Theses and Dissertations (Zoology)
http://hdl.handle.net/10386/74
2024-03-28T08:50:55ZMolecular phylogeny of South African gobiid fishes of the genus Caffrogobius Smitt, 1900 and intraspecific genetic variation of Caffrogobius gilchristi boulenger,1900
http://hdl.handle.net/10386/4434
Molecular phylogeny of South African gobiid fishes of the genus Caffrogobius Smitt, 1900 and intraspecific genetic variation of Caffrogobius gilchristi boulenger,1900
Mavimbela, Caswell
The molecular phylogeny of the southern African endemic genus Caffrogobius and
the variability in intraspecific DNA sequences of the prison goby, Caffrogobius gilchristi, from the South African coastline, were investigated. The genus Caffrogobius (Gobiidae) consists of seven nominal western Indian Ocean species, six of which occur in the southern African region (from Mozambique to Namibia) with the seventh species, C. dubius, from Seychelles and do not form part of this study. These are small, benthic fishes that generally inhabit shallow-water habitats in estuaries while their larvae are marine. There is a high degree of morphological similarity among the species of this genus, hampering species identification using traditional dichotomous morphological keys. In a study of the phylogeny of the genus,the cytochrome b (cyt-b) and cytochrome oxidase subunit I (COI) loci were employed to resolve taxonomic problems.Six Caffrogobius species (C. gilchristi, C. nudiceps, C. saldanha, C. agulhensis, C. caffer and C. natalensis) were used for molecular phylogenetic analyses. Two partial mitochondrial DNA genes, cyt-b (281 bp) and COI (535bp) were amplified for 28 specimens using Polymerase Chain Reaction (PCR). Three phylogenetic tree reconstruction methods were employed namely, maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) using Bathygobius sp. 1 and Bathygobius sp. 2 as outgroups. According to the estimated topologies from the family Gobiidae, the genus Caffrogobius is monophyletic and consists of three clades, the C. agulhensis and C. saldanha clade with C. natalensis as sister group, the sister groups C. gilchristi and C. caffer and the basal clade C. nudiceps.
Phylogeographic patterns of the prison goby, C. gilchristi using sequences from cyt-b
(425 bp from 63 specimens) and COI (524 bp from 109 specimens) may reveal patterns related to intraspecific population genetic structure. Demographic history was investigated with neutrality tests (Tajima‘s D, Fu‘s Fs and Ramos-Onsins & Rozas R2), mismatch distributions and haplotype networks which all indicated population expansion. Spatial groupings of populations were examined using AMOVA. Coalescent analyses were used to estimate gene flow between sampling locations and indicated a high level of gene flow among localities. AMOVA showed no consistent iv patterns of differences in the genetic structure within populations and thus AMOVA and parsimony network analyses revealed panmictic populations (i.e. no significant population structure detected), suggesting a recent divergence. Furthermore, parsimony networks support recent population expansion of only one population amongst all the localities analysed. Several possible life-history adaptations could be responsible for maintaining gene flow across phylogeographical distribution range. These may include a long pelagic larval stage and larval behavior, as well as oceanographic features such as the flow of sea currents. The presence of a marine pelagic larval stage in gobies may account for this lack of population structuring. It is also reasonable to assume that estuaries farther away from a particular spawning site
would receive fewer recruits from that site, than would be the case for estuaries situated at a closer proximity to the breeding event. This means that conservation should not be focused on individual estuaries, but on a wider geographical scale. However this must still be tested further
Thesis (M.Sc.( Zoology)) -- University of Limpopo, 2011
2011-01-01T00:00:00ZA taxonomic study of selected representatives of siphonostomatoida (copepoda) from ostechthyes in coastal waters off Southern Africa
http://hdl.handle.net/10386/4294
A taxonomic study of selected representatives of siphonostomatoida (copepoda) from ostechthyes in coastal waters off Southern Africa
Sebone, Makwena Melita
Currently Copepoda consists of 14 600 species of which 2 275 species are members
of the Siphonostomatoida. Siphonostomatoida consists of 40 families, with 17 families
symbiotic on fish. Sphyriidae has 44 accepted species in eight reported genera, of
which four genera infect teleosts and the remaining four infect elasmobranchs. Adult
females undergo transformation through loss of locomotory appendages to suit their
mesoparasitic lifestyle and develop outgrowths on the cephalothorax or neck for
attachment to the host. To date, only 176 marine siphonostomatoid species have been
reported from South African waters, with only nine sphyriid species.
