Biology subjects

Digby, A.

Publications and source records attributed to Digby, A..

7 recordsLinked to original sources

bioRxiv2026

Unexpected post-release behaviours of reintroduced kakapo

Translocations are commonly used to reduce the risk of extinction of threatened species, and often to reintroduce animals to their former habitats. If extirpation occurred a long time ago, individuals may be placed into novel environments outside of conditions they have previously experienced, which can affect translocation success. To measure success of translocations, particularly those to novel habitats, it is important to monitor post-release spatial behaviour. In 2023, ten critically endangered k[a]k[a]p[o] (Strigops habroptilus) were released to form a new population at the fenced mainland island of Sanctuary Mountain Maungatautari (hereafter Maungatautari) in the North Island of New Zealand, an area from which they were extirpated approximately a century earlier. The spatial behaviour and habitat selection of these k[a]k[a]p[o] was analysed using dynamic space use and step selection functions with temporally dynamic responses applied to GPS logger data recorded over a seven month period. These showed three unexpected results: k[a]k[a]p[o] were highly mobile and used larger areas compared to other sites; there was synchronicity of movement, with most individuals simultaneously moving toward the perimeter fence in spring; and when near the fence k[a]k[a]p[o] selected for areas of pasture and exotic vegetation more than anticipated. While direct comparisons are difficult due to varying data availability, this unexpected spatial behaviour and habitat selection suggests that k[a]k[a]p[o] behavioural responses were different at Maungatautari compared to other sites. This may indicate that k[a]k[a]p[o] released at Maungatautari had a longer exploratory stage than elsewhere; that there were behavioural effects influenced by conspecific density or the availability of novel and exotic vegetation; or that there were specific breeding habitat requirements not met at the site during the study period. These results highlight the importance of high-resolution spatial monitoring to evaluate the success of translocations, particularly those to novel environments.

animal behavior and cognition↗

bioRxiv2024

Evidence for a role of extraintestinal pathogenic Escherichia coli, Enterococcus faecalis and Streptococcus gallolyticus in the aetiology of exudative cloacitis in the critically endangered kakapo (Strigops habroptilus)

The k[a]k[a]p[o] is a critically endangered flightless parrot which suffers from exudative cloacitis, a debilitating disease resulting in inflammation of the vent margin or cloaca. Despite this disease emerging over 20 years ago, the cause of exudative cloacitis remains elusive. We used total RNA sequencing and metatranscriptomic analysis to characterise the infectome of lesions and cloacal swabs from nine k[a]k[a]p[o] affected with exudative cloacitis, and compared this to cloacal swabs from 45 non-diseased k[a]k[a]p[o]. We identified three bacterial species - Streptococcus gallolyticus, Enterococcus faecalis and Escherichia coli - as significantly more abundant in diseased k[a]k[a]p[o] compared to healthy individuals. The genetic diversity observed in both S. gallolyticus and E. faecalis among diseased k[a]k[a]p[o] suggests that these bacteria originate from exogenous sources rather than from k[a]k[a]p[o]-to-k[a]k[a]p[o] transmission. The presence of extraintestinal pathogenic E. coli (ExPEC)-associated virulence factors in the diseased k[a]k[a]p[o] population suggests that E. coli may play a critical role in disease progression by facilitating iron acquisition and causing DNA damage in host cells, possibly in association with E. faecalis. No avian viral, fungal nor other parasitic species were identified. These results, combined with the consistent presence of one E. coli gnd sequence type across multiple diseased birds, suggests that this species may be the primary cause of exudative cloacitis. These findings shed light on possible causative agents of exudative cloacitis, and offer insights into the interplay of microbial factors influencing the disease.

microbiology↗

bioRxiv2023

The ghost of selection past: evolution and conservation relevance of the kakapo color polymorphism

The information contained in population genomic data can tell us much about the past ecology and evolution of species. We leveraged detailed phenotypic and genomic data of nearly all living k[a]k[a]p[o] to understand the evolution of its remarkable feather color polymorphism. The k[a]k[a]p[o] is an endangered and culturally significant parrot endemic to Aotearoa New Zealand, and the green and olive feather colorations are present at similar frequencies in the population. The presence of such a neatly balanced color polymorphism is remarkable because the entire population currently numbers less than 250 birds, which means it has been exposed to severe genetic drift. We dissected the color phenotype, demonstrating that the two colors differ in their light reflectance patterns due to differential feather structure. We used quantitative genomics methods to identify two genetic variants whose epistatic interaction can fully explain the species color phenotype. Our genomic forward simulations show that balancing selection might have been pivotal to establish the polymorphism in the ancestrally large population, and to maintain it during population declines that involved a severe bottleneck. We hypothesize that an extinct apex predator was the likely agent of balancing selection, making the color polymorphism in the k[a]k[a]p[o] a "ghost of selection past".

