Understanding how species respond to population declines is a central question in conservation and evolutionary biology. Population declines are often associated with loss of genetic diversity, inbreeding and accumulation of deleterious mutations, which can lead to a reduction in fitness and subsequently contribute to extinction. Using temporal approaches can help us understand the effects of population declines on genetic diversity in real time. Sequencing pre-decline as well as post-decline mitogenomes representing all the remaining mitochondrial diversity, we estimated the loss of genetic diversity in the critically endangered kākāpō (Strigops habroptilus). We detected a signal of population expansion coinciding with the end of the Pleistocene last glacial maximum (LGM). Also, we found some evidence for northern and southern lineages, supporting the hypothesis that the species may have been restricted to isolated northern and southern refugia during the LGM. We observed an important loss of neutral genetic diversity associated with European settlement in New Zealand but we could not exclude a population decline associated with Polynesian settlement in New Zealand. However, we did not find evidence for fixation of deleterious mutations. We argue that despite high pre-decline genetic diversity, a rapid and range-wide decline combined with the lek mating system, and life-history traits of kākāpō contributed to a rapid loss of genetic diversity following severe population declines.


  • Significant attention has been devoted to examining the effects of extrinsic processes such as habitat modification, over-hunting or persecution on species persistence

  • Genetic diversity was high among historical samples but very low among modern samples

  • Our results highlight the use of temporal approaches to examine the genomic consequences of population declines

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Significant attention has been devoted to examining the effects of extrinsic processes such as habitat modification, over-hunting or persecution on species persistence. There is still a gap in our understanding on how intrinsic genetic processes contribute to extinctions [1,2,3]. Theory predicts that small and isolated populations will lose genetic diversity, become exposed to the effects of inbreeding and accumulate deleterious mutations. Recent studies of extinct species have shown an increase in inbreeding [3] and accumulation in deleterious mutations in both nuclear [6] and mitochondrial DNA [7] immediately before their extinction, suggesting that geographical isolation and the associated effects of genetic drift and inbreeding may have contributed to the extinction event. In the current 6th mass extinction [8], it is crucial to understand how these intrinsic genetic processes affect species extinction risk because many species are surviving in the form of


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