Sphyriids previously collected from marine bony fish off the east, south and west
coasts of southern Africa and preserved in 70% ethanol were studied. Specimens
were examined with stereo- and compound microscopes and identified using
published literature. Selected specimens were stained in lactic acid with added lignin
pink, appendages were dissected and illustrated with the aid of a drawing tube.
Selected specimens were also studied through scanning electron microscopy.
The examined specimens were identified as species of Sphyrion and Lophoura. Re descriptions were done for all valid Sphyrion species females (S. laevigatum, S. lumpi
and S. quadricornis) and new descriptions for the males of S. laevigatum and S.
quadricornis. Post-metamorphosis females of Sphyrion species can be differentiated
by the shape of cephalothorax, length of the neck in relation to the length of the trunk
and the length of posterior processes in relation to the trunk length, while males are
mostly very similar. New information is provided regarding the appendages of S.
laevigatum and S. quadricornis. The appendages of the three species bear close
resemblance to one another. Additionally, an identification key for the post metamorphosis females of Sphyrion species is provided.
Re-descriptions were done for five female Lophoura species (L. caparti, L. cornuta, L.
cf edwardsi, L. tetraloba and Lophoura sp.) and a new description of the male of L.
tetraloba. Differences between young and post-metamorphosis females of L. cf
edwardsi and L. tetraloba were observed in the width of the holdfast organ processes
and the length of porous peduncle and stalks of the posterior processes which appear
to grow with age. The difference between the young and adult male of L. tetraloba lies
in the lengths of the cephalothorax in relation to the trunk length and segmentation
visible on the trunk of the young male but not adult male. The post-metamorphosis
females of Lophoura species can be differentiated by the shape and number of
processes on the holdfast organ, in combination with the cephalothorax length in
relation to the neck length, neck length in relation to the trunk length, shape of the
trunk, and the length and structure of the posterior processes. An identification key
was drawn up for all species of the Lophoura post-metamorphosis females.
An attempt was made to provide the COI barcodes for all the species of Sphyrion and
five species of Lophoura. These would have confirmed the species identification of
morphologically variable species e.g. S. laevigatum and S. lumpi and also provide an
estimation of the interspecific divergence amongst the different species. Additionally,
it would have assisted in distinguishing between L. tetraloba and L. cf edwardsi and
provided an estimation of the amount of sequence divergence between the two
genera. Unfortunately sequencing of apparently successfully amplified products was
unsuccessful probably due to low DNA quality which possibly degraded due to
collection methods used for the fish hosts and parasites and prolonged preservation
of specimens.
This study provides new host records i.e. Coelorinchus simorhynchus, Coelorinchus
trunovi and Saurida undosquamis for Sphyrion quadricornis off South Africa which is
also a new geographical record. Allocyttus verrucosus, Coelorinchus simorhynchus,
Coelorinchus trunovi, Mesovagus antipodum and Ventrifossa nasuta are also new
host records for S. lumpi. Additionally, Epigonus denticulatus and Bassanago
albescens are new host records for Lophoura caparti and L. cornuta respectively off
South Africa, which is a new geographical record for both species. Furthermore,
Coelorinchus fasciatus and Lucigadus ori are new host records for Lophoura tetraloba
and L. cf edwardsi off South Africa, which is also a new geographic record for both
species. Thus, the results of the study improve the current knowledge of the marine
siphonostomatoid biodiversity off South Africa as well as their distribution and infected
hosts.
Thesis (M.Sc. (Zoology)) -- University of Limpopo , 2023
2023-01-01T00:00:00ZAssessing the effects of water and sediment quality on aquatic macro-invertebrate diversity in the Steelpoort River, Olifants River System, Limpopo Province
http://hdl.handle.net/10386/4268
Assessing the effects of water and sediment quality on aquatic macro-invertebrate diversity in the Steelpoort River, Olifants River System, Limpopo Province
Matlou, Katlego Shirley
In this study data was collected to establish if the water and sediment quality of the
Steelpoort River has any effects on macro-invertebrate species. The Steelpoort River
is a tributary of the Olifants River system but not much data about the water quality is
available. The Steelpoort River is a perennial river (Ashton et al. 2001) situated west
of Burgersfort and from there it flows in a north- easterly direction and converges
with the Olifants River in the Drakensberg near Kromellenboog. High silt levels in the
river, increases the risk of flooding and leads to the smothering of in-stream habitats
resulting in loss of some invertebrate and fish species.
