Thesis (MSc)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Deciphering patterns of intraspecies population genetic structuring in commercially
important shark species is essential for an integrated fisheries management approach to
conservation of regional biodiversity. The common smoothhound shark, Mustelus mustelus,
is an overexploited, commercially and recreationally important shark species in South Africa.
Considering the vulnerable status of the common smoothhound shark and due to very limited
available genetic information, this study aimed to develop molecular markers, assess patterns
of genetic diversity and population connectivity along the South African coast using
multilocus data generated from 12 microsatellite markers and the mitochondrial gene, NADH
dehydrogenase subunit 4 (ND4). The cross-species amplification of microsatellites proved
useful for genetic diversity and population genetic analysis of the common smoothhound
shark. These microsatellites could aid in the molecular characterisation of other endemic and
cosmopolitan species and provide valuable tools for the conservation of potentially
threatened or exploited shark species. For the microsatellite data, moderate levels of genetic
diversity based on the heterozygosity, allelic richness and haplotype diversity were found in a
total of 144 individuals sampled across eight study populations. Estimates for pairwise
population differentiation, F-statistics, AMOVA and factorial correspondence analysis (FCA)
indicated significant genetic structure within and between west- and east coast populations.
Additionally, Bayesian clustering analyses detected two putative ancestral gene pools,
supporting the presence of a biogeographic barrier at the Cape Agulhas region and therefore
genetic discontinuity between the Indian and Atlantic Ocean samples. On the contrary,
mitochondrial data indicated that common smoothhound shark is genetically homogenous with substantial interoceanic gene flow. Such conflicting signals found between nuclear and
mitochondrial DNA (mitonuclear discordance) can be attributed to a number of factors and
could simply be due to the inherent differences in marker properties or an indication of sex
biased dispersal. Despite an indication of an expanding common smoothhound shark
population based on both marker types, a contemporary genetic bottleneck may have gone
undetected as genetic divergence was very low in some of the study populations.
Nonetheless, contemporary restriction to gene flow and historical demographics such as
range expansion are proposed as the most likely forces explaining genetic structure in
present-day common smoothhound sharks in South Africa. For future sustainable exploitation of common smoothhound shark, the possible existence of two genetically differentiated
populations and observed asymmetric gene flow along the South African coast should be
taken into consideration. It is also recommended that in the future further evaluations of finescale
genetic structure and seasonal migration patterns in this commercially important species
are conducted in order to allow integration of this knowledge into existing fisheries
management practices. / AFRIKAANSE OPSOMMING: Die ontsyfering van patrone van intraspesie populasie genetiese struktuur in kommersieel
belangrike haai spesies is noodsaaklik vir 'n geïntegreerde bestuursbenadering tot visserue en
bewaring van plaaslike biodiversiteit. Die hondhaai, Mustelus mustelus, is 'n oorbenutte,
kommersiële en sporthengelary belangrike haai spesie in Suid-Afrika. Met inagneming van
die kwesbare status van die hondhaai en as gevolg van baie beperkte beskikbare genetiese
inligting, het hierdie studie gepoog om molekulêre merkers te ontwikkel, asook om die
patrone van genetiese diversiteit en populasie struktuur te ondersoek langs die Suid-
Afrikaanse kus deur middel van multilokus data gegenereer uit 12 mikrosatelliet merkers en
die mitokondriale geen, NADH dehidrogenase subeenheid 4 (ND4). Die kruis-spesie
amplifisering van mikrosatelliete was nuttig vir genetiese diversiteit en populasie genetiese
analise van die hondhaai. Hierdie mikrosatelliete kan moontlik help met die molekulêre
karakterisering in ander inheemse en kosmopolitaanse spesies en kan as waardevolle
hulpmiddels dien in die bewaring van potensieel bedreigde en oorbenutte haai spesies. Vir die
mikrosatelliet data is matige vlakke van genetiese diversiteit gevind gebaseer op
heterosigositeit, alleliese rykheid en haplotipe diversiteit gevind in 'n totaal van 144 individue
getoets oor agt studie populasies. Skattings vir paarsgewyse populasie differensiasie, Fstatistieke,
AMOVA en faktoriale ooreenstemming analise het betekenisvolle genetiese
struktuur aangedui binne en tussen wes- en ooskus populasies. Daarbenewens, het Bayesian
groepering analise twee potensiele voorvaderlike geenpoele waargeneem, ter ondersteuning
van die teenwoordigheid van 'n biogeografiese versperring by die Cape Agulhas gebied en
dus genetiese diskontinuïteit tussen die Indiese en Atlantiese Oseaan monsters. In teenstelling
het die mitokondriale data aangedui dat hierdie haai spesie geneties homogeen is met aansienlike interoseaniese geenvloei. Sulke teenstrydige tekens tussen kern en mitokondriale
DNS (mitokern onenigheid) kan toegeskryf word aan 'n aantal faktore en kan eenvoudig wees
as gevolg van die inherente verskille in merker eienskappe of 'n aanduiding van geslags
sydigeverspreiding. Ten spyte van 'n aanduiding van 'n groeiende hondhaai populasie
gebaseer op beide merker tipes, kon 'n hedendaagse genetiese bottelnek onopgemerk gegaan
het aangesien genetiese divergensie baie laag was in sommige van die studie populasies.
Nietemin, hedendaagse restriksie van geenvloei en historiese demografie soos verbreding van
reeks voorkoming word voorgestel as die mees waarskynlike dryfkragte wat genetiese struktuur in die hedendaagse hondhaaie in Suid-Afrika verduidelik. Vir toekomstige
volhoubare benutting van die spesie, moet die moontlike bestaan van twee geneties
verskillende populasies en waargenome asimmetriese geenvloei langs die Suid-Afrikaanse
kus in ag geneem word. Vir die toekoms word dit ook aanbeveel dat verdere evaluerings van
fyn-skaal genetiese struktuur en seisoenale migrasie patrone in hierdie kommersiël belangrike
spesie uitgevoer word om die integrasie van hierdie kennis in die bestaande bestuur van
visserye praktyke toe te laat. / National Research Foundation (NRF)
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:sun/oai:scholar.sun.ac.za:10019.1/95783 |
| Date | 12 1900 |
| Creators | Maduna, Simo Njabulo |
| Contributors | Bester-van der Merwe, Aletta Elizabeth, Roodt-Wilding, Rouvay, Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics. |
| Publisher | Stellenbosch : Stellenbosch University |
| Source Sets | South African National ETD Portal |
| Language | en_ZA |
| Detected Language | Unknown |
| Type | Thesis |
| Format | 182 pages : illustrations, maps |
| Rights | Stellenbosch University |
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