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Prioritization of communities for monitoring was based on the following criteria: representativeness, extent, fragmentation, endangerment and threats. Aggregated communities that received high priority rankings based on several criteria include CSS and meadows & freshwater wetlands. Communities with high endangerment or threats should also receive high priority and include: Southern foredunes, Southern coastal salt marsh, Southern coastal bluff scrub, Maritime succulent scrub, Diegan coastal sage scrub, Southern maritime chaparral, Valley needlegrass grassland, Cismontane alkali marsh, Southern arroyo willow riparian forest, Southern willow scrub, Engelmann oak woodland, Torrey Pine forest, and Tecate Cypress forest. This report will: describe the current state of the MSCP Preserve, discuss natural community assemblages and alternative vegetation community classifications for the MSCP, describe the use of landscape stratification based on environmental variables as an alternative to vegetation classification, discuss the grouping of communities for the monitoring program, and prioritize natural communities for monitoring protocol development.