Justification: Perennial shrubs and annual herbs form the foundation of California Sage Scrub (CSS) habitat (structure and food). Monitoring both perennial shrubs and annual plants is critical because diversity and abundance of shrubs tend to respond slowly to many stressors, whereas annual plants show large response to inter-annual variation in climate. Focusing on both perennial and annual plant species should allow us both to determine how short-term stressors influence plant diversity and abundance and to identify shifts associated with climate change and other disturbances.

Monitoring Protocol: The plant diversity protocol was designed to annually record percent cover, species composition, and species richness at sampling sites within CSS fragments. Sampling is conducted in spring when most annual plants are flowering. To standardize our data across CSS fragments, surveys will be conducted in April during peaks in annual diversity, particularly in inland CSS sites.

While site managers will decide the level of effort that is feasible, we recommend that each CSS fragment run a minimum of three transects in various locations. One should be in the area with the most intact CSS habitat. A second transect is recommended to be run in a different plant habitat type (e.g., non-native grassland or chaparral), if one exists adjacent to the CSS fragment. Additional transects should focus on CSS and chose sites based on the needs of the respective institution/site. With increased resources, we recommend increasing the number of transects and focusing efforts on CSS habitats. Additional transects, however, should only be run if managers can commit the effort to survey the sites over multiple years.

Permanent transects are 40 m long. Location of the beginning and the end of each transect will be staked and GPS locations recorded. It is recommended that photographs be taken at the beginning point of each transect each year prior to conducting the plant survey.

Plant surveys combine three elements:

  1. First, researchers will mark the species present, the number of times each species touches, and the maximum height of each species at every meter along the transect using the point-intercept method to provide an estimate of both basal and canopy cover. To standardize data, point-intercept data should be collected using a pole that is ¾ inches (~1.9 cm) in diameter. A PVC pole with 10-cm heights marked on the pole to 2 m is most often used. Previous work suggests that point-intercept data are more precise than those taken via visual cover estimates (Godinez-Alvarez et al. 2009) and are especially appropriate for studies in chaparral (Bauer 1943). Also, point-intercept methods are easy to teach quickly, as well as more objective and repeatable than visual cover estimates when carried out by multiple observers (Elzinga et al. 2009).
  2. Following the point-intercept method data collection, 1 m2-quadrats will be placed every 2 m along each transect. In each quadrat, all species will be identified to better record species richness of annuals. From 2017 forward, all quadrats will be placed on the right side of the transect, i.e., the side that is on the researcher’s right looking from the beginning of the transect to the end of the transect.
  3. Following quadrat measurements, researchers will record all additional species not recorded using previous methods within 5 m on either side of the transect line. This last step will allow us to make comparisons to surveys conducted by the CNPS (https://www.cnps.org/cnps/vegetation/pdf/rapid_assessment_protocol.pdf) using the rapid protocol. Identifications of all plants should be to species. When individuals cannot be identified to species, individuals should be identified to lowest taxonomic level, photographed and flagged for expert identification. Since species identification may require flower morphology, individual plants may need to be tracked and collaboration with experts within the network will be utilized.

For details on data management, please refer to the PRISSM plant diversity data management plan [link coming soon!].

PRISSM Plant Diversity Data 2015 – 2017


  • Bauer, H. L. 1943. The statistical analysis of chaparral and other plant communities by means of transect samples. Ecology 24: 45-60.
  • Elzinga, C.L., D.W. Salzer, J.W. Willoughby & J.P. Gibbs. 2009. Monitoring Plant and Animal Populations: A Handbook for Field Biologists. John Wiley & Sons, New York, USA.
  • Godinez-Alvarez, H., J.E. Herrick, M. Mattocks, D. Toledo & J. Van Zee. Comparison of three vegetation monitoring methods: Their relative utility for ecological assessment and monitoring. Ecological Indicators 9: 1001-1008.