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Techniques and Challenges in Conservation Genomics

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  • Techniques and Challenges in Conservation Genomics

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    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research has been focused on developing tools for conservation genomics. With his love of birds and fascination with their migration, DeSaix supported various conservation projects on avian species. Uniting this passion with genomics and its evolving technologies was the perfect combination for his conservation work.

    A key technique utilized in his research was low-coverage whole genome sequencing (lcWGS). While noting the utility of methods like RAD-seq and ddRAD-seq, DeSaix shared that lcWGS stands out for its ability to analyze numerous organisms at a significantly reduced cost. This approach has enhanced the understanding of population genetic structures and facilitated broader sampling across diverse geographic ranges. Additionally, lcWGS has greatly benefited large-scale projects like the Bird Genoscape Project undertaken by the Ruegg Lab, an initiative that aims to map the genoscapes of at least 100 bird species and use these insights to assist in the conservation of declining migratory bird populations.

    In the course of his doctoral research with lcWGS data, DeSaix identified a gap in the field: the lack of tools for conducting population assignment analysis using genotype likelihood data. To fill this gap, DeSaix began a collaboration with Eric Anderson, a statistical geneticist with NOAA, to develop a new software called WGSassign. This tool allows the calculation of allele frequencies in different reference groups, provides the ability for users to conduct leave-one-out cross-validation with these groups, and assists in classifying individuals of unknown origin into the appropriate reference groups. Importantly, WGSassign has shown uses outside of avian research and has been aiding researchers with similar challenges in fields such as fisheries management.

    More recently, DeSaix is utilizing his extensive knowledge in his new role at the USDA's Animal Plant Health Inspection Service (APHIS) to manage the movement of feral swine. While focused on a very different species, this work utilizes similar genomic methods to understand and manage wildlife populations effectively. His current work also contributes to our knowledge of diseases like African swine fever and their impact on agriculture. DeSaix noted how the crossover between his work with birds and the management of feral swine demonstrates the broad applicability of genomic tools in various aspects of conservation genomics.


    Advancements and Applications
    After recently obtaining her doctoral degree from the Meek Lab at Michigan State University, Miranda Wade began a postdoctoral position at the University of Hong Kong. Her dissertation work examined the effects of microplastics on gene expression and methylation in minnows; she utilized model organisms to draw broader conclusions about species of conservation concern. Although the official findings are still pending publication, Wade noted that there were significant differences observed between minnows exposed to microplastics and controls, which highlights the potential impact of environmental pollutants.

    In her postdoctoral research, Wade shifted her focus to the evolution of sexual dimorphism in the bird family Cardinalidae, along with projects investigating amphibians from Hong Kong. Throughout her academic career, Wade employed a diverse range of methodologies, including RAD-seq, mRNA sequencing for expression analysis, and enzyme-based methylation sequencing for epigenetics research. Despite the intensive learning required to master each of these methods, Wade has continued to expand her genomics toolkit, most recently with whole genome resequencing data analysis.

    “The field of genomics, in general, has really benefitted from the exponential increase in technology, even from the time I started my Ph.D. to now,” explained Wade. “The dramatic decrease in sequencing costs has allowed people to transition to using whole-genome methods instead of SNPs (or even microsatellites) to investigate questions.” However, Wade has raised important questions about the implications of managing and storing large volumes of data in conservation efforts and wonders whether there is a limit on how much information is truly needed to make conservation decisions. Given the increased technical knowledge required to analyze and interpret results, Wade ponders the true applicability of these new methods for decision-makers and resource managers.

    Nonetheless, Wade expressed enthusiasm for numerous advancements within her field, especially the development of the CRISPR-based SHERLOCK method for species identification. This technique employs cellular machinery to identify species-specific genetic variations. Additionally, the results can be analyzed using qPCR, specialized instruments, or, more recently, through test strips similar to at-home COVID-19 testing kits. Wade praised that this is a prime demonstration of how technologies from various genetic research areas are being combined to improve conservation efforts.


    Challenges and the Future of Conservation Genomics
    Outside of the more obvious issues like a lack of funding, both Wade and DeSaix emphasized several other obstacles in the field of conservation genomics. In particular, Wade stressed the constant race against time to address biodiversity crises. She pointed out the inherent delays in genomics research between sample collection and extensive analysis that slow down timely conservation actions. These lag times are further compounded when it comes to sharing scientific findings with non-experts and various organizations in a way that is accessible and clear. Furthermore, Wade acknowledged that conservation genomics is a discipline that is continually racing against the ongoing climate crisis and that the stress from this race can often sap motivation and lead to the fear of failure. She recommends fostering a supportive community and suggests that this is key to success in science and life in general.

    For DeSaix, two primary challenges in the field hinder the application and impact of research. The first challenge is the increased complexity and technical demands of genomics research that often require specialized staff with extensive bioinformatics knowledge and advanced computing tools. This can be a huge barrier for conservation organizations that lack the training, infrastructure, or funds to perform this work. According to DeSaix, interdisciplinary partnerships are crucial for overcoming these hurdles and driving the field forward.

    Similar to Wade’s comments, the second major challenge is the difficulties involved in translating research findings into actionable strategies for conservation experts, decision-makers, and policymakers. He explained that the gap between generating scientific knowledge and its practical application has been bridged in initiatives like the Bird Genoscape Project, where each study was paired with a management agency that ensured the research outcomes were utilized for conservation planning and action. DeSaix remains hopeful about others overcoming this disconnect and believes that the decreasing cost of genomics research will make it more accessible to conservation groups and lead to its broader application in conservation policy.

    As for the future of the field, Wade shared, “I would love to see conservation genetics head toward more field-deployable genotyping methods for immediate species or even population delimitation.” She highlighted her excitement for the methods currently being tested and refined, like iCatch, which is being developed by her former Ph.D. lab colleagues. These advancements could greatly benefit natural resource managers by providing immediate data on the conservation status of organisms encountered in the field.
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    About the Author

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    seqadmin Benjamin Atha holds a B.A. in biology from Hood College and an M.S. in biological sciences from Towson University. With over 9 years of hands-on laboratory experience, he's well-versed in next-generation sequencing systems. Ben is currently the editor for SEQanswers. Find out more about seqadmin

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      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

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