Abstract:
Reintroduction is the translocation of animals to their historic range. Reintroduced populations are usually small and commonly have low population genetic diversity. They are particularly susceptible to the effects of inbreeding and genetic drift. This can lead to inbreeding depression and the loss of genetic variation, limiting population growth and adaptation respectively. Genetic diversity can be further impacted during a reintroduction both in a source population as it loses individuals and in the translocated population as it has lower genetic diversity and population size than the source. I look at the reintroduction of an endangered New Zealand passerine, hihi (Notiomystis cincta, ‘stitchbird’). I develop a single nucleotide polymorphism array (50K SNP array) to measure genetic diversity and inbreeding in reintroduced hihi populations. SNPs can be found in large numbers throughout the whole genome and are becoming more common in the fields of ecological and conservation genetics due to their decreasing costs and reproducibility across labs. In conservation studies, samples from endangered species are often limited in the quantity and quality of DNA available. I found that a SNP array of 50K markers could genotype samples of low quantity or quality and was not affected by tissue type (feather or blood). Earlier studies on hihi relied on a panel of microsatellites from non-coding locations of the genome. I show that SNPs measure genetic diversity and inbreeding as well as microsatellites. Furthermore, SNPs can reveal the locations of long runs of homozygosity (ROHs) in a genome, i.e. parts of the genome that are more inbred. These regions mark areas of potential autozygosity, where sequences are identical due to having a common ancestor. ROH patterns in a population can result from their demographic history, with shorter ROHs from more distant ancestors and long ROHs illustrating recent inbreeding events. This is one of the first studies of ROHs in a reintroduced population of endangered animals. Looking at a hihi population over 11 years, I show that removing individuals has no effect on the inbreeding measure FIS. Small but significant changes in FIS could be seen across cohorts in SNP data only (0.003, Adjusted R2 = 0.5486, p-value = 0.005511). Small but significant changes could be seen in the number of SNPs in ROHs (increased by 0.02859 SNPs per year, adjusted R2 : 0.000574, p-value: 0.007625) and number of ROHs per 2 individual per year (increased by 0.14728 per year, adjusted R2 : 0.00231, p-value:0.05345) but there were no significant changes in ROH length. I show previously unseen increases in inbreeding across translocation bottlenecks. I found that across populations, hihi have short ROHs with a median length of 528 kb indicating no recent strong bottlenecks. Some individuals have very long ROHs, perhaps as a result of a recent consanguineous mating. A genetic marker of bottlenecks, the summed length of ROHs per individual, increases across each translocation bottleneck, indicating the genetic impact that recent repeated translocations are having on this species.