Genomic insights into the evolutionary relationships and demographic history of kiwi

Kiwi are a unique and emblematic group of birds endemic to New Zealand. Deep-time evolutionary relationships among the five extant kiwi species have been difficult to resolve, in part due to the absence of pre-Quaternary fossils to inform speciation events among them. Here, we utilise single representative nuclear genomes of all extant kiwi species (great spotted kiwi, little spotted kiwi, Okarito brown kiwi, North Island brown kiwi, and southern brown kiwi) and investigate their evolutionary histories with phylogenomic, genetic diversity, and deep-time (past million years) demographic analyses. We uncover low levels of gene-tree phylogenetic discordance across the genomes, suggesting clear distinction between species. However, we also find indications of post-divergence gene flow, concordant with recent reports of interspecific hybrids. The four species with available reference assemblies show relatively low levels of genetic diversity, which we suggest reflects a combination of older environmental as well as more recent anthropogenic influence. In addition, we uncover similarities and differences in the demographic histories of the five kiwi species over the past million years, and suggest hypotheses regarding the impact of known past environmental events, such as volcanic eruptions and glacial periods, on the evolutionary history of the group.