Dryad
Published April 11, 2021 | Version v1
Dataset Open

Unifying community detection across scales from genomes to landscapes

Creators

  • 1. Boise State University
  • 2. Conservation International
  • 3. Washington State University
  • 4. Agricultural Research Service
  • 5. University of Nevada Reno

Description

Biodiversity science encompasses multiple disciplines and biological scales from molecules to landscapes. Nevertheless, biodiversity data are often analyzed separately with discipline-specific methodologies, constraining resulting inferences to a single scale. To overcome this, we present a topic modeling framework to analyze community composition in cross-disciplinary datasets, including those generated from metagenomics, metabolomics, field ecology, and remote sensing. Using topic models, we demonstrate how community detection in different datasets can inform the conservation of interacting plants and herbivores. We show how topic models can identify members of molecular, organismal, and landscape-level communities that relate to wildlife health, from gut microbes to forage quality. We conclude with a future vision for how topic modeling can be used to design cross-scale studies that promote a holistic approach to detect, monitor, and manage biodiversity.

Notes

Please see ReadMe file and Supporting Information for methodologcal and modeling details.

Funding provided by: National Aeronautics and Space Administration
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000104
Award Number: 80NSCCC17K0738

Funding provided by: Idaho State Board of Education
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100013375
Award Number: IGEM19-002

Funding provided by: Semiconductor Research Corporation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000028
Award Number: SRC 2018-SB-2842

Funding provided by: Idaho Department of Fish and Game
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100010374
Award Number: Pittman-Robertson 683 Funds

Funding provided by: Sigma Xi Grants-In-Aid*
Crossref Funder Registry ID:
Award Number:

Funding provided by: U.S. Bureau of Land Management
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100007149
Award Number: L09AC16253

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: IOS-1258217

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: DEB-1146194

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: DEB-1146368

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: OIA-1826801

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: OIA-1757324

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: OIA-1738865

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: ECCS-1807809

Funding provided by: Sigma Xi Grants-In-Aid
Crossref Funder Registry ID:

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