connectivity of two scleractinian corals in the south west Indian Ocean.
(2010) Macdonald, Angus Hector Harold.; Schleyer, Michael H.; Lamb, Jennifer Margaret.
Generations of hard corals have built the complex reef ecosystems that harbour a huge diversity of sea-life in the world’s shallow tropical oceans. These undergo both sexual and clonal reproduction, and may contain signatures in their genomes which help to decipher the riddles of past population dynamics and evolutionary history. Two species of coral, Acropora austera and Platygyra daedalea, were collected from sites along the east African coastline from Kenya in the north to Maputaland, South Africa in the south, and from the Chagos Archipelago. Sequences of two different DNA regions were tested, in a preliminary study, for their potential ability to elucidate connectivity and differentiation among these coral populations. These were the nuclear ribosomal ITS region of P. daedalea populations, and a previously-unused marker, the carbonic anhydrase 3/550 nuclear intron of A. austera. These molecular markers indicated high levels of connectivity amongst populations in a preliminary study based on limited sample sizes and a subset of populations. It was decided to further explore the variability of the carbonic anhydrase 3/550 intron, which showed evidence of subdivision and structuring within Mozambique populations relative to South African populations, in a study in which both the sample size per site and the number and range of sampled sites were increased. ITS sequences, although highly variable, revealed no population differentiation in P. daedalea; STR markers were used in subsequent studies of population differentiation in this species. Populations of both A. austera and P. daedalea showed signs of high connectivity along the region of the coastline sampled in this study. However, there appeared to be a disjunction in ecological connectivity between reefs in Maputaland, South Africa and those in southern Mozambique, between Durban and Maputo where the Agulhas Current originates. This was reinforced in A. austera populations which displayed a region of genetic discontinuity between Inhaca Island and Maputaland reefs of the central reef complex, in the region of Rabbit Rock. Northern reef complexes also harboured unique haplotypes in contrast to southern reefs which shared all haplotypes with those in the north, an indication that northern reefs have seeded the southern (Maputaland) reefs. P. daedalea populations appeared evolutionarily panmictic over scales relevant to this study. Evidence for fine-scale structure indicated that populations were separated from one another over ecologically relevant time-scales. These populations were defined by both their habitats and their sampling location. There was a possibility that the Platygyra species complex included cryptic species that were not distinguishable from P. daedalea. However, the disjunction in the connectivity between northern and southern population groups was also evident in the population structure of P. daedalea. There was a net immigration of propagules of both P. daedalea and A. austera into populations north of the disjunction between groups, where the prevailing current regime is dictated by the Mozambique Channel eddies. In contrast populations to the south of the disjunction (the southern population group) which are subject to the swiftly flowing Agulhas Current, showed a net emigration of propagules from Maputaland reefs. These emigrants were likely to be lost to inhospitable habitat south of the marginal Maputaland region. Although there was evidence for migration of both Platygyra and Acropora propagules between the Bazaruto Archipelago reefs and certain Maputaland reefs, genetic exchange between Mozambique and Maputaland reefs appeared to be limited and may have occurred primarily at evolutionary rather than demographic levels. Managers may need to treat the regional Maputaland reefs as separate stocks and manage them accordingly, as the relative isolation of these corals in the central and southern reef complexes in Maputaland, South Africa, means that they are at risk to losing species to evolutionary extinction. It is also important that reef health in northern Mozambique and Tanzania is maintained as, despite evidence of a break in demographic connectivity, between reefs in these regions and those in Maputaland, there was evidence to suggest that reefs were connected at evolutionary scales, thus maintaining levels of genetic diversity on southern African reefs.
DNA cleavage, photoinduced by benzophenone-based sunscreens.
(2003) Sewlall, Avashnee.; Martincigh, Bice Susan.; Lamb, Jennifer Margaret.
