Conservation genetics of kakapo (Strigops habroptilus): Contemporary and historic samples reveal founder relationships and patterns of genetic diversity

Small populations that have experienced a bottleneck often suffer from low genetic diversity and inbreeding, the effects of which may threaten persistence over time. The iconic kakapo (Strigops habroptilus) is an endemic parrot of New Zealand, which has been successfully brought back from the brink of extinction, but experienced a severe bottleneck of 51 individuals. The population has since recovered to 125 individuals, but exhibits high hatching failure and other signs of inbreeding depression, which have been supported by studies indicating that contemporary kakapo possess low genetic diversity. Therefore, quantifying and maintaining existing genetic diversity are high priorities in kakapo management. Kakapo are currently genetically managed using molecular estimates of relatedness, but the goal is to move to pedigree-based genetic management. An assumption common to most pedigrees is that founding individuals are unrelated. However, this is unlikely to be the case for kakapo, as most founders originate from one area of Stewart Island. I examined kakapo founders for potential relationships using several molecular techniques. Founders were genotyped using 25 microsatellites, which were used to generate relatedness estimates and assign relationships. I assigned 107 relationships in total, including 6 full sibling and 22 parent-offspring relationships. Sequencing the mitochondrial DNA (mtDNA) control region revealed three haplotypes in Stewart Island founders. All of these sources of genetic information were combined into a matrix of pairwise relatedness estimates, which can inform the generation of a pedigree. The improved pedigree will be used by the New Zealand Department of Conservation to manage the kakapo population genetically through artificial insemination and planned matings. Knowledge of founder relationships can also inform which kakapo are placed on which islands to avoid mating between close relatives. Historical samples lend insight into past genetic diversity and phylogeography, which can inform how current genetic diversity is managed. Historic levels and patterns of genetic diversity in kakapo were examined using museum samples from both Stewart Island and the South Island. DNA was extracted from toepads, and the mtDNA control region was sequenced and compared with that of contemporary kakapo. Loss of haplotype diversity over time was observed, and there were no haplotypes shared in common between historic and contemporary samples. Haplotype networks were used to explore phylogeographic patterns, but there was no clear association between haplotype and geographic location of samples. Historic population structure was also investigated by calculating FST values and examining populations for isolation by distance, neither of which indicated strong population structure. There was evidence for a historic population expansion, which could be explained by a kakapo radiation following the Last Glacial Maximum, approximately 10,000 years ago. The higher diversity in historic South Island kakapo lends support to the current management strategy of prioritizing the Fiordland lineage. This study shows the importance of a historic perspective in the genetic management of populations, both for identifying founder relationships in the recent past and for examining historic genetic diversity and phylogeography in museum samples