ORCID Profile
0000-0001-8095-4282
Current Organisation
University of Canterbury
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Publisher: Wiley
Date: 12-09-2021
DOI: 10.1111/MEC.16141
Abstract: Structural variants (SVs) are large rearrangements ( bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on in idual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future‐focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP‐based approaches to enhance species recovery. We also leverage the existing literature–predominantly in human health, agriculture and ecoevolutionary biology–to identify approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we manage some of the world's most threatened species.
Publisher: Cold Spring Harbor Laboratory
Date: 24-10-2022
DOI: 10.1101/2022.10.22.513130
Abstract: The kākāpō 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 in iduals living in early 2018 (169 in iduals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to quantify genome-wide ersity 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 ersity and ersity in breeding values, and hence, evolutionary potential. We provide new pathways for informing future conservation management decisions for kākāpō, including prioritizing in iduals for translocation and monitoring in iduals with poor growth or high disease risk. Overall, by explicitly addressing the challenge of small s le size, we provide a template for the inclusion of genomic data that will be transformational for species recovery efforts around the globe.
Publisher: Wiley
Date: 22-10-2021
DOI: 10.1111/MEC.16192
Abstract: Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long‐standing tools available to manage genetics—the pedigree—has been widely used to characterize ersity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome‐wide functional ersity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well‐informed s ling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities.
Publisher: Springer Science and Business Media LLC
Date: 28-08-2023
No related grants have been discovered for Jana Renee Wold.