The topical application of sunscreens is widely practised to protect healthy and photosensitive skins from the sun. The benzophenone-derived sunscreens, e.g. 2-hydroxy-4-methoxy benzophenone-5-sulphonic acid (or benzophenone-4) and 2-hydroxy-4-methoxy benzophenone (or benzophenone-3), were ranked as the second and third most frequently used sunscreens, respectively, by the United States Food and Drug Administration (FDA) in 1996. These sunscreens are categorised as being 'safe' and 'effective'. However, it is well known that the parent compound, benzophenone, undergoes rapid hydrogen abstraction reactions on irradiation and is an extremely powerful radical generator. In addition, benzophenone has been shown to be a potent photosensitizer of thymine dimers in deoxyribose nucleic acid (DNA). More astounding to the sunscreen industry is the recent discovery that a group of non-steroidal anti- inflammatory drugs (NSAIDs) having the benzophenone backbone, e.g. ketoprofen, not only form thymine dimers when irradiated with DNA in vitro, but also photosensitize double stranded supercoiled DNA making it prone to single-strand break formation. Both these lesions, if unrepaired, may contribute to mutagenesis, carcinogenesis, inherited disease and eventually cell death. The purpose of this investigation was to determine if a group of benzophenone-derived sunscreen agents has the ability to photosensitize the cleavage of DNA, whereby supercoiled DNA is converted to the relaxed circular and linear forms. The group of UV absorbers investigated in this study included benzophenone-4, benzophenone-3 , 2,4 dihydroxybenzophenone (or benzophenone-l), 2,2'-dihydroxy-4,4'-dimethoxy benzophenone sulphonic acid (or trade name Uvinul DS49) and 2-phenylbenzimidazole-5-sulphonic acid (or trade name Eusolex 232). For comparison the parent compound benzophenone and the NSAID ketoprofen, a well-known photocleaver, were also studied. Buffered aqueous solutions of the benzophenones were irradiated in the presence of DNA at wavelengths greater than 300 nm with an Osram 500 W/2 high-pressure mercury lamp in conjunction with a 10 mm thick Pyrex filter. The irradiated samples were analysed for DNA cleavage by agarose gel electrophoresis and for DNA binding by fluorescence spectroscopy. The photostability of the UV absorbers was also investigated. In addition, computational studies were conducted to obtain the lowest energy geometrical structures of these UV absorbers and hence determine if intercalation of these UV absorbers with DNA was possible. From the photostability experiments conducted, it is apparent that the benzophenone-based UV absorbers were stable to photodecomposition when irradiated with UV light. They behaved in a manner different from their parent compound benzophenone, and from ketoprofen, where substantial photodegradation occurred upon UV irradiation. This is indicative of the rapid photoreactivity of the benzophenone backbone. The relative photostability of the UV absorbers was not anticipated and was attributed to the substituents present on the benzophenone backbone. The agarose gel electrophoresis experiments however clearly showed that benzophenone, ketoprofen, benzophenone-l, Uvinul DS49 and Eusolex 232 cleave ?X174 DNA when irradiated with UV light at wavelengths greater than 300 nm, while benzophenone-3 and benzophenone-4 did not. For these UV absorbers with the exception of benzophenone-3 and benzophenone-4, the number of single strand breaks in the DNA increased compared to when it was irradiated in their absence. In addition, the supercoiled DNA was converted to the relaxed circular and linear forms, the latter of which was undetected in the absence of the UV absorbers. Binding of benzophenone, ketoprofen, benzophenone-l and Uvinul DS49 to calf thymus DNA was also detected by the fluorescence spectroscopy technique. However, this was not observed for Eusolex 232, benzophenone-3 and benzophenone-4, since they did not compete with ethidium bromide for DNA binding sites. Where DNA cleavage did occur, the mechanism of this interaction had to be determined hence the motivation for the computational studies. From computational studies using PM3 semi- empirical calculations, it was determined that the benzophenone-based UV absorbers investigated, apart from Eusolex 232, displayed non-planar geometrical structures. This indicated that DNA intercalation of these sunscreen agents with DNA would at best be very limited, since only one half of the molecule could possibly interact with the bases of DNA. For benzophenone, ketoprofen, benzophenone-l and Uvinul DS49, photosensitised type I and type II processes involving triplet energy transfer reactions has been identified in literature as being responsible for DNA cleavage. It was determined by ab initio calculations that Eusolex 232 exists in a planar structure unlike the other UV absorbers mentioned above that were non- planar. It was concluded that although Eusolex 232 has the ability to intercalate with the base pairs of DNA, it does not do so, as shown by its lack of binding to calf thymus DNA by the fluorescence spectroscopy study. Literature alludes to photooxidation by singlet oxygen in single stranded DNA via the type II reaction and type I electron transfer reactions in double stranded DNA as the mechanism responsible for DNA cleavage induced by Eusolex 232.
Genetic diversity of symbiodinium in selected corals in the Western Indian Ocean.
(2007) Starzak, Dorota Ewa.; Schleyer, Michael H.; Lamb, Jennifer Margaret.
Coastal communities along the east African coastline rely on coral reefs and their associated resources for food security and income. However, increases in the frequency and severity of episodes of coral bleaching have resulted in mass coral moralities in many locations around the world including the western Indian Ocean (WIO). Reef corals obligately host dinoflagellate algal symbionts of the genus Symbiodinium. Coral bleaching is caused by the loss of these symbionts from the host, resulting from a variety of stresses, the major ones being increased seawater temperature and irradiance. The Symbiodinum genus is diverse and the distribution of symbionts is influenced by the host biology, external light environment and geographic location. Ten distinct clades of Symbiodinium have been identified. Although the Caribbean and Great Barrier Reef have been studied intensively with respect to Symbiodinium diversity in many locations in the WIO Symbiodinium diversity is unknown. The aim of this study was to determine diversity, distribution and prevalence of Symbiodinium types in corals along the east African coastline. The Symbiodinium ssrDNA region was analysed using restriction fragment length polymorphism (RFLP) in order to assess the cladal diversity of Symbiodinium. The results showed all samples analysed to belong to clade C. To gain more insight into Symbiodinium genetic diversity, the ITS region was employed to assess Symbiodinium diversity at the subcladal level. Twenty ITS types were identified. The most prevalent type was found to be subclade C1. No phylogeographic structuring was found amongst the symbiont types, however, specificity of symbiont types to coral hosts was demonstrated indicating potential susceptibility to perturbations such as increased seawater temperature.
