Abstract
The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in kākāpō indicate that present-day island kākāpō have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ∼10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into kākāpō breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species.
Highlights
New Zealand was one of the last landmasses colonized by humans.[1]
We present the reference genome for kakapo, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP),[18] and a population genomics analysis of 49 kakapo from Stewart Island and the extinct mainland population
Island and mainland populations are distinct and separated after the last glaciation We generated a high-quality chromosome-level genome assembly for a female kakapo (Figures S1–S3) and sequenced the genomes from 36 individuals that survived the bottleneck at its most severe phase in the 1990s (Richard Henry and 35 Stewart Island birds) as well as 13 genomes from $130-year-old museum specimens that originated from the extinct mainland population (Figure 1A; Table S1)
Summary
New Zealand was one of the last landmasses colonized by humans.[1] Following Polynesian colonization circa 1360 CE and European colonization in the 1800s, and the resulting overhunting and introduction of mammalian predators, New Zealand experienced major extinction events of endemic species.[2] The kakapo (Strigops habroptilus), a flightless parrot species, was. Cell Genomics 1, 100002, October 13, 2021 a 2021 The Author(s). Gemmell,[4] Fiona Robertson,[6] Ron Moorhouse,[22] Andrew Digby,[22] Daryl Eason,[22] Deidre Vercoe,[22] Jason Howard,[15,23] Erich D. Robertson,6,* and Love Dalen1,2,3,* 17Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA 18Genomics Aotearoa and Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, PO Box 56, Dunedin
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