Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Zygophyllum orbiculatum Welwitsch ex Oliv. from Angola and Zygophyllum stapffii Schinz
from Namibia were described in the late 1800’s. Recent comparisons of these two species
revealed that they were morphologically very similar except that Zygophyllum orbiculatum has
unifoliolate leaves and Zygophyllum stapffii has bifoliolate leaves. The similarity of these two
species was investigated using nuclear ITS (Internal Transcribed Spacer, i.e. ITS1, 5.8SrDNA,
ITS2) region sequence data as phylogenetic markers. Due to almost identical sequences and
phylogenetic grouping, it was concluded that they were conspecific. However, the phylogenetic
relationships of the major groups within the subfamily Zygophylloideae based on ITS sequences,
were unresolved and unsupported, as was found in previous studies using chloroplast gene
marker sequences.
To resolve the phylogenetic relationships of the major groups within the subfamily
Zygophylloideae, a next generation sequencing (NGS) approach was taken. Chloroplasts of taxa
representing the major groups within the subfamily were isolated and chloroplast genome
sequence data were generated using the Ion Torrent™ sequencer. Additional nuclear ITS
cassette data (18SrDNA, ITS1, 5.8SrDNA, ITS2, 26SrDNA) were generated as a by-product and
used to produce a large combined aligned sequence matrix for phylogenetic analysis.
Model-based phylogenetic programs were able to retrieve strongly supported and resolved
phylogenetic relationships of the major groups within Zygophylloideae. Two basal groupings
were retrieved in the subfamily. The first grouping consisted of the genera Tetraena, Fagonia
and Melocarpum. The second grouping consisted of the monotypic genus Augea and
Zygophyllum orbiculatum/stapffii which were embedded within the genus Roepera. Using a gene
duplication approach, the chloroplast marker data of genus Zygophyllum sensu stricto placed this
genus basal to the Augea, Zygophyllum orbiculatum/stapffii, Roepera clade whilst the nuclear
marker data of Zygophyllum sensu stricto, was found in a basal position to the entire subfamily. From this it is concluded that Zygophyllum sensu stricto shows evidence of incomplete lineage
sorting. A revised taxonomy for the entire subfamily Zygophylloideae is proposed. / AFRIKAANSE OPSOMMING: Zygophyllum orbiculatum Welwitsch ex Oliv. uit Angola en Zygophyllum stapffii Schinz van
Namibië is in die laat 1800's beskryf. Onlangse vergelykings van hierdie twee spesies het getoon
dat hulle morfologies baie eners is, behalwe dat Zygophyllum orbiculatum unifoliolate blare
besit en dat Zygophyllum stapffii bifoliolate blare besit. Hierdie ooreenkoms is ondersoek, met
behulp van die nukleêre “ITS” (Internal Transcribed Spacer d.w.s. ITS1, 5.8SrDNA, ITS2)
DNS-strook volgordedata as filogenetiese merkers. As gevolg van feitlik identiese
geenopeenvolgings is bevind dat die twee spesies konspesifiek is. Die filogenetiese
verwantskappe van die groot binnegroepe van die subfamilie Zygophylloideae, gebaseer op ITS
geenopeenvolgings, was egter onopgelos en nie ondersteun nie, net soos in vorige studies waarin
chloroplast geenmerkervolgordes gebruik was.
Om die filogenetiese verwantskappe van die groot binnegroepe van die subfamilie
Zygophylloideae op te los, was ‘n betreklik nuwe DNS volgordebepalingstegniek, naamlik
“Next Generation Sequencing” (NGS), gebruik. Chloroplaste van taksa, wat die groot groepe
binne-in die subfamilie verteenwoordig, is geïsoleer en chloroplast genoomdata is gegenereer
met behulp van die Ion Torrent ™ (NGS) DNS-volgordebepaler. Bykomend was die nukleêre
“ITS”-kasset volgordedata (18SrDNS, ITS1, 5.8SrDNS, ITS2, 26SrDNS) ook as 'n by-produk
gegenereer en ook gebruik om 'n groot gesamentlike DNS oplyningmatriks vir filogenetiese
doeleindes.
Model-gebaseerde filogenetiese programme was in staat was om sterk ondersteuning en
opgeloste filogenetiese verwantskappe van die groot groepe binne-in Zygophylloideae te
ontravel. Die subfamilier toon twee basale groeperinge. Die eerste groepering bestaan uit die
genera Tetraena, Fagonia en Melocarpum. Die tweede groepering bestaan uit die monotipiese
genus Augea en Zygophyllum orbiculatum/stapffii, wat ingebed is binne-in die genus Roepera.
Deur ‘n geendupliseringsbenadering te gebruik op die DNS geenopeenvolgings van die
verteenwoordigende takson van Zygophyllum sensu stricto, is bevind dat die chloroplast DNS
volgordes hierdie groep basaal aan ‘n Roepera/Augea/Zygophyllum orbiculatum/stapffii klade
plaas, terwyl die nukleêre DNS volgordes hierdie groep basaal aan die hele subfamilie
Zygophylloideae plaas. Hieruit is die gevolgtrekking gemaak dat Zygophyllum sensu scricto
bewyse van onvolledige afstammelingsortering toon. ‘n Gewysigde taksonomie vir die hele
subfamilie Zygophylloideae word voorgestel.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:sun/oai:scholar.sun.ac.za:10019.1/96877 |
| Date | 04 1900 |
| Creators | Van Der Merwe, Pieter de Wet |
| Contributors | Bellstedt, Dirk Uwe, Pirie, Michael David, Stellenbosch University. Faculty of Science. Dept. of Biochemistry. |
| Publisher | Stellenbosch : Stellenbosch University |
| Source Sets | South African National ETD Portal |
| Language | en_ZA, en_ZA |
| Detected Language | English |
| Type | Thesis |
| Format | x, 193 pages : colour illustrations |
| Rights | Stellenbosch University |
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