Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project

H Bradley Shaffer; Erin Toffelmier; Russ B Corbett-Detig; Merly Escalona; Bjorn Erickson; Peggy Fiedler; Mark Gold; Ryan J Harrigan; Scott Hodges; Tara K Luckau; Courtney Miller; Daniel R Oliveira; Kevin E Shaffer; Beth Shapiro; Victoria L Sork; Ian J Wang

doi:10.1093/jhered/esac020

Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project

J Hered. 2022 Nov 30;113(6):577-588. doi: 10.1093/jhered/esac020.

Authors

H Bradley Shaffer^{1

2

3}, Erin Toffelmier^{1

2}, Russ B Corbett-Detig⁴, Merly Escalona⁴, Bjorn Erickson⁵, Peggy Fiedler⁶, Mark Gold⁷, Ryan J Harrigan^{2

8}, Scott Hodges⁹, Tara K Luckau^{1

2}, Courtney Miller^{1

2}, Daniel R Oliveira^{1

2}, Kevin E Shaffer³, Beth Shapiro^{10

11}, Victoria L Sork^{1

2}, Ian J Wang^{12

13}

Affiliations

¹ Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.
² La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.
³ California Department of Fish and Wildlife, Fisheries Branch, West Sacramento, CA 95605, USA.
⁴ Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
⁵ U.S. Fish and Wildlife Service, Sacramento, CA 95825, USA.
⁶ Natural Reserve System, Office of the President, University of California, Oakland, CA 94607, USA.
⁷ California Natural Resources Agency, 1416 Ninth Street, Suite 1311, Sacramento, CA 95814, USA.
⁸ Center for Tropical Research, Institute for Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.
⁹ Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA.
¹⁰ Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
¹¹ Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
¹² Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA.
¹³ Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA.

PMID: 35395669
DOI: 10.1093/jhered/esac020

Abstract

The California Conservation Genomics Project (CCGP) is a unique, critically important step forward in the use of comprehensive landscape genetic data to modernize natural resource management at a regional scale. We describe the CCGP, including all aspects of project administration, data collection, current progress, and future challenges. The CCGP will generate, analyze, and curate a single high-quality reference genome and 100-150 resequenced genomes for each of 153 species projects (representing 235 individual species) that span the ecological and phylogenetic breadth of California's marine, freshwater, and terrestrial ecosystems. The resulting portfolio of roughly 20 000 resequenced genomes will be analyzed with identical informatic and landscape genomic pipelines, providing a comprehensive overview of hotspots of within-species genomic diversity, potential and realized corridors connecting these hotspots, regions of reduced diversity requiring genetic rescue, and the distribution of variation critical for rapid climate adaptation. After 2 years of concerted effort, full funding ($12M USD) has been secured, species identified, and funds distributed to 68 laboratories and 114 investigators drawn from all 10 University of California campuses. The remaining phases of the CCGP include completion of data collection and analyses, and delivery of the resulting genomic data and inferences to state and federal regulatory agencies to help stabilize species declines. The aspirational goals of the CCGP are to identify geographic regions that are critical to long-term preservation of California biodiversity, prioritize those regions based on defensible genomic criteria, and provide foundational knowledge that informs management strategies at both the individual species and ecosystem levels.

Keywords: California Floristic Province; climate change; landscape genetics; non-model organism; whole-genome resequencing.

Publication types

Review
Research Support, Non-U.S. Gov't

MeSH terms

Biodiversity*
California
Conservation of Natural Resources
Ecosystem*
Fresh Water
Genomics
Phylogeny