Inheritance of Telomere Length in a Bird

Telomere dynamics are intensively studied in human ageing research and epidemiology, with many correlations reported between telomere length and age-related diseases, cancer and death. While telomere length is influenced by environmental factors there is also good evidence for a strong heritable component. In human, the mode of telomere length inheritance appears to be paternal and telomere length differs between sexes, with females having longer telomeres than males. Genetic factors, e.g. sex chromosomal inactivation, and non-genetic factors, e.g. antioxidant properties of oestrogen, have been suggested as possible explanations for these sex-specific telomere inheritance and telomere length differences. To test the influence of sex chromosomes on telomere length, we investigated inheritance and sex-specificity of telomere length in a bird species, the kakapo (Strigops habroptilus), in which females are the heterogametic sex (ZW) and males are the homogametic (ZZ) sex. We found that, contrary to findings in humans, telomere length was maternally inherited and also longer in males. These results argue against an effect of sex hormones on telomere length and suggest that factors associated with heterogamy may play a role in telomere inheritance and sex-specific differences in telomere length

Population genomics of the critically endangered kākāpō

Summary 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

Sex allocation theory aids species conservation

Supplementary feeding is often a key tool in the intensive management of captive and threatened species. Although it can increase such parameters as breeding frequency and individual survival, supplementary feeding may produce undesirable side effects that increase overall extinction risk. Recent attempts to increase breeding frequency and success in the kakapo Strigops habroptilus using supplementary feeding inadvertently resulted in highly male-biased chick sex ratios. Here, we describe how the inclusion of sex allocation theory has remedied this conservation dilemma. Our study is the first to manipulate chick sex ratios in an endangered species by altering maternal condition and highlights the importance of incorporating evolutionary theory into modern conservation practice

Paper 11 NEW.indd

Abstract The reproduction of kakapo (Strigops habroptilus) on offshore island refuges was monitored between 1990 and 2002. Productivity was primarily determined by the proportion of females that nested each breeding year. Within the same island, the proportion of females nesting each breeding year ranged between 33 -95% but, as a proportion of the total female population, was just 5 -42% between 1990 and 1999. The deliberate placement of the entire adult female population on Codfi sh Island (Whenua Hou) in anticipation of an exceptional fruit crop resulted in 95% of them nesting in 2002, raising 24 fl edglings and increasing the total population by 39%. Although efforts to increase the frequency of kakapo breeding by providing supplementary food have been unsuccessful, nesting and fl edging success increased signifi cantly following the introduction of new, more intensive, management methods in 1995. Hatching success has, however, remained poor, with just 42% of eggs hatching. Comparison with related parrot species suggests that the kakapo's hatching success is unusually low, perhaps because of inbreeding. Despite infrequent breeding and poor hatching success, the kakapo population has increased by 69% from 51 birds i

Non-invasive real-time genomic monitoring of the critically endangered kākāpō

We used non-invasive real-time genomic approaches to monitor one of the last surviving populations of the critically endangered kākāpō (Strigops habroptilus). We first established an environmental DNA metabarcoding protocol to identify the distribution of kākāpō and other vertebrate species in a highly localized manner using soil samples. Harnessing real-time nanopore sequencing and the high-quality kākāpō reference genome, we then extracted species-specific DNA from soil. We combined long read-based haplotype phasing with known individual genomic variation in the kākāpō population to identify the presence of individuals, and confirmed these genomically informed predictions through detailed metadata on kākāpō distributions. This study shows that individual identification is feasible through nanopore sequencing of environmental DNA, with important implications for future efforts in the application of genomics to the conservation of rare species, potentially expanding the application of real-time environmental DNA research from monitoring species distribution to inferring fitness parameters such as genomic diversity and inbreeding

Hidden impacts of conservation management on fertility of the critically endangered kākāpō

Funding Information: Andrew Digby, Daryl Eason, Deidre Vercoe, Michael Lierz, Tineke Joustra and Caroline Lees were supported by the Ka¯ka¯po¯ Recovery Programme, which is funded by the New Zealand government, public donations and commercial partners. Michael Lierz was also supported by the European Association of Avian Veterinarians. Alejandro Catalina was funded by the Finnish Center for Artificial Intelligence (FCAI) and supported by Aalto-Science IT project. Stephanie Galla and Tammy E. Steeves were funded by the Ministry of Business, Innovation and Employment (MBIE) Endeavour Fund (UOCX1602, awarded to Tammy E. Steeves). Stephanie Galla was also supported by a National Science Foundation Track 2 EPSCoR Program under award number OIA-1826801. Lara Urban was funded by a Feodor Lynen Research Fellowship provided by the Alexander von Humboldt Foundation. Marissa F. Le Lec was also supported by a University of Otago doctoral scholarship. Joseph Guhlin, Marissa F. Le Lec, Lara Urban, Tammy E. Steeves and Peter K. Dearden were supported by Genomics Aotearoa through their High-Quality Genomes and Population Genomics project. Tane Davis was supported by Te Ru¯nanga o Nga¯i Tahu. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: Copyright 2023 Digby et al.Background. Animal 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. Methods. We 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. Results. The 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. Conclusions. These 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.Peer reviewe