Differential patterns of diversity at microsatellite, MHC, and TLR loci in bottlenecked South Island saddleback populations

For populations that experienced historical population bottlenecks, subsequent contemporary bottlenecks may continue to degrade genetic diversity at loci that are still variable. However, it is currently unclear how different types of contemporary bottlenecks may affect diversity at functional versus neutral loci. In this study, we examine genetic diversity of microsatellite, major histocompatibility complex (MHC), and toll-like receptor (TLR) loci of three New Zealand South Island saddleback (Philesturnus carunculatus) populations: Big Island, Kaimohu Island and Motuara Island. One population, Motuara, experienced two sets of contemporary bottlenecks (translocation event followed by a disease-outbreak and population crash) and was sampled in three different years. For all populations and sampling periods, we compare patterns of diversity across the three sets of loci to infer the effects of contemporary bottlenecks. We found that translocation-induced bottlenecks resulted in greater losses of microsatellite than MHC diversity, whereas temporal (encompassing a potential disease-induced bottleneck) fluctuations in diversity were greater for MHC markers than microsatellite loci. Both translocation- and disease-induced contemporary bottlenecks affected TLR diversity to a greater extent than diversity of either microsatellites or MHC. We found significant temporal changes in the frequencies of two TLR1LA alleles on Motuara Island (coincident with the population crash), but no further subsequent change. These alleles differ by an amino acid variant (associated with the leucine-rich repeat region of TLR1LA). Since TLR1LA may initiate an innate immune response in the presence of haemosporidia parasites, it is possible that a selection event has contributed to the observed patterns at TLR1LA. Our results indicate that patterns of genetic diversity loss at microsatellite, MHC and TLR loci are not equally affected by contemporary population bottlenecks, and may be influenced by bottleneck type.