Dataset Information

Population genomics of the critically endangered kakapo.

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.

SUBMITTER: Dussex N

PROVIDER: S-EPMC9903828 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature

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Population genomics of the critically endangered kākāpō.

Dussex Nicolas N van der Valk Tom T Morales Hernán E HE Wheat Christopher W CW Díez-Del-Molino David D von Seth Johanna J Foster Yasmin Y Kutschera Verena E VE Guschanski Katerina K Rhie Arang A Phillippy Adam M AM Korlach Jonas J Howe Kerstin K Chow William W Pelan Sarah S Mendes Damas Joanna D JD Lewin Harris A HA Hastie Alex R AR Formenti Giulio G Fedrigo Olivier O Guhlin Joseph J Harrop Thomas W R TWR Le Lec Marissa F MF Dearden Peter K PK Haggerty Leanne L Martin Fergal J FJ Kodali Vamsi V Thibaud-Nissen Françoise F Iorns David D Knapp Michael M Gemmell Neil J NJ Robertson Fiona F Moorhouse Ron R Digby Andrew A Eason Daryl D Vercoe Deidre D Howard Jason J Jarvis Erich D ED Robertson Bruce C BC Dalén Love L

Cell genomics 20210908 1

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 geno ...[more]

PMID: 36777713

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Project description:BackgroundAnimal conservation often requires intensive management actions to improve reproductive output, yet any adverse effects of these may not be immediately apparent, particularly in threatened species with small populations and long lifespans. Hand-rearing is an example of a conservation management strategy which, while boosting populations, can cause long-term demographic and behavioural problems. It is used in the recovery of the critically endangered kākāpō (Strigops habroptilus), a flightless parrot endemic to New Zealand, to improve the slow population growth that is due to infrequent breeding, low fertility and low hatching success.MethodsWe applied Bayesian mixed models to examine whether hand-rearing and other factors were associated with clutch fertility in kākāpō. We used projection predictive variable selection to compare the relative contributions to fertility from the parents' rearing environment, their age and previous copulation experience, the parental kinship, and the number of mates and copulations for each clutch. We also explored how the incidence of repeated copulations and multiple mates varied with kākāpō density.ResultsThe rearing status of the clutch father and the number of mates and copulations of the clutch mother were the dominant factors in predicting fertility. Clutches were less likely to be fertile if the father was hand-reared compared to wild-reared, but there was no similar effect for mothers. Clutches produced by females copulating with different males were more likely to be fertile than those from repeated copulations with one male, which in turn had a higher probability of fertility than those from a single copulation. The likelihood of multiple copulations and mates increased with female:male adult sex ratio, perhaps as a result of mate guarding by females. Parental kinship, copulation experience and age all had negligible associations with clutch fertility.ConclusionsThese results provide a rare assessment of factors affecting fertility in a wild threatened bird species, with implications for conservation management. The increased fertility due to multiple mates and copulations, combined with the evidence for mate guarding and previous results of kākāpō sperm morphology, suggests that an evolutionary mechanism exists to optimise fertility through sperm competition in kākāpō. The high frequency of clutches produced from single copulations in the contemporary population may therefore represent an unnatural state, perhaps due to too few females. This suggests that opportunity for sperm competition should be maximised by increasing population densities, optimising sex ratios, and using artificial insemination. The lower fertility of hand-reared males may result from behavioural defects due to lack of exposure to conspecifics at critical development stages, as seen in other taxa. This potential negative impact of hand-rearing must be balanced against the short-term benefits it provides.

Dataset Information

Population genomics of the critically endangered kakapo.

Publications

Population genomics of the critically endangered kākāpō.

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