Significance of population genetics for managing small natural and reintroduced populations in New Zealand

Conservation biology has had a long-standing debate about the relative importance of genetic processes in increasing the risk of extinction in threatened species. We assume that priority should be given to securing a species from extinction by stopping significant declines in numbers and then managing the secured populations to recovery by creating opportunities for population growth. This two-prong approach endorses the importance of ameliorating the agents that are causing populations to decline and then understanding the genetic issues that can arise once populations become small but stable or slowly recovering. This starting point was the initiator for the research we commenced in the mid-1990s and continue to this day. The review covers six sections: (1) We identified inbreeding depression (using pedigree relatedness and molecular loci) in takahē (Porphyrio hochstetteri), robins (Petroica australis and P. longipus), and kākāpō (Strigops habroptilus), and both negative and positive effects of relatedness on fitness in the highly inbred Chatham Island black robins (Petroica traversi); (2) We found no relationship between pedigree inbreeding, molecular heterozygosity and fitness (HFC) in the genetically depauperate takahē, but we did find such effects in the more diverse robins; (3) We found that all threatened species in New Zealand had lost genetic diversity over time, compared with more recent bottlenecks associated with reintroductions; (4) AlleleRetain employs user-specified parameters to simulate demography, allele retention and inbreeding in animals with overlapping generations, and is particularly useful for identifying the maximum retention of allelic diversity of a reintroduced population. DOC is currently developing a website to assist with simulation in AlleleRetain to assist both DOC and community-led reintroductions; (5) A meta-analysis of 109 populations indicated that loss of neutral and functional diversity was correlated during prolonged bottlenecks, but overall loss of MHC diversity is 15% greater than neutral diversity. We found support for this pattern when we investigated the loss of genetic diversity from historical museum to contemporary samples in saddlebacks and robins. Further prioritising of individuals for targeted breeding on the basis of adaptive immune alleles in yellow-fronted parakeets (Cyanoramphus auriceps) and kākāpō may allow the maintenance of important functional genetic diversity over a species’ recovery; (6) We described the diversity of toll-like receptor (TLR) genes that mediate innate immune responses in avian species, and note they may be simpler to use than the more complicated MHC immunity genes. We found evidence of episodic positive selection in the evolution of most avian TLRs, but within 10 bottlenecked species more evidence of genetic drift occurred than balancing selection at TLR loci.