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Abstract Phylogenetic diversity offers critical insights into the ecological dynamics shaping species composition and ecosystem function, thereby informing conservation strategies. Despite its recognized importance in ecosystem management, the assessment of phylogenetic diversity in endangered habitats, such as vernal pools, remains limited. Vernal pools, characterized by cyclical inundation and unique plant communities, present an ideal system for investigating the interplay between ecological factors and phylogenetic structure. This study aims to characterize the phylogenetic patterns of vernal pools and their associated vegetation zones, addressing questions about taxonomic and phylogenetic community discreteness, the role of flooding as a habitat filter, the influence of invasive species on phylogenetic structure, and the impact of seasonal variation on phylogenetic diversity. I find that zones‐of‐vegetation exhibit high between zone taxonomic and phylogenetic beta diversity whereas each zone forms a unique cluster, suggesting that zones are taxonomically and phylogenetically discrete units. Regions of high‐inundation pressure exhibit phylogenetic clustering, indicating that flooding is a habitat filter in vernal pool habitats. Competition between native species conform to the ‘competitive relatedness hypothesis’ and, conversely, communities dominated by invasive Eurasian grass species are phylogenetically clustered. In addition, I find that phylogenetic diversity within zones fluctuates across the spring season in response to changing water levels, precipitation, and temperature. By analyzing three pools within the Merced Vernal Pool and Grassland Reserve, this research elucidates the phylogenetic dynamics of vernal pools. The findings underscore the need for tailored conservation strategies that account for the unique ecological characteristics of each vegetation zone within vernal pool habitats. |
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