Mid-Term Assessment of Progress on the 2015 Strategic Vision for Antarctic and Southern Ocean Research (2021) / Chapter Skim
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3 Priority II: Using Genomics to Understand How Antarctic Biota Evolve and Adapt
3 Priority II: Using Genomics to Understand How Antarctic Biota Evolve and Adapt
Pages 55-76
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From page 55... ...
identified "How do Antarctic biota evolve and adapt to the changing environment? Decoding the genomic and transcriptomic bases of biological adaptation" as Strategic Priority II, outlining three key areas under Priority II that were primed for transformational advances: i.
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From page 56... ...
In early 2019, OPP issued a "Dear Colleague Letter" (NSF 19-045, Genetic Underpinnings for Life in Antarctica or ANT-LIA) to advance Priority II, which encouraged Antarctic research focused on "understanding the genetic underpinnings of organismal adaptations to their current environment and ways in which extant biota and ecosystems respond to changing conditions over different spatial and temporal scales." The letter emphasized integration of Priority II goals with three of NSF's 10 Big Ideas: Understanding the Rules of Life, Harnessing the
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From page 57... ...
Genetics and genomics are not synonymous, and many organisms that cannot be analyzed genetically are nonetheless amenable to genomic analysis and other omics technologies that yield important biological insights. Furthermore, the Dear Colleague Letter specifically excluded proposals that "simply describe species presence or construct genomes," in contrast to the 2015 report, which stated "the fundamental unexplored frontier is the genomic information encoded within Antarctic organisms." Sequences from viruses to mammals are often required to reveal genetic diversity prior to understanding functional and evolutionary implications.
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From page 58... ...
that address Priority II either fully or in part. The funding plot reflects the total sum of project awards, rather than a fractional estimate of project funding that addressed Priority II.
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From page 59... ...
This increase in funding was less evident when NSF's original classifications were used, likely because NSF's broader definition of genomics blurred the distinction between molecular and genetic research, which has long been supported by the AOE program, and genomics and omics research, which was the emphasis of the 2015 NASEM report. Because omics research has rapidly increased over the past 10 years, the committee was not able to parse the extent to which the increased OPP funding of Antarctic omics research reflected greater interest in, and use of, these technologies by investigators versus a concerted effort by OPP to address Priority II.
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From page 60... ...
The Antarctic Genomics Initiative has yet to be realized due to numerous reasons, including the broad scope of Priority II in the context of organismal diversity and the limitations in OPP resources. Priority II implementation challenges are discussed in more detail later in the chapter.
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SCIENTIFIC COMMUNITY AND PARTNERSHIPS The U.S. Antarctic biology community has yet to organize itself to develop large-scale genome initiatives that are organized around phylogenetically informed
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From page 62... ...
Studies of the shelled pteropod Limacina helicina (e) underscore the sensitivity of calcification processes to Southern Ocean acidification.
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From page 63... ...
The 2019 Dear Colleague Letter called for proposals to fund conferences that would "advance understanding of how Antarctic biota evolve and adapt to unique and ever-changing Antarctic environments." One collaborative research project, which included a training workshop, has been funded. Two other workshops related to Priority II were funded3 between 2017 and 2019.
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From page 64... ...
, rather than the traditional OPP research model based on individual investigators or small teams. To elucidate the genomic and phenotypic mechanisms that have allowed, and will continue to allow, Antarctic biota to evolve and adapt in a changing Antarctic environment, researchers will need to advance interdisciplinary collaborative approaches.
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From page 65... ...
Beyond data standards, access to Antarctic omics datasets and associated contextual information is currently an onerous task, mostly limited to literature or targeted National Center of Biotechnology Information (NCBI) searches.
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From page 66... ...
This committee was not able to determine the extent to which previously collected samples were used in new omics projects, and NSF did not promote sample sharing until recently. However, NSF's recent call for reuse of samples and data (Dear Colleague Letter, NSF DCL 21-041)
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From page 67... ...
Although this aspect of omics research was not extensively developed in the NASEM (2015) report, the present committee judges that concurrent measurements of dynamic Antarctic environments are crucial because they provide the context for understanding the omics of organisms and assemblages.
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From page 68... ...
, the American Geophysical Union, the Association for Sciences of Limnology and Oceanography, the Society for Integrative and Comparative Biology International Polar and Alpine Microbiology Conference, and the American Society for Microbiology) , generating a critical mass of principal investigators to promote Antarctic omics research in any given organization is extremely difficult.
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From page 69... ...
Foundational, phylogenetically informed genome "collections" would establish new Antarctic model organisms and organismal assemblages and set the stage for derived omics studies that embrace questions of adaptation and response. Historically, NSF has discouraged non-hypothesis-driven proposals, and the 2019 Dear Colleague Letter excluded genome-only projects.
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From page 70... ...
NSF could also build capacity by supporting U.S.-based courses that focus on omics technologies and recruit polar biology researchers to participate in them. There are also pressing needs to train Antarctic life scientists in bioinformatics.
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From page 71... ...
Progress in this area has been initiated through the SCAR Biodiversity Informatics data portal.8 A seed project targeting Antarctic microbial diversity and genomics has been initiated in which environmental datasets can be uploaded and associated with microbial genomics data deposited in publicly accessible data bases.9 Enhancements along these lines could significantly foster communication and comparative genomics across the field of Antarctic life sciences. 8 See http://biodiversity.aq.
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From page 72... ...
Community guidance to NSF and an Antarctic Genomics Initiative are the key missing links to advance Priority II omics research. The Antarctic biology community should conduct a series of workshops to develop a phylogenetically informed strategy to prioritize representative taxa and species assemblages for omics analyses that address the three Priority II emphases.
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From page 73... ...
NSF could encourage Antarctic life science researchers to link to, or develop, programs to address big data questions for Antarctic biology and build data-access-enabled resources through the Polar Cyberinfrastructure program in coordination with the NSF Office of Advanced Cyberinfrastructure. Reaching outside of NSF to build partnerships for omics resources, infrastructure sharing, and access will also be essential to realize the research objectives identified in NASEM (2015)
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From page 74... ...
A call for proposals with clear and updated objectives, emphasizing the use of omics technologies to understand diversity, adaptation, and evolution in the context of environmental change, could expand interest both inside and beyond the Antarctic sciences community -- particularly if larger, coordinated, multi-investigator submissions are encouraged. NSF should evaluate opportunities to enhance access to organisms, samples, and data to advance Priority II science and address logistics challenges that limit access.
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From page 75... ...
Upgrades to Antarctic research facilities and vessels to allow real-time genomic analyses to inform ongoing experiments and to facilitate more process-oriented research of biota in their environment so that evolutionary adaptations can be understood in context. In all cases, additional attention to data management is needed to improve access to ‘omics data, metadata, and associated contextual information.
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