Biology subjects

Santure, A. W.

Publications and source records attributed to Santure, A. W..

7 recordsLinked to original sources

bioRxiv2024

Joint consideration of selection and microbial generation count provides unique insights into evolutionary and ecological dynamics of holobionts

The relationship between, and joint selection on, a host and its microbes - the holobiont - can impact evolutionary and ecological outcomes of the host and its microbial community. Here we present a novel agent-based modelling framework for understanding the ecological dynamics of hosts and their microbiomes. Our model explicitly incorporates numerous microbial generations per host generation allowing for selection on both host and microbe. We apply our model to explore community fitness and diversity in the face of rapid environmental change. We demonstrate that multiple microbial generations can buffer changes experienced across host lifetimes by smoothing environmental transitions. Our simulations reveal that microbial fitness and host fitness may be at odds with each other when considering the impact of vertical inheritance of microbial communities from a host to its offspring - where high values favour microbial fitness, while low values favour host fitness - these tradeoffs are minimized when microbial generation count per host generation is high. We suggest that these results arise from cross-generational priority effects which maintain diversity within the community and can subsequently be acted upon by selection. Our model is readily extensible into new areas of holobiont research and provides novel insights into holobiont evolution under variable environmental conditions.

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↗

bioRxiv2023

The genome of a globally invasive passerine, the common myna (Acridotheres tristis)

In an era of global climate change and massive environmental disturbance, biodiversity conservation is receiving increased attention. Conservation efforts are being greatly aided by genetic tools and approaches, which seek to understand patterns of genetic diversity and how they impact species health and ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions around adaptive potential, with a particular focus on how changes in genetic diversity and effective population size interact with the novel selection regime of the invaded range to drive rapid evolution. The common myna (Acridotheres tristis) is a globally invasive passerine, which has undergone multiple concurrent and sequential bottlenecks across its globally invasive range, and yet has established itself across a diverse array of ecological conditions. It is therefore an excellent model species for research both into the persistence of low-diversity populations and the mechanics of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna, assembled using a backbone of Oxford Nanopore Technologies long reads, alongside an RNA-seq based transcriptome and genome annotation. To provide genomic context for future studies, we describe the genomic landscape of this species, including genome wide allelic diversity, methylation, repeats, and recombination rate, as well as an examination of gene family expansions and contractions. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, but also reveal artefactual impacts of genetic bottlenecks on demographic analysis.

genomics↗

bioRxiv2023

Including the Invisible Fraction in Whole Population Studies: a Guide to the Genetic Sampling of Unhatched Bird Eggs

Early embryo mortality has recently been proven to be a significant component of avian reproductive failure. Due to the difficulty in distinguishing eggs which have suffered early embryo mortality from unfertilised eggs, this cause of reproductive failure has historically been underestimated and overlooked. We describe methods for recognising and collecting undeveloped, unhatched eggs from wild bird populations, identifying and isolating embryonic material in unhatched eggs, and efficiently extracting DNA from those samples. We test these methods on unhatched eggs collected from the field which have undergone post-mortem incubation. We obtained DNA yields from early-stage embryos that are sufficient for a wide range of molecular techniques, including microsatellite genotyping for parentage analysis and sex-typing. The type of tissue sample taken from the egg affected downstream DNA yields and microsatellite amplification rates. Species-specific microsatellite markers had higher amplification success rates than cross-species markers. We make key recommendations for each stage of the sampling and extraction process and suggest improvements potential and protocol modifications. Genetic and possibly genomic analysis of embryos that die early in development has the potential to advance many fields. The methods described here will allow a more in-depth exploration of the previously overlooked causes of early embryo mortality in wild populations of birds, including threatened species.

genetics↗

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↗

bioRxiv2019

A comparison of pedigree, genetic, and genomic estimates of relatedness for informing pairing decisions in two critically endangered birds.

Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimise relatedness between individuals in an effort to avoid inbreeding, maximise diversity, and maintain evolutionary potential. However, conservation breeding programmes struggle to use this approach when pedigrees are shallow or incomplete. While genetic data (i.e., microsatellites) can be used to estimate relatedness to inform pairing decisions, emerging evidence indicates this approach lacks precision in genetically depauperate species, and more effective estimates will likely be obtained from genomic data (i.e., thousands of genome-wide single nucleotide polymorphisms, or SNPs). Here, we compare relatedness estimates using pedigree-, genetic-, and genomic-based approaches for making pairing decisions in two critically endangered birds endemic to New Zealand: kak[i]/black stilt (Himantopus novaezelandiae) and k[a]k[a]riki karaka/orange-fronted parakeet (Cyanoramphus malherbi). Our findings indicate genetic-based estimates of relatedness are indeed the least precise when assessing known parent-offspring and full sibling relationships. Furthermore, our results show that relatedness estimates and subsequent pairing recommendations using PMx are most similar between pedigree- and genomic-based approaches. These combined results indicate that in lieu of robust pedigrees, SNPs are an effective tool for informing pairing decisions, which has exciting implications for many poorly pedigreed conservation breeding programmes worldwide.

molecular biology↗