Sampling of the water, sediment and macroinvertebrates was conducted quarterly at
the Steelpoort River at five sites. One site was above the impoundment (De Hoop
Dam) and the rest were below the impoundment. A handheld YSI 556™ Multi Probe
System (MPS instrument and a Mettler Toledo SevenGo™ conductivity meter were
used to measure the physico-chemical characteristics at the sites. The
macroinvertebrates were sampled using the SASS 5 bio-assessment protocol
(Goodyear & McNeill 1999, Dickens & Graham 2002). Macro-invertebrate samples
were collected using a 400 mm x 400 mm SASS net with a 250 μm mesh size. The
substrate was disturbed for a period of two minutes to free macro-invertebrates from
the substrate. The SASS score for each site was evaluated in the field for three of
the five samples. The macro-invertebrate samples were preserved in 70% ethanol
and sorted to family level in the University of Limpopo’s Biodiversity laboratory.
For the majority of the physico-chemical parameters the most elevated were
detected downstream and lowest concentrations were detected upstream. Analysis
of variance (ANOVA) indicated that there were no significant differences for electrical
conductivity, salinity, and TDS, between the sites (p>0.05). There were however
significant differences in the temperature, dissolved oxygen, turbidity, and pH
concentrations (p<0.05). The majority of the metals and metalloids in the water (Fe,
Mn, V, Co, Zn, Ba, and Cu) were highest at Tiershoek (Site1) and lowest at
Steelpoort (Site 4) and Burgersfort Bridge (Site 5).The mean metal concentrations
collected showed elevated levels for chromium, copper and zinc, which were above
the CCME sediment guidelines.
The most abundant macroinvertebrates were from the family Ephemeroptera which
are pollution sensitive and good indicators of pollution in aquatic ecosystems. When
using the interpretation of the SASS 5 results from Chutter 1995, the mean Average
Score Per Taxa (ASPT) scores show that the water quality for Tiershoek (Site 1) and
Polopark (Site 3) is natural but the habitat diversity has been reduced. For De Hoop
(Site 2) and Steelpoort (Site 4), the mean ASPT score shows that there is some
deterioration in the water quality. Finally, for Burgersfort Bridge (Site 5), the mean
ASPT score indicates that there is major deterioration in the water quality.
Primer statistical analysis indicated that the average dissimilarity between sites
showed that the highest dissimilarity was between Tiershoek (Site 1) and Burgersfort
Bridge (Site 5) which was conclusive with the results from the macro-invertebrate
count and SASS, indicating that there is diverse difference from upstream to
downstream.
CCA indicated positive correlations between nutrients detected at Steelpoort with
Athericidae, Tabanidae, Gomphidae, Baetidae, Elmidae, Planaria, Psephenidae, and
Libellulidae which was indicated that water chemistry characteristics exert influence
on macroinvertebrates. The results showed that there is degradation of the water
quality in river from upstream to downstream with more pollution tolerant species
being abundant at Steelpoort (Site 4) and Burgersfort Bridge (Site 5). The most
favourable season was autumn and the least summer/spring and this may be
attributed to the life cycle of the macro-invertebrate communities
Thesis (M.Sc. (Zoology)) -- University of Limpopo, 2017
2017-01-01T00:00:00ZSystematics of the Southern African larks (alaudidae) : syringeal and vocalisation perspective
http://hdl.handle.net/10386/3735
Systematics of the Southern African larks (alaudidae) : syringeal and vocalisation perspective
Nthangeni, Aluwani
The larks (Passeriformes, Passeri, Alaudidae) are small to medium-sized (10-23 cm)
birds that are primarily terrestrial and cryptically plumaged hence they are difficult to
encounter and recognise. The current taxonomic circumscription places these birds in
a group that is comprised of 21 genera and 98 species, with all the genera occurring
in Africa, 13 in Eurasia, and a single genus occurs in Australia and the Americas. Up
until Alström et al. (2013), morphologically, the lark family was distinguished by having
two unique and primitive features: i) the tarsus morphology (latiplantar and scutellate)
consisting of the flat posterior surface covered with prominent scales, instead of being
narrow and smooth as in other families, and ii) the syrinx (voice-generating organ).
