We compiled phytoplankton data from the Global Biodiversity Information Facility (GBIF; https://www.gbif.org, retrieved on 7 December 2015), the Ocean Biogeographic Information System (OBIS; https://www.obis.org, retrieved on 5 December 2015), Villar et al. (36), and the MAREDAT initiative (table S3) (37). The final dataset contained 1,056,363 presence observations from 1298 species and two genera (collectively termed “species”), which were recorded at an average depth of 5.41 ± 6.95 m (mean ± SD) at 182,392 locations in space and time. Observation densities were spatially biased, with 49% of total observations originating from the north Atlantic and only 0.9% originating from the south Atlantic. Methods involved in original data collection included filters (38), microscopy (36, 39), and flow cytometers (37), among others. We retrieved all species observations for seven phyla: Cyanobacteria, Chlorophyta (excluding macroalgae), Cryptophyta, Myzozoa, Haptophyta, Ochrophyta, and Euglenozoa. More specifically, among the Ochrophyta, we included the classes Bacillariophyceae, Chrysophyceae, Pelagophyceae, and Raphidophyceae. Among the Myzozoa, we considered the class Dinophyceae. Among the Euglenozoa, we considered the class Euglenoidea. In addition, we compiled observations of Prochlorococcus and Synechococcus from the data sources. These genera are globally abundant but rarely identified to a species level. We excluded records (i) if they were listed as “fossil specimen” or “preserved specimen,” (ii) if they were associated with year of collection >2015 or <1800, (iii) if they were associated with negative depths, or (iv) if they were associated with nonsensible coordinates. We removed data below the monthly climatological mixed layer based on the temperature criterion (40), as data at depth were insufficient to develop species models. However, for “mixed-layer species” (i.e., species recorded in the mixed layer), we assumed that data without depth indication stem from the mixed layer as well. Species names in the original data were harmonized following expert opinion (see Supplementary Materials and Methods). The dataset spanned all major phytoplankton taxa of the marine realm (41) and reflected, within the bounds of uncertainty, roughly similar factions of the total species known among key taxa (table S4).

Independent data (<2.9% of the observations overlap with the above dataset) (39), primarily based on Atlantic transect cruises, served for validation of results obtained from the main dataset. These independent data were collected on the basis of a consistent methodology by the same taxonomist, containing 4217 presence observations from 303 phytoplankton species within the mixed layer (39).

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