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.