<p>The rainbow trout (Oncorhynchus mykiss) of Lake Taupo, New Zealand provide an exceptional opportunity to explore the contemporary adaptation of an introduced aquatic species. Recently it has become evident that their spawning migration time has shifted to later in the season. I investigated the genetic basis of these changes in spawning time by (1) using genetic markers to determine the origins of Taupo trout in California, (2) determining the pattern and extent of spatial population genetic variation throughout the Lake Taupo catchment and in comparison to nearby Lake Tarawera in the Rotorua district, (3) analysing genetic variation at the OtsClock1b spawning time gene in temporal replicates from several sites from Taupo, and (4) comparing contemporary genetic variation at this gene and microsatellite markers to genetic variation from three Taupo tributaries in 1980s. I compared the ability of single nucleotide polymorphism (SNP) and microsatellite markers to determine the origins of Lake Taupo rainbow trout, translocated from California around 120 years ago. Data were collected from 15 microsatellite and 93 SNP markers, using samples from the Lake Taupo population and ten populations throughout California, which included all historically indicated populations of origin. Results revealed that the Lake Taupo population has significantly diverged from Californian populations at both microsatellite and SNP loci. These analyses also showed that the Lake Taupo population was probably derived from several sources in California (the most likely origins being the McCloud River and Lake Almanor), and an indeterminate California coastal population. This conclusion was supported with simulations of founder events, which suggested that the genetic patterns of a single source of introduction would still be detectable 100 years post-founding, but with multiple introductions exact source populations become more difficult to detect. Approximately 50 individuals from 10 locations throughout the catchment were then analysed using 15 microsatellite loci to determine if there was any spatial population genetic differentiation. There was no significant difference in genetic distance between locations within Lake Taupo, although there was a significant difference between these populations and Rotorua and Waipakihi, which are isolated by geographic barriers. Lake Taupo rainbow trout do appear to diverge at markers potentially under selection, though, because genotyping of the poly-Q region of the timing locus OtsClock1b shows significant differentiation between individuals sampled at different times in the Waipa River. Two other sites, however, did not show the same pattern of significant seasonal variation in OtsClock1b allele frequencies. This suggests that genotypes at this locus could be influencing spawning migration time, but that this variation could also be site specific, and therefore have a strong environmental component. Scale samples from the 1980s show no significant divergence at 5 microsatellites and OtsClock1b, indicating that allele frequencies have not changed significantly over the last 20 years at neutral markers or markers under selection. I therefore conclude that while Taupo rainbow trout have diverged from their origins in California, they have only slightly diverged within their new environment, and do not show a consistent pattern of genetic change over time. This information will contribute not only to the management of the Taupo fishery but also to the current understanding of the population genetic structuring of introduced salmonids.</p>
The Sensitiveness of Expected Heterozygosity and Allelic Richness Estimates for Analyzing Population Genetic Diversity