Thesis (PhD (Genetics))--University of Stellenbosch, 2009. / ENGLISH ABSTRACT: South African abalone, Haliotis midae, has been the subject of major concern
regarding its survival and conservation over the last decade or more. Being the only
one of five endemic species with commercial value, there is considerable interest and
urgency in genetic management and improvement of this species. Limited genetic
information and the increasing conservation concern of this species are considered
the key motivations for generating information on the micro- and macro-evolutionary
processes of H. midae, the overall objective of this study.
This study reported the first microsatellite and Single Nucleotide Polymorphism
(SNP) markers developed specifically for Haliotis midae. Both these marker types
were applied to elucidate the degree of gene flow in nine natural abalone populations
whilst testing for two contrasting hypotheses; panmixia versus restricted gene flow.
Data was analysed using a series of methodological approaches ranging from
traditional summary statistics to more advanced MCMC based Bayesian clustering
methods with and without including spatial information. Using only microsatellite data,
the historical demography of the species was also examined in terms of effective
population size and population size fluctuations. Finally, the evolutionary positioning
and origin of Haliotis midae with regards to other Haliotis species was investigated
based on mitochondrial and nuclear sequence data.
Both microsatellite and SNP data gave evidence for subtle differentiation between
West and East coast populations that correlates with a hydrogeographic barrier in the
vicinity of Cape Agulhas. Population substructure was supported by AMOVA, FCA
and Bayesian clustering analysis. Clustering utilizing spatial information further
indicated clinal variation on both sides of the proposed barrier with a region in the
middle coinciding with a secondary contact zone, indicating possible historical isolation during glacial periods. Overall, the similar degree of substructure observed
with both microsatellites and SNPs supported the existence of contemporary and/or
historical factors with genome-wide effect on gene flow. The population expansion
measured with the microsatellites was inconsistent with the known recent decline but
taking the species’ life cycle and large effective population size into account, a
shrinkage in population size will probably only be apparent in a few generations time.
On a macro-evolutionary scale, this study presents the first classification of South
African abalone as a monophyletic group within the Haliotidae family. The topology
based on the combined mitochondrial and nuclear dataset is highly suggestive of a
relatively recent radiation of the SA species from the Indo-Pacific basin.
The study concludes by describing the most likely factors that could have affected
overall population structure and makes suggestions on how the given genetic
information should be incorporated into strategies aimed towards the effective
management and conservation of Haliotis midae. / AFRIKAANSE OPSOMMING: Die Suid-Afrikaanse perlemoen, Haliotis midae, is oor die laaste dekade of meer
die onderwerp van groot bekommernis betreffende die spesie se oorlewing en
bewaring. Aangesien dit die enigste van vyf endemiese SA spesies is met
kommersiёle waarde, is daar besonderse belang en erns in die genetiese beheer en
verbetering van die spesie. Beperkte genetiese inligting en ‘n toenemende behoefte
om die spesie te bewaar is die hoof motivering agter die generering van informasie
rakende mikro- en makro-evolusionêre prosesse in Haliotis midae en is die oorhoofse
doel van hierdie studie.
Hierdie studie beskryf die eerste mikrosatelliete en enkel basispaar polimorfismes
wat ontwikkel is spesifiek vir Haliotis midae. Beide tipe merkers is aangewend om die
mate van gene vloei in nege wilde perlemoen populasies te ondersoek terwyl twee
hipoteses ondersoek is; panmiksie versus beperkte gene vloei. Data is geanaliseer
deur gebruik te maak van ‘n reeks metodieke benaderings wat wissel van tradisionele
opsommings statistieke tot meer gevorderde MCMC gebasseerde groeperings
metodes met of sonder die gebruik van geografiese data. Mikrosatelliet data is ook
aangewend om die historiese demografie van die spesie te bepaal in terme van
effektiewe populasie grootte asook veranderinge in populasie groottes. Laastens is
die evolusionêre posisionering en oorsprong van Haliotis midae teenoor ander
Haliotis spesies ondersoek deur gebruik te maak van mitokondriale en nukleêre DNA
volgorde data.
Beide mikrosatelliet en enkel basispaar polimorfisme data lewer bewys van ‘n
subtiele genetiese verskil tussen wes en ooskus populasies wat verband hou met ‘n
hidrografiese skeiding in die omgewing van Kaap Agulhas. Populasie struktuur is
ondersteun deur die analise van molekulêre variansie (AMOVA), faktoriale komponente analise asook Bayesiese groeperings analise. Groeperings analise wat
geografiese informasie insluit dui klinale genetiese variasie aan beide kante van die
skeiding aan met ‘n area in die middel wat ooreenstem met ‘n sekondêre kontak
gebied. In totaal, ondersteun die soortgelyke mate van struktuur verkry met beide die
mikrosatelliete en enkel basispaar polimorfismes die bestaan van hedendaagse en/of
historiese faktore met genoom wye invloed op gene vloei. Die toename in populasie
grootte vasgestel deur die mikrosatelliet data stem nie ooreen met die onlangse
afname waargeneem in die spesie nie, maar met inagneming van Haliotis midae se
lewenssiklus en groot effektiewe populasie grootte, sal die afname in populasie
grootte moontlik eers oor ‘n paar generasies na vore kom.
Op ‘n makro-evolusionêre skaal lewer hierdie studie die eerste klassifikasie van
Suid-Afrikaanse perlemoen as ‘n monofiletiese groep binne die Haliotidae familie. Die
topologie gebaseer op ‘n gesamentlike mitkondriale en nukleêre datastel is hoogs
aanduidend van ‘n relatiewe onlangse verspreiding van die Suid-Afrikaanse spesies
uit die Stille-Indiese Oseaan.
Die studie sluit af deur die mees algemene faktore te bespreek wat populasie
struktuur kon beïnvloed het en maak voorstelle op watter wyse hierdie genetiese
inligting aangewend kan word vir die effekiewe beheer en bewaring van Haliotis
midae.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:sun/oai:scholar.sun.ac.za:10019.1/3974 |
| Date | 03 1900 |
| Creators | Van der Merwe, Aletta Elizabeth |
| Contributors | Roodt-Wilding, R., D'Amato, M. E., Volckaert, F., Bester, Aletta Elizabeth, University of Stellenbosch. Faculty of Agrisciences. Dept. of Genetics. |
| Publisher | Stellenbosch : University of Stellenbosch |
| Source Sets | South African National ETD Portal |
| Language | English |
| Detected Language | English |
| Type | Thesis |
| Rights | University of Stellenbosch |
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