Genetic diversity of the Chaerephon leucogaster/pumilus complex from mainland Africa and the western Indian Ocean islands.
(2013) Naidoo, Theshnie.; Lamb, Jennifer Margaret.; Schoeman, Marthinus Cornelius.; Taylor, Peter John.; Goodman, Steven Michael.
Chaerephon (Dobson, 1874), an Old World genus belonging to the family Molossidae, is part of the suborder Vespertilioniformes. Members of this genus are distributed across mainland Africa (sample sites; Tanzania, Yemen, Kenya, Botswana, South Africa and Swaziland), its offshore islands (Zanzibar, Pemba and Mozambique Island), Madagascar and the surrounding western Indian Ocean islands (Anjouan, Mayotte, Moheli, Grande Comore, Aldabra and La Reunion). A multifaceted approach was used to elucidate the phylogenetic and population genetic relationships at varying levels amongst these different taxa. Working at the subspecific level, I analysed the phylogenetics and phylogeography of Chaerephon leucogaster from Madagascar, based on mitochondrial cytochrome b and control region sequences. Cytochrome b genetic distances among C. leucogaster samples were low (maximum 0.35 %). Genetic distances between C. leucogaster and C. atsinanana ranged from 1.77 % to 2.62 %. Together, phylogenetic and distance analyses supported the classification of C. leucogaster as a separate species. D-loop data for C. leucogaster samples revealed significant but shallow phylogeographic structuring into three latitudinal groups (13º S, 15 - 17º S, 22 - 23º S) showing exclusive haplotypes which correlated with regions of suitable habitat defined by ecological niche modelling. Population genetic analysis of D-loop sequences indicated that populations from Madagascar have been expanding since 5 842 - 11 143 years BP. At the infra-generic level, I carried out analyses of sequences of the mitochondrial cytochrome b gene and control region, and the nuclear RAG2 region, to resolve the evolutionary history and taxonomy of the C. pumilus species complex from Africa and the western Indian Ocean islands. The nominate form comprised C. pumilus from Massawa, Eritrea, and this was genetically distinct from all other forms of Chaerephon. Our molecular evidence does not support that the syntype of C. limbatus and the holotypes of C. elphicki and C. langi and topotype of C. naivashae are specifically distinct from C. pumilus s.s. There is evidence of introgression of both C. pusillus and C. pumilus s.l. (south eastern Africa) mitochondrial haplotypes into C. leucogaster. The C. pumilus species complex has several attributes of a ring species, but appears to differ from this model in some important respects. It occurs on the African mainland and western Indian Ocean Islands, including Madagascar, ringing a potential barrier to gene flow, the Mozambique Channel. The taxa within the species complex form a ring in which the differentiated terminal forms, C. pusillus and C. leucogaster, occur in sympatry on Mayotte (Comoro Islands). Although there is evidence of isolation by distance around the ring, there is also a relatively high degree of genetic structure and limited gene flow. It appears that the island-based component species may have differentiated in allopatry, with some gene flow by over water dispersal, whereas the African mainland species may have differentiated through isolation by distance. A further study was aimed at re-examining the phylogeny of C. pumilus sensu lato from south eastern Africa based on a considerably larger sample set with a wider geographic range; I confirmed the previously-reported phylogenetic structure, and identified an additional strongly-supported control region clade. Discriminant Function Analysis based on four echolocation parameters could not discriminate between these clades. The hypothesised existence of cryptic species with distinct echolocation characteristics was not supported. Indices of diversity and neutrality, combined with a ragged multimodal mismatch distribution, are inconsistent with demographic expansion of a single C. pumilus south eastern African population and suggest that the control region lineages are stable populations at demographic equilibrium that were established during the late Pleistocene between 60 000 and 13 000 years ago. Further, more variable markers (microsatellites) were employed for finer-scale resolution of population genetic structure among the five genetic lineages of C. pumilus sensu lato found in the Durban area of KwaZulu-Natal, and to search for hybridization between these lineages. We recovered strong mitochondrial genetic structure, with 90% of the molecular variance occurring among four phylogenetically-defined groups, and a high significant Fst (0.897). Microsatellite data recovered three admixed populations with 3% of the nuclear variance occurring among populations, and global (Fst=0.037) and pairwise Fst values among populations were low and not significant. This is indicative of little genetic structure among the groups of C. pumilus s.l., which appear to comprise a single interbreeding population. Such high levels of mitochondrial genetic structure in the absence of significant nuclear structure are consistent with social isolation mechanisms such as female philopatry, and may reflect introgression of mitochondrial genes due to past hybridisation events with mitochondrially-distinct forms from outside the sampled area.
Genetic diversity of the Rattus complex (Rodentia: Muridae) in KwaZulu-Natal.
