The application of new technologies in conservation genetics

[摘要] English: Over the past decade, the development of high-throughput DNA techniques has expanded thescope of conservation genetics and molecular markers have become indispensable tools for themanagement of wildlife species and populations. There are several molecular markers available forbiodiversity analysis, but their selection depends on the objective of the study, the molecularinformation sought (and reliability thereof) and the facilities and/or resources available. In order todevelop and apply new genetic techniques I have decided on using one bird and one mammalspecies of interest in South Africa. The bird species chosen is the African Penguin (Spheniscusdemersus) which has suffered serious population declines and is listed in the IUCN Red Data Bookas an endangered species. Due to world-wide attention to rhinoceros conservation and populationdecline, the white rhinoceros (Ceratotherium simum) was selected as mammal species. Threedifferent markers and their utility in aid of South African wildlife biodiversity conservation wereinvestigated in these diverse species. The complete mitochondrial genome of the African Penguinwas sequenced. The Spheniscus demersus mtDNA genome is very similar, both in compositionand length, to both the Eudyptes chrysocome and E. minor genomes. This is the first report of thecomplete nucleotide sequence for the mitochondrial genome of the African Penguin. These resultscan be subsequently used to provide information for penguin phylogenetic studies and insights intothe evolution of genomes. Furthermore, the study reported eight species specific microsatellitemarkers as well as 31 SNP markers as new molecular tools for the investigation, management andreintroduction of African penguin. Utilising these new tools, the study generated molecular geneticinformation to verify/complement studbook-based pedigree data from ex-situ populations of AfricanPenguin. In addition, we compared the relative and combined utility of MS and SNP markers forparentage 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 34novel SNP markers for the white rhinoceros, identified through sequencing of CATS loci as well asSNP enriched libraries. The utility of 33 Single Nucleotide Polymorphisms and 10 microsatellites inisolation and in combination for assigning parentage in captive white rhinoceros were compared. Itwas found that a combined dataset of SNPs and microsatellites was most informative and showedthe highest confidence level. This study thus provides a useful set of SNP and MS markers forparentage and relatedness testing in white rhinoceros. Furthermore, assessment of the utility ofSNP and MS markers over multiple (> three) generations and the incorporation of a larger varietyof 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, forforensic applications and to determine population structure and variability when other markersprove problematic.

[发布机构] University of the Free State