The application of new technologies in conservation genetics
Abstract
English: Over the past decade, the development of high-throughput DNA techniques has expanded the
scope of conservation genetics and molecular markers have become indispensable tools for the
management of wildlife species and populations. There are several molecular markers available for
biodiversity analysis, but their selection depends on the objective of the study, the molecular
information sought (and reliability thereof) and the facilities and/or resources available. In order to
develop and apply new genetic techniques I have decided on using one bird and one mammal
species of interest in South Africa. The bird species chosen is the African Penguin (Spheniscus
demersus) which has suffered serious population declines and is listed in the IUCN Red Data Book
as an endangered species. Due to world-wide attention to rhinoceros conservation and population
decline, the white rhinoceros (Ceratotherium simum) was selected as mammal species. Three
different markers and their utility in aid of South African wildlife biodiversity conservation were
investigated in these diverse species. The complete mitochondrial genome of the African Penguin
was sequenced. The Spheniscus demersus mtDNA genome is very similar, both in composition
and length, to both the Eudyptes chrysocome and E. minor genomes. This is the first report of the
complete nucleotide sequence for the mitochondrial genome of the African Penguin. These results
can be subsequently used to provide information for penguin phylogenetic studies and insights into
the evolution of genomes. Furthermore, the study reported eight species specific microsatellite
markers as well as 31 SNP markers as new molecular tools for the investigation, management and
reintroduction of African penguin. Utilising these new tools, the study generated molecular genetic
information to verify/complement studbook-based pedigree data from ex-situ populations of African
Penguin. In addition, we compared the relative and combined utility of MS and SNP markers for
parentage assignment. We found that a combined subset of these two types of markers attained a
> 99% correct cumulative parentage assignment probability. This study further reported on 34
novel SNP markers for the white rhinoceros, identified through sequencing of CATS loci as well as
SNP enriched libraries. The utility of 33 Single Nucleotide Polymorphisms and 10 microsatellites in
isolation and in combination for assigning parentage in captive white rhinoceros were compared. It
was found that a combined dataset of SNPs and microsatellites was most informative and showed
the highest confidence level. This study thus provides a useful set of SNP and MS markers for
parentage and relatedness testing in white rhinoceros. Furthermore, assessment of the utility of
SNP and MS markers over multiple (> three) generations and the incorporation of a larger variety
of relationships among individuals (e.g. half-siblings or cousins) is strongly recommended.
Developed SNP markers could be used to define the genetic mating system of this species, for
forensic applications and to determine population structure and variability when other markers
prove problematic. Afrikaans: Oor die afgelope dekade, het die ontwikkeling van hoë-deurset DNA tegnieke die omvang van
bewaringsgenetika aansienlik uitgebrei en molekulêre merkers het onontbeerlike hulpmiddels vir
die bestuur van wild spesies en bevolkings geword. Daar is verskeie molekulêre merkers
beskikbaar vir die ontleding van biodiversiteit, maar die keuse hang af van die doel van die studie,
die vereisste molekulêre inligting (en betroubaarheid daarvan) en die fasiliteite en / of hulpbronne
beskikbaar. Een voël en een soogdier spesie van belang in Suid-Afrika was gekies vir die
ontwikkeling en toepassing van nuwe genetiese tegnieke. Die Afrika pikkewyn (Spheniscus
demersus), wat ernstige bevolkings afnames toon en gelys is in die IUCN Rooidataboek as 'n
bedreigde spesie, was gekies as voëlspesie. Die Witrenoster (Ceratotherium simum) is gekies as
soogdier spesies as gevolg van die wêreld-wye aandag aan renoster bewaring en bevolkings
afname. Drie verskillende klasse merkers en hul nut vir die Suid-Afrikaanse wilds-biodiversiteit
bewaring was ondersoek in hierdie diverse spesies. Die volledige mitochondriale genoom volgorde
van die Afrika pikkewyn was bepaal. Die S. demersus mtDNA genoom is baie soortgelyk, beide in
samestelling en lengte, aan beide die Eudyptes chrysocome en E. minor genome. Hierdie is die
eerste verslag van die volledige nukleotiedvolgorde vir die mitochondriale genoom van die Afrika
pikkewyn. Hierdie resultate kan gebruik word as inligting vir pikkewyn filogenetiese studies en kan
insigte in die evolusie van genome te verskaf. Verder het die studie agt spesie-spesifieke
mikrosatelliet merkers asook 31 SNP-merkers geidentifiseer as nuwe molekulêre hulpmiddels vir
die ondersoek, bestuur en hervestiging van Afrika-pikkewyne. Deur gebruik te maak van die
merkers het die studie genetiese inligting gegenereer om stamboom data van ex-situ bevolkings
van Afrika pikkewyne aan te vul en te verifieer. Daarbenewens is die relatiewe en gekombineerde
nut van MS en SNP-merkers vir ouerskap-bepaling vergelyk. Daar is bevind dat 'n gekombineerde
substel van hierdie twee tipe merkers 'n > 99% kumulatiewe ouerskap waarskynlikheid moontlik
maak. Hierdie studie het verder 34 nuwe SNP-merkers vir die Wit renoster geïdentifiseer deur
volgorde bepaling van CATS lokusse sowel as SNP verrykingsbiblioteke. Die nut van 33 SNPmerkers
en 10 mikrosatelliete was afsonderlik en in kombinasie vergelyk vir toepassing in
ouerskap-bepaling op Witrenosters in gevangeneskap. Daar is gevind dat 'n gekombineerde
datastel van SNPs en mikrosatelliete die mees insiggewend was en die hoogste vlak van
betroubaarheid bied. Hierdie studie bied dus 'n nuttige stel SNP en MS merkers vir ouerskap en
verwantskap bepaling in Witrenostesr. Verder word die assessering van die nut van SNP en MS
merkers oor verskeie (>3) generasies en met 'n groter verskeidenheid van moontlike verhoudings
tussen individue (bv half-broers en susters of neefs) sterk aanbeveel. Die ontwikkelde SNPmerkers
kan gebruik word om die genetiese paringstelsel van hierdie spesie te definieer, vir
forensiese ondersoeke en om die bevolking-struktuur en verskeidenheid te bepaal wanneer ander
merkers problematies is.
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