The kākāpō (Strigops habroptilus)

Abstract

The kākāpō, Strigops habroptilus, is a flightless and critically endangered parrot from New Zealand. The species belongs to a unique lineage of parrots, endemic to the archipelago that diverged from other parrots ~82 million years ago (mya), as New Zealand split from Gondwana. The kākāpō genome represents one of the first high-quality chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP) and is an important resource for future studies on evolution and conservation. Analyses of this new genome provide key insights into kākāpō breeding and recovery. Comparison of modern and historical genomes show that kākāpō experienced a reduction in mutational load through genetic drift and purging. These findings indicate that even extremely inbred and bottlenecked species can survive in the wild, but also caution about the future management strategy for the species. Because kākāpō is a taonga, or treasure for Māori, the project was established in collaboration with Te Rūnanga o Ngāi Tahu. The kākāpō genome comprises 23 chromosomes (2n), making for a total genome size of ~1.19 Gbp. It has a repeat content of 15% and a GC content of 42%. A total of 16 053 annotated protein-coding genes were identified. Kākāpō is one of the most inbred species on earth with 0.4–0.5 heterozygote sites per 1000 bp and an inbreeding coefficient (FROH) of ~53%. The kākāpō diverged from flying New Zealand parrots (kea and kākā) ~28 mya. Population genomics analyses revealed that the divergence time between the extinct mainland and the extant Stewart Island populations dates back to the end of the last glaciation ~15 thousand years ago (kya). The kākāpō used to be one of most common and widespread birds in New Zealand. There are now only 202 kākāpō surviving on island sanctuaries that are part of an intense breeding program. Only one mainland bird, called Richard Henry, and 39 Stewart Island birds survived an extreme bottleneck in 1995 and reproduced. Kākāpō are flightless, nocturnal with a probable well-developed sense of smell and with a pronounced sexual dimorphism in body size. Contrary to other parrots, kākāpō have a polygynous lek breeding system. They only reproduce every 2–5 years, during years of heavy rimu (Dacrydium cupressinum) fruiting. Females reach sexual maturity between 5 and 18 years and males between 11 and 23 years. Kākāpō are believed to be exceedingly long-lived, with one male, Richard Henry, having lived up to ~80 years old. The Z sex chromosome fused with the chromosome 11 equivalent of other bird species, and this since has been found for other parrot species, indicating that the fusion may have occurred at the origin of parrots. KINGDOM: Animalia PHYLUM: Chordata CLASS: Aves ORDER: Psittaciformes FAMILY: Psittacidae GENUS: Strigops