The conservation genetics of the hihi (Notiomystis cincta) and epidemiology of coccidian infection

Abstract

In this thesis I investigated both neutral and functional genetic diversity and the disease epidemiology of the threatened New Zealand hihi (Notiomystis cincta). By sampling birds in the remnant population of Te Hauturu-o-Toi from a much broader set of geographical locations than has ever been done previously, I determined that there was no significant population structure. However, simulations revealed that sampling different regions of the island affected the rate at which genetic diversity was captured due to the distribution of low frequency alleles in the population. Analysis of genetic diversity through time suggests a recent population bottleneck. I compared the level of genetic variation between Te Hauturu-o-Toi and the reintroduced population on Tiritiri Matangi using microsatellite and toll-like receptor (TLR) loci. Although putatively neutral microsatellite loci were less diverse in Tiritiri Matangi, the functional TLR loci had higher diversity in the reintroduced population, likely as a result of sample size differences. However, I found no evidence of selection acting on the TLR loci and a resampling analysis suggests that genetic drift is the strongest force shaping variation at these loci. I found an annual pattern in coccidian prevalence driven by the age structure of the population. Juveniles were most susceptible to infection, thus following the breeding season when there is a large influx of juveniles into the population, the prevalence of coccidia increases, and prior to the breeding season prevalence is low. This pattern was apparent in both populations but more pronounced in Tiritiri Matangi. We also found variation at TLR1B to have a significant effect on susceptibility to coccidian infection in females, but only in the Tiritiri Matangi population. Finally, I demonstrate that detection of coccidial DNA using PCR is more sensitive compared to visual assessment via microscopy. Overall, these results provide critical information for the ongoing management of the species, including informing future translocation strategies, providing important baseline information for assessing the impact of coccidia, and highlight the need to consider both neutral and functional diversity in assessments of the genetic health and adaptive potential of threatened populations.