(2010) Nair, Deenadayalan.; Lamb, Jennifer Margaret.; Contraffato, Giancarlo.; Taylor, Peter John.
The rodent genus Rattus is considered to be the single largest genus of mammals in the world. One species of Rattus is usually more dominant than another within a specific geographical area; however within the province of KwaZulu-Natal South Africa current observations indicate that Norway rats (R. norvegicus), black rats (R. rattus) and the indistinct Asian house rat (R. tanezumi) exist sympatrically. DNA sequencing of the cytochrome b and D-loop regions of the mitochondrion were used in conjunction with karyotyping of bone marrow and tissue culture cells to analyse the genetic diversity of selected Rattus populations from KwaZulu-Natal. Comparison of sequence data obtained during the study to reference sequences obtained from the NCBI GenBank revealed three well-supported monophyletic groups in maximum parsimony and Bayesian analyses. These three monophyletic groups indicated the existence of three species of the Rattus complex within KwaZulu-Natal, namely Rattus rattus, Rattus norvegicus and Rattus tanezumi. Analysis of cytochrome b sequence data revealed the presence of 6, 3 and 2 haplotypes in 20 R. norvegicus, 8 R. rattus and 5 R. tanezumi specimens, respectively. The R. norvegicus haplotypes were separated from R. rattus and R. tanezumi haplotypes by 60 mutational steps, while R. rattus haplotypes were separated from R. tanezumi haplotypes by 24 mutational steps. Analysis of D-loop sequence data revealed the presence of 6, 2 and 1 haplotypes in 14 R. norvegicus, 4 R. rattus and 3 R. tanezumi specimens, respectively. R. norvegicus haplotypes were separated from R. rattus and R. tanezumi haplotypes by 15 mutational steps, while R. rattus haplotypes were separated from R. tanezumi haplotypes by 11 mutational steps. Karyotype analysis of specimens revealed that: (1) R. rattus specimens sampled presented with a karyotype of either 2n = 38 or 2n = 40; (2) R. tanezumi specimens sampled presented with a karyotype of 2n = 42 and (3) R. norvegicus specimens sampled presented with a karyotype of 2n = 42 which was very distinct from that of R. tanezumi.
Genetic variability of Chaerephon atsinanana (Chiroptera) within the context of the Afro-Malagasy Molossidae : a mitochondrial and nuclear perspective.
(2013) Napier, Melanie Carmel.; Lamb, Jennifer Margaret.
This study has focused on genetic variability and structure in Chaerephon atsinanana, a newly-described molossid bat found in the mid to southern region of the eastern watershed of Madagascar. As these bats are strong fliers, and are able to traverse the riverine and mountain barriers within the landscape, it was hypothesized that they would show relatively low levels of intraspecific genetic structure, consistent with patterns shown for other Molossidae on Madagascar (Mormopterus jugularis, Mops midas, Mops leucostigma, and C. lecuogaster. Phylogenetic (neighbor-joining, parsimony and Bayesian inference) and population genetic analyses of maternally-inherited mitochondrial control region sequences revealed the presence of 6 distinct haplotype groups separated by genetic distances of up to 8.14% (mean 4.95%). There were high levels of genetic structure among the haplotype groups (overall FST= 0.994). Thus the hypothesis of low levels of genetic structure was rejected. Bayesian skyline analyses and significantly ragged mismatch distributions were consistent with ancient stable C. atsinanana populations which were of constant size during the last two major Pleistocene glacial periods. This made retreat into and expansion from glacial refugia an unlikely explanation for such high levels of structure. An alternative hypothesis is that C. atsinanana haplotype groups are spatially structured as a result of philopatry. As mitochondria are maternally-inherited, this data is consistent with the existence of female philopatry in C. atsinanana. The second aim of this study was to examine the genetic structure of C. atsinanana with nuclear sequence markers, which are biparentally-inherited, in order to provide information on the male contribution to gene flow and the possible presence of male philopatry in this molossid bat species. The initial objective was to amplify and sequence candidate nuclear markers in order to identify those which were variable among C. atsinanana samples. I attempted to amplify and sequence a set of 12 nuclear markers, identified from the literature, which had been reported to show high levels of variability, or which were untested and showed the potential for high levels of variability. Of these, the intron markers PNPO-3, SLC38A7-8, CARHSP1-1, GAD2-1, OSTA-5 had not previously been used in phylogenetic analyses while FES, GHR, RHO1 CHRNA1, STAT5, PRKC1 and THY had been. I was not able to amplify and/or sequence SLC38A7-8, CARHSP1-1, GAD2-1, OSTA-5, CHRNA1, STAT5 and THY across the range of the C. atsinanana samples. PNPO-3, FES, GHR, RHO1 and PRKC1were successfully amplified and sequenced, but showed no variability and very little polymorphism, and were therefore unsuitable for testing hypotheses related to genetic variability of C. atsinanana populations. These five nuclear sequence markers