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Molecular phylogenetics and phylogeography of sand lizards, Pedioplanis (Sauria: Lacertidae) in southern AfricaMakokha, Jane Sakwa 12 1900 (has links)
Thesis (MSc)--University of Stellenbosch, 2006. / ENGLISH ABSTRACT: The present study aims to determine the phylogenetic relationships among the sand lizards, Pedioplanis. In addition, a single mitochondrial gene is used to investigate the geographic genetic structure of the widey distributed P. burchelli. With 11 species, Pedioplanis is the most speciose genus among the southern African genera of the family Lacertidae. All the species are restricted to the subcontinent with the exception of three (P. namaquensis, P. undata and P. benguellensis), which extend their range northwards into Angola. A total of 2200 nucleotide positions derived from two mitochondrial markers (ND2 and 16S rRNA) and one nuclear gene (RAG-1) are used to determine the phylogenetic relationships among ten of the eleven Pedioplanis species. The first well resolved gene tree for the genus, drawn from 100 individuals, is presented and this is largely congruent with a phylogeny derived from morphology. Contrary to some previous suggestions, Pedioplanis forms a monophyletic assemblage with Heliobolus and Nucras. The genus Pedioplanis is monophyletic with P. burchelli/P. laticeps forming a sister clade to all the remaining congeners. Two distinct geographic lineages can be identified within the widespread P. namaquensis; one occurs in Namibia, while the other occurs in South Africa. The “P. undata” species complex is monophyletic, but one of its constituent species, P. inornata, is paraphyletic. Relationships among the subspecies of P. lineoocellata are much more complex than previously documented. An isolated population previously assigned to P. l. pulchella is paraphyletic and sister to the three named subspecies. The phylogeny identifies two biogeographical groupings that probably diverged during the mid-Miocene. The development of the Benguella Current could have initiated isolation mechanisms associated with changes in habitat that could have generated barriers and played a role in the evolution of this group.
At the lower taxonomic level, the mtDNA phylogeographic structure of the wide spread P. burchelli in South Africa reveal at least six distinct clades that are geographically partitioned. The first one is restricted to the eastern mountains along the Great Escarpment (GE). The next three are found along the Cape Fold Mountains (CFM): the north-west CFM, central CFM and eastern CFM. The fifth one shares samples from central CFM and GE. The last clade is restricted to the eastern central mountains of the GE. These six geographic groupings are genetically divergent from each other and they started separating in the early Pliocene period. Phylogeographic studies on other taxa in the region have found different levels of genetic structuring among or within taxa. The fact that P. burchelli is restricted to high altitude areas could have resulted in limited dispersal and consequently contributed to its geographic structure. However, the exact cause of the pattern obtained is not readily apparent. Habitat fragmentation in the past is probably one of the most influential factors shaping the genetic distribution of the species across South Africa. The inclusion of nuclear markers will shed more light on the evolutionary history of P. burchelli in South Africa. / AFRIKAANSE OPSOMMING: Die huidige studie stel ten doel om ‘n filogenie daar te stel vir die Sand akkedisse, Pedioplanis. ‘n Enkele mitochondriale geen is ook gebruik om die geografiese genetiese struktuur van die wydverspreide P. burchelli vas te stel. Met 11 spesies is Pedioplanis die mees spesieryke genus onder die suidelike Afrika genera wat aan die Lacertidae familie behoort. Al die spesies is beperk tot die subkontinent met die uitsondering van drie (P. namaquensis, P. undata en P. benguellensis), wat ‘n uitgebreide verspreiding het noordwaarts tot in Angola. ‘n Totaal van 2200 nukleotied posisies wat afkomstig is van twee mitochondriale merkers (ND2 en 16S rRNA) en een nukluêre geen (RAG-1) is gebruik om die filogenetiese verwantskappe tussen 10 van die 11 Pedioplanis spesies vas te stel. Die eerste goed geondersteunde geen boom vir die genus, gebasseer op 100 individue, is verkry en dit is meestal ooreenstemmend met ‘n filogenie gebasseer op morfologie. In teenstelling met sekere voorstelle van die verlede vorm Pedioplanis ‘n monofiletiese groep tesame met Heliobolus en Nucras. Die genus Pedioplanis is monofileties met P. burchelli/P. laticeps wat ‘n suster groep vorm van al die oorblywende lede van die genus. Twee herkenbare geografiese lyne kan geidentifiseer word in die wydverspreide P. namaquensis; een kom in Namibia voor, terwyl die ander een in Suid Afrika voorkom. Die “P. undata” spesies kompleks is monofileties, maar een van die spesies wat deel uitmaak van die groep, P. inornata, is parafileties. Verwantskappe tussen die subspesies van P. lineoocellata is meer kompleks as wat aanvanklik aanvaar is. ‘n Geisoleerde bevolkimg wat voorheen toegesê is aan P. l. pulchella is parafileties en verteenwoordig ‘n suster groep van die benaamde subspesies. Die filogenie identifiseer twee biogeografiese groeperings wat moontlik gedivergeer het gedurende die middel-Miocene. Die ontwikkeling van die Benguella stroom het dalk versperrings geinisiëer as gevolg van die gesamentlike veranderinge in habitat wat dalk ook ‘n rol gespeel het in die evolusie van die groep.
