Stephanodiscus yellowstonensis is distinguished from S. niagarae based on the number of spines / diameter (see Theriot and Stoermer 1984). Stephanodiscus niagarae has marginal spines positioned every 2-3 costae, while S. yellowstonensis tends tends to have marginal spines positioned every 2-5 costae. Stephanodiscus yellowstonensis also has thicker marginal spines and extensions of the rimoportulae (SEM features), as compared to S. niagarae. Stephanodiscus reimeri is smaller in size, with more regular placement of spines on every second to third costae and coarser polygonal areolae (8-12 in 10 µm).
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