Preliminary Results: Genomic surveys of six rare plant species in San Diego County Amy Vandergast, Elizabeth Milano, Jon Rebman and Margie Mulligan USGS Western Ecological Research Center; San Diego Natural History Museum Western Ecological Research Center San Diego Field Station Conservation Genetics Lab Assess genetic impacts of landscape and environmental change on animal and plant populations. • Coastal Cactus Wren • California Gnatcatcher • Southern Mule Deer • Western Pond Turtle https://portal.sdmmp.com/ Acanthomintha ilicfolia Baccharis vanessae Dicranostegia orcuttiana San Diego thornmint Encinitas baccharis Orcutt’s bird’s-beak Chloropyron maritimum ssp. Deinandra conjugens Monardella viminea maritimum Otay tarplant Willowy monardella Salt Marsh bird’s-beak Project Goals • Status of species and occurrences • Ploidy differences • Genetic diversity and connectivity • Baseline estimate for future monitoring Why is connectivity important? Discrete plant occurrences may be linked by pollen and seed dispersal Genetic connectivity Avoid inbreeding Maintenance of genetic diversity Flow of adaptive traits Impacts: spread of disease, invasives, disruption of local adaptation. Why is genetic diversity important? • Genetic diversity provides the raw materials for adaptation and evolution. • In outbreeding species, fitness is positively correlated with genetic diversity. Seed banking and reintroduction Introduce new genetic material into threatened population Three outcomes Population will recover and thrive Population will stay the same Population will decline Field Collections 99 total sites, ~450 individuals ploidy, ~1000 sequenced • Deinandra conjugens 17 sites • Baccharis vanessae 11 sites • Chloropyron maritimum ssp. maritimum 9 (27) sites • Dicranostegia orcuttiana 6 sites • Acanthomintha ilicifolia 24 sites • Monardella viminea 12 sites Flow Cytometry: Ploidy and Genome Size Genome Size Species N Ratio Mean Ratio St. Dev. (Gb) D. conjugens 79 4.14 0.26 6.7 Aster B. vanessae 55 4.10 0.28 6.5 Aster C. maritimum 45 (108) 1.50 0.25 2.3 Orobanchaceae ssp. maritimum D. orcuttiana 25 2.15 0.21 3.3 Orobanchaceae A. Ilicifolia 130 1.13 0.06 1.8 Mint M. viminea 58 1.21 0.08 2.1 Mint • No evidence of mixed ploidy Genetic Population Structure • Genetic data generated using RADseq • Diversity statistics • Principle component analysis • Genetic isolation by geographic distance • Genetic habitat associations, landscape features San Diego Thornmint Preliminary Results Encinitas Baccharis Preliminary Results Salt Marsh Bird’s Beak Preliminary Results Salt Marsh Bird’s Beak Preliminary Results Species Range Metrics for prioritization and decision-making • FST: Genetic differentiation • He: Genetic diversity • FIS: Inbreeding coefficient • Isolation by distance Future Work • Complete genetic analyses; final report Spring 2018 • Hold a workshop with experts, Spring 2018 • Review genetic data and other species information. • Categorize species into management priority groups, seed banking strategies. • Data will be incorporated into individual species management plans to be drafted by SDMMP. Partner Agencies and Land Preserves Back Country Land Trust The Nature Conservancy Conservation Biology Institute U.S. Fish and Wildlife Service California Department of Fish and Bureau of Land Management Wildlife City Encinitas Caltrans Escondido Creek Conservancy City of Chula Vista Helix Environmental City of Poway Olivenheim Water District City of San Diego Otay Water District County of San Diego NAVFAC SW Endangered Habitats Conservancy Marine Corps Base Camp Pendleton Marine Corps Air Station Miramar U.S. Forest Service Center for Natural Lands Management Western Ecological Research Center • Ecology • Conservation • Restoration • Monitoring • Modeling • Spatial Ecology • GIS Flow Cytometry www.abcam.com • Lower genetic diversity in reintroduced vs. natural populations in Sweetwater Marsh.