Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project
2022/04/08 by H. Bradley Shaffer, H Bradley Shaffer, Erin Toffelmier +21 · 1 voice · 164 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Biodiversity #Biology #Ecology #Environmental DNA in Biodiversity Studies #Environmental resource management #Genetic diversity and population structure #Genetics #Genome #Genomics #Geography #Species Distribution and Climate Change
paper · pdf · doi:10.1093/jhered/esac020
published in Journal of Heredity 113(6), 577-588 (Oxford University Press)
openalex publication_date 2022/04/08 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/30
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.
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