Better tools, better resources, better conservation: integrating genome data into the conservation of the pink pigeon Nesoenas mayeri

Ryan, Camilla (2021) Better tools, better resources, better conservation: integrating genome data into the conservation of the pink pigeon Nesoenas mayeri. Doctoral thesis, University of East Anglia.

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Humans are driving the sixth mass extinction causing biodiversity to decline at an unprecedented rate. To halt these declines effective conservation strategies are vital, if possible, these should include genetic data to ensure that the extinction risk of a population is not being underestimated. This thesis presents resources and tools that have been used to integrate genetic data into the management of the endangered pink pigeon (Nesoenas mayeri). A pseudo-chromosome assembly enabled the first whole genome analyses of the pink pigeon (Chapter 2), these analyses provided insight into their past demography and revealed a surprisingly large amount of variation within its genome. This challenges previous results obtained using restriction site associated DNA sequencing (RAD-Seq) data from wild pink pigeons but current methods for processing RAD data produce biased data sets that under-estimate diversity. A novel tool, RADiKal is presented (Chapter 3), which extracts information directly from raw RAD reads and avoids biasing data sets with complex parameterisation. The painted chromosomes produced by RADiKal provide an overview about the levels of variation present in the wild population which are comparable to those observed from whole genome analyses. Despite increasing access to genetic data one of the greatest challenges is its integration into management, one solution is the use of population viability analysis (PVA). An updated PVA was produced for pink pigeons showing that without genetic rescue they could face extinction within 100 years (Chapter 4). Selecting which individuals are most valuable for a genetic rescue is not trivial, especially in the absence of empirical data. I Choose You (I.C.Y) is an easy-to-use tool that allows practitioners to select individuals for genetic rescue based on their genetic diversity measured using founder equivalents calculated from studbook data (Chapter 5). Overall this thesis aims to demonstrate how better tools can lead to better resources and better conservation.

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Science > School of Environmental Sciences
Depositing User: Chris White
Date Deposited: 09 Mar 2022 11:41
Last Modified: 10 Mar 2022 14:50


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