Despite that the structure of the syrinx of larks has been studied, literature reveals
confusion pertaining to either the presence or absence of the pessulus, its level of
development and size. To date, the work in Alström et al. (2013) remains the most
comprehensive multi-locus phylogeny of the larks in which three strongly supported
major clades (clade A – hereafter the Alaudid, clade B – the Mirafrid, clade C – the
Ammomanid) emerged though with some uncertainty in some parts of the tree. In this
study, the aim was to investigate the utility of syringeal and vocal characters in
classifying the species of larks, finding out how syringeal and vocal characters evolved
and identifying characters that define clades. The gross morphology and histology of
the syringes and song strophes of larks and their putative outgroups were studied.
Gross morphologically and histologically, the larks were found to possess a
typical syrinx classified as a ‘syrinx tracheo-bronchialis’ and pessulus was observed
in larks and the outgroups studied. There were differences observed in the syringeal
gross morphological structure across all the three major clades (A, B and C). This is
with regard to the presence or absence of the divided or double bronchial rings variably
observed in clade A, B and C. In clade B and C, the ossification is variably restricted
to the centre of bronchial rings forming a serial pattern while in clade A, bronchial rings
are variably almost fully ossified without forming any serial pattern. The prominent
oblique muscle-like structure runs ventrally and it was only observed in clade C in
Chersomanes albofasciata. On the other hand, the syringeal histology revealed
differences in the shape of the pessulus (blunt, pointy or sharp), the pessulus position
relative to bronchial rings 1, 2 and 3 (B1, B2 and B3 respectively), length of the internal tympaniform membranes and connective tissue along the internal tympaniform
membrane. The position of the pessulus was variably found to align with B2, to be
below B2 and to be positioned beyond B2. One-way Anova clearly showed that among
the three clades (A, B and C) identified in Alström et al. (2013), a statistically highly
significant difference (P < 0.01) was found between the song strophes of species in
clade C and A. The species in clade A generally give song strophes defined by high
maximum frequency, high peak frequency and broad bandwidth frequency. The
species in clade B have a similar trend with those in clade A, possibly explaining the
overlap between these clades and the statistically significantly difference between
clade A and C. These findings may be in support of the phylogenetic findings in
Alström et al. (2013) and this study wherein clade A and B shared a sister relationship
while clade C was placed basally. Clade C, on the other hand, comprises song
strophes that are defined by low maximum frequency, lower peak frequency and
narrow bandwidth frequency and this clade differed significantly from clade A. Despite
that not all of the species could be correctly classified to their respective clades based
on the Discriminant Function Analysis’ partition plot, the largest number of correct
classifications were for clade A (70%). In addition, the distinction among the clades
was also observed in either the presence or the absence of wing clappings in the song
strophes, either being detached from or attached to the song strophes. Clade B is the
only one which was marked by the presence of wing clappings particularly, genus
Mirafra, although they are reported in Chersophilus duponti which belongs to clade A
but not included in this study. With regard to the vocal phylogeny, the topology was
highly unresolved, and no relationships could be inferred. The tracing of the evolution
of characters of eight vocal and five syringeal characters revealed that among the 13
characters for which the ancestral state reconstructions were performed, 12 are
polymorphic that is, they underwent multiple state changes ranging from four to 18.
Most character states were found to plesiomorphous and mainly leading to clades of
which their ancestral nodes were defined largely by autapormorphic and
symplesiomorphic states. These do not assist in explaining how the various characters
evolved. In conclusion, the findings have shed some light concerning the general
syringeal morphology and histological structures of larks, revealed that lark songs are
not suitable for reconstructing the phylogeny, shed light on the evolution of the
selected vocal and syringeal characters as well as identifying characters that define
the three major clades of larks (the Alaudid, Mirafrid and the Ammomanid).
Thesis (M. Sc. (Zoology)) -- University of Limpopo, 2021
2021-01-01T00:00:00Z