genomics↗

bioRxiv2022

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

We used non-invasive real-time genomic approaches to monitor one of the last surviving populations of the critically endangered k[a]k[a]p[o] (Strigops habroptilus). We first established an environmental DNA metabarcoding protocol to identify the distribution of k[a]k[a]p[o] and other vertebrate species in a highly localized manner using soil samples. Harnessing real-time nanopore sequencing and the high-quality k[a]k[a]p[o] reference genome, we then extracted species-specific DNA from soil. We combined long read-based haplotype phasing with known individual genomic variation in the k[a]k[a]p[o] population to identify the presence of individuals, and confirmed these genomically informed predictions through detailed metadata on k[a]k[a]p[o] 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.

genomics↗

bioRxiv2022

Capturing species-wide diversity of the gut microbiota and its relationship with genomic variation in the critically endangered kakapo

The gut microbiota plays an essential role in host health that has important implications for the conservation management of threatened wildlife. While factors such as diet, medication, and habitat are known to shape the microbiota, our understanding of the entirety of factors, including the complex role of the host genomic background, remains incomplete. Our research on the gut microbiota of the critically endangered k[a]k[a]p[o] (Strigops habroptilus), a flightless parrot species endemic to Aotearoa New Zealand, represents, to our knowledge, the first study to describe the gastrointestinal bacterial diversity for virtually an entire species and to assess the relationship between gut microbiota and host genomic diversity in a highly threatened population. Here we report a 16S rRNA gene-based analysis of k[a]k[a]p[o] faecal samples representing the gut microbiota for 84% of k[a]k[a]p[o] (n = 133). This survey was then leveraged with exceptional metadata to tease apart the impact of host genomic diversity and factors such as sex, diet, antibiotic treatment, disease status, habitat, and time of sampling on the k[a]k[a]p[o] gut microbiota, with sex being the only covariate significantly associated with gut microbiota diversity. We find evidence of a highly polygenic genomic architecture of the gut microbiota and further identify putative associations between gut bacterial diversity and functional biological pathways related to intestinal homeostasis, inflammation, immune response and metabolism. This improved understanding of the k[a]k[a]p[o] gut microbiota - and its relationship with host genomics - can directly benefit k[a]k[a]p[o] management and conservation by providing new insights into the role of the gut microbiome in k[a]k[a]p[o] health and disease mitigation. Overall, we anticipate that an integration of microbiome studies in conservation research and management will improve our understanding of how the concept of One Health with its implications for human, animal and environmental welfare can be achieved.

microbiology↗

bioRxiv2022

Species-wide genomics of kakapo provides transformational tools to accelerate recovery

The k[a]k[a]p[o] is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analyzed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to quantify genome-wide diversity of the species over time and present new approaches using probabilistic programming, combined with a phenotype dataset spanning five decades, to disentangle phenotypic variance into environmental and genetic effects while quantifying uncertainty in small populations. We find associations for growth, disease susceptibility, clutch size, and egg fertility within genic regions previously shown to influence these traits in other species. Finally, we generate breeding values to predict phenotype and illustrate that active management over the past 45 years has maintained both genome-wide diversity and diversity in breeding values, and hence, evolutionary potential. We provide new pathways for informing future conservation management decisions for k[a]k[a]p[o], including prioritizing individuals for translocation and monitoring individuals with poor growth or high disease risk. Overall, by explicitly addressing the challenge of small sample size, we provide a template for the inclusion of genomic data that will be transformational for species recovery efforts around the globe.

genomics↗

bioRxiv2020

Towards complete and error-free genome assemblies of all vertebrate species

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are only available for a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling the most accurate and complete reference genomes to date. Here we summarize these developments, introduce a set of quality standards, and present lessons learned from sequencing and assembling 16 species representing major vertebrate lineages (mammals, birds, reptiles, amphibians, teleost fishes and cartilaginous fishes). We confirm that long-read sequencing technologies are essential for maximizing genome quality and that unresolved complex repeats and haplotype heterozygosity are major sources of error in assemblies. Our new assemblies identify and correct substantial errors in some of the best historical reference genomes. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an effort to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species and help enable a new era of discovery across the life sciences.

genomics↗