Finding needles in haystacks: Linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.B.R. and C.L.S. acknowledge support from the Intramural Research Program of the National Institutes of Health, National Library of MedicinePeer Reviewe

Strong floristic distinctiveness across Neotropical successional forests

Forests that regrow naturally on abandoned fields are important for restoring biodiversity and ecosystem services, but can they also preserve the distinct regional tree floras? Using the floristic composition of 1215 early successional forests (≤20 years) in 75 human-modified landscapes across the Neotropic realm, we identified 14 distinct floristic groups, with a between-group dissimilarity of 0.97. Floristic groups were associated with location, bioregions, soil pH, temperature seasonality, and water availability. Hence, there is large continental-scale variation in the species composition of early successional forests, which is mainly associated with biogeographic and environmental factors but not with human disturbance indicators. This floristic distinctiveness is partially driven by regionally restricted species belonging to widespread genera. Early secondary forests contribute therefore to restoring and conserving the distinctiveness of bioregions across the Neotropical realm, and forest restoration initiatives should use local species to assure that these distinct floras are maintained

Multidimensional tropical forest recovery

Tropical forests disappear rapidly because of deforestation, yet they have the potential to regrow naturally on abandoned lands. We analyze how 12 forest attributes recover during secondary succession and how their recovery is interrelated using 77 sites across the tropics. Tropical forests are highly resilient to low-intensity land use; after 20 years, forest attributes attain 78% (33 to 100%) of their old-growth values. Recovery to 90% of old-growth values is fastest for soil (12 decades). Network analysis shows three independent clusters of attribute recovery, related to structure, species diversity, and species composition. Secondary forests should be embraced as a low-cost, natural solution for ecosystem restoration, climate change mitigation, and biodiversity conservation

Multidimensional tropical forest recovery

Tropical forests disappear rapidly because of deforestation, yet they have the potential to regrow naturally on abandoned lands. We analyze how 12 forest attributes recover during secondary succession and how their recovery is interrelated using 77 sites across the tropics. Tropical forests are highly resilient to low-intensity land use; after 20 years, forest attributes attain 78% (33 to 100%) of their old-growth values. Recovery to 90% of old-growth values is fastest for soil (12 decades). Network analysis shows three independent clusters of attribute recovery, related to structure, species diversity, and species composition. Secondary forests should be embraced as a low-cost, natural solution for ecosystem restoration, climate change mitigation, and biodiversity conservation