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Already in ancient times, all life on Earth was classified into two "kingdoms": plants and animals. This division remained in place until relatively modern times, including in Linnaeus's work. By the mid-20th century, life was typically divided into five "kingdoms": prokaryotic life (bacteria, etc.), animals, plants, fungi, and protists. However, recent research has shown that "protists" is merely a catch-all category for eukaryotic organisms that are neither plants, animals, nor fungi. Some protists are more closely related to animals and fungi, while others are closer to plants, and some are not closely related to any of these groups. Today, the classification of life is far more complex than the traditional "kingdom" system.

Now, to my question: Historically, many organisms have been classified under the name "algae." Roughly speaking, any organism capable of photosynthesis that was not a land plant was grouped under this term. Traditionally, all such organisms were placed in the plant kingdom. However, we now know that while some, such as green and red algae, are indeed closely related to plants (in fact, "green algae" is now recognized as paraphyletic since plants evolved from them), others, like brown algae, are not, and belong to entirely different branches of the tree of life. While this has been confirmed through molecular genetic studies, I believe it was recognized earlier that certain groups, such as brown algae, possess distinctive features that set them apart from plants.

Historically, when was it first recognized that some groups of algae, such as brown algae, are not closely related to plants? Can anyone provide insights into the timeline and development of algae classification outside the plant kingdom?

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The timeline of the classification is outlined by Boll in A Brief History of the Kingdoms of Life. In brief, Haeckel proposed a third kingdom (Protista) for unicellular organisms in 1866, Chatton distinguished Prokaryota (without a nucleus) and Eukaryota (with a nucleus) in 1925, adding Monera as the fourth kingdom, Whittaker separated Fungi into a fifth kingdom in 1969. This got us the popular 5, with Protista turned into a pseudo-kingdom of leftovers under Eukaryota. Around 1970, Woese subdivided Prokaryota into Eubacteria and Archaeobacteria based on cell membrane structure, among other things, producing 6 kingdoms, but that did not affect the unsatisfactory status of Protista.

Brown algae were separated from more plant-like algae only in 1990-s by Cavalier-Smith, who rearranged the 6 kingdoms, dissolving the Protista in particular, see his Only six kingdoms of life (2004). Here is Boll's summary:

"By the end of the 20th century, Thomas Cavalier-Smith, after intense study of protists, created a new model with 6 kingdoms. Bacteria and Archaea were put together in the same kingdom, called Bacteria. Protists were divided in two kingdoms: (1) Chromista, including Alveolates (Apicomplexa, parasitic protozoa like Plasmodium; Ciliates and Dinoflagellates), Heterokonts or Stramenopiles (brown algae, golden algae, diatoms, water moulds, etc) and Rhizarians (like Radiolaria and Foraminifera), among others; and (2) Protozoa, including Amoebozoa (amoebas and slime moulds), Choanozoa (choanoflagellates) and a set of flagellated protozoa called Excavata. Glaucophytes, red and green algae were classified inside the kingdom Plantae."

Since then molecular analysis led to at least six more refined subdivisions of Eukaryota alone (so 8 kingdoms total together with Woese's 2), but their full classification is considered unfinished.

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    $\begingroup$ I have no disagreements with this answer as a general overview, but the answer to the question "when was the first time some groups of algae were recognized as not closely related to plants", without taking brown algae specifically as the test case, would probably be Chatton in 1925, which categorized the blue-green algae as Prokaryota. They were still considered plants by Haeckel. $\endgroup$
    – brendan
    Commented Sep 14 at 19:45

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