Stramenopile
The heterokont problem

The term 'heterokont' is used as both an adjective – indicating that a cell has two dissimilar flagella – and as the name of a taxon. The taxon 'Heterokontae' was introduced in 1899 by Alexander Luther for algae that are now considered the Xanthophyceae. But the same term was used for other groupings of algae. For example, in 1956, Copeland used it to include the xanthophytes (using the name Vaucheriacea), a group that included what became known as the chrysophytes, the silicoflagellates, and the hyphochytrids. Copeland also included the unrelated collar flagellates (as the choanoflagellates) in which he placed the bicosoecids. He also included the not-closely related haptophytes. The consequence of associating multiple concepts to the taxon 'heterokont' is that the meaning of 'heterokont' can only be made clear by making reference to its usage: Heterokontae sensu Luther 1899; Heterokontae sensu Copeland 1956, etc. This contextual clarification is rare, such that when the taxon name is used, it is unclear how it should be understood. The term 'Heterokont' has lost its usefulness in critical discussions about the identity, nature, character and relatedness of the group. The term 'stramenopile' sought to identify a clade (monophyletic and holophyletic lineage) using the approach developed by transformed cladists of pointing to a defining innovative characteristic or apomorphy.

Over time, the scope of application has changed, especially when in the 1970s ultrastructural studies revealed greater diversity among the algae with chromoplasts (chlorophylls a and c) than had previously been recognized. At the same time, a protistological perspective was replacing the 19th century one based on the division of unicellular eukaryotes into animals and plants. One consequence was that an array of heterotrophic organisms, many not previously considered as 'heterokonts', were seen as related to the 'core heterokonts' (those having anterior flagella with stiff hairs). Newly recognized relatives included the parasitic opalines, proteromonads, and actinophryid heliozoa. They joined other heterotrophic protists, such as bicosoecids, labyrinthulids, and oomycete fungi, that were included by some as heterokonts and excluded by others. Rather than continue to use a name whose meaning had changed over time and was hence ambiguous, the name 'stramenopile' was introduced to refer to the clade of protists that had tripartite stiff (usually flagellar) hairs and all their descendants. Molecular studies confirm that the genes that code for the proteins of these hairs are exclusive to stramenopiles.
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