Community phylogeny of the globally critically imperiled pine rockland ecosystem

Management of a Globally Imperiled and Fire-Dependent Ecosystem in the Urban Matrix of Miami–Dade County, Florida: A Case Study of the Richmond Tract Pine Rocklands

Pine rockland habitat of South Florida is among the most highly threatened terrestrial ecosystems in the neo-subtropics and is among the rarest worldwide. With only 1.2% of its original extent remaining outside Everglades National Park, fewer than 780 hectares of this ecosystem remains across all of South Florida. This fire-dependent ecosystem—habitat for many rare, endemic species—has experienced substantial deforestation and defaunation due to urbanization, land use change, habitat fragmentation, fire suppression, and exotic plant invasions. Owing to the small size of remaining fragments, and the fact that most are surrounded by urbanization, adequate burning regimes are suppressed. The Richmond Tract, a complex of twelve separate parcels under multiple private and public ownership partially surrounding Zoo Miami, is the largest tract of pine rockland outside the federal protection of Everglades National Park. In this article, we take inventory of the threatened biodiversity at the Richmond Tract and focus on the policy and management landscape. We take a close look at threats to the pine rockland’s persistence here and review approaches that either help maintain the health of this ecosystem or those that may need to be reconsidered. We end by discussing coordination among multiple stakeholder groups, the potential use for incentive-based conservation practices, and suggesting ways to improve management in highly urbanized South Florida.

Native ectomycorrhizal fungi from the endangered pine rocklands are superior symbionts to commercial inoculum for slash pine seedlings

The south Florida pine rocklands is a critically endangered, fire-dependent ecosystem dominated by the overstory tree Pinus densa (South Florida slash pine). Because pine recruitment in this ecosystem has proven problematic, restoration efforts need to include replanting slash pine trees. Even though ectomycorrhizal fungi are known to be critical symbionts of young pines and are necessary for the development of healthy pines, virtually nothing is known about these mutualists and their role in pine establishment and survival in the pine rocklands. One approach to improve pine establishment is to grow seedlings in a nursery before outplanting, facilitating early associations with ectomycorrhizae, and therefore improving seedling health. In this study, we compared health metrics (height, stem diameter, final needle length, root length, root colonization, needle greenness, root volume, and root:shoot ratio) of seedlings grown in soil amended with five commercially available mycorrhizal inocula versus field soil collected from three pine rockland fragments. Seedlings grown with native field soil from the pine rocklands generally performed better than those grown with commercial inoculum in all metrics except root length. According to their labels, each commercial inoculum contained between 4 and 10 ectomycorrhizal fungi species. However, no ectomycorrhizal fungi were recovered from two of the inoculum products and only three ectomycorrhizal fungi in total were recovered from the other three products. In contrast, seedlings grown with field soil are associated with ten ectomycorrhizal species. Our results highlight the importance of incorporating native ectomycorrhizal fungi into pine seedling replanting as part of restoration efforts in the pine rocklands.

For common community phylogenetic analyses, go ahead and use synthesis phylogenies

Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort, expertise, and cost than subsetting an already available phylogeny (synthesis-based phylogeny). However, we still lack a comparison of how these two approaches to building phylogenetic trees influence common community phylogenetic analyses such as comparing community phylogenetic diversity and estimating trait phylogenetic signal. Here, we generated three purpose-built phylogenies and their corresponding synthesis-based trees (two from Phylomatic and one from the Open Tree of Life, OTL). We simulated 1,000 communities and 12,000 continuous traits along each purpose-built phylogeny. We then compared the effects of different trees on estimates of phylogenetic diversity (alpha and beta) and phylogenetic signal (Pagel's λ and Blomberg's K). Synthesis-based phylogenies generally yielded higher estimates of phylogenetic diversity when compared to purpose-built phylogenies. However, resulting measures of phylogenetic diversity from both types of phylogenies were highly correlated (Spearman's ρ  > 0.8 in most cases). Mean pairwise distance (both alpha and beta) is the index that is most robust to the differences in tree construction that we tested. Measures of phylogenetic diversity based on the OTL showed the highest correlation with measures based on the purpose-built phylogenies. Trait phylogenetic signal estimated with synthesis-based phylogenies, especially from the OTL, was also highly correlated with estimates of Blomberg's K or close to Pagel's λ from purpose-built phylogenies when traits were simulated under Brownian motion. For commonly employed community phylogenetic analyses, our results justify taking advantage of recently developed and continuously improving synthesis trees, especially the Open Tree of Life.