Multiplex PCR reveals population structure in an inbred communal bird

Studying the effects of inbreeding in wild avian populations can be challenging due to attendant concerns and restrictions when working with endangered species. Therefore, naturally inbreeding species listed as Not of Concern, such as the communally breeding pūkeko (Porphyrio melanotus melanotus, family Rallidae), may provide an excellent model for experimental analyses of inbreeding. We hope that this work will eventually inform conservation efforts directed at endangered species. We sampled pūkeko populations on the North Island (Tāwharanui Park) and South Island (Otokia Reserve) of Aotearoa New Zealand that differ in climate and breeding behaviour. North Island populations are philopatric, living on year-round territories, and in kin groups, leading to inbreeding once the young become breeders. South Island populations have seasonal territories, high dispersal rates, and form non-kin groups, resulting in outbreeding. Given behavioural evidence of inbreeding at a nearby North Island population, we predicted that the North Island population would exhibit lower heterozygosity and higher inbreeding coefficients than the South Island population. To test these predictions, we developed microsatellite primers, optimised multiplex PCRs, and genotyped breeding groups from the North and South Island. In this pilot study we found that breeding groups from North Island were genetically differentiated, whereas population structure was not detected in the South Island groups. North Island birds also had higher inbreeding coefficients and levels of within-group kinship than South Island birds. This pilot study validated microsatellite markers and multiplex PCR methods and is, to our knowledge, the first genetic analysis of population structure and relatedness within communal breeding pūkeko. These genetic tools will be used for larger-scale studies to understand interactions between breeding behaviour and inbreeding.