Population Structure, Conservation Genetics and Evolution of the Kaka (Nestor Meridionalis): a Microsatellite Study

Abstract

This thesis describes the isolation of microsatellite DNA loci from the kaka (Nestor meridionalis), and investigates the population genetics of kaka using these molecular tools. This thesis also describes the evolutionary dynamics of this class of repeat DNA sequence using allele frequency spectra and DNA sequence data from kaka and phylogenetic comparisons among parrot species. The kaka is a threatened, endemic New Zealand, parrot with a fragmented distribution and North Island and South Island subspecies. A PCR-based technique was used to isolate six polymorphic microsatellite loci from the kaka genome. This study presents data from these loci and two more first characterised in other parrot species. A total of 126 kaka from nine regional populations were available for study. Substantial levels of genetic diversity were found across all eight loci, but reveal little population structure in kaka, with most variation (93.7%) shared across populations, rather than divided among populations, and no differentiation between subspecies. Further, most of the inter-population genetic differentiation is attributed to the divergence of the Kapiti Island population from all other kaka populations surveyed. The Kapiti Island population has relatively low diversity consistent with a possible previous genetic bottleneck. The low population divergence in kaka probably reflects historic population structure. Conservation management of N. meridionalis should reflect this New Zealand-wide metapopulation, although special consideration might be given to Kapiti Island. It was possible to examine evolution at seven microsatellite loci in N. meridionalis by statistical testing and DNA sequence analysis of a total of 350 allele copies representing 39 different electromorphs. Length polymorphism at these loci reflects changes in repeat number, although size homoplasy resulting from single nucleotide polymorphisms was also detected. Allele number is predicted by the Infinite Allele Model (Kimura & Crow 1964) for all seven loci examined. Therefore, it is appropriate to estimate population genetic parameters (e.g.FST) based on these features. In contrast, inter-specific microsatellite evolution was found to be a more complex phenomenon limiting the use of these microsatellite loci in phylogenetic studies. In general, heterologous amplification using the kaka primer pairs was rare, reflecting the deep evolutionary divergence of N. meridionalis from most other parrots. Microsatellite evolution over inter-specific time spans was examined at two test loci by DNA sequence analysis of 44 alleles across 26 different parrot species. Structural changes comprising insertions, deletions and substitutions as well as changes in repeat number were Observed.