were further used to investigate phylogenetic relationships among 5 genera (Chaerephon, Mops, Mormopterus, Otomops and Sauromys) and 13 species of Afro-Malagasy molossid bats, and to provide a nuclear phylogenetic perspective on the newly-described C. atsinanana. PNPO-3 is a novel nuclear intron marker, previously unused in phylogenetic studies. This intron provides resolution primarily at the genus level, and is less informative at interspecific level. These five nuclear markers were combined with already existing mitochondrial cytochrome b (Cyt b) and nuclear Rag2 data retrieved from GenBank. This study provides strong support for the monophyly of the Chaerephon and Mops taxa included, with the exception of C. jobimena, which was weakly associated with this group. There was no support for the generic affiliation of C. jobimena or for the monophyly of either of the genera Chaerephon or Mops individually. This leads to the suggestion that Mops and Chaerephon be combined into a single genus, with crown age of 14.82 (6.44-25.54) MYA, or 21.97 (12.16-33.44) MYA if C. jobimena is included. Otomops forms a strongly supported clade consistent with its generic status, comprising two subclades corresponding to the recognised sister species O. martiensseni and O. madagascariensis, which last shared a common ancestor 8.35 (2.87-17.47) MYA. This study provides good nuclear support for the mitochondrially-defined subclades of O. martiensseni, which last shared a common ancestor 4.18 (1.08-9.96) MYA. It would appear appropriate to name the clade from north east Africa and Arabia as a new species of Otomops, as the clade from southern and western Africa includes the type locality. This study provides weak support based on individual gene regions for associations of Sauromys with Otomops and Mormopterus, although these do not stand up in the concatenated datasets which offer better resolving power, indicating that Sauromys is not phylogenetically associated with Chaerephon/Mops, Otomops and Mormopterus. These results provide some support for the membership of Mormopterus in the proposed Old World Molossid tribe, Tadarini, but also support Mormopterus as a basal genus within the Molossidae, consistent with its designation as a separate tribe, Mormopterini.
Mitochondrial DNA variability between selected populations of Otomys irroratus (Muridae:Otomyinae)
(1993) Raubenheimer, Janine.; Lamb, Jennifer Margaret.; Contrafatto, Giancarlo.
An interpopulation study was done on the rodent species Otamys irroratus (Muridae:Otomyinae) using restriction fragment length Polymorphisms to examine the mitochondrial DNA (mtDNA) of 30 vlei rats (Otamys irroratus) from three South African locations and 12 Angoni vlei rats (O.angoniensis) from two locations which were included as an outgroup. The three O.irroratus Populations originated from Karkloof and Kamberg in the Natal midlands and from Rietvlei in the Southern Transvaal. Mitochondrial DNA was extracted and purified by cesium-chloride/ethidium-bromide ultracentrifugation and digested with 19 class 11 restriction endonucleases. The fragments were end-labelled with 32P-dCTP, separated by electrophoresis on horizontal 1% agarose gels and the bands detected by autoradiography. The resultant individual-specific fragment patterns were analysed using the Restsite analysis program (v 1.1; Nei and Miller, 1990) to obtain a measure of the percent sequence divergences between and within the 3 POpulations of O.irroratus as well as between this species and the outgroup. The 19 endonucleases detected 19 distinct O.irroratus mtDNA maternal lineages and 3 O.angoniensis lineages. The O.irroratus lineages were clearly geographical ly structured and most closely reflected the Avise et al. (1987) category I (phylogenetic discontinuity with spatial separation). The only exception was a possible ancestral lineage represented by single individuals from Kamberg and Karkloof. Phylogenetic affinities between the most diverse lineages found at Kamberg and most Karkloof clones appear to be consistent with the finding of Pillay et al. (1993) and Contrafatto et al. (1992b) that Kamberg O.irroratus is an incipient sibling species of Karkloof O.irroratus. The mtDNA data indicates that the O.irroratus Populations at Karkloof and Kamberg last shared a common ancestor approximately 365 000 years ago. By contrast, O.angoniensis showed no evidence of geographic mtDNA structuring and is best described by the Avise et al. (1987) category Ill, which reflects phylogenetic continuity with spatial separation. These classifications must be regarded with caution given the limited distributional range of each species covered by this investigation. The interspecific mtDNA sequence divergence between O.irroratus and O.angoniensis of 11.57% substaniates morphological, karyotypic and allozymic evidence that these two sympatric species are also sibling species and they appear to have last shared a common ancestor between 1.2 and 2.4 million years ago.
Molecular identification of hookworm isolates from stray dogs, humans and selected wildlife from KwaZulu-Natal and Mpumalanga provinces of South Africa.
(2019) Ngcamphalala, Philile Ignecious.; Mukaratirwa, Samson.; Lamb, Jennifer Margaret.
