Browsing by Author "Taylor, Peter John."

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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.
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.
The influence of abiotic processes, competition and predation on the community structure of rodents and shrews.
(2012) Delcros, Gwenaelle.; Schoeman, Marthinus Cornelius.; Taylor, Peter John.
Predation and abiotic processes rather than competition should influence the community structure of rodents and shrews with life histories characterised by high fecundity, short longevity and unstable populations. I investigated the influence of abiotic processes, predation and competition on three parameters of community structure (species composition, phenotypic and phylogenetic niches) of rodents and shrews at Mkhuze and Kube Yini, two game reserves in KwaZulu-Natal, South Africa, using null models and multivariate analyses. Rodents and shrews were sampled between 2007 and 2009. Sample-based rarefaction curves indicated that rodent species richness was higher at Mkhuze than at Kube Yini, while shrew species richness was identical at both reserves. Species richness estimators indicated that estimates of species richness were fairly accurate, hence strengthening the results from my null model analyses. I found evidence that immigration and extinction operating at a regional scale influenced rodent species composition. Moreover, habitat filtering operating at a local scale influenced rodent and shrew species composition. These processes produced nested assemblages: species present at species-poor sites were subsets of species present at species-rich sites. Habitat filtering also influenced the phenotypic niche of rodents and shrews: sympatric species showed similar phenotypic adaptations (phenotypic niches were underdispersed), probably in response to similar food requirements. Furthermore, shrew phenotypic traits showed a convergent evolution, and local assemblages comprised distantly related species (phylogenetic evenness), suggesting the influence of habitat filtering on the phylogenetic niche structure of shrews. Predation influenced shrew phenotypes. Bullae and ears were underdispersed and larger than expected by chance, probably to reduce predation risk through increased hearing sensitivity. In contrast, I found no evidence that predation influenced the rodent phenotypic niche. Competition influenced the phenotypic niches of rodents and shrews in species-rich assemblages (phenotypic niches were overdispersed). In these assemblages, the coexistence of species was facilitated by dietary and microhabitat partitioning. Competition also influenced the phylogenetic niche of rodents: phenotypic traits showed a convergent evolution, and local assemblages comprised closely related species (phylogenetic clustering). In conclusion, both abiotic and biotic processes influenced different parameters of the community structure of rodents and shrews. However, despite similar life-history traits, the community structure of local assemblages differed between rodents and shrews. Comparing patterns and processes of community structure across taxa would help find general trends of community organisation.
Infraspecific systematics of the yellow mongoose Cynictis penicillata.
(1990) Taylor, Peter John.; Meester, Jurgens Anthonie Jansen.; Rautenbach, Ignatius Lourens.
Geographic variation was analysed in morphological (colour, morphometric) and genetic (electrophoretic, chromosomal) characters in the yellow mongoose cynictis penicillata, a diurnal, colonial, burrow-dwelling viverrid, endemic to and widespread throughout Southern Africa. The causal bases of observed geographic patterns were investigated, and a taxonomic revision of the species was undertaken. Three physical properties of pelage colour (hue, value and chroma) were measured independently using Munsell colour charts and a tristimulus colorimeter. Hue and chroma varied from yellowish (hue) and bleached (chroma) in the north to a brighter, (chroma) tawny-orange (hue) in the south. A zone of rapid colour change separated northern and southern groups. Specimens from the drier western areas were paler (in value) than specimens from more easterly localities. Colour patterns were interpreted in terms in the principle of metachromism. Environmental correlates of colour were analysed. Non-geographic (age, sex, individual) and geographic variation was analysed in 14 cranial and two external characters, using multivariate and univariate techniques. The species does not show secondary sexual dimorphism. Multivariate analyses resulted in the description of four parapatric subspecies, three of which were distinguished on the basis of skull size (which accounted for 93% of geographic variation). Subspecies were separated by continuous zones of craniometric differentiation (transition zones). Craniometric overlap (intergradation) occurred across transition zones. The geographic pattern of craniometric variation in C. penicillata could be explained by either an allopatric or a parapatric mode of speciation. A cladistic analysis of coded cranial characters was used to infer the historical pattern of range expansion in the species. The population genetical structure, based on electrophoretic analysis of 28 loci in eight populations of yellow mongooses, was characterised by the absence of genetic divergence between morphometrically-defined subspecies, a mean expected heterozygosity of 3.4%, low genetic distances between populations (0.000--0.105 for Nei's genetic distance), and a surprisingly high fixation index (FST) of 0.585. The basic karyotype of the yellow mongoose was invariant geographically (2n = 36, NF = 72), although a single, supernumerary microchromosome was detected in four out of the five populations sampled. G- and C-banded karyotypes are presented. Evolutionary relationships among eight Southern African viverrid species, including the yellow mongoose, were inferred from phenetic and cladistic analyses of allelic variation at 18 protein loci. These data suggested the separate evolution of social and solitary lineages of mongooses.