Op die laer taksonomiese vlak het die mtDNA filogeografiese struktuur van die wydverspreide P. burchelli in Suid Afrika ten minste ses groepe aangetoon wat geografies van mekaar geskei is. Die eerste een is beperk tot die oostelike berge wat aan die Groot Eskarpement (GE) behoort. Die volgende drie word gevind in die Kaapse Vouberge (KVB): die noord-westelike KVB, sentrale KVB en oostelike KVB. Die vyfde een deel eksemplare van beide die GE en die KVB. Die laaste groep is beperk tot die oostelike en sentrale berge van die GE. Hierdie ses geografiese groepe is geneties geskei van mekaar en hulle het begin om apart te ontwikkel gedurende die vroë Pliocene periode. Ander filogeografiese studies in die area het verskillende vlakke van genetiese struktuur vertoon tussen en binne taksa. Die feit dat P. burchelli beperk is tot hoogliggende dele kon moontlik bygedrae het tot die geografiese struktuur. Die presiese oorsaak van die patroon wat verkry is, is nie ooglopend nie. Habitat fragmentasie in die verlede is moontlik een van die mees invloedrykste faktore wat die genetiese verspreiding van die spesie in Suid Afrika beinvloed het. Die insluiting van nukluêre merkers sal meer lig warp op die evolusionêre geskiedenis van P. burchelli in Suid Afrika.
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Biodiversity of saproxylic Coleoptera in 'old-growth' and managed forests in southeastern OntarioZeran, Rebecca January 2004 (has links)
The species richness, abundance and composition of saproxylic Coleoptera was compared between 'old-growth' and mature-managed hemlock-hardwood forests in southeastern Ontario, Canada. Beetles were sampled weekly from 29 April until 3 October 2003 using large-area flight-intercept traps (FITs) and trunk-window traps (TTs). Analyses were conducted using the Fisher's alpha and Simpson's diversity indices, rarefaction, indicator species analysis and cluster analysis. A total of 11,888 fungivorous Coleoptera was collected from 11 families and 73 species (excluding Nitidulidae). Nitidulidae were analysed separately with traps yielding 2,129 sap beetles comprising 30 species. The species richness and abundance of fungivorous Coleoptera did not differ significantly between the two forest types. Conversely, the species abundance of nitidulid beetles was higher in managed forests and the species richness higher in 'old-growth' forests. Several species were strongly associated with either managed or 'old-growth' forest types. Certain species such as Anisotoma inops (Leiodidae) and Glischrochilus sanguinolentus (Nitidulidae) were much more frequently caught in TTs than in FITs.
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Biodiversity of saproxylic Coleoptera in 'old-growth' and managed forests in southeastern OntarioZeran, Rebecca January 2004 (has links)
No description available.
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The evolutionary history and taxonomy of the Kobus leche species complex of South-Central Africa in the context of palaeo-drainage dynamicsCotterill, Fenton P. D. 12 1900 (has links)
Dissertation (PhD)--University of Stellenbosch, 2006. / ENGLISH ABSTRACT: This multi-disciplinary study compiled taxonomic and biogeographical data to elucidate the
extant diversity of lechwe antelopes (Kobus leche complex), and reconstruct their evolutionary
history. Their diversification has been confined to wetlands across the south-central Africa
plateaux. Lechwes are specialist grazers in water meadow floodplains; these stenotopic habitat
requirements are invoked to explain why their evolution is atypical of terrestrial large mammals.
