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A Biodiversity Composition Map of California Derived from Environmental DNA Metabarcoding and Earth Observation

View ORCID ProfileMeixi Lin, View ORCID ProfileAriel Levi Simons, Emily E. Curd, Ryan J. Harrigan, View ORCID ProfileFabian D. Schneider, View ORCID ProfileDannise V. Ruiz-Ramos, Zack Gold, View ORCID ProfileMelisa G. Osborne, View ORCID ProfileSabrina Shirazi, Teia M. Schweizer, View ORCID ProfileTiara N. Moore, Emma A. Fox, View ORCID ProfileRachel Turba, Ana E. Garcia-Vedrenne, Sarah K. Helman, Kelsi Rutledge, Maura Palacios Mejia, View ORCID ProfileMiroslava N. Munguia Ramos, View ORCID ProfileRegina Wetzer, Dean Pentcheff, View ORCID ProfileEmily Jane McTavish, View ORCID ProfileMichael N. Dawson, View ORCID ProfileBeth Shapiro, Robert K. Wayne, View ORCID ProfileRachel S. Meyer
doi: https://doi.org/10.1101/2020.06.19.160374
Meixi Lin
1Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
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Ariel Levi Simons
2Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA 90089, USA
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Emily E. Curd
1Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
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Ryan J. Harrigan
1Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
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Fabian D. Schneider
3Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91009, USA
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Dannise V. Ruiz-Ramos
4U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO 65201, USA
5Department of Life & Environmental Sciences, University of California-Merced, Merced, CA 95343, USA
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Zack Gold
1Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
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Melisa G. Osborne
6Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
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  • ORCID record for Melisa G. Osborne
Sabrina Shirazi
7Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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Teia M. Schweizer
1Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
8Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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Tiara N. Moore
1Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
9School of Environmental and Forestry Sciences, University of Washington, Seattle, WA 98195, USA
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Emma A. Fox
1Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
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Rachel Turba
1Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
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Ana E. Garcia-Vedrenne
1Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
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Sarah K. Helman
1Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
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Kelsi Rutledge
1Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
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Maura Palacios Mejia
1Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
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Miroslava N. Munguia Ramos
1Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
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Regina Wetzer
10Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
11Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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Dean Pentcheff
10Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
11Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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Emily Jane McTavish
5Department of Life & Environmental Sciences, University of California-Merced, Merced, CA 95343, USA
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Michael N. Dawson
5Department of Life & Environmental Sciences, University of California-Merced, Merced, CA 95343, USA
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Beth Shapiro
7Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
12Howard Hughes Medical Institute, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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Robert K. Wayne
1Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
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Rachel S. Meyer
1Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
7Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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  • For correspondence: rsmeyer@ucla.edu
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Abstract

Unique ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. We offer a way to use environmental DNA, community science and remote sensing together as methods to reduce the discrepancy between the magnitude of change and historical approaches to measure it. Taking advantages of modern ecological models, we integrate environmental DNA and Earth observations to evaluate regional biodiversity patterns for a snapshot of time, and provide critical community-level characterization. We collected 278 samples in Spring 2017 from coastal, shrub and lowland forest sites in California, a large-scale biodiversity hotspot. We applied gradient forest to model 915 family occurrences and community composition together with environmental variables and multi-scalar habitat classifications to produce a statewide biodiversity-based map. 16,118 taxonomic entries recovered were associated with environmental variables to test their predictive strength on alpha, beta, and zeta diversity. Local habitat classification was diagnostic of community composition, illuminating a characteristic of biodiversity hotspots. Using gradient forest models, environmental variables predicted 35% of the variance in eDNA patterns at the family level, with elevation, sand percentage, and greenness (NDVI32) as the top predictors. This predictive power was higher than we found in published literature at global scale. In addition to this indication of substantial environmental filtering, we also found a positive relationship between environmentally predicted families and their numbers of biotic interactions. In aggregate, these analyses showed that strong eDNA community-environment correlation is a general characteristic of temperate ecosystems, and may explain why communities easily destabilize under disturbances. Our study provides the first example of integrating citizen science based eDNA with biodiversity mapping across the tree of life, with promises to produce large scale, high resolution assessments that promote a more comprehensive and predictive understanding of the factors that influence biodiversity and enhance its maintenance.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/meixilin/caledna_transect

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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A Biodiversity Composition Map of California Derived from Environmental DNA Metabarcoding and Earth Observation
Meixi Lin, Ariel Levi Simons, Emily E. Curd, Ryan J. Harrigan, Fabian D. Schneider, Dannise V. Ruiz-Ramos, Zack Gold, Melisa G. Osborne, Sabrina Shirazi, Teia M. Schweizer, Tiara N. Moore, Emma A. Fox, Rachel Turba, Ana E. Garcia-Vedrenne, Sarah K. Helman, Kelsi Rutledge, Maura Palacios Mejia, Miroslava N. Munguia Ramos, Regina Wetzer, Dean Pentcheff, Emily Jane McTavish, Michael N. Dawson, Beth Shapiro, Robert K. Wayne, Rachel S. Meyer
bioRxiv 2020.06.19.160374; doi: https://doi.org/10.1101/2020.06.19.160374
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A Biodiversity Composition Map of California Derived from Environmental DNA Metabarcoding and Earth Observation
Meixi Lin, Ariel Levi Simons, Emily E. Curd, Ryan J. Harrigan, Fabian D. Schneider, Dannise V. Ruiz-Ramos, Zack Gold, Melisa G. Osborne, Sabrina Shirazi, Teia M. Schweizer, Tiara N. Moore, Emma A. Fox, Rachel Turba, Ana E. Garcia-Vedrenne, Sarah K. Helman, Kelsi Rutledge, Maura Palacios Mejia, Miroslava N. Munguia Ramos, Regina Wetzer, Dean Pentcheff, Emily Jane McTavish, Michael N. Dawson, Beth Shapiro, Robert K. Wayne, Rachel S. Meyer
bioRxiv 2020.06.19.160374; doi: https://doi.org/10.1101/2020.06.19.160374

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