Biology subjects

Vercoe, D.

Publications and source records attributed to Vercoe, D..

3 recordsLinked to original sources

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

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↗