Aulacoseira subarctica is similar in cell size and proportions to A. ambigua, but does not have a hollow ringleiste and has large pointy spines with a row of mantle areolae running into the middle of each spine. Linking spines of A. ambigua are small, bifurcated or triangular and are easily distinguished from the pointy spines of A. subarctica, but the separation spines of A. ambigua can be difficult to distinguish from those of A. subarctica under LM. Often the rows of mantle areolae in A. ambigua merge close to valve face and thus give an impression of a single row of areolae running into the base of the spine as in A. subarctica, but the spines of A. subarctica are larger than separation spines in A. ambigua and even if two rows of mantle areolae merge into a single row that runs into the base of the spine, this merge happens far from the valve face. A. subarctica is similar in frustule structure to A. pusilla, which has, however, lower mantle height/valve diameter ratio and shorter spines. The initial and post-initial cells of A. subarctica can also have a low (0.4-0.8) mantle height/valve diameter ratio, but they are larger in diameter (> 7.5 mm) than valves of A. pusilla.
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