Combined analyses of morphological (171 adult males), genetic (208 genotyped individuals)
and palaeo-environmental datasets, revealed a recent (Middle Pleistocene) pulse of speciation in
the K. leche complex. Multivariate morphometric analyses revealed the presence of five distinct
groups that could be tied to the geography of the region. Furthermore, the genetic analyses
supported the existence of at least four of these lineages, which show significant population
separation at the level of the mtDNA control region. Most of the differences among populations
were confined to frequency differences among populations and Bayesian analyses strongly
suggest that the pattern obtained is the result of the retention of ancestral haplotypes with
limited female geneflow among the extant populations. Evolution of the five lineages identified
by the morphological and population genetic analyses were further investigated by making use
of additional genetic data (mtDNA cyt b, SPTNB, SRY, Protamine 1, and b-Fibrinogen) and a
subset of the samples. Topologies were largely unresolved due to the recent common ancestry
of the lineages. Following the Evolutionary Species Concept, which was motivated by a
philosophical review, five allopatric species could be recognized (anselli, kafuensis, leche,
robertsi and smithemani). A model of drainage evolution compiled disparate facets of biological
and geological evidence to detail interlinked histories of wetlands and their biota across the
south-central Africa plateaux. This wetland archipelago is recognized as a distinct
biogeographical unit in its own right - the Katanga-Chambeshi region. Evolutionary
diversification of lechwes represents a dominant biogeographical signal reflecting how the
aquatic biota have evolved in tandem with palaeo-drainage dynamics across this evolutionary
theatre. Delimitation of key events in lechwe and drainage evolution was refined by
archaeological dating of the Victoria Falls Formation, to decipher when the Zambezi river
eroded the Batoka gorge. Demographic expansion in K. leche s.s (early Middle Pleistocene)
corresponds to dessication of Palaeo-Lake Makakgadikgadi while more recent phylogeographic
signals correspond to the tenure of Palaeo-Lake Bulozi. These speciation events in the Middle
Pleistocene preceded peripatric speciation of K. kafuensis that accompanied the morphosis of
the Kafue Flats (from palaeo-lake to floodplain), when the Kafue River attained its modern
topology. The present study highlights that Lechwes represent a biota of evolutionary vibrant
clades, rich in endemic species. As ecologically-dominant species in wetlands, lechwes deserve priority conservation attention, which is challenged to perpetuate evolutionary and ecological
processes across an archipelago straddling five countries. / AFRIKAANSE OPSOMMING: Die multidisiplinêre studie bring saam taksonomiese en biogeografiese data om die evolusionêre
geskiedenis en huidige diversitiet van basterwaterbokke (Kobus leche kompleks) te verklaar.
Hulle diversifikasie is beperk to vleilande regoor die suid-sentraal Afrika plato.
Basterwaterbokke is gespesialiseerde grasvreters in grasvloedvlaktes; hierdie stenotipiese
habitatsvereiste word voorgehou om te verduidelik hoekom die evolusie van hierdie diere atipies
is vir terrestriële groot soogdiere. Gekombineerde analise van morfologie (171 volwasse
manlike diere), geneties (208 genotipes) en plaeo-omgewings datstelle toon aan dat daar ‘n
onlangse (middel Pleistoseen) pols van spesiasie plaasgevind het in die K. lechwe kompleks.
Multivariate morfometriese analyses het aangetoon dat vyf verskillende groepe diere bestaan
wat ook sin gemaak het op grond van geografiese ligging. Verdermeer, die genetiese analise het
die bestaan van ten minste vier van hierdie lyne geondersteun wat betekenisvolle bevolkings
isolasie vertoon het op die vlak van die mtDNA kontrole gebied. Meeste van die verskille tussen
bevolkings was beperk to frekwensieverkille tussen die bevolkings en Bayesian analise het sterk
aanduidings getoon dat die patroon wat gekry is die gevolg was van die behoud van
voorvaderlike haplotiepes met beperkte vroulike geenvloei tussen die huidige bevolkings.