Hookworms are nematodes that cause infections to the host via skin penetration of the third stage larvae and they are widely distributed in the tropical and subtropical regions. They parasitize a wide range of host species including humans and companion animals such as dogs and cats. An estimated 740 million people are infected worldwide, with sub-Saharan Africa having the highest documented prevalence. With the exception of the study conducted by Lamb et al. (2012), Ancylostoma species identification in Southern Africa was solely based on egg morphology and morphological characteristics of adult worms. This study therefore aimed at using molecular techniques to identify the hookworm species and their prevalence in stray dogs, school-going children from KwaZulu-Natal province, and selected wild canids and felids from Mpumalanga province of South Africa. A total of 356 faecal samples were collected and screened for the presence of hookworm eggs using coproscopy and coproculture, which yielded prevalence of 23.04% and 21.67%, respectively. Larvae derived from coproculture of a total of 55 samples were subjected to molecular analysis. DNA was isolated and subjected to PCR amplification, PCR-RFLP and sequencing of the nuclear ribosomal internal transcribed spacer (ITS1) and 5.8S rRNA region. PCR-RFLP showed an overall prevalence of 72.7% (40/55) for A. caninum, 12.7% (7/55) for a mixture of A. caninum, A. ceylanicum, and A. braziliense, 7.27% (4/55) for A. caninum and A. ceylanicum mixed infection, and 7. 27% (4/55) for A. caninum and unidentifiable species. These results are consistent with other studies which show that A. caninum is the most dominant hookworm species worldwide even though A. braziliense is regarded as a more important zoonotic species. Phylogenetic analyses of alignments based on the DNA sequences were also used to identify isolates which were sequenced. However, results of phylogenetic analysis were not consistent with results from PCR-RFLP analysis as none of the sequences matched with A. ceylanicum. Sequencing also showed a 0.68% prevalence for both A. caninum and A. braziliense (mixed infections) in dogs. Of great importance was the revelation that A. caninum can now cause a patent infection in South African (Ingwavuma area) school-aged children as all human isolates matched with A. caninum with a prevalence of 6%. For wildlife, a prevalence of 10% was recorded. However, due to the small sample size, these results cannot be regarded as a true reflection of the prevalence in wildlife. Thus there is a need for future studies that will increase sample sizes, broaden ranges as well as look into finding better detection methods, primers and/or restriction enzymes that are specific to hookworm species isolated in South Africa.
On the vacuolar system in maize roots.
(1979) Lamb, Jennifer Margaret.; Berjak, Patricia.
Root-cap cells of Zea mays L proliferate by division in the cap meristem, and subsequently differentiate and mature as they move towards the periphery of the cap, where ' they undergo autolysis and are sloughed. Vacuolar ontogeny has been shown to be complex, several different mechanisms operating not only within the root cap tissue, but within the single cells. Vacuolar initials (provacuoles) are formed in the meristem by the pinching off of single- or doublemembrane bound vesiculations of the E.R. In some instances large vacuoles appear to be formed in the mature region of the cap through the sequestering of large organelle-free regions of cytoplasm by vesicles and small cisternae, thought to be of E.R. origin. Further development of provacuoles comprises their expansion and extensive fusion, this process culminating in the formation, in a mature cell, of just one large vacuole. The vacuoles of the mature region are autophagically active, engulfing all types of cytoplasmic organelle which are subsequently lysed; these vacuoles show a positive cytochemical reaction for acid-phosphatase, further indicating that they are lysosomal in nature. The dictyosomes of the late mature cells are hypersecretory and autoradiographic and cytochemical evidence indicates that the vesicles contain an accumulation of polysaccharide. These vesicles appear to follow two secretory pathways; firstly fusion with the plasmalemma, with secretion of their content into the extra-protoplasmic space where it accumulates, finally penetrating the cell wall and middle-lamella and forming viscous polysaccharide slime on the exterior of the cap. Secondly, these vesicles appear to be engulfed by and broken down within the vacuoles. At this stage the vacuole expands considerably, and it has been postulated (Berjak and Villiers, pers. corom.) that hydrolysis of the dictyosomally-derived polysaccharide within the vacuole to monosaccharide units results in osmotic. changes leading to an influx of water into the vacuole, and its consequent expansion. Autoradiographic, cytochemical and chromatographic evidence is not inconsistent with an accumulation of monosaccharide units being at least partially responsible for the osmotic uptake of water into the swelling vacuole. Finally, the vacuolar membrane becomes discontinuous, allowing hydrolytic enzymes p~esumably contained within the vacuole to come into contact with the cytoplasm, which consequently undergoes autolysis. At this stage the cell is sloughed from the cap.
Patterns of genetic variation in Mops leucostigma (Molossidae) from Madagascar and the Comoros.
(2008) Hoosen, Nikhat.; Lamb, Jennifer Margaret.
