Tropical South America Diatom Database (TSADB)

Determining the mechanisms of community assembly forms the foundation of biogeography and community ecology. Studies of the biodiversity of Neotropical macro-organisms have helped recognized the roles of environmental, spatial, and historical factors in structuring communities at different spatial and temporal scales, but these roles on microorganisms are still poorly unknown. Diatoms are a very species-rich group of algae, disperse widely, and sensitive to environmental variation due to their position in the base of aquatic food webs. Here, we present the Tropical South American Diatom Database (TSADB) which contains distributional patterns of species across lentic and lotic environments, including predictors that describe local (limnology) and regional (geo-climatic) factors. The information contained can be used to tackle fundamental questions in macroecology using diatoms as model organisms, including metacommunity ecology and biogeography research. From an applied perspective, the consideration of niche and dispersal factors can be used to develop multiple hypotheses on the mechanisms driving microbial diversity and community assembly, with special emphasis on biomonitoring, long-term ecological change, and biodiversity trends. The TSADB includes 326 sites containing 437 samples distributed across 26 regions (0 to 5,070 m a.s.l, and between 8°N–35°S; 58–90°W). In addition, long-term, diatom-based paleolimnological records are presented as a complementary tool for identifying well-resolved regions with modern and paleorecords for a truly long-term limnological change observatory in tropical Americas. We describe the TSADB structure and functionality, as well as R codes to manipulate and visualize the data. Each of the 26 study regions includes 3 data matrices: sampling site information, environmental variables (limnology, climate, and landscape), and diatom community data (relative abundance or presence/absence). Access to data is through publicly available repositories, providing opportunities for complementing existing databases on diatoms and allowing optimal usage of the TSADB by the user community: diatomists, limnologists, aquatic ecologists, and tropical ecologists in general.The TSADB is stored in a zipped folder which contains: Excel spreadsheets: 26 excel files (one for each study region). Depending on the original information, each file has three sheets containing the three data matrices (site information, environmental variables, and diatom community data). A metadata sheet describing sources and descriptions of environmental variables is common in all excel files. R folder: files consisting in the TSADB's region datasets as a R list object ("TSABD.RData"), three R scripts for data processing, plotting (Figs. 1-4) and updating taxon nomenclature, and two R shiny apps for dynamic visualization and consultation of the database ("TSADB_shiny_sites.R" and "TSADB_shiny_species.R". The "TSADB.Rdata" is a list of objects, in which each element refers to a data matrix ($sites, $environment, $diatoms) that itself contains a list of study regions. The R script "1-cleaning and formatting.R" allows for data preparation, checking the correct format (i.e., numeric, text, ordered factors, region name spelling), and linking the original datasets by unique IDs. Database manipulation, plotting and generating metadata is available via the R script "2-visualization.R". Finally, the R script "3-taxonomic-harmonisation.R" run steps for nomenclature synchronization and authority harmonization (see above). The R code routines generate output files and plots that can be turned on/off by commenting/uncommenting lines. All steps were conducted using several R packages, including tidyverse (Wickham et al. 2019), ggplot2 (Wilke et al. 2019), cowplot (Wilke et al. 2019), and shiny (Winston et al. 2021). Funding provided by: the Secretary of Universities and Research (Government of Catalonia) and the Horizon 2020 programme*Crossref Funder Registry ID: Award Number: 801370The Tropical South America Diatom Database (TSADB) includes 326 sites containing 437 samples distributed across 26 regions (0 to 5,070 m a.s.l, and between 8°N–35°S; 58–90°W). The database comprises published and unpublished studies from lentic and lotic environments sampled by different authors for different purposes (e.g. paleoclimatic reconstructions, taxonomy, biodiversity). Diatom samples correspond to multiple habitats (e.g. sediment surface, periphyton, and plankton) and cover the period 1978–2017, including predictors that describe local (limnology) and regional (geo-climatic) factors