Evolusie van die vyf lyne wat deur die morfologie en bevolkingsgenetika studies geidentifiseer
is was verder ondersoek deur gebruik te maak van addisionele genetiese data (mtDNA cytb,
SPTBN, SRY, Protamien 1, en b-Fibrinogeen) en ‘n subset van die monsters. Topologieë was
hoofsaaklik onopgelos as gevolg van die kort tyd tot die onlangse gemeenskaplike voorouer van
lyne. Deur die Evolusionêre Spesies Konsep aan te hang, wat gemotiveer is deur ‘n filosofiese
oorsig, is vyf allopatriese spesies herken (anselli, kafuensis, leche, robertsi and smithemani). ‘n
Model wat dreinerings evolusie voorstel het verskeie fasette van biologiese en geologiese
bewyse saamgvat om die verbindingsgeskiedenis van vleilande en hulle biota oor die suidsentraal
Afrika plato te beskryf. Die vleiland argipelago word herken as ‘n onafhanklike
biogeografiese eenheid in sy eie reg – die Katanga-Chambeshi streek. Evolusionêre
diversifikasie van basterwaterbokke verteenwoordig ‘n dominante biogeografiese sein wat
voortsel hoe die akwatiese biota ontwikkel het in tandem met die palaeo-dreinerings dinamika
in hierdie evolusionêre konsert. Die afbakening van sleutelgebeure in basterwaterbok en
dreinerigsevolusie is beter toegelig deur argeologiese datering wat gebasseer was op die
vorming van die Victoria Valle om te bepaal waneer die Zambezi rivier die Batoka skeurgroef gevorm het. Demografiese uitbreiding binne K. leche s.s (gedurende die vroë Middel
Pleistoseen) stem ooreen met die uitdroging van Palaeo-Meer Makakgadikgadi terwyl meer
onlangse filogeografiese syne ooreenstem met die ontstaan van Palaeo-Meer Bulozi. Hierdie
spesiasie gebeure in die Middel Pleistoseen het die peripatriese spesiasie van K. kafuensis
voorafgegaan wat die morfose van die Kafue Vlaktes vergesel het (van palaeo-meer na
vloedvlakte), toe die Kafue Rivier sy huidige vorm aangeneem het. Die huidige studie het
uitgelig dat basterwaterbokke verteenwoordig ‘n biota van evolusionêre energieke eenhede, ryk
aan endemiese spesies. As ‘n ekologiese dominante spesie in vleilande, moet basterwaterbokke
as ‘n prioriteit gesien word in bewaring, waar dit dan die geleentheid sal hê om voort te bou op
die evolusionêre en ekologiese prossese van die archipelago wat oor vyf lande strek.
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The development of a geographic information systems based atlas of southern African freshwater fish, and its application to biogeographic analysisScott, Lucy Elizabeth Powell January 2000 (has links)
A Geographic Information Systems (GIS) atlas of southern African freshwater fish was developed for the SADC countries from natural history collection specimens, hydrological, topographical and climatological data. The primary purpose of the development of the atlas of freshwater fish was the construction of a practical framework to transform vast amounts of existing biological data for use in research and management of aquatic resources. The database of freshwater fish collection specimens that was incorporated into the atlas, was developed in association with ALCOM (Aquatic Resources Management for Local Community Development Programme). The development of advanced computing and GIS technology has increased the scope of biological atlas projects by facilitating the integration of large amounts of spatial data to produce derived databases for specific applications. The atlas of freshwater fish was constructed using TNTmips GIS software as the most practical system available for managing and analysing biological data with a spatial component. The atlas contains 35 180 comprehensive distribution records of 735 species of fish. It has many applications as an inventory of ichthyofaunal spatial biodiversity, including those of conservation planning, environmental assessment and biogeographic research. Biogeographic studies have traditionally been subjective due to the logistical problems of working with large amounts of distribution data, although some small-scale quantitative research has been carried out in the past. The content of the atlas of freshwater fish is tested with respect to these previous studies, on known patterns of freshwater fish distributions, and the analytical capability of the atlas is tested and demonstrated with some new preliminary approaches to the analysis of freshwater fish distributions in southern Africa.
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Population genetics and phylogeography of the pygmy nuthatch in Southern CaliforniaBenson, Thomas Alan 01 January 2006 (has links)
Uses mitochondrial DNA sequence data to examine the degree of genetic differentiation among sky island populations of two subspecies of pygmy nuthatch (Sitta pygmaea melanotis and Sitta pygmaea leuconucha) occurring in Southern California. Assesses the hypothesis that sky islands are genetically isolated and that migration (gene flow) is restricted among them. Eleven sampling locations throughout Southern California were selected based on representation of subspecies, availability of specimens, and feasibility of collection. Results indicate that pygmy nuthatch populations fragmented in the disjunct mountain ranges of Southern California exhibit low but significant levels of genetic differentiation.
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