The synanthropic molossid bat, Mops leucostigma (Allen 1918), is widely distributed across Madagascar and has recently been described from the Comoros. M. leucostigma individuals from eastern Malagasy populations are markedly larger than those from the west, and Mops leucostigma populations from Madagascar are morphologically distinct from populations of its putative sister species, Mops condylurus from mainland Africa (Ratrimomanarivo et al. in press, Genetic diversity was assessed by sequencing the mitochondrial cytochrome b (n = 56) and displacement loop (D-loop) (n = 64) regions of Mops leucostigma individuals from a broad range of locations across Madagascar, and Mohéli and Anjouan in the Comoros. Specimens of Mops condylurus (n =3), Mops midas (n =3) and Otomops martiensseni (n = 1) were included in the study for comparative purposes as outgroups. Phenetic and cladistic analysis of cytochrome b and D-loop sequences strongly supported the reciprocally-monophyletic status of Mops condylurus and M. leucostigma. Comorian (Mohéli and Anjouan) and Malagasy M. leucostigma samples formed a monophyletic Mops leucostigma group, within which Comorian samples formed a poorly-supported subclade in the cytochrome b analysis only. Cytochrome b genetic distances of 13.8 % separated M. midas from M. condylurus and M. leucostigma, which formed reciprocally-monophyletic sister groups separated by genetic distances of 2.5 % for cytochrome b and 13 % for the D-loop. 49 M. leucostigma cytochrome b sequences yielded seven haplotypes, two of which were exclusive to the Comoros. D-loop haplotype analysis did not support the distinctiveness of the Comorian samples. Genetic distances within M. leucostigma samples were low (0.22 % for cytochrome b and 1.91 % for the D-loop). Comorian samples were found to be genetically attributable to M. leucostigma. Clear phylogenetic separation between M. condylurus and M. leucostigma was found in all analyses, consistent with their status as phylogenetic species within the genus Mops. There was no clear correlation between haplotype distribution and aspect (east/west-facing slopes), elevation or gender. Low mtDNA variation (cytochrome b and D-loop) and lack of phylogeographic concordance indicates that the observed morphometric variation between eastern and western Mops leucostigma populations may possibly be explained in terms of adaptation to local environmental conditions.
Population genetic studies of Fasciola species from cattle and selected wildlife species in Zimbabwe and localities of KwaZulu-Natal and Mpumalanga provinces of South Africa.
(2014) Mucheka, Vimbai Tendai.; Mukaratirwa, Samson.; Lamb, Jennifer Margaret.; Pfukenyi, Davies M.
The objective of the study was to confirm the species and determine the genetic diversity of the confirmed Fasciola species from cattle and selected wildlife hosts from Zimbabwe and KwaZulu-Natal and Mpumalanga provinces of South Africa. This was based on analysis of DNA sequences of the nuclear ribosomal internal transcribed spacer (ITS) and mitochondrial cytochrome oxidase 1 (CO1) regions. Flukes were collected from livers of 57 cattle at four abattoirs in Zimbabwe and 47 cattle at four abattoirs in South Africa. DNA was extracted from each fluke and 3 wildlife, alcohol preserved, duiker, antelope and eland samples from Zimbabwe. The ITS and CO1 regions of individual flukes were amplified by the polymerase chain reaction (PCR) and sequenced. Aligned sequences (ITS 506 base pairs and CO1 381 base pairs) were analyzed by neighbour-joining, maximum parsimony and bayesian inference methods. The phylogenetic trees revealed the presence of Fasciola gigantica in cattle from Zimbabwe and F. gigantica and Fasciola hepatica in the samples from South Africa. Fasciola hepatica was more prevalent (64%) in South Africa than F. gigantica. Fasciola gigantica was the only species found in Zimbabwe save one sample and an antelope and a duiker which were found to be F. hepatica. This is the first molecular confirmation of Fasciola species in Zimbabwe and South Africa. Knowledge on the identity and distribution of these liver flukes at molecular level will allow disease surveillance and control in the studied areas.
Restriction patterns of mitochondrial DNA in natural populations of the murid species Otomys irroratus.
(1994) Rimmer, Alison.; Lamb, Jennifer Margaret.; Contrafatto, Giancarlo.
Mitochondrial DNA (mtDNA) was isolated from 8 different natural populations of the rodent species Otomys irroratus (Muridae: Otomyinae) and from one population of the species 0. angoniensis occurring in South Africa. MtDNA samples were cleaved with five different restriction endonucleases, end-labelled with phosphorous-32, separated by electrophoresis on horizontal 1 % agarose gels and the resulting fragment bands were detected by autoradiography. The individual-specific fragment banding patterns were analysed and compared among the various populations. The percent sequence divergence among and between the populations was calculated using the formula of Nei (1979). A matrix of sequence divergence values for all intergenomic pairwise comparisons was subjected to a clustering analysis by the unweighted pair group method with arithmetic means (UPGMA, Sneath and Sokal, 1973), using the computer programme NTSYS (Rohlf: 1988). The results of these analyses allowed for a preliminary identification of phenetic groupings in the data set. A matrix generated by scoring the restriction endonuclease fragments as present or absent was used to generate a phylogenetic dendogram using the BIOSYS (Swofford and Selander, 1989) programme. The overall restriction fragment variation uncovered in this study revealed 15 different mtDNA haplotypes within the 20 individuals examined. This corresponded to a high degree of polymorphism in the populations where more than one specimen was available, as well as within the species 0. irroratus. There were no clones that were shared between any of the populations sampled. The intrapopulation sequence divergence values uncovered in this study were high (range 0.35 % to 5.08 %), but also consistent with some other reports in the literature for intrapopulation variation. The outgroup, 0. angoniensis revealed the highest divergence values when compared to the mtDNA clones found in 0. irroratus. The phenetic and cladistic cluster diagrams revealed overall similarity with one another. There appeared to be little correlation between the topology of the mtDNA haplotype phenograms and the geographic distance of the sample localities. There was, however, a marked congruence between the distribution of mtDNA haplotypes and the distribution of three distinct cytotypes occurring over the species range. A possible polyphyletic evolution of populations of 0. irroratus was inferred from the cladistic analysis.
Y-STR studies of genetic genealogy, population and forensic genetics of Indian and Zulu groups in the Durban, KwaZulu-Natal area of South Africa.
(2018) Singh, Surina.; Lamb, Jennifer Margaret.
The combination of molecular genetics and surname analysis of short tandem repeat (STR) data has the potential to shed light on population structure and history, falling within the field of forensic deoxyribonucleic acid (DNA) analysis. Since the Y-chromosome DNA along with surnames are paternally inherited, non-related males sharing a surname should be more closely related in comparison to the general population. Currently, no surname studies based on the Indian population in South Africa exist. This study aimed to explore the genetic genealogy, population and forensic genetics of Indian (different geographic origin, religion and language) and Zulu males with different common surnames from Durban, KwaZulu-Natal. This was achieved by: (1) Collecting samples from 224 non-paternal lineage related North Indians males and generating DNA profiles, using the Yfiler® Plus kit to amplify 27 Y-chromosome STR (Y-STR) loci; (2) Comparing the genetics of the North Indian group to that of other groups with South Indian and Zulu African surnames found in the forensic lab database. Hypotheses were formulated to analyse differences in relationships at ethnic, region, religion, language and surname-based levels (Figure 1). Population and forensic genetic analyses revealed that the Yfiler® Plus gave a higher number of unique haplotypes and discrimination capacity and a lower haplotype match probability, validating its use in this study. Genetic structure was found amongst examined sub-groupings. AMOVA was significant for all levels tested, with exception to between South Indian surnames. There are no known barriers to intermarriage among people bearing these South Indian surnames. Structure and PCoA analysis showed the presence of two significant sub-populations, which were ethnic based. Population structure and diversity were not surname based, but rather at an ethic level. This could be attributed to polyphyletic origin (many surname origin) of the analysed surnames. Surname transmission was polyphyletic for all surname groups, showing overlapping haplotypes and clades, implying multiple founders/ lineages for each specific surname investigated. The data generated in this study will contribute to the Indian DNA profiling database and could potentially serve as a baseline for further research. Further research could include sequencing autosomal STRs and hypervariable regions of mtDNA. enetic genealogy is a field of growing interest, involving genealogical testing to determine genetic relationships between individuals. The combination of molecular genetics and surname analysis of Y-STR data has the potential to shed light on population structure and history and is within the field of HID (human Identification) forensic DNA analysis. Since DNA along with surnames are passed down from our ancestors, people with the same surname should have a greater chance of sharing common ancestry when compared with the general population. There are currently no surname studies based on the Indian or Zulu populations of SA. The primary focus of this study was on genetic genealogy, i.e. co-inheritance of surnames and Y-STRs. In addition, population and forensic genetics of a sample group of mainly Indian and Zulu people from the greater Durban area of KwaZulu-Natal (KZN), SA, was investigated to search for genetic structure in comparisons of groups based on (1) Ethnicity (Indian vs Zulu), (2) Region of origin in India (North vs South), (3) Religion (Hindu vs Muslim), (4) Language (Hindi vs Muslim (Urdu) vs Tamil Indians) and, (5) Surname-based groups originating from North India (surnames Khan, Maharaj and Singh), South India (surnames Govender, Naidoo and Pillay), and Africa (surnames Buthelezi, Cele, Dlamini, Mkhize and Zulu). Further, an attempt was made to establish baseline aspects of the social history of the North Indian groups in Durban, which relate to genetic genealogy. The age profile and number of generations since the first family member arrived in the Durban area from India were investigated, along with information on whether a North Indian individual shares his surname, city, religion and language with his child and paternal and maternal forefathers. DNA samples were collected from 224 non-parentally related North Indian males with the surnames Khan, Maharaj and Singh and the Yfiler® Plus Polymerase chain reaction (PCR) amplification kit was used to amplify 27 Y-STR loci, from which DNA profiles were generated. In order to extend the basis for comparison to other Durban area ethnic groups, Y-STR profiles, from the lab database, of South Indians (n = 90, surnames Govender, Naidoo and Pillay) and Zulus (n = 100, surnames Buthelezi, Cele, Dlamini, Mkhize and Zulu) were included in the sample set. Null Alleles were observed at 77.8 % (21 out of 27) of the different loci analysed, with most contained in loci DYS391, DYS389II and DYS448.