Population genetics of the striped-mouse, Rhabdomys Pumilio (Sparrman, 1784)
(1999) Mahida, Harendra.; Campbell, Glen Kerry.; Taylor, Peter John.
The striped-mouse, Rhabdomys pumilio, is widely distributed throughout southern Africa within a variety of habitats and rainfall regimes. It is found at sea level in the Eastern and Western Cape regions and at altitudes above 2700 m in the Drakensberg mountains. The attraction of R.pumilio to cultivated land and crops has resulted in extensive damage to plants and cultivated crops. A study of the genetic variation between populations of R.pumilio from different regions of southern Africa was undertaken by protein electrophoresis and randomly amplified polymorphic DNA using the polymerase chain reaction (PCR-RAPD). A cytogenetic study was also undertaken. The mean heterozygosity (H=0.074) for R.pumilio was more than twice that estimated for mammals (H=0.036) while the mean percent polymorphism (P=16.1%) was only slightly higher than the mean percent polymorphism obtained for mammals (P=14.7%). The highest heterozygosities were recorded in the Potchefstroom (H=0 .145) and Zimbabwe (H=0 .118) samples and the lowest mean heterozygosity was recorded in the peninsular Western Cape (H=0. 032). A mean Fst value of 0.459 was obtained, suggesting a high degree of genetic differentiation between the samples of R.pumilio but the negative Fis (-0.01) value emphasized that R.pumilio retained an outbreeding population structure. The similarity coefficient between the samples of R.pumilio using PCR-RAPD's ranged between 0.471 and 0.853 and substantiated the argument for genetic divergence between the samples of R.pumilio. An isolation by distance model for the population genetic structure of R.pumilio was supported by the allozymes (r=0.58, p<0.00l) and PCR-RAPD's (0.75, p<0.00l). Temperature and rainfall also had an influence on the allelic frequency distribution of certain loci of R.pumilio. Rogers (1972) genetic similarity varied between 0.796 and 0.988 while the values for Nei's (1978) unbiased genetic distance varied between 0.000 and 0.189 for the different samples of R.pumilio. Subgrouping of the KwaZulu-Natal samples, the peninsular Western Cape and Eastern Cape samples of R.pumilio was evident with the allozymes. With the PCR-RAPD' s the Zimbabwe sample showed the least similarity to the other samples with a KwaZulu-Natal/Potchefstroom subgroup separating from the less well defined Eastern Cape and Western Cape subgroup. Cytogenetic studies of specimens of R.pumilio from some of the localities in southern Africa revealed a chromosomal number of 2n=48 , while the Potchefstroom and Zimbabwe specimens displayed a chromosomal number of 2n=46. Homology in G-and C-banding was recorded. The allozymes, PCR-RAPD's and chromosomal studies suggested subspecies status for the Zimbabwe population of R.pumilio. The Potchefstroom sample displayed a greater genetic similarity to the remaining South African samples of R.pumilio than the Zimbabwe samples and therefore could not be considered for subspecies status. Although the South African samples of R.pumilio displayed a certain degree of genetic divergence, it was insufficient to warrant subspecies status although evolution in this direction was suggested.
Systematic revision of Southern African species in the genera Eptesicus, Neoromicia, Hypsugo and Pipistrellus (Chiroptera: Vespertilionidae).
(2005) Kearney, Teresa Catherine.; Contrafatto, Giancarlo.; Taylor, Peter John.